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1. The "nitrogenase-protective" FeSII protein of Azotobacter vinelandii: overexpression, characterization, and crystallization

Author:
Moshiri, F.; Crouse, B.R.; Johnson, M.K.; Maier, R.J.
Source:
Biochemistry 1995 v.34 no.40 pp. 12973-12982
ISSN:
0006-2960
Subject:
Azotobacter vinelandii; Escherichia coli; X-ray diffraction; absorption; chloroplasts; crystallization; cysteine; ferredoxins; iron; nitrogenase; oxidative stress; recombinant proteins; solvents; spectral analysis; spectroscopy; temperature; vibrational properties
Abstract:
... The Azotobacter vinelandii FeSII protein confers conformational protection to nitrogenase by binding to the MoFe and Fe proteins under periods of oxidative stress to create an inactive but O2-stabilized tripartite complex. In this work the FeSII protein has been overexpressed in Escherichia coli, and the recombinant protein has been purified to homogeneity, crystallized, and characterized in terms ...
DOI:
10.1021/bi00040a007
PubMed:
7548055

2. (1,3;1,4)-β-Glucan Biosynthesis by the CSLF6 Enzyme: Position and Flexibility of Catalytic Residues Influence Product Fine Structure

Author:
Dimitroff George; Little Alan; Lahnstein Jelle; Schwerdt Julian G.; Srivastava Vaibhav; Bulone Vincent; Burton Rachel A.; Fincher Geoffrey B.
Source:
Biochemistry 2016 v.55 no.13 pp. 2054-2061
ISSN:
1520-4995
Subject:
Hordeum vulgare; Nicotiana benthamiana; Sorghum bicolor; active sites; amino acids; barley; biosynthesis; carbohydrate structure; cellulose; complementary DNA; dietary fiber; genes; grasses; leaves; models; solubility
Abstract:
... Cellulose synthase-like F6 (CslF6) genes encode polysaccharide synthases responsible for (1,3;1,4)-β-glucan biosynthesis in cereal grains. However, it is not clear how both (1,3)- and (1,4)-linkages are incorporated into a single polysaccharide chain and how the frequency and arrangement of the two linkage types that define the fine structure of the polysaccharide are controlled. Through transient ...
DOI:
10.1021/acs.biochem.5b01384

3. The (Not Completely Irreversible) Population of a Misfolded State of Cytochrome c under Folding Conditions

Author:
Soffer Jonathan B.; Fradkin Emma; Pandiscia Leah A.; Schweitzer-Stenner Reinhard
Source:
Biochemistry 2013 v.52 no.8 pp. 1397-1408
ISSN:
1520-4995
Subject:
circular dichroism spectroscopy; cytochrome c; gel electrophoresis; heart; heme iron; horses; isomers; pH; spectral analysis
Abstract:
... This paper reports the discovery of a (meta)stable partially unfolded state of horse heart ferricytochrome c that was obtained after exposing the protein to a solution with an alkaline pH of 11.5 for 1 week. Thereafter, the protein did not undergo any detectable change in its secondary and tertiary structure upon adjusting the solution to folding promoting conditions at neutral pH. Spectroscopic d ...
DOI:
10.1021/bi301586e

4. The -Cys-X1-X2-Cys- Motif of Reduced Glutaredoxins Adopts a Consensus Structure That Explains the Low pKa of Its Catalytic Cysteine

Author:
Foloppe Nicolas; Vlamis-Gardikas Alexios; Nilsson Lennart
Source:
Biochemistry 2012 v.51 no.41 pp. 8189-8207
ISSN:
1520-4995
Subject:
Escherichia coli; active sites; cysteine; enzymes; humans; hydrogen bonding; models; molecular dynamics; mutants; nuclear magnetic resonance spectroscopy; prediction; viruses
Abstract:
... The -Cys-X1-X2-Cys- active site motif is central to the function of enzymes of the thioredoxin superfamily, including glutaredoxins. Their chemistry depends on the lowered pKₐ of the N-terminal thiolate cysteine of the -Cys-X1-X2-Cys- sequence; therefore its structure, dynamics, and electrostatics matter. Much information about the glutaredoxin structures was obtained by nuclear magnetic resonance ...
DOI:
10.1021/bi3006576

5. 1 alpha-hydroxylation of 24-hydroxyvitamin D2 represents a minor physiological pathway for the activation of vitamin D2 in mammals

Author:
Horst, R.L.; Koszewski, N.J.; Reinhardt, T.A.
Source:
Biochemistry 1990 v.29 no.2 pp. 578-582
ISSN:
0006-2960
Subject:
rats; vitamin deficiencies; ergocalciferol
DOI:
10.1021/bi00454a035
PubMed:
2154251

6. 1,2,3-Triazole–Heme Interactions in Cytochrome P450: Functionally Competent Triazole–Water–Heme Complexes

Author:
Conner Kip P.; Vennam Preethi; Woods Caleb M.; Krzyaniak Matthew D.; Bowman Michael K.; Atkins William M.
Source:
Biochemistry 2012 v.51 no.32 pp. 6441-6457
ISSN:
1520-4995
Subject:
cytochrome P-450; electron paramagnetic resonance spectroscopy; enthalpy; entropy; heme; heme iron; hydrogen bonding; ligands; metabolism; models; risk
Abstract:
... In comparison to imidazole (IMZ) and 1,2,4-triazole (1,2,4-TRZ), the isosteric 1,2,3-triazole (1,2,3-TRZ) is unrepresented among cytochrome P450 (CYP) inhibitors. This is surprising because 1,2,3-TRZs are easily obtained via “click” chemistry. To understand this underrepresentation of 1,2,3-TRZs among CYP inhibitors, thermodynamic and density functional theory computational studies were performed ...
DOI:
10.1021/bi300744z
PubMed:
22809252
PubMed Central:
PMC3448000

7. 1-Methylthio-d-xylulose 5-Phosphate Methylsulfurylase: A Novel Route to 1-Deoxy-d-xylulose 5-Phosphate in Rhodospirillum rubrum

Author:
Warlick Benjamin P.; Evans Bradley S.; Erb Tobias J.; Ramagopal Udipi A.; Sriram Jaya; Imker Heidi J.; Sauder J. Michael; Bonanno Jeffrey B.; Burley Stephen K.; Tabita F. Robert; Almo Steven C.; Sweedler Jonathan S.; Gerlt John A.
Source:
Biochemistry 2012 v.51 no.42 pp. 8324-8326
ISSN:
1520-4995
Subject:
Rhodospirillum rubrum; S-adenosylmethionine; active sites; adenine; biosynthesis; dimethyl disulfide; isomerization; isoprenoids; polyamines
Abstract:
... Rhodospirillum rubrum produces 5-methylthioadenosine (MTA) from S-adenosylmethionine in polyamine biosynthesis; however, R. rubrum lacks the classical methionine salvage pathway. Instead, MTA is converted to 5-methylthio-d-ribose 1-phosphate (MTR 1-P) and adenine; MTR 1-P is isomerized to 1-methylthio-d-xylulose 5-phosphate (MTXu 5-P) and reductively dethiomethylated to 1-deoxy-d-xylulose 5-phosph ...
DOI:
10.1021/bi301215g
PubMed:
23035785
PubMed Central:
PMC3490199

8. The 15-Amino Acid Repeat Region of Adenomatous Polyposis Coli Is Intrinsically Disordered and Retains Conformational Flexibility upon Binding β-Catenin

Author:
Aaron J. Rudeen; Justin T. Douglas; Minli Xing; W. Hayes McDonald; Audrey L. Lamb; Kristi L. Neufeld
Source:
Biochemistry 2020 v.59 no.41 pp. 4039-4050
ISSN:
1520-4995
Subject:
binding sites; biochemistry; carcinoma; chemical elements; colon; dynamics; mutants; mutation; rectum
Abstract:
... The tumor suppressor Adenomatous polyposis coli (APC) is a large, multidomain protein with many identified cellular functions. The best characterized role of APC is to scaffold a protein complex that negatively regulates Wnt signaling via β-catenin destruction. This destruction is mediated by β-catenin binding to centrally located 15- and 20-amino acid repeat regions of APC. More than 80% of cance ...
DOI:
10.1021/acs.biochem.0c00479

9. 19F NMR Studies of a Desolvated Near-Native Protein Folding Intermediate

Author:
Kitevski-LeBlanc Julianne L.; Hoang Joshua; Thach William; Larda Sacha Thierry; Prosser R. Scott
Source:
Biochemistry 2013 v.52 no.34 pp. 5780-5789
ISSN:
1520-4995
Subject:
calmodulin; circular dichroism spectroscopy; deuterium oxide; dissolved oxygen; hydrophobicity; isotopes; nuclear magnetic resonance spectroscopy; phase transition; protein folding; solvents; temperature
Abstract:
... Although many proteins are recognized to undergo folding via an intermediate, the microscopic nature of folding intermediates is less understood. In this study, ¹⁹F NMR and near-UV circular dichroism (CD) are used to characterize a transition to a thermal folding intermediate of calmodulin, a water-soluble protein, which is biosynthetically enriched with 3-fluorophenylalanine (3F-Phe). ¹⁹F NMR sol ...
DOI:
10.1021/bi4010057

10. 19F Nuclear Magnetic Resonance and Crystallographic Studies of 5-Fluorotryptophan-Labeled Anthrax Protective Antigen and Effects of the Receptor on Stability

Author:
Chadegani Fatemeh; Lovell Scott; Mullangi Vennela; Miyagi Masaru; Battaile Kevin P.; Bann James G.
Source:
Biochemistry 2014 v.53 no.4 pp. 690-701
ISSN:
1520-4995
Subject:
Bacillus anthracis; anthrax toxin; binding proteins; morphogenesis; nuclear magnetic resonance spectroscopy; oligomerization; pH; temperature
Abstract:
... The anthrax protective antigen (PA) is an 83 kDa protein that is one of three protein components of the anthrax toxin, an AB toxin secreted by Bacillus anthracis. PA is capable of undergoing several structural changes, including oligomerization to either a heptameric or octameric structure called the prepore, and at acidic pH a major conformational change to form a membrane-spanning pore. To follo ...
DOI:
10.1021/bi401405s
PubMed:
24387629
PubMed Central:
PMC3985773

11. 1H NMR assignment and global fold of napin BnIb, a representative 2S albumin seed protein

Author:
Rico, M.; Bruix, M.; Gonzalez, C.; Monsalve, R.I.; Rodriguez, R.
Source:
Biochemistry 1996 v.35 no.49 pp. 15672-15682
ISSN:
0006-2960
Subject:
albumins; allergenicity; calmodulin; corn; cysteine; disulfide bonds; genetic engineering; geometry; hydrophobicity; lipid transfer proteins; nuclear magnetic resonance spectroscopy; phospholipids; polypeptides; sequence homology; soybeans; spectral analysis; structure-activity relationships; transgenic plants; wheat
Abstract:
... Napin BnIb is a representative member of the 2S albumin seed proteins, which consists of two polypeptide chains of 3.8 and 8.4 kDa linked by two disulfide bridges. In this work, a complete assignment of the 1H spectra of napin BnIb has been carried out by two-dimensional NMR sequence-specific methods and its secondary structure determined on the basis of spectral data. A calculation of the tertiar ...
DOI:
10.1021/bi961748q
PubMed:
8961930

12. 1H NMR studies of plastocyanin from Scenedesmus obliquus: complete sequence-specific assignment, secondary structure analysis, and global fold

Author:
Moore, J.M.; Chazin, W.J.; Powls, R.; Wright, P.E.
Source:
Biochemistry 1988 v.27 no.20 pp. 7806-7816
ISSN:
0006-2960
Subject:
Scenedesmus; nuclear magnetic resonance spectroscopy; amino acids
DOI:
10.1021/bi00420a033
PubMed:
3207712

13. 1H and 31P nuclear magnetic resonance and kinetic studies of the active site structure of chloroplast CF1 ATP synthase

