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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. 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

7. 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

8. 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

9. 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

10. 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

11. 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

12. 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

13. 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

14. 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

15. 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

16. 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

17. 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

18. 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

19. 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

20. 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

21. 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

22. 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

23. 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

24. 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

25. 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

26. 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

27. 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

28. 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

29. 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

30. 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

31. 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

32. 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

33. 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

34. 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

35. 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

36. 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

37. 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

38. 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

39. 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

40. 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

41. 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

42. 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

43. 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

44. 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

45. 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

46. 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

47. 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

48. 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

49. 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

50. 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

51. 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

52. 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

53. 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

54. 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

55. 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

56. 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

57. 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

58. 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

59. 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

60. 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

61. 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

62. 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

63. 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

64. 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

65. 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

66. 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

67. 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

68. 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

69. 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

70. 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

71. 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

72. Activation of a Unique Flavin-Dependent tRNA-Methylating Agent

Author:
Hamdane Djemel; Bruch Eduardo; Un Sun; Field Martin; Fontecave Marc
Source:
Biochemistry 2013 v.52 no.49 pp. 8949-8956
ISSN:
1520-4995
Subject:
Bacillus subtilis; active sites; cysteine; flavin-adenine dinucleotide; hydroquinone; methylation; methyltransferases; pH; spectroscopy; sulfur; transfer RNA
Abstract:
... TrmFO is a tRNA methyltransferase that uses methylenetetrahydrofolate (CH₂THF) and flavin adenine dinucleotide hydroquinone as cofactors. We have recently shown that TrmFO from Bacillus subtilis stabilizes a TrmFO–CH₂–FADH adduct and an ill-defined neutral flavin radical. The adduct contains a unique N–CH₂–S moiety, with a methylene group bridging N⁵ of the isoalloxazine ring and the sulfur of an ...
DOI:
10.1021/bi4013879

73. Activation of the Class Ib Ribonucleotide Reductase by a Flavodoxin Reductase in Bacillus cereus

Author:
Lofstad Marie; Gudim Ingvild; Hammerstad Marta; Røhr ÅsmundKjendseth; Hersleth Hans-Petter
Source:
Biochemistry 2016 v.55 no.36 pp. 4998-5001
ISSN:
1520-4995
Subject:
Bacillus cereus; aerobic conditions; catalytic activity; ferredoxin-NADP reductase; flavoproteins; ribonucleotide reductase; ribonucleotides; spectral analysis
Abstract:
... To reduce ribonucleotides to deoxyribonucleotides, the manganese-bound form of class Ib ribonucleotide reductase (RNR) must be activated via a pathway that involves redox protein(s). The reduced flavoprotein NrdI is an important protein in this pathway, as it reduces dioxygen to superoxide. Superoxide then reacts with the RNR Mnᴵᴵ₂ site to generate a tyrosyl radical that is required for catalysis. ...
DOI:
10.1021/acs.biochem.6b00699

74. Activation of the Epidermal Growth Factor Receptor: A Series of Twists and Turns

Author:
Poger David; Mark Alan E.
Source:
Biochemistry 2014 v.53 no.16 pp. 2710-2721
ISSN:
1520-4995
Subject:
carcinogenesis; dimerization; epidermal growth factor; epidermal growth factor receptors; models; molecular dynamics; plasma membrane; protein subunits; transforming growth factor alpha
Abstract:
... The cell surface epidermal growth factor receptor (EGFR) plays a critical role in cell development and oncogenesis. The binding of growth factors to the EGFR results in a mechanical signal being transmitted through the plasma membrane. In this study, atomistic molecular dynamics simulations have been used to investigate the conformational changes associated with the binding of the epidermal growth ...
DOI:
10.1021/bi401632z

75. Activation of the glmS Ribozyme Nucleophile via Overdetermined Hydrogen Bonding

Author:
Bingaman Jamie L.; Gonzalez Inanllely Y.; Wang Bo; Bevilacqua Philip C.
Source:
Biochemistry 2017 v.56 no.33 pp. 4313-4317
ISSN:
1520-4995
Subject:
Lewis bases; acidification; active sites; hydrogen bonding; oxygen; phosphates; ribozymes
Abstract:
... RNA enzymes, or ribozymes, catalyze internal phosphodiester bond cleavage using diverse catalytic strategies. These include the four classic strategies: in-line nucleophilic attack, deprotonation of the 2′-OH nucleophile, protonation of the 5′-O leaving group, and stabilization of developing charge on the nonbridging oxygen atoms of the scissile phosphate. In addition, we recently identified two a ...
DOI:
10.1021/acs.biochem.7b00662