Author:
Devlin, C.C.; Grisham, C.M.
Source:
Biochemistry 1990 v.29 no.26 pp. 6192-6203
ISSN:
0006-2960
Subject:
Spinacia; chloroplasts; adenosine triphosphate; ligases; manganese; kinetics; spectral analysis; nuclear magnetic resonance spectroscopy; binding sites
DOI:
10.1021/bi00478a012
PubMed:
2145032

14. 2-Amino-1,3-benzothiazole-6-carboxamide Preferentially Binds the Tandem Mismatch Motif r(UY:GA)

Author:
Andrew T. Chang; Lu Chen; Luo Song; Shuxing Zhang; Edward P. Nikonowicz
Source:
Biochemistry 2020 v.59 no.35 pp. 3225-3234
ISSN:
1520-4995
Subject:
RNA; chemical compounds; hydrogen bonding; screening
Abstract:
... RNA helices are often punctuated with non-Watson–Crick features that may be targeted by chemical compounds, but progress toward identifying such compounds has been slow. We embedded a tandem UU:GA mismatch motif (5′-UG-3′:5′-AU-3′) within an RNA hairpin stem to identify compounds that bind the motif specifically. The three-dimensional structure of the RNA hairpin and its interaction with a small m ...
DOI:
10.1021/acs.biochem.0c00369

15. The 2-Aminopyridine Nucleobase Improves Triple-Helical Recognition of RNA and DNA When Used Instead of Pseudoisocytosine in Peptide Nucleic Acids

Author:
Christopher A. Ryan; Nikita Brodyagin; Justin Lok; Eriks Rozners
Source:
Biochemistry 2021 v.60 no.24 pp. 1919-1925
ISSN:
1520-4995
Subject:
DNA; biotechnology; cytosine; double-stranded RNA; pH; peptides; therapeutics
Abstract:
... Pseudoisocytosine (J), a neutral analogue of protonated cytosine, is currently the gold standard modified nucleobase in peptide nucleic acids (PNAs) for the formation of J·G-C triplets that are stable at physiological pH. This study shows that triple-helical recognition of RNA and DNA is significantly improved by using 2-aminopyridine (M) instead of J. The positively charged M forms 3-fold stronge ...
DOI:
10.1021/acs.biochem.1c00275

16. 24,25,28-trihydroxyvitamin D2 and 24,25,26-trihydroxyvitamin D2: novel metabolites of vitamin D2

Author:
Reddy, G.S.; Tserng, K.Y.
Source:
Biochemistry 1990 v.29 no.4 pp. 943-949
ISSN:
0006-2960
Subject:
rats; vitamin D; spectral analysis; metabolites
DOI:
10.1021/bi00456a014
PubMed:
2340285

17. 24,26-Dihydroxyvitamin D2: a unique physiological metabolite of vitamin D2

Author:
Koszewski, N.J.; Reinhardt, T.A.; Napoli, J.L.; Beitz, D.C.; Horst, R.L.
Source:
Biochemistry 1988 v.27 no.15 pp. 5785-5790
ISSN:
0006-2960
Subject:
ergocalciferol; metabolites; rats; blood plasma; metabolism
DOI:
10.1021/bi00415a058
PubMed:
3263145

18. 245 GHz high-field EPR study of tyrosine-D and tyrosine-Z in mutants of photosystem II

Author:
Un, S.; Tang, X.S.; Diner, B.A.
Source:
Biochemistry 1996 v.35 no.3 pp. 679-684
ISSN:
0006-2960
Subject:
Atta; Synechocystis sp. PCC 6803; free radicals; hydrogen bonding; mutants; photosystem II; ribonucleotide reductase; spinach
Abstract:
... A 245 GHz 8.7 T high-field EPR study of tyrosine-D (TyrD degrees) and tyrosine-Z (TyrZ degrees) radicals of photosystem II (PSII) from Synechocystis PCC 6803 was carried out. Identical principal g values for the wild-type Synechocystis and spinach TyrD degrees showed that the two radicals were in similar electrostatic environments. By contrast, the principal g values of the TyrD degrees in the D2- ...
DOI:
10.1021/bi9523769

19. 2H Solid-State Nuclear Magnetic Resonance Investigation of Whole Escherichia coli Interacting with Antimicrobial Peptide MSI-78

Author:
Pius James; Morrow MichaelR.; Booth Valerie
Source:
Biochemistry 2012 v.51 no.1 pp. 118-125
ISSN:
1520-4995
Subject:
Escherichia coli; adenosine monophosphate; anti-infective properties; antimicrobial peptides; bacteria; bioassays; cell growth; deuterium; lipid bilayers; lipids; nuclear magnetic resonance spectroscopy; stable isotopes
Abstract:
... A key aspect of the activity of antimicrobial peptides (AMPs) is their interaction with membranes. Efforts to elucidate their detailed mechanisms have focused on applying biophysical methods, including nuclear magnetic resonance (NMR), to AMPs in model lipid systems. However, these highly simplified systems fail to capture many of the features of the much more complex cell envelopes with which AMP ...
DOI:
10.1021/bi201569t

20. The 3-His Metal Coordination Site Promotes the Coupling of Oxygen Activation to Cysteine Oxidation in Cysteine Dioxygenase

Author:
Dianna L. Forbes; Kathleen M. Meneely; Annemarie S. Chilton; Audrey L. Lamb; Holly R. Ellis
Source:
Biochemistry 2020 v.59 no.21 pp. 2022-2031
ISSN:
1520-4995
Subject:
X-ray diffraction; crosslinking; cysteamine; cysteine; cysteine dioxygenase; geometry; glutamic acid; iron; ligands; oxidation; oxygen; testing; tyrosine
Abstract:
... Cysteine dioxygenase (CDO) structurally resembles cupin enzymes that use a 3-His/1-Glu coordination scheme. However, the glutamate ligand is substituted with a cysteine (Cys93) residue, which forms a thioether bond with tyrosine (Tyr157) under physiological conditions. The reversion variant, C93E CDO, was generated in order to reestablish the more common 3-His/1-Glu metal ligands of the cupin supe ...
DOI:
10.1021/acs.biochem.9b01085

21. 3-Phosphoglycerate Is an Allosteric Activator of Pyruvate Kinase from the Hyperthermophilic Archaeon Pyrobaculum aerophilum

Author:
Solomons J. T. Graham; Johnsen Ulrike; Schönheit Peter; Davies Christopher
Source:
Biochemistry 2013 v.52 no.34 pp. 5865-5875
ISSN:
1520-4995
Subject:
Archaea; arginine; bacteria; crystal structure; evolution; fructose; glyceraldehyde 3-phosphate; glycolysis; mutation; phosphates; phosphofructokinases; pyruvate kinase; sulfates; tyrosine
Abstract:
... Pyruvate kinase (PK) is a highly regulated enzyme that catalyzes the final step of glycolysis. PK from the hyperthermophilic archaeon Pyrobaculum aerophilum (PaPK) is distinguished from most PK enzymes of eukarya and bacteria by not responding to any known allosteric effectors and apparently exhibiting only cooperative regulation. We determined the crystal structure of PaPK to 2.2 Å resolution and ...
DOI:
10.1021/bi400761b

22. 3-Phosphoglycerate Transhydrogenation Instead of Dehydrogenation Alleviates the Redox State Dependency of Yeast de Novol-Serine Synthesis

Author:
Nicole Paczia; Julia Becker-Kettern; Jean-François Conrotte; Javier O. Cifuente; Marcelo E. Guerin; Carole L. Linster
Source:
Biochemistry 2019 v.58 no.4 pp. 259-275
ISSN:
1520-4995
Subject:
Escherichia coli; NAD (coenzyme); Pseudomonas; Saccharomyces cerevisiae; alpha-ketoglutaric acid; carbon metabolism; dehydrogenation; enzyme activity; enzymes; genes; humans; in vitro studies; oxidation; phenotype; reaction mechanisms; serine; yeasts
Abstract:
... The enzymatic mechanism of 3-phosphoglycerate to 3-phosphohydroxypyruvate oxidation, which forms the first step of the main conserved de novo serine synthesis pathway, has been revisited recently in certain microorganisms. While this step is classically considered to be catalyzed by an NAD-dependent dehydrogenase (e.g., PHGDH in mammals), evidence has shown that in Pseudomonas, Escherichia coli, a ...
DOI:
10.1021/acs.biochem.8b00990

23. The 3.2 Å Resolution Structure of a Receptor:CheA:CheW Signaling Complex Defines Overlapping Binding Sites and Key Residue Interactions within Bacterial Chemosensory Arrays

Author:
Li Xiaoxiao; Fleetwood Aaron D.; Bayas Camille; Bilwes Alexandrine M.; Ortega Davi R.; Falke Joseph J.; Zhulin Igor B.; Crane Brian R.
Source:
Biochemistry 2013 v.52 no.22 pp. 3852-3865
ISSN:
1520-4995
Subject:
Thermotoga maritima; binding sites; bioinformatics; chemoreceptors; chemotaxis; cryo-electron microscopy; crystal structure; genomics; histidine kinase; hydrophobicity; mastication; models; mutagenesis; nuclear magnetic resonance spectroscopy; proteins; sequence analysis
Abstract:
... Bacterial chemosensory arrays are composed of extended networks of chemoreceptors (also known as methyl-accepting chemotaxis proteins, MCPs), the histidine kinase CheA, and the adaptor protein CheW. Models of these arrays have been developed from cryoelectron microscopy, crystal structures of binary and ternary complexes, NMR spectroscopy, mutational, data and biochemical studies. A new 3.2 Å reso ...
DOI:
10.1021/bi400383e
PubMed:
23668907
PubMed Central:
PMC3694592

24. 31P NMR measurements of the ADP concentration in yeast cells genetically modified to express creatine kinase

Author:
Brindle, K.; Braddock, P.; Fulton, S.
Source:
Biochemistry 1990 v.29 no.13 pp. 3295-3302
ISSN:
0006-2960
Subject:
Saccharomyces cerevisiae; genetic engineering; plasmids; gene expression; creatine kinase; genetic transformation; adenosine diphosphate; nuclear magnetic resonance spectroscopy; rabbits
DOI:
10.1021/bi00465a021
PubMed:
2185836

25. 31P NMR studies of enzyme-bound substrate complexes of yeast 3-phosphoglycerate kinase. 1. Effects of sulfate and pH. Mg(II) affinity at the two ATP sites

Author:
Ray, B.D.; Rao, B.D.N.
Source:
Biochemistry 1988 v.27 no.15 pp. 5574-5578
ISSN:
0006-2960
Subject:
yeasts; phosphoglycerate kinase; nuclear magnetic resonance spectroscopy; adenosine triphosphate; adenosine diphosphate; magnesium; binding sites
DOI:
10.1021/bi00415a027
PubMed:
3052580

26. 31P and 13C NMR studies of intermediates of aerobic and anaerobic glycolysis in Saccharomyces cerevisiae

Author:
Hollander, J.A. den.; Ugurbil, K.; Shulman, R.G.
Source:
Biochemistry 1986 v.25 no.1 pp. 212-219
ISSN:
0006-2960
Subject:
Saccharomyces cerevisiae; glycolysis; aerobiosis; anaerobiosis; nuclear magnetic resonance spectroscopy
DOI:
10.1021/bi00349a030
PubMed:
3513824

27. 3′-Phosphoadenosine 5′-Phosphosulfate Allosterically Regulates Sulfotransferase Turnover

Author:
Wang Ting; Cook Ian; Leyh Thomas S.
Source:
Biochemistry 2014 v.53 no.44 pp. 6893-6900
ISSN:
1520-4995
Subject:
active sites; catalytic activity; drugs; humans; liver; primary amines; sulfotransferases
Abstract:
... Human cytosolic sulfotransferases (SULTs) regulate the activities of thousands of small moleculesmetabolites, drugs, and other xenobioticsvia the transfer of the sulfuryl moiety (-SO₃) from 3′-phosphoadenosine 5′-phosphosulfate (PAPS) to the hydroxyls and primary amines of acceptors. SULT1A1 is the most abundant SULT in liver and has the broadest substrate spectrum of any SULT. Here we present t ...
DOI:
10.1021/bi501120p
PubMed:
25314023
PubMed Central:
PMC4230322

28. The 5'-linked termini of plant ribosomal ribonucleic acids

Author:
Halloin, J.M.; Pollard, C.J.; Becker, V.E.; Fowlks, E.R.
Source:
Biochemistry 1969 v.8 no.5 pp. 1940-1947
ISSN:
0006-2960
Subject:
plant anatomy; RNA; acids
DOI:
10.1021/bi00833a025

29. 5-Methylcytosine (5mC) and 5-Hydroxymethylcytosine (5hmC) Enhance the DNA Binding of CREB1 to the C/EBP Half-Site Tetranucleotide GCAA

Author:
Syed Khund Sayeed; He Ximiao; Tillo Desiree; Wang Jun; Durell Stewart R.; Vinson Charles
Source:
Biochemistry 2016 v.55 no.49 pp. 6940-6948
ISSN:
1520-4995
Subject:
DNA; DNA probes; X-radiation; binding proteins; brain; humans; mice; microarray technology; nucleotide sequences; stem cells; transcription (genetics); transcription factors
Abstract:
... In human and mouse stem cells and brain, 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) can occur outside of CG dinucleotides. Using protein binding microarrays (PBMs) containing 60-mer DNA probes, we evaluated the effect of 5mC and 5hmC on one DNA strand on the double-stranded DNA binding of the mouse B-ZIP transcription factors (TFs) CREB1, ATF1, and JUND. 5mC inhibited binding of CRE ...
DOI:
10.1021/acs.biochem.6b00796

30. 5-Methylcytosine Recognition by Arabidopsis thaliana DNA Glycosylases DEMETER and DML3

Author:
Brooks Sonja C.; Fischer Robert L.; Huh Jin Hoe; Eichman Brandt F.
Source:
Biochemistry 2014 v.53 no.15 pp. 2525-2532
ISSN:
1520-4995
Subject:
Arabidopsis thaliana; DNA; DNA methylation; X chromosome; active sites; animals; cytosine; gene expression; genes; glycosylases; models; transposons
Abstract:
... Methylation of cytosine to 5-methylcytosine (5mC) is important for gene expression, gene imprinting, X-chromosome inactivation, and transposon silencing. Active demethylation in animals is believed to proceed by DNA glycosylase removal of deaminated or oxidized 5mC. In plants, 5mC is removed from the genome directly by the DEMETER (DME) family of DNA glycosylases. Arabidopsis thaliana DME excises ...
DOI:
10.1021/bi5002294
PubMed:
24678721
PubMed Central:
PMC4004242

31. 500-MHz 1H NMR studies of ragweed allergen Ra5

Author:
Vidusek, D.A.; Roberts, M.F.; Goodfriend, L.
Source:
Biochemistry 1985 v.24 no.11 pp. 2747-2753
ISSN:
0006-2960
Subject:
Ambrosia artemisiifolia; nuclear magnetic resonance spectroscopy; allergens
DOI:
10.1021/bi00332a023
PubMed:
4027223

32. 500-MHz Proton NMR evidence for two solution structures of the common arm base-paired of wheat germ 5S ribosomal RNA

Author:
Wu, J.J.; Marshall, A.G.
Source:
Biochemistry 1990 v.29 no.7 pp. 1722-1730
ISSN:
0006-2960
Subject:
Triticum aestivum; RNA; ribosomes; nucleotide sequences; spectral analysis; nuclear magnetic resonance spectroscopy
DOI:
10.1021/bi00459a009

33. 500-MHz proton homonuclear overhauser evidence for additional base pairs in the common arm of eukaryotic ribosomal 5S RNA: wheat germ

Author:
Li, S.J.; Wu, J.; Marshall, A.G.
Source:
Biochemistry 1987 v.26 no.6 pp. 1578-1585
ISSN:
0006-2960
Subject:
Triticum aestivum; wheat germ; ribosomes; RNA; binding sites
DOI:
10.1021/bi00380a014

34. 5S,15S-Dihydroperoxyeicosatetraenoic Acid (5,15-diHpETE) as a Lipoxin Intermediate: Reactivity and Kinetics with Human Leukocyte 5-Lipoxygenase, Platelet 12-Lipoxygenase, and Reticulocyte 15-Lipoxygenase-1

Author:
Abigail R. Green; Cody Freedman; Jennyfer Tena; Benjamin E. Tourdot; Benjamin Liu; Michael Holinstat; Theodore R. Holman
Source:
Biochemistry 2018 v.57 no.48 pp. 6726-6734
ISSN:
1520-4995
Subject:
arachidonic acid; catalytic activity; enzymes; humans; inhibitory concentration 50; leukocytes; platelet aggregation
Abstract:
... The reaction of 5S,15S-dihydroperoxyeicosatetraenoic acid (5,15-diHpETE) with human 5-lipoxygenase (LOX), human platelet 12-LOX, and human reticulocyte 15-LOX-1 was investigated to determine the reactivity and relative rates of producing lipoxins (LXs). 5-LOX does not react with 5,15-diHpETE, although it can produce LXA₄ when 15-HpETE is the substrate. In contrast, both 12-LOX and 15-LOX-1 react w ...
DOI:
10.1021/acs.biochem.8b00889

35. 6-Fluorocholesterol as a growth factor for the yeast mutant GL7

Author:
Zundel, M.; Nambiar, K.P.; Boswell, G.; Bloch, K.
Source:
Biochemistry 1989 v.28 no.12 pp. 5161-5164
ISSN:
0006-2960
Subject:
Saccharomyces cerevisiae; cholesterol; growth factors; mutants
DOI:
10.1021/bi00438a037
PubMed:
2669969

36. 7-Methylguanosine Diphosphate (m7GDP) Is Not Hydrolyzed but Strongly Bound by Decapping Scavenger (DcpS) Enzymes and Potently Inhibits Their Activity

Author:
Wypijewska Anna; Bojarska Elzbieta; Lukaszewicz Maciej; Stepinski Janusz; Jemielity Jacek; Davis Richard E.; Darzynkiewicz Edward
Source:
Biochemistry 2012 v.51 no.40 pp. 8003-8013
ISSN:
1520-4995
Subject:
Nematoda; binding capacity; biochemical pathways; enzyme inhibition; enzymes; humans; hydrolysis; messenger RNA; nucleosides; proteins; yeasts
Abstract:
... Decapping scavenger (DcpS) enzymes catalyze the cleavage of a residual cap structure following 3′ → 5′ mRNA decay. Some previous studies suggested that both m⁷GpppG and m⁷GDP were substrates for DcpS hydrolysis. Herein, we show that mononucleoside diphosphates, m⁷GDP (7-methylguanosine diphosphate) and m₃²,²,⁷GDP (2,2,7-trimethylguanosine diphosphate), resulting from mRNA decapping by the Dcp1/2 c ...
DOI:
10.1021/bi300781g
PubMed:
22985415
PubMed Central:
PMC3495079

37. The AAA+ FtsH Protease Degrades an ssrA-Tagged Model Protein in the Inner Membrane of Escherichia coli

Author:
Hari Sanjay B.; Sauer Robert T.
Source:
Biochemistry 2016 v.55 no.40 pp. 5649-5652
ISSN:
1520-4995
Subject:
Escherichia coli; polypeptides; protein synthesis; proteinases; proteins; proteolysis; quality control; ribosomes
Abstract:
... In eubacteria, the tmRNA system frees ribosomes that stall during protein synthesis and adds an ssrA tag to the incompletely translated polypeptide to target it for degradation. The AAA+ ClpXP protease degrades most ssrA-tagged proteins in the Escherichia coli cytoplasm and was recently shown to degrade an ssrA-tagged protein in the inner membrane. However, we find that tmRNA-mediated tagging of E ...
DOI:
10.1021/acs.biochem.6b00920
PubMed:
27677373
PubMed Central:
PMC5218843

38. ABC Transporters and Immunity: Mechanism of Self-Defense

Author:
Hinz Andreas; Tampé Robert
Source:
Biochemistry 2012 v.51 no.25 pp. 4981-4989
ISSN:
1520-4995
Subject:
ABC transporters; adenosine triphosphate; antigens; cytosol; endoplasmic reticulum; hydrolysis; immunity; major histocompatibility complex; peptides; solutes
Abstract:
... The transporter associated with antigen processing (TAP) is a prototype of an asymmetric ATP-binding cassette (ABC) transporter, which uses ATP binding and hydrolysis to translocate peptides from the cytosol to the lumen of the endoplasmic reticulum (ER). Here, we review molecular details of peptide binding and ATP binding and hydrolysis as well as the resulting allosteric cross-talk between the n ...
DOI:
10.1021/bi300128f

39. ABHD12 and LPCAT3 Interplay Regulates a Lyso-phosphatidylserine-C20:4 Phosphatidylserine Lipid Network Implicated in Neurological Disease

Author:
Taka-Aki Ichu; Alex Reed; Daisuke Ogasawara; Olesya Ulanovskaya; Amanda Roberts; Carlos A. Aguirre; Liron Bar-Peled; Jie Gao; Jason Germain; Sabrina Barbas; Kim Masuda; Bruno Conti; Peter Tontonoz; Benjamin F. Cravatt
Source:
Biochemistry 2020 v.59 no.19 pp. 1793-1799
ISSN:
1520-4995
Subject:
carboxylic ester hydrolases; cataract; cells; cerebellum; genes; hearing disorders; humans; metabolites; mice; mutation; phosphatidylserines; retinitis pigmentosa
Abstract:
... PHARC (polyneuropathy, hearing loss, cerebellar ataxia, retinitis pigmentosa, and cataract) is a human neurological disorder caused by deleterious mutations in the ABHD12 gene, which encodes an integral membrane lyso-phosphatidylserine (lyso-PS) lipase. Pharmacological or genetic disruption of ABHD12 leads to higher levels of lyso-PS lipids in human cells and the central nervous system (CNS) of mi ...
DOI:
10.1021/acs.biochem.0c00292

40. ABHD4 Regulates Multiple Classes of N-Acyl Phospholipids in the Mammalian Central Nervous System

Author:
Lee Hyeon-Cheol; Simon Gabriel M.; Cravatt Benjamin F.
Source:
Biochemistry 2015 v.54 no.15 pp. 2539-2549
ISSN:
1520-4995
Subject:
brain; carboxylic ester hydrolases; cell membranes; metabolism; mice; phosphatidylethanolamines
Abstract:
... N-Acyl phospholipids are atypical components of cell membranes that bear three acyl chains and serve as potential biosynthetic precursors for lipid mediators such as endocannabinoids. Biochemical studies have implicated ABHD4 as a brain N-acyl phosphatidylethanolamine (NAPE) lipase, but in vivo evidence for this functional assignment is lacking. Here, we describe ABHD4–/– mice and their characteri ...
DOI:
10.1021/acs.biochem.5b00207
PubMed:
25853435
PubMed Central:
PMC4767004

41. ADP binding induces long-distance structural changes in the beta polypeptide of the chloroplast ATP synthase

Author:
Mills, D.A.; Seibold, S.A.; Squier, T.C.; Richter, M.L.
Source:
Biochemistry 1995 v.34 no.18 pp. 6100-6108
ISSN:
0006-2960
Subject:
H+/K+-exchanging ATPase; H-transporting ATP synthase; adenosine diphosphate; adenosine triphosphate; beef; binding sites; catalytic activity; chloroplasts; crystal structure; cysteine; dissociation; energy transfer; fluorescence; heart; information exchange; mitochondria; polypeptides
Abstract:
... Binding of ADP to the beta polypeptide isolated from the catalytic F1 portion (CF1) of the chloroplast ATP synthase caused an increase of 10-20% in the steady state fluorescence intensity of fluorescent maleimides attached to the cysteine residue at position 63. Fluorescence lifetime distributions indicated that the beta polypeptide switched between two conformational states depending on the prese ...
DOI:
10.1021/bi00018a013
PubMed:
7742314