76. Activation of the multicatalytic endopeptidase by oxidants. Effects on enzyme structure

Author:
Strack, P.R.; Waxman, L.; Fagan, J.M.
Source:
Biochemistry 1996 v.35 no.22 pp. 7142-7149
ISSN:
0006-2960
Subject:
benzenesulfonic acid; cysteine proteinase inhibitors; dissociation; dithiothreitol; enzyme activity; functional properties; hydrogen peroxide; hydrophobicity; metabolites; oxidants; peptides; polyacrylamide gel electrophoresis; proteasome endopeptidase complex; proteins; proteolysis; reducing agents; serine proteinases
Abstract:
... It is well established that the functional properties of proteins can be compromised by oxidative damage and, in vivo, proteins modified by oxidants are rapidly degraded. It was hypothesized that oxidants may also affect the ability of proteases to hydrolyze peptides and proteins. We therefore examined the effect of oxidants on the endopeptidase activities of the 650 kDa 20S proteasome or multicat ...
DOI:
10.1021/bi9518048
PubMed:
8679541

77. Active Site Architecture of a Sugar N-Oxygenase

Author:
Thoden James B.; Branch Megan C.; Zimmer Alex L.; Bruender Nathan A.; Holden Hazel M.
Source:
Biochemistry 2013 v.52 no.19 pp. 3191-3193
ISSN:
1520-4995
Subject:
active sites; antibiotics; apoproteins; models; sugars
Abstract:
... KijD3 is a flavin-dependent N-oxygenase implicated in the formation of the nitro-containing sugar d-kijanose, found attached to the antibiotic kijanimicin. For this investigation, the structure of KijD3 in complex with FMN and its dTDP-sugar substrate was solved to 2.1 Å resolution. In contrast to the apoenzyme structure, the C-terminus of the protein becomes ordered and projects into the active s ...
DOI:
10.1021/bi400407x

78. Active Site Binding and Catalytic Role of Bicarbonate in 1,4-Dihydroxy-2-naphthoyl Coenzyme A Synthases from Vitamin K Biosynthetic Pathways

Author:
Sun Yueru; Song Haigang; Li Jie; Jiang Ming; Li Yan; Zhou Jiahai; Guo Zhihong
Source:
Biochemistry 2012 v.51 no.22 pp. 4580-4589
ISSN:
1520-4995
Subject:
Escherichia coli; Synechocystis; active sites; aspartic acid; bicarbonates; binding sites; biochemical pathways; biosynthesis; coenzyme A; crystal structure; electrostatic interactions; enzyme activity; hydrogen bonding; hydrophobic bonding; nitrates; phylloquinone
Abstract:
... 1,4-Dihydroxy-2-naphthoyl coenzyme A (DHNA-CoA) synthase, or MenB, catalyzes a carbon–carbon bond formation reaction in the biosynthesis of both vitamin K1 and K2. Bicarbonate is crucial to the activity of a large subset of its orthologues but lacks a clearly defined structural and mechanistic role. Here we determine the crystal structure of the holoenzymes from Escherichia coli at 2.30 Å and Syne ...
DOI:
10.1021/bi300486j

79. Active Site Desolvation and Thermostability Trade-Offs in the Evolution of Catalytically Diverse Triazine Hydrolases

Author:
Sugrue Elena; Carr Paul D.; Scott Colin; Jackson Colin J.
Source:
Biochemistry 2016 v.55 no.45 pp. 6304-6313
ISSN:
1520-4995
Subject:
Nocardioides; active sites; atrazine chlorohydrolase; catalytic activity; crystal structure; evolution; glutamic acid; glutamine; hydrophilicity; hydrophobicity; mutants; mutation; pH; thermal stability; triazines
Abstract:
... The desolvation of ionizable residues in the active sites of enzymes and the subsequent effects on catalysis and thermostability have been studied in model systems, yet little about how enzymes can naturally evolve to include active sites with highly reactive and desolvated charges is known. Variants of triazine hydrolase (TrzN) with significant differences in their active sites have been isolated ...
DOI:
10.1021/acs.biochem.6b00731