42. ADP-Ribose Pyrophosphatase Reaction in Crystalline State Conducted by Consecutive Binding of Two Manganese(II) Ions as Cofactors

Author:
Furuike Yoshihiko; Akita Yuka; Miyahara Ikuko; Kamiya Nobuo
Source:
Biochemistry 2016 v.55 no.12 pp. 1801-1812
ISSN:
1520-4995
Subject:
Thermus thermophilus; X-ray diffraction; adenosine monophosphate; cations; crystals; divalent metals; hydrolysis; magnesium; manganese; proteins; zinc
Abstract:
... Adenosine diphosphate ribose pyrophosphatase (ADPRase), a member of the Nudix family proteins, catalyzes the metal-induced and concerted general acid–base hydrolysis of ADP ribose (ADPR) into AMP and ribose-5′-phosphate (R5P). The ADPR-hydrolysis reaction of ADPRase from Thermus thermophilus HB8 (TtADPRase) requires divalent metal cations such as Mn²⁺, Zn²⁺, or Mg²⁺ as cofactors. Here, we report t ...
DOI:
10.1021/acs.biochem.5b00886

43. The ANF-RGC Gene Motif 669WTAPELL675 Is Vital for Blood Pressure Regulation: Biochemical Mechanism

Author:
Duda Teresa; Pertzev Alexandre; Sharma Rameshwar K.
Source:
Biochemistry 2013 v.52 no.13 pp. 2337-2347
ISSN:
1520-4995
Subject:
adrenal glands; aldosterone; animal models; apoptosis; blood pressure; cyclic GMP; genes; guanosine monophosphate; guanylate cyclase; hypertension; hypertrophy; kidneys; metabolic syndrome; mice; obesity; secretion; signal transduction
Abstract:
... ANF-RGC is the prototype membrane guanylate cyclase, both the receptor and the signal transducer of the hormones ANF and BNP. After binding them at the extracellular domain, it, at its intracellular domain, signals activation of the C-terminal catalytic module and accelerates production of the second messenger, cyclic GMP. This, in turn, controls the physiological processes of blood pressure, card ...
DOI:
10.1021/bi400175d
PubMed:
23464624
PubMed Central:
PMC3636714

44. AP-Endonuclease 1 Accelerates Turnover of Human 8-Oxoguanine DNA Glycosylase by Preventing Retrograde Binding to the Abasic-Site Product

Author:
Esadze Alexandre; Rodriguez Gaddiel; Cravens Shannen L.; Stivers James T.
Source:
Biochemistry 2017 v.56 no.14 pp. 1974-1986
ISSN:
1520-4995
Subject:
DNA; DNA damage; DNA repair; cations; crosslinking; humans; phosphates; protein-protein interactions; thymine-DNA glycosylase
Abstract:
... A major product of oxidative DNA damage is 8-oxoguanine. In humans, 8-oxoguanine DNA glycosylase (hOGG1) facilitates removal of these lesions, producing an abasic (AP) site in the DNA that is subsequently incised by AP-endonuclease 1 (APE1). APE1 stimulates turnover of several glycosylases by accelerating rate-limiting product release. However, there have been conflicting accounts of whether hOGG1 ...
DOI:
10.1021/acs.biochem.7b00017
PubMed:
28345889
PubMed Central:
PMC5526596

45. APEX Proximity Labeling as a Versatile Tool for Biological Research

Author:
Thanh My Thi Nguyen; Junhyung Kim; Thi Tram Doan; Min-Woo Lee; Mihye Lee
Source:
Biochemistry 2019 v.59 no.3 pp. 260-269
ISSN:
1520-4995
Subject:
amino acids; ascorbate peroxidase; cells; endoplasmic reticulum; fractionation; free radicals; immunohistochemistry; mass spectrometry; mitochondrial membrane; proteomics; research; streptavidin; transcriptome
Abstract:
... Most proteins are specifically localized in membrane-encapsulated organelles or non-membrane-bound compartments. The subcellular localization of proteins facilitates their functions and integration into functional networks; therefore, protein localization is tightly regulated in diverse biological contexts. However, protein localization has been mainly analyzed through immunohistochemistry or the ...
DOI:
10.1021/acs.biochem.9b00791

46. APEX, a Master Key To Resolve Membrane Topology in Live Cells

Author:
Chang-Mo Yoo; Hyun-Woo Rhee
Source:
Biochemistry 2019 v.59 no.3 pp. 250-259
ISSN:
1520-4995
Subject:
ascorbate peroxidase; cells; endoplasmic reticulum; information; lead; methodology; mitochondria; proteins; proteome; topology
Abstract:
... Determining the topology of the membrane proteome is fundamental for understanding its function at the membrane. However, conventional methods involving test tube reactions often lead to unreliable results, which do not accurately reflect membrane topology under physiological conditions, as perturbations occur during lysis. In this Perspective, we introduce a new method using engineered ascorbate ...
DOI:
10.1021/acs.biochem.9b00785

47. APOBEC2 Is a Monomer in Solution: Implications for APOBEC3G Models

Author:
Krzysiak Troy C.; Jung Jinwon; Thompson James; Baker David; Gronenborn Angela M.
Source:
Biochemistry 2012 v.51 no.9 pp. 2008-2017
ISSN:
1520-4995
Subject:
Human immunodeficiency virus; antiretroviral properties; crystal structure; crystallization; models; nuclear magnetic resonance spectroscopy; pathogenicity; prediction
Abstract:
... Although the physiological role of APOBEC2 is still largely unknown, a crystal structure of a truncated variant of this protein was determined several years ago [Prochnow, C. (2007) Nature445, 447–451]. This APOBEC2 structure had considerable impact in the HIV field because it was considered a good model for the structure of APOBEC3G, an important HIV restriction factor that abrogates HIV infectiv ...
DOI:
10.1021/bi300021s
PubMed:
22339232
PubMed Central:
PMC3316327

48. APOBEC3A Loop 1 Is a Determinant for Single-Stranded DNA Binding and Deamination

Author:
Samantha J. Ziegler; Yingxia Hu; Swapnil C. Devarkar; Yong Xiong
Source:
Biochemistry 2019 v.58 no.37 pp. 3838-3847
ISSN:
1520-4995
Subject:
CRISPR-Cas systems; apolipoprotein B; deamination; deoxycytidine; enzymes; innate immunity; interferons; lead; length; mutation; single-stranded DNA; substrate specificity; technology
Abstract:
... The apolipoprotein B mRNA editing enzyme catalytic polypeptide-like 3 (APOBEC3 or A3) family of proteins functions in the innate immune system. The A3 proteins are interferon inducible and hypermutate deoxycytidine to deoxyuridine in foreign single-stranded DNA (ssDNA). However, this deaminase activity cannot discriminate between foreign and host ssDNA at the biochemical level, which presents a si ...
DOI:
10.1021/acs.biochem.9b00394
PubMed:
31448897
PubMed Central:
PMC7211764

49. The ATF3 Transcription Factor Is a Short-Lived Substrate of the Arg/N-Degron Pathway

Author:
Tri T. M. Vu; Alexander Varshavsky
Source:
Biochemistry 2020 v.59 no.30 pp. 2796-2812
ISSN:
1520-4995
Subject:
adults; assays; autophagy; cell lines; degradation; genes; genotype; humans; leucine zipper; mechanics; mice; mutants; strains; transactivators; ubiquitin-protein ligase
Abstract:
... The Arg/N-degron pathway targets proteins for degradation by recognizing their specific N-terminal residues or, alternatively, their non-N-terminal degrons. In mammals, this pathway is mediated by the UBR1, UBR2, UBR4, and UBR5 E3 ubiquitin ligases, and by the p62 regulator of autophagy. UBR1 and UBR2 are sequelogous, functionally overlapping, and dominate the targeting of Arg/N-degron substrates ...
DOI:
10.1021/acs.biochem.0c00514

50. ATP Acyl Phosphate Reactivity Reveals Native Conformations of Hsp90 Paralogs and Inhibitor Target Engagement

Author:
Nordin Brian E.; Liu Yongsheng; Aban Arwin; Brown Heidi E.; Wu Jiangyue; Hainley Anna K.; Rosenblum Jonathan S.; Nomanbhoy Tyzoon K.; Kozarich John W.
Source:
Biochemistry 2015 v.54 no.19 pp. 3024-3036
ISSN:
1520-4995
Subject:
adenosine triphosphate; adenosinetriphosphatase; drugs; humans; inhibitory concentration 50; phosphates; protein kinases; proteins
Abstract:
... Hsp90 is an ATP-dependent chaperone of widespread interest as a drug target. Here, using an LC-MS/MS chemoproteomics platform based on a lysine-reactive ATP acyl phosphate probe, several Hsp90 inhibitors were profiled in native cell lysates. Inhibitor specificities for all four human paralogs of Hsp90 were simultaneously monitored at their endogenous relative abundances. Equipotent inhibition of p ...
DOI:
10.1021/acs.biochem.5b00148

51. ATP Allosterically Activates the Human 5-Lipoxygenase Molecular Mechanism of Arachidonic Acid and 5(S)-Hydroperoxy-6(E),8(Z),11(Z),14(Z)-eicosatetraenoic Acid

Author:
Smyrniotis Christopher J.; Barbour Shannon R.; Xia Zexin; Hixon Mark S.; Holman Theodore R.
Source:
Biochemistry 2014 v.53 no.27 pp. 4407-4419
ISSN:
1520-4995
Subject:
adenosine triphosphate; arachidonic acid; humans; hydrogen; hydrogen bonding; inflammation; isotopes; leukotrienes; oxidation; solvents
Abstract:
... 5-Lipoxygenase (5-LOX) reacts with arachidonic acid (AA) to first generate 5(S)-hydroperoxy-6(E),8(Z),11(Z),14(Z)-eicosatetraenoic acid [5(S)-HpETE] and then an epoxide from 5(S)-HpETE to form leukotriene A₄, from a single polyunsaturated fatty acid. This work investigates the kinetic mechanism of these two processes and the role of ATP in their activation. Specifically, it was determined that epo ...
DOI:
10.1021/bi401621d
PubMed:
24893149
PubMed Central:
PMC4215895

52. ATP Hydrolysis in the RecA–DNA Filament Promotes Structural Changes at the Protein–DNA Interface

Author:
Reymer Anna; Babik Sándor; Takahashi Masayuki; Nordén Bengt; Beke-Somfai Tamás
Source:
Biochemistry 2015 v.54 no.30 pp. 4579-4582
ISSN:
1520-4995
Subject:
DNA; adenosine triphosphate; binding sites; homologous recombination; hydrogen bonding; hydrolysis
Abstract:
... To address the mechanistic roles of ATP hydrolysis in RecA-promoted strand exchange reaction in homologous recombination, quantum mechanical calculations are performed on key parts of the RecA–DNA complex. We find that ATP hydrolysis may induce changes at the protein–DNA interface, resulting in the rearrangement of the hydrogen bond network connecting the ATP and the DNA binding sites. ...
DOI:
10.1021/acs.biochem.5b00614

53. ATP Is an Allosteric Inhibitor of Coxsackievirus B3 Polymerase

Author:
Karr Jonathan P.; Peersen Olve B.
Source:
Biochemistry 2016 v.55 no.28 pp. 3995-4002
ISSN:
1520-4995
Subject:
Flaviviridae; Picornaviridae; RNA; RNA-directed RNA polymerase; active sites; adenosine triphosphate; binding sites; catalytic activity; fluorescence; guanosine; guanosine triphosphate; mutation; progeny; uridine triphosphate; viruses
Abstract:
... The RNA-dependent RNA polymerases from positive-strand RNA viruses, such as picornaviruses and flaviviruses, close their active sites for catalysis via a unique NTP-induced conformational change in the palm domain. Combined with a fully prepositioned templating nucleotide, this mechanism is error-prone and results in a distribution of random mutations in the viral progeny often described as a quas ...
DOI:
10.1021/acs.biochem.6b00467
PubMed:
27319576
PubMed Central:
PMC5749642

54. ATP Transport through VDAC and the VDAC–Tubulin Complex Probed by Equilibrium and Nonequilibrium MD Simulations

Author:
Noskov Sergei Yu.; Rostovtseva Tatiana K.; Bezrukov Sergey M.
Source:
Biochemistry 2013 v.52 no.51 pp. 9246-9256
ISSN:
1520-4995
Subject:
adenosine diphosphate; adenosine triphosphate; algorithms; binding capacity; binding sites; electric field; lipids; mitochondria; mitochondrial membrane; molecular dynamics; permeability; probability; thermodynamics; tubulin
Abstract:
... Voltage-dependent anion channel (VDAC), the major channel of the mitochondrial outer membrane, serves as a principal pathway for ATP, ADP, and other respiratory substrates across this membrane. Using umbrella-sampling simulations, we established the thermodynamic and kinetic components governing ATP transport across the VDAC1 channel. We found that there are several low-affinity binding sites for ...
DOI:
10.1021/bi4011495

55. ATP and Magnesium Promote Cotton Short-Form Ribulose-1,5-bisphosphate Carboxylase/Oxygenase (Rubisco) Activase Hexamer Formation at Low Micromolar Concentrations

Author:
Kuriata Agnieszka M.; Chakraborty Manas; Henderson J. Nathan; Hazra Suratna; Serban Andrew J.; Pham Tuong V. T.; Levitus Marcia; Wachter Rebekka M.
Source:
Biochemistry 2014 v.53 no.46 pp. 7232-7246
ISSN:
1520-4995
Subject:
Gossypium hirsutum; adenosine diphosphate; adenosine triphosphate; adenosinetriphosphatase; binding sites; carbon dioxide fixation; cations; cotton; data collection; diffusivity; fluorescence; magnesium; protein content; ribulose-bisphosphate carboxylase; spectroscopy; thermodynamics; titration
Abstract:
... We report a fluorescence correlation spectroscopy (FCS) study of the assembly pathway of the AAA+ protein ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) activase (Rca), a ring-forming ATPase responsible for activation of inhibited Rubisco complexes for biological carbon fixation. A thermodynamic characterization of simultaneously populated oligomeric states appears critical in understan ...
DOI:
10.1021/bi500968h

56. ATP synthase of chloroplasts: selective action of agents binding to F1 on partial reactions of proton transfer in F0

Author:
Groth, G.; Junge, W.
Source:
Biochemistry 1995 v.34 no.27 pp. 8589-8596
ISSN:
0006-2960
Subject:
H+/K+-exchanging ATPase; H-transporting ATP synthase; active sites; adenosine triphosphate; binding agents; pH; protons; thylakoids
Abstract:
... We studied the basic steps of proton transfer through ATP synthase of chloroplasts, CF0CF1, under conditions of proton slip, a conducting state in the absence of added nucleotides. On the background of a steady transmembrane pH difference, voltage steps were induced by flashing light. Proton intake, transfer, and release by CF0CF1 were kinetically resolved by spectrophotometric probes. Kinetic dis ...
DOI:
10.1021/bi00027a008
PubMed:
7612600

57. ATP-Dependent Electron Activation Module of Benzoyl-Coenzyme A Reductase from the Hyperthermophilic Archaeon Ferroglobus placidus

Author:
Schmid Georg; Auerbach Hendrik; Pierik Antonio J.; Schünemann Volker; Boll Matthias
Source:
Biochemistry 2016 v.55 no.39 pp. 5578-5586
ISSN:
1520-4995
Subject:
Thauera aromatica; adenosine triphosphate; adenosinetriphosphatase; air; amino acids; benzene; denitrifying bacteria; electron transfer; fermentation; hydrolysis; iron; phylogeny; redox potential; spectral analysis; spectroscopy
Abstract:
... The class I benzoyl-coenzyme A (BzCoA) reductases (BCRs) are key enzymes in the anaerobic degradation of aromatic compounds that catalyze the ATP-dependent dearomatization of their substrate to a cyclic dienoyl-CoA. The phylogenetically distinct Thauera- and Azoarcus-type BCR subclasses are iron–sulfur enzymes and consist of an ATP-hydrolyzing electron activation module and a BzCoA reduction modul ...
DOI:
10.1021/acs.biochem.6b00729

58. ATP-Induced Dimerization of the F0F1 ε Subunit from Bacillus PS3: A Hydrogen Exchange–Mass Spectrometry Study

Author:
Rodriguez Antony D.; Dunn Stanley D.; Konermann Lars
Source:
Biochemistry 2014 v.53 no.24 pp. 4072-4080
ISSN:
1520-4995
Subject:
H+/K+-exchanging ATPase; H-transporting ATP synthase; adenosine triphosphate; adenosinetriphosphatase; antibiotics; bacteria; circular dichroism spectroscopy; crystallography; deuterium; dimerization; electrochemistry; hydrolysis; mass spectrometry; multiprotein complexes; thermophilic microorganisms; ultracentrifugation
Abstract:
... F₀F₁ ATP synthase harnesses a transmembrane electrochemical gradient for the production of ATP. When operated in reverse, this multiprotein complex catalyzes ATP hydrolysis. In bacteria, the ε subunit is involved in regulating this ATPase activity. Also, ε is essential for coupling ATP hydrolysis (or synthesis) to proton translocation. The ε subunit consists of a β sandwich and two C-terminal heli ...
DOI:
10.1021/bi5004684

59. ATR-FTIR Spectroelectrochemical Study on the Mechanism of the pH Dependence of the Redox Potential of the Non-Heme Iron in Photosystem II

Author:
Yuki Kato; Hiroki Watanabe; Takumi Noguchi
Source:
Biochemistry 2021 v.60 no.27 pp. 2170-2178
ISSN:
1520-4995
Subject:
Fourier transform infrared spectroscopy; amino acids; deprotonation; electrodes; iron; ligands; pH; photosystem II; plastoquinones; protonation; redox potential; redox reactions; temperature
Abstract:
... The non-heme iron that bridges the two plastoquinone electron acceptors, QA and QB, in photosystem II (PSII) is known to have a redox potential (Eₘ) of ∼+400 mV with a pH dependence of ∼−60 mV/pH. However, titratable amino acid residues that are coupled to the redox reaction of the non-heme ion and responsible for its pH dependence remain unidentified. In this study, to clarify the mechanism of th ...
DOI:
10.1021/acs.biochem.1c00341

60. ATR–FTIR Detection of Metal-Sensitive Structural Changes in the Light-Harvesting 1 Reaction Center Complex from the Thermophilic Purple Sulfur Bacterium Thermochromatium tepidum

Author:
Li Yong; Kimura Yukihiro; Arikawa Teruhisa; Wang-Otomo Zheng-Yu; Ohno Takashi
Source:
Biochemistry 2013 v.52 no.50 pp. 9001-9008
ISSN:
1520-4995
Subject:
Allochromatium vinosum; Fourier transform infrared spectroscopy; Thermochromatium tepidum; amino acids; bacteria; barium; cadmium; calcium; light harvesting complex; polypeptides; strontium; sulfur; temperature; thermal stability
Abstract:
... Thermochromatium tepidum grows at the highest temperature among purple bacteria, and the light-harvesting 1 reaction center (LH1-RC) complex enhances the thermal stability by utilizing Ca²⁺, although the molecular mechanism has yet to be resolved. Here, we applied perfusion-induced attenuated total reflection (ATR) Fourier transform infrared (FTIR) spectroscopy to highly purified LH1-RC complexes ...
DOI:
10.1021/bi401033y

61. Aberrantly Large Single-Channel Conductance of Polyhistidine Arm-Containing Protein Nanopores

Author:
Thakur Avinash Kumar; Larimi Motahareh Ghahari; Gooden Kristin; Movileanu Liviu
Source:
Biochemistry 2017 v.56 no.36 pp. 4895-4905
ISSN:
1520-4995
Subject:
electrophysiology; lipid bilayers; monoclonal antibodies; nanopores; outer membrane proteins; potassium chloride
Abstract:
... There have been only a few studies reporting on the impact of polyhistidine affinity tags on the structure, function, and dynamics of proteins. Because of the relatively short size of the tags, they are often thought to have little or no effect on the conformation or activity of a protein. Here, using membrane protein design and single-molecule electrophysiology, we determined that the presence of ...
DOI:
10.1021/acs.biochem.7b00577
PubMed:
28812882
PubMed Central:
PMC5595664

62. Abietane-Type Diterpenoids Inhibit Protein Tyrosine Phosphatases by Stabilizing an Inactive Enzyme Conformation

Author:
Michael K. Hjortness; Laura Riccardi; Akarawin Hongdusit; Sophia Ruppe; Mengxia Zhao; Edward Y. Kim; Peter H. Zwart; Banumathi Sankaran; Haribabu Arthanari; Marcelo C. Sousa; Marco De Vivo; Jerome M. Fox
Source:
Biochemistry 2018 v.57 no.40 pp. 5886-5896
ISSN:
1520-4995
Subject:
abietic acid; active sites; diterpenoids; drugs; human diseases; inhibitory concentration 50; insulin; molecular dynamics; nuclear magnetic resonance spectroscopy; protein-tyrosine-phosphatase; simulation models; therapeutics
Abstract:
... Protein tyrosine phosphatases (PTPs) contribute to a striking variety of human diseases, yet they remain vexingly difficult to inhibit with uncharged, cell-permeable molecules; no inhibitors of PTPs have been approved for clinical use. This study uses a broad set of biophysical analyses to evaluate the use of abietane-type diterpenoids, a biologically active class of phytometabolites with largely ...
DOI:
10.1021/acs.biochem.8b00655
PubMed:
30169954
PubMed Central:
PMC6219988

63. The Ability of Insulin To Inhibit the Formation of Amyloid by Pro-Islet Amyloid Polypeptide Processing Intermediates Is Significantly Reduced in the Presence of Sulfated Glycosaminoglycans

Author:
Wang Hui; Raleigh Daniel P.
Source:
Biochemistry 2014 v.53 no.16 pp. 2605-2614
ISSN:
1520-4995
Subject:
amyloid; extracellular matrix; glycosaminoglycans; insulin; islets of Langerhans; noninsulin-dependent diabetes mellitus; polypeptides; proteoglycans
Abstract:
... Islet amyloid polypeptide (IAPP) is responsible for amyloid deposition in type 2 diabetes and plays an important role in the loss of β-cell mass associated with the disease and in the failure of islet transplants, but the mechanism of islet amyloid formation is not understood. The incorrect processing of proIAPP to produce partially processed forms of the peptide has been proposed to play a role i ...
DOI:
10.1021/bi4015488
PubMed:
24654599
PubMed Central:
PMC4010284

64. Abscisic Acid Acts as a Blocker of the Bitter Taste G Protein-Coupled Receptor T2R4

Author:
Pydi Sai P.; Jaggupilli Appalaraju; Nelson Ken M.; Abrams Suzanne R.; Bhullar Rajinder P.; Loewen Michele C.; Chelikani Prashen
Source:
Biochemistry 2015 v.54 no.16 pp. 2622-2631
ISSN:
1520-4995
Subject:
abscisic acid; agonists; antagonists; calcium; central nervous system; functional foods; gamma-aminobutyric acid; humans; image analysis; inhibitory concentration 50; molecular models; mouth; neurotransmitters; phaseic acid; quinine; reproductive system; respiratory system; site-directed mutagenesis; taste; taste receptors; yohimbine
Abstract:
... Bitter taste receptors (T2Rs) belong to the G protein-coupled receptor superfamily. In humans, 25 T2Rs mediate bitter taste sensation. In addition to the oral cavity, T2Rs are expressed in many extraoral tissues, including the central nervous system, respiratory system, and reproductive system. To understand the mechanistic roles of the T2Rs in oral and extraoral tissues, novel blockers or antagon ...
DOI:
10.1021/acs.biochem.5b00265

65. Abscisic Acid Analogues That Act as Universal or Selective Antagonists of Phytohormone Receptors

Author:
Rajagopalan Nandhakishore; Nelson Ken M.; Douglas Amy F.; Jheengut Vishal; Alarcon Idralyn Q.; McKenna Sean A.; Surpin Marci; Loewen Michele C.; Abrams Suzanne R.
Source:
Biochemistry 2016 v.55 no.36 pp. 5155-5164
ISSN:
1520-4995
Subject:
Arabidopsis thaliana; abscisic acid; antagonists; flowering; plant growth; receptors; screening
Abstract:
... The plant hormone abscisic acid (ABA) plays many important roles in controlling plant development and physiology, from flowering to senescence. ABA is now known to exert its effects through a family of soluble ABA receptors, which in Arabidopsis thaliana has 13 members divided into three clades. Homologues of these receptors are present in other plants, also in relatively large numbers. Investigat ...
DOI:
10.1021/acs.biochem.6b00605

66. Accessibility and External versus Intercalative Binding to DNA As Assessed by Oxygen-Induced Quenching of the Palladium(II)-Containing Cationic Porphyrins Pd(T4) and Pd(tD4)

Author:
Bork Matthew A.; Gianopoulos Christopher G.; Zhang Hanyu; Fanwick Phillip E.; Choi Jong Hyun; McMillin David R.
Source:
Biochemistry 2014 v.53 no.4 pp. 714-724
ISSN:
1520-4995
Subject:
DNA; X-ray diffraction; absorbance; cations; circular dichroism spectroscopy; ligands; oxygen; palladium; porphyrins; singlet oxygen
Abstract:
... Studies reveal that it is possible to design a palladium(II)-containing porphyrin to bind exclusively by intercalation to double-stranded DNA while simultaneously enhancing the ability to sensitize the formation of singlet oxygen. The comparisons revolve around the cations [5,10,15,20-tetra(N-methylpyridinium-4-yl)porphyrin]palladium(II), or Pd(T4), and [5,15-di(N-methylpyridinium-4-yl)porphyrin]p ...
DOI:
10.1021/bi401610t

67. Accessibility from the Cytoplasm Is Critical for ssrA Tag-Mediated Degradation of Integral Membrane Proteins by ClpXP Protease

Author:
Thilini Abeywansha; Qian Chai; Xinyi Zhang; Zhaoshuai Wang; Yinan Wei
Source:
Biochemistry 2018 v.57 no.38 pp. 5602-5608
ISSN:
1520-4995
Subject:
cytosol; membrane proteins; models; proteinases; ribosomes
Abstract:
... The AAA+ protease ClpXP has long been established as the cellular rescue system that degrades ssrA-tagged proteins resulting from stalled ribosomes. Until recently, in all of these studies soluble proteins were used as model substrates, since the ClpXP complex and the related adapter SspB are all cytosolic proteins. In a previous study, we found that the introduction of an ssrA tag can facilitate ...
DOI:
10.1021/acs.biochem.8b00641

68. Accumulation and Pulse Electron Paramagnetic Resonance Spectroscopic Investigation of the 4-Oxidobenzyl Radical Generated in the Radical S-Adenosyl-l-methionine Enzyme HydG

Author:
Guodong Rao; Nanhao Chen; David A. Marchiori; Lee-Ping Wang; R. David Britt
Source:
Biochemistry 2022 v.61 no.2 pp. 107-116
ISSN:
1520-4995
Subject:
S-adenosylmethionine; byproducts; electron paramagnetic resonance spectroscopy; enzymes; ligands; p-cresol; protonation; spectral analysis; tyrosine
Abstract:
... The radical S-adenosyl-l-methionine (SAM) enzyme HydG cleaves tyrosine to generate CO and CN– ligands of the [FeFe] hydrogenase H-cluster, accompanied by the formation of a 4-oxidobenzyl radical (4-OB•), which is the precursor to the HydG p-cresol byproduct. Native HydG only generates a small amount of 4-OB•, limiting detailed electron paramagnetic resonance (EPR) spectral characterization beyond ...
DOI:
10.1021/acs.biochem.1c00619

69. Accurate and Efficient One-Pot Reverse Transcription and Amplification of 2′-Fluoro-Modified Nucleic Acids by Commercial DNA Polymerases

Author:
Arianna S. Thompson; Susanna E. Barrett; Aurora G. Weiden; Ananya Venkatesh; Madison K. C. Seto; Simone Z. P. Gottlieb; Aaron M. Leconte
Source:
Biochemistry 2020 v.59 no.31 pp. 2833-2841
ISSN:
1520-4995
Subject:
DNA; DNA-directed DNA polymerase; RNA; RNA-directed DNA polymerase; biotechnology; frequency; materials; oligonucleotides; researchers; reverse transcription; sequence analysis; synthesis; synthetic biology
Abstract:
... DNA is a foundational tool in biotechnology and synthetic biology but is limited by sensitivity to DNA-modifying enzymes. Recently, researchers have identified DNA polymerases that can enzymatically synthesize long oligonucleotides of modified DNA (M-DNA) that are resistant to DNA-modifying enzymes. Most applications require M-DNA to be reverse transcribed, typically using a RNA reverse transcript ...
DOI:
10.1021/acs.biochem.0c00494

70. Acetylated Ubiquitin Modulates the Catalytic Activity of the E1 Enzyme Uba1

Author:
Rachel E. Lacoursiere; Gary S. Shaw
Source:
Biochemistry 2021 v.60 no.16 pp. 1276-1285
ISSN:
1520-4995
Subject:
DNA damage; acetylation; catalytic activity; energy transfer; enzymes; fluorescent dyes; lysine; protein degradation; proteomics; ubiquitin; ubiquitination
Abstract:
... Ubiquitin (Ub) signaling requires the covalent passage of Ub among E1, E2, and E3 enzymes. The choice of E2 and E3 enzymes combined with multiple rounds of the cascade leads to the formation of polyubiquitin chains linked through any one of the seven lysines on Ub. The linkage type and length act as a signal to trigger important cellular processes such as protein degradation or the DNA damage resp ...
DOI:
10.1021/acs.biochem.1c00145

71. Acetylation by Eis and Deacetylation by Rv1151c of Mycobacterium tuberculosis HupB: Biochemical and Structural Insight

Author:
Keith D. Green; Tapan Biswas; Allan H. Pang; Melisa J. Willby; Matthew S. Reed; Olga Stuchlik; Jan Pohl; James E. Posey; Oleg V. Tsodikov; Sylvie Garneau-Tsodikova
Source:
Biochemistry 2018 v.57 no.5 pp. 781-790
ISSN:
1520-4995
Subject:
Mycobacterium tuberculosis; acetylation; acetyltransferases; chromosomes; genome; mammals; post-translational modification; proteins
Abstract:
... Bacterial nucleoid-associated proteins (NAPs) are critical to genome integrity and chromosome maintenance. Post-translational modifications of bacterial NAPs appear to function similarly to their better studied mammalian counterparts. The histone-like NAP HupB from Mycobacterium tuberculosis (Mtb) was previously observed to be acetylated by the acetyltransferase Eis, leading to genome reorganizati ...
DOI:
10.1021/acs.biochem.7b01089
PubMed:
29345920
PubMed Central:
PMC5971062

72. Acetylation of Gly1 and Lys2 Promotes Aggregation of Human γD-Crystallin

Author:
DiMauro Michael A.; Nandi Sandip K.; Raghavan Cibin T.; Kar Rajiv Kumar; Wang Benlian; Bhunia Anirban; Nagaraj Ram H.; Biswas Ashis
Source:
Biochemistry 2014 v.53 no.46 pp. 7269-7282
ISSN:
1520-4995
Subject:
acetylation; cysteine; denaturation; glycine (amino acid); humans; hydrophobicity; lysine; mass spectrometry; proteins
Abstract:
... The human lens contains three major protein families: α-, β-, and γ-crystallin. Among the several variants of γ-crystallin in the human lens, γD-crystallin is a major form. γD-Crystallin is primarily present in the nuclear region of the lens and contains a single lysine residue at the second position (K2). In this study, we investigated the acetylation of K2 in γD-crystallin in aging and cataracto ...
DOI:
10.1021/bi501004y
PubMed:
25393041
PubMed Central:
PMC4245984

73. Acetylation of Lysine 92 Improves the Chaperone and Anti-apoptotic Activities of Human αB-Crystallin

Author:
Nahomi Rooban B.; Huang Rong; Nandi Sandip K.; Wang Benlian; Padmanabha Smitha; Santhoshkumar Puttur; Filipek Slawomir; Biswas Ashis; Nagaraj Ram H.
Source:
Biochemistry 2013 v.52 no.45 pp. 8126-8138
ISSN:
1520-4995
Subject:
acetylation; apoptosis; binding capacity; heart; humans; hydrodynamics; hydrophobicity; kidneys; lysine; molecular models; molecular weight; pro-apoptotic proteins; protein subunits; retina; tissues
Abstract:
... αB-Crystallin is a chaperone and an anti-apoptotic protein that is strongly expressed in many tissues, including the lens, retina, heart, and kidney. In the human lens, several lysine residues in αB-crystallin are acetylated. We have previously shown that such acetylation is predominant at lysine 92 (K92) and lysine 166 (K166). We have investigated the effect of lysine acetylation on the structure ...
DOI:
10.1021/bi400638s
PubMed:
24128140
PubMed Central:
PMC3889837

74. Acetylene is an active-site-directed, slow-binding, reversible inhibitor of Azotobacter vinelandii hydrogenase

Author:
Hyman, M.R.; Arp, D.J.
Source:
Biochemistry 1987 v.26 no.20 pp. 6447-6454
ISSN:
0006-2960
Subject:
Azotobacter vinelandii; enzyme inhibitors; acetylene; kinetics; binding sites
DOI:
10.1021/bi00394a023

75. The Achilles’ Heel of “Ultrastable” Hyperthermophile Proteins: Submillimolar Concentrations of SDS Stimulate Rapid Conformational Change, Aggregation, and Amyloid Formation in Proteins Carrying Overall Positive Charge

Author:
Khan Javed M.; Sharma Prerna; Arora Kanika; Kishor Nitin; Kaila Pallavi; Guptasarma Purnananda
Source:
Biochemistry 2016 v.55 no.28 pp. 3920-3936
ISSN:
1520-4995
Subject:
Pyrococcus furiosus; ambient temperature; amyloid; anionic surfactants; circular dichroism spectroscopy; electrostatic interactions; hydrophobic bonding; molecular weight; sodium dodecyl sulfate
Abstract:
... Low concentrations (<3.0 mM) of the anionic surfactant sodium dodecyl sulfate (SDS) have been shown to induce the formation of amyloid fibers in more than 20 different mesophile-derived proteins in the cationic state. It is not known whether SDS has similar effects on hyperthermophile-derived proteins, which are otherwise thought to be “ultrastable” and inordinately resistant to structural perturb ...
DOI:
10.1021/acs.biochem.5b01343

76. The Acidic Ribosomal Stalk Proteins Are Not Required for the Highly Specific Inactivation Exerted by α-Sarcin of the Eukaryotic Ribosome

Author:
Olombrada Miriam; Rodríguez-Mateos María; Prieto Daniel; Pla Jesús; Remacha Miguel; Martínez-del-Pozo Álvaro; Gavilanes José G.; Ballesta Juan P. G.; García-Ortega Lucía
Source:
Biochemistry 2014 v.53 no.10 pp. 1545-1547
ISSN:
1520-4995
Subject:
Saccharomyces cerevisiae; fungi; ribosomes; ricin; viability
Abstract:
... The ribosomal sarcin/ricin loop (SRL) is the target of ribosome-inactivating proteins like the N-glycosidase ricin and the fungal ribotoxin α-sarcin. The eukaryotic ribosomal stalk directly interacts with several members of the N-glycosidase family, favoring their disruption of the SRL. Here we tested this hypothesis for the ribotoxin α-sarcin. Experiments with isolated ribosomes, cell-free transl ...
DOI:
10.1021/bi401470u

77. Acid–Base Catalysis and Crystal Structures of a Least Evolved Ancestral GFP-like Protein Undergoing Green-to-Red Photoconversion

Author:
Kim Hanseong; Grunkemeyer Timothy J.; Modi Chintan; Chen Liqing; Fromme Raimund; Matz Mikhail V.; Wachter Rebekka M.
Source:
Biochemistry 2013 v.52 no.45 pp. 8048-8059
ISSN:
1520-4995
Subject:
active sites; breathing; carbon; catalytic activity; color; crystal structure; dissociation; fluorescent proteins; histidine; hydrogen bonding; pH; sequence analysis
Abstract:
... In green-to-red photoconvertible fluorescent proteins, a three-ring chromophore is generated by the light-activated incorporation of a histidine residue into the conjugated π-system. We have determined the pH–rate profile and high- and low-pH X-ray structures of a least evolved ancestor (LEA) protein constructed in the laboratory based on statistical sequence analysis. LEA incorporates the minimal ...
DOI:
10.1021/bi401000e

78. AcpM, the Meromycolate Extension Acyl Carrier Protein of Mycobacterium tuberculosis, Is Activated by the 4′-Phosphopantetheinyl Transferase PptT, a Potential Target of the Multistep Mycolic Acid Biosynthesis

Author:
Zimhony Oren; Schwarz Alon; Raitses-Gurevich Maria; Peleg Yoav; Dym Orly; Albeck Shira; Burstein Yigal; Shakked Zippora
Source:
Biochemistry 2015 v.54 no.14 pp. 2360-2371
ISSN:
1520-4995
Subject:
Mycobacterium tuberculosis; acids; acyl carrier protein; biosynthesis; catalytic activity; cell walls; electrostatic interactions; fatty-acid synthase; hydrophobicity; mass spectrometry; models; polyacrylamide gel electrophoresis; polyketide synthases
Abstract:
... Modification of acyl carrier proteins (ACP) or domains by the covalent binding of a 4′-phosphopantetheine (4′-PP) moiety is a fundamental condition for activation of fatty acid synthases (FASes) and polyketide synthases (PKSes). Binding of 4′-PP is mediated by 4′ phosphopantetheinyl transfersases (PPTases). Mycobacterium tuberculosis (Mtb) possesses two essential PPTases: acyl carrier protein synt ...
DOI:
10.1021/bi501444e

79. Acrolein Modification Impairs Key Functional Features of Rat Apolipoprotein E: Identification of Modified Sites by Mass Spectrometry

Author:
Tran Tuyen N.; Kosaraju Malathi G.; Tamamizu-Kato Shiori; Akintunde Olayemi; Zheng Ying; Bielicki John K.; Pinkerton Kent; Uchida Koji; Lee Yuan Yu; Narayanaswami Vasanthy
Source:
Biochemistry 2014 v.53 no.2 pp. 361-375
ISSN:
1520-4995
Subject:
acrolein; air; antibodies; apolipoprotein E; blood lipids; cholesterol; crosslinking; guanidines; homeostasis; lipid metabolism; lipid peroxidation; low density lipoprotein; lysine; macrophages; males; mass spectrometry; oils; pollutants; precipitin tests; rats; smoking (habit)
Abstract:
... Apolipoprotein E (apoE), an antiatherogenic apolipoprotein, plays a significant role in the metabolism of lipoproteins. It lowers plasma lipid levels by acting as a ligand for the low-density lipoprotein receptor (LDLr) family of proteins, in addition to playing a role in promoting macrophage cholesterol efflux in atherosclerotic lesions. The objective of this study is to examine the effect of acr ...
DOI:
10.1021/bi401404u
PubMed:
24325674
PubMed Central:
PMC3937454

80. The Actin Binding Affinity of the Utrophin Tandem Calponin-Homology Domain Is Primarily Determined by Its N-Terminal Domain

Author:
Singh Surinder M.; Bandi Swati; Winder Steve J.; Mallela Krishna M. G.
Source:
Biochemistry 2014 v.53 no.11 pp. 1801-1809
ISSN:
1520-4995
Subject:
actin; binding capacity; centrifugation; humans
Abstract:
... The structural determinants of the actin binding function of tandem calponin-homology (CH) domains are poorly understood, particularly the role of individual domains. We determined the actin binding affinity of isolated CH domains from human utrophin and compared them with the affinity of the full-length tandem CH domain. Traditional cosedimentation assays indicate that the C-terminal CH2 domain b ...
DOI:
10.1021/bi500149q

81. Actin Stimulates Reduction of the MICAL-2 Monooxygenase Domain

Author:
McDonald Claudia A.; Liu Ying Yi; Palfey Bruce A.
Source:
Biochemistry 2013 v.52 no.35 pp. 6076-6084
ISSN:
1520-4995
Subject:
NAD (coenzyme); NADP (coenzyme); actin; catalytic activity; enzymology; hydrides; hydrogen peroxide; isotopes; methionine; prostatic neoplasms; pyridines; sulfur
Abstract:
... MICALs are large, multidomain flavin-dependent monooxygenases that use redox chemistry to cause actin to depolymerize. Little enzymology has been reported for MICALs, and none has been reported for MICAL-2, an enzyme vital for the proliferation of prostate cancer. The monooxygenase domains of MICALs resemble aromatic hydroxylases, but their substrate is the sulfur of a methionine of actin. In orde ...
DOI:
10.1021/bi4008462

82. Actin–Curcumin Interaction: Insights into the Mechanism of Actin Polymerization Inhibition

Author:
Dhar Gopa; Chakravarty Devlina; Hazra Joyita; Dhar Jesmita; Poddar Asim; Pal Mahadeb; Chakrabarti Pinak; Surolia Avadhesha; Bhattacharyya Bhabatarak
Source:
Biochemistry 2015 v.54 no.4 pp. 1132-1143
ISSN:
1520-4995
Subject:
Curcuma longa; actin; aqueous solutions; binding sites; calorimetry; curcumin; fluorescence; medicinal properties; microtubules; molecular dynamics; molecular models; oxazoles; polymerization; receptors; rhizomes; thermodynamics; titration
Abstract:
... Curcumin, derived from rhizomes of the Curcuma longa plant, is known to possess a wide range of medicinal properties. We have examined the interaction of curcumin with actin and determined their binding and thermodynamic parameters using isothermal titration calorimetry. Curcumin is weakly fluorescent in aqueous solution, and binding to actin enhances fluorescence several fold with a large blue sh ...
DOI:
10.1021/bi5014408

83. Action and Timing of BacC and BacD in the Late Stages of Biosynthesis of the Dipeptide Antibiotic Bacilysin

Author:
Parker Jared B.; Walsh Christopher T.
Source:
Biochemistry 2013 v.52 no.5 pp. 889-901
ISSN:
1520-4995
Subject:
Bacillus subtilis; alanine; antibiotics; biosynthesis; diastereomers; enzymes; genes; in vitro studies; mutants; oxidation
Abstract:
... Biosynthesis of the dipeptide antibiotic bacilysin, encoded by the seven Bacillus subtilis genes bacA–G, involves diversion of flux from prephenate to the noncognate amino acid anticapsin. The anticapsin warhead is then ligated to the C-terminus of l-alanine to produce mature bacilysin. We have previously noted the formation of two diastereomers of tetrahydrotyrosine (4S- and 4R-H₄Tyr) by tandem a ...
DOI:
10.1021/bi3016229
PubMed:
23317005
PubMed Central:
PMC3568925

84. The Action of Cytochrome b5 on CYP2E1 and CYP2C19 Activities Requires Anionic Residues D58 and D65

Author:
Peng Hwei-Ming; Auchus Richard J.
Source:
Biochemistry 2013 v.52 no.1 pp. 210-220
ISSN:
1520-4995
Subject:
cytochrome P-450; electrons; hydrophilicity; mutation; phosphatidylcholines; phosphatidylethanolamines; phosphatidylserines
Abstract:
... The capacity of cytochrome b₅ (b₅) to influence cytochrome P450 activities has been extensively studied and physiologically validated. Apo-b₅ enhances the activities of CYP3A4, CYP2A6, CYP2C19, and CYP17A1 but not that of CYP2E1 or CYP2D6, suggesting that the b₅ interaction varies among P450s. We previously showed that b₅ residues E48 and E49 are required to stimulate the 17,20-lyase activity of C ...
DOI:
10.1021/bi301384n
PubMed:
23193974
PubMed Central:
PMC3596112

85. Activation Barrier-Limited Folding and Conformational Sampling of a Dynamic Protein Domain

Author:
Dogan Jakob; Toto Angelo; Andersson Eva; Gianni Stefano; Jemth Per
Source:
Biochemistry 2016 v.55 no.37 pp. 5289-5295
ISSN:
1520-4995
Subject:
Gibbs free energy; chemical reactions; ligands; nuclear magnetic resonance spectroscopy; protein-protein interactions; proteins; reaction mechanisms
Abstract:
... Folding reaction mechanisms of globular protein domains have been extensively studied by both experiment and simulation and found to be highly concerted chemical reactions in which numerous noncovalent bonds form in an apparent two-state fashion. However, less is known regarding intrinsically disordered proteins because their folding can usually be studied only in conjunction with binding to a lig ...
DOI:
10.1021/acs.biochem.6b00573

86. Activation Loop Dynamics Are Coupled to Core Motions in Extracellular Signal-Regulated Kinase-2

Author:
Dylan B. Iverson; Yao Xiao; David N. Jones; Elan Z. Eisenmesser; Natalie G. Ahn
Source:
Biochemistry 2020 v.59 no.29 pp. 2698-2706
ISSN:
1520-4995
Subject:
X-radiation; active sites; arginine; dynamics; enzyme activation; mitogen-activated protein kinase; mutation; nuclear magnetic resonance spectroscopy; phosphorylation; threonine; tyrosine
Abstract:
... The activation loop segment in protein kinases is a common site for regulatory phosphorylation. In extracellular signal-regulated kinase 2 (ERK2), dual phosphorylation and conformational rearrangement of the activation loop accompany enzyme activation. X-ray structures show the active conformation to be stabilized by multiple ion pair interactions between phosphorylated threonine and tyrosine resi ...
DOI:
10.1021/acs.biochem.0c00485

87. Activation Mechanism of the Bacteroides fragilis Cysteine Peptidase, Fragipain

Author:
Herrou Julien; Choi Vivian M.; Bubeck Wardenburg Juliane; Crosson Sean
Source:
Biochemistry 2016 v.55 no.29 pp. 4077-4084
ISSN:
1520-4995
Subject:
Bacteroides fragilis; active sites; alanine; arginine; cysteine proteinases; lysine; metalloproteinases; proteolysis; substrate specificity
Abstract:
... Enterotoxigenic Bacteroides fragilis produces a secreted metalloprotease known as B. fragilis toxin (BFT), which contributes to anaerobic sepsis, colitis, and colonic malignancy in mouse models of disease. A C11 family cysteine protease, fragipain (Fpn), directly activates BFT in the B. fragilis cell by removing the BFT prodomain. Fpn is itself a proenzyme and is autoactivated upon cleavage at an ...
DOI:
10.1021/acs.biochem.6b00546
PubMed:
27379832
PubMed Central:
PMC5053104

88. Activation Mechanism of the Streptomyces Tyrosinase Assisted by the Caddie Protein

Author:
Matoba Yasuyuki; Kihara Shogo; Muraki Yoshimi; Bando Naohiko; Yoshitsu Hironari; Kuroda Teruo; Sakaguchi Miyuki; Kayama Kure’e; Tai Hulin; Hirota Shun; Ogura Takashi; Sugiyama Masanori
Source:
Biochemistry 2017 v.56 no.41 pp. 5593-5603
ISSN:
1520-4995
Subject:
Streptomyces; aerobic conditions; anaerobic conditions; copper; electron paramagnetic resonance spectroscopy; melanogenesis; monophenol monooxygenase; phenol; quinones; reducing agents; spectral analysis; transportation; tyrosine
Abstract:
... Tyrosinase (EC 1.14.18.1), which possesses two copper ions at the active center, catalyzes a rate-limiting reaction of melanogenesis, that is, the conversion of a phenol to the corresponding ortho-quinone. The enzyme from the genus Streptomyces is generated as a complex with a “caddie” protein that assists the transport of two copper ions into the active center. In this complex, the Tyr⁹⁸ residue ...
DOI:
10.1021/acs.biochem.7b00635

89. Activation Microswitches in Adenosine Receptor A₂A Function as Rheostats in the Cell Membrane

Author:
Ning Ma; Sangbae Lee; Nagarajan Vaidehi
Source:
Biochemistry 2020 v.59 no.42 pp. 4059-4071
ISSN:
1520-4995
Subject:
cations; design; detergents; dynamics; heat; lipid bilayers; lipids; micelles; models; molecular dynamics; purinergic receptors
Abstract:
... Although multiple components of the cell membrane modulate the stability and activation of G protein-coupled receptors (GPCRs), insights into the dynamics of GPCR structures come from biophysical studies conducted in detergents. This is because of the challenges of studying activation in a multicomponent lipid bilayer. To understand the role of cellular membrane lipids and cations in GPCR activati ...
DOI:
10.1021/acs.biochem.0c00626

90. The Activation Parameters of a Cold-Adapted Short Chain Dehydrogenase Are Insensitive to Enzyme Oligomerization

Author:
Lucien Koenekoop; Florian van der Ent; Miha Purg; Johan Åqvist
Source:
Biochemistry 2022 v.61 no.7 pp. 514-522
ISSN:
1520-4995
Subject:
Gibbs free energy; catalytic activity; cold; computers; enthalpy; entropy; enzyme activity; evolution; oligomerization; oxidoreductases; temperature
Abstract:
... The structural principles of enzyme cold adaptation are of fundamental interest both for understanding protein evolution and for biotechnological applications. It has become clear in recent years that structural flexibility plays a major role in tuning enzyme activity at low temperatures, which is reflected by characteristic changes in the thermodynamic activation parameters for psychrophilic enzy ...
DOI:
10.1021/acs.biochem.2c00024

91. Activation and Loading of the Starter Unit during Thiocoraline Biosynthesis

Author:
Mori Shogo; Shrestha Sanjib K.; Fernández Javier; Álvarez San Millán María; Garzan Atefeh; Al-Mestarihi Ahmad H.; Lombó Felipe; Garneau-Tsodikova Sylvie
Source:
Biochemistry 2017 v.56 no.34 pp. 4457-4467
ISSN:
1520-4995
Subject:
active sites; acyl carrier protein; adenosine monophosphate; biochemical pathways; biosynthesis; fatty-acid synthase; multigene family; mutants; sequence homology
Abstract:
... The initiation of the nonribosomal peptide synthetase (NRPS) assembly of the bisintercalator natural product thiocoraline involves key enzymatic steps for AMP activation and carrier protein loading of the starter unit 3-hydroxyquinaldic acid (3HQA). Gene cluster data combined with protein sequence homology analysis originally led us to propose that TioJ could be responsible for the AMP activation ...
DOI:
10.1021/acs.biochem.7b00661

92. Activation of 11R-Lipoxygenase Is Fully Ca2+-Dependent and Controlled by the Phospholipid Composition of the Target Membrane

Author:
Järving Reet; Lõokene Aivar; Kurg Reet; Siimon Liina; Järving Ivar; Samel Nigulas
Source:
Biochemistry 2012 v.51 no.15 pp. 3310-3320
ISSN:
1520-4995
Subject:
arachidonic acid; calcium; enzyme activity; fluorometry; lipid composition; phosphatidylethanolamines; phosphatidylserines; surface plasmon resonance; synergism
Abstract:
... Activation of some lipoxygenases (LOX) is found to be related to the selective membrane binding upon cell stimulation. In this study, a systematic analysis of the effect of the lipid composition on the membrane binding efficiency, Ca²⁺ affinity, and enzymatic activity of 11R-LOX was performed. The analysis of the membrane targeting by fluorometric and surface plasmon resonance measurements in the ...
DOI:
10.1021/bi201690z

93. Activation of BNGR-A24 by Direct Interaction with Tachykinin-Related Peptides from the Silkworm Bombyx mori Leads to the Gq- and Gs-Coupled Signaling Cascades

Author:
He Xiaobai; Zang Jiashu; Li Xiangmei; Shao Jiajie; Yang Huipeng; Yang Jingwen; Huang Haishan; Chen Linjie; Shi Liangen; Zhu Chenggang; Zhang Guozheng; Zhou Naiming
Source:
Biochemistry 2014 v.53 no.42 pp. 6667-6678
ISSN:
1520-4995
Subject:
Bombyx mori; G-protein coupled receptors; calcium; cyclic AMP; ligands; mammals; neuropeptides; phosphorylation; reverse transcriptase polymerase chain reaction; silkworms
Abstract:
... Tachykinins constitute one of the largest peptide families in the animal kingdom and exert their diverse actions via G protein-coupled receptors (GPCRs). In this study, the Bombyx tachykinin-related peptides (TKRPs) were identified as specific endogenous ligands for the Bombyx neuropeptide GPCR A24 (BNGR-A24) and thus designated BNGR-A24 as BmTKRPR. Using both mammalian cell line HEK293 and insect ...
DOI:
10.1021/bi5007207

94. Activation of Chlamydomonas rhodopsin in vivo does not require isomerization of retinal

Author:
Foster, K.W.; Saranak, J.; Derguini, F.; Zarrilli, G.R.; Johnson, R.; Okabe, M.; Nakanishi, K.
Source:
Biochemistry 1989 v.28 no.2 pp. 819-824
ISSN:
0006-2960
Subject:
Chlamydomonas reinhardtii; isomerization; vitamin A
DOI:
10.1021/bi00428a061
PubMed:
2713348

95. Activation of Human Mitochondrial Lysyl-tRNA Synthetase upon Maturation of Its Premitochondrial Precursor

Author:
Dias José; Octobre Guillaume; Kobbi Lydia; Comisso Martine; Flisiak Sebastian; Mirande Marc
Source:
Biochemistry 2012 v.51 no.4 pp. 909-916
ISSN:
1520-4995
Subject:
Human immunodeficiency virus 1; alternative splicing; binding properties; dissociation; genes; humans; lysine-tRNA ligase; mitochondria; polypeptides; transfer RNA; virion
Abstract:
... The cytoplasmic and mitochondrial species of human lysyl-tRNA synthetase are encoded by a single gene by means of alternative splicing of the KARS1 gene. The cytosolic enzyme possesses a eukaryote-specific N-terminal polypeptide extension that confers on the native enzyme potent tRNA binding properties required for the vectorial transfer of tRNA from the synthetase to elongation factor EF1A within ...
DOI:
10.1021/bi201337b

96. Activation of Phenylalanine Hydroxylase by Phenylalanine Does Not Require Binding in the Active Site

Author:
Roberts Kenneth M.; Khan Crystal A.; Hinck Cynthia S.; Fitzpatrick Paul F.
Source:
Biochemistry 2014 v.53 no.49 pp. 7846-7853
ISSN:
1520-4995
Subject:
active sites; catecholamines; diet; fluorescence; hydroxylation; iron; liver; lysine; mutants; phenylalanine; phenylalanine 4-monooxygenase; tryptophan; tyrosine
Abstract:
... Phenylalanine hydroxylase (PheH), a liver enzyme that catalyzes the hydroxylation of excess phenylalanine in the diet to tyrosine, is activated by phenylalanine. The lack of activity at low levels of phenylalanine has been attributed to the N-terminus of the protein’s regulatory domain acting as an inhibitory peptide by blocking substrate access to the active site. The location of the site at whic ...
DOI:
10.1021/bi501183x
PubMed:
25453233
PubMed Central:
PMC4270383

97. Activation of Phosphorylase Kinase by Physiological Temperature

Author:
Herrera Julio E.; Thompson Jackie A.; Rimmer Mary Ashley; Nadeau Owen W.; Carlson Gerald M.
Source:
Biochemistry 2015 v.54 no.51 pp. 7524-7530
ISSN:
1520-4995
Subject:
adenosine diphosphate; behavior change; body temperature; hysteresis; orthophosphates; pH; phosphorylase kinase; phosphorylation; rabbits; skeletal muscle
Abstract:
... In the six decades since its discovery, phosphorylase kinase (PhK) from rabbit skeletal muscle has usually been studied at 30 °C; in fact, not a single study has examined functions of PhK at a rabbit’s body temperature, which is nearly 10 °C greater. Thus, we have examined aspects of the activity, regulation, and structure of PhK at temperatures between 0 and 40 °C. Between 0 and 30 °C, the activi ...
DOI:
10.1021/acs.biochem.5b01032
PubMed:
26632861
PubMed Central:
PMC5014378

98. The Activation of Protein Kinase A by the Calcium-Binding Protein S100A1 Is Independent of Cyclic AMP

Author:
Melville Zephan; Hernández-Ochoa Erick O.; Pratt Stephen J. P.; Liu Yewei; Pierce Adam D.; Wilder Paul T.; Adipietro Kaylin A.; Breysse Daniel H.; Varney Kristen M.; Schneider Martin F.; Weber David J.
Source:
Biochemistry 2017 v.56 no.17 pp. 2328-2337
ISSN:
1520-4995
Subject:
adenosine monophosphate; cAMP-dependent protein kinase; calcium; calmodulin; cyclic AMP; gene expression regulation; knockout mutants; skeletal muscle
Abstract:
... Biochemical and structural studies demonstrate that S100A1 is involved in a Ca²⁺-dependent interaction with the type 2α and type 2β regulatory subunits of protein kinase A (PKA) (RIIα and RIIβ) to activate holo-PKA. The interaction was specific for S100A1 because other calcium-binding proteins (i.e., S100B and calmodulin) had no effect. Likewise, a role for S100A1 in PKA-dependent signaling was es ...
DOI:
10.1021/acs.biochem.7b00117
PubMed:
28409622
PubMed Central:
PMC5415871

99. Activation of Proton Translocation by Respiratory Complex I

Author:
Belevich Nikolai; von Ballmoos Christoph; Verkhovskaya Marina
Source:
Biochemistry 2017 v.56 no.42 pp. 5691-5697
ISSN:
1520-4995
Subject:
NAD (coenzyme); NAD(P)H dehydrogenase (quinone); NADP (coenzyme); adenosinetriphosphatase; ambient temperature; enzyme activity; membrane permeability; protons; quinones
Abstract:
... Activation of proton pumping by reconstituted and native membrane-bound Complex I was studied using optical electric potential- and pH-sensitive probes. We find that reconstituted Complex I has a delay in proton translocation, which is significantly longer than the delay in quinone reductase activity, indicating an initially decoupled state of Complex I. Studies of the amount of NADH required for ...
DOI:
10.1021/acs.biochem.7b00727

100. Activation of UbcH5c∼Ub Is the Result of a Shift in Interdomain Motions of the Conjugate Bound to U-Box E3 Ligase E4B

Author:
Soss Sarah E.; Klevit Rachel E.; Chazin Walter J.
Source:
Biochemistry 2013 v.52 no.17 pp. 2991-2999
ISSN:
1520-4995
Subject:
dynamic models; nitrogen; nuclear magnetic resonance spectroscopy; post-translational modification; stable isotopes; ubiquitin; ubiquitin-protein ligase
Abstract:
... Post-translational modification of proteins with ubiquitin is mediated by dynamic multienzyme machinery (E1, E2, and E3). E3 ubiquitin ligases play a key role acting as both scaffolds to bring reactants together and activators to catalyze ubiquitin (Ub) transfer from E2∼Ub conjugates to substrates. Our recent studies provided insights into the mechanism of the activation event; binding of an E3 to ...
DOI:
10.1021/bi3015949
PubMed:
23550736
PubMed Central:
PMC3666176