80. Active Site Hydrogen Bonding Induced in Cytochrome P450cam by Effector Putidaredoxin

Author:
Claire C. Mammoser; Sashary Ramos; Megan C. Thielges
Source:
Biochemistry 2021 v.60 no.21 pp. 1699-1707
ISSN:
1520-4995
Subject:
active sites; catalytic activity; cytochrome P-450; electron transfer; hydrogen; hydrogen bonding; infrared spectroscopy; ligands; oxygen; solvents
Abstract:
... Cytochrome P450s are diverse and powerful catalysts that can activate molecular oxygen to oxidize a wide variety of substrates. Catalysis relies on effective uptake of two electrons and two protons. For cytochrome P450cam, an archetypal member of the superfamily, the second electron must be supplied by the redox partner putidaredoxin (Pdx). Pdx also plays an effector role beyond electron transfer, ...
DOI:
10.1021/acs.biochem.1c00075

81. Active Site Midpoint Potentials in Different Cytochrome c Oxidase Families: A Computational Comparison

Author:
Margareta R.A. Blomberg
Source:
Biochemistry 2019 v.58 no.15 pp. 2028-2038
ISSN:
1520-4995
Subject:
Gibbs free energy; active sites; catalytic activity; chemical bonding; cytochrome-c oxidase; electrochemistry; electron transfer; electron transport chain; heme; models; oxygen; quantum mechanics; tyrosine
Abstract:
... Cytochrome c oxidase (CcO) is the terminal enzyme in the respiratory electron transport chain, reducing molecular oxygen to water. The binuclear active site in CcO comprises a high-spin heme associated with a CuB complex and a redox active tyrosine. The electron transport in the respiratory chain is driven by increasing midpoint potentials of the involved cofactors, resulting in a release of free ...
DOI:
10.1021/acs.biochem.9b00093

82. Active Site Structure and Peroxidase Activity of Oxidatively Modified Cytochrome c Species in Complexes with Cardiolipin

Author:
Capdevila Daiana A.; Oviedo Rouco Santiago; Tomasina Florencia; Tortora Verónica; Demicheli Verónica; Radi Rafael; Murgida Daniel H.
Source:
Biochemistry 2015 v.54 no.51 pp. 7491-7504
ISSN:
1520-4995
Subject:
active sites; apoptosis; binding capacity; cytochrome c; enzyme activity; heme; lipid peroxidation; methionine; oxidative stress; peroxidase; post-translational modification; spectroscopy; tyrosine
Abstract:
... We report a resonance Raman and UV–vis characterization of the active site structure of oxidatively modified forms of cytochrome c (Cyt-c) free in solution and in complexes with cardiolipin (CL). The studied post-translational modifications of Cyt-c include methionine sulfoxidation and tyrosine nitration, which lead to altered heme axial ligation and increased peroxidase activity with respect to t ...
DOI:
10.1021/acs.biochem.5b00922

83. Active Site Substitution A82W Improves the Regioselectivity of Steroid Hydroxylation by Cytochrome P450 BM3 Mutants As Rationalized by Spin Relaxation Nuclear Magnetic Resonance Studies

Author:
Rea V.; Kolkman A. J.; Vottero E.; Stronks E. J.; Ampt K. A. M.; Honing M.; Vermeulen N. P. E.; Wijmenga S. S.; Commandeur J. N. M.
Source:
Biochemistry 2012 v.51 no.3 pp. 750-760
ISSN:
1520-4995
Subject:
Bacillus megaterium; active sites; alanine; cytochrome P-450; heme iron; hydroxylation; mutants; mutation; nuclear magnetic resonance spectroscopy; protons; steroids; testosterone; tryptophan
Abstract:
... Cytochrome P450 BM3 from Bacillus megaterium is a monooxygenase with great potential for biotechnological applications. In this paper, we present engineered drug-metabolizing P450 BM3 mutants as a novel tool for regioselective hydroxylation of steroids at position 16β. In particular, we show that by replacing alanine at position 82 with a tryptophan in P450 BM3 mutants M01 and M11, the selectivity ...
DOI:
10.1021/bi201433h

84. Active Sites of Spinoxin, a Potassium Channel Scorpion Toxin, Elucidated by Systematic Alanine Scanning

Author:
Peigneur Steve; Yamaguchi Yoko; Kawano Chihiro; Nose Takeru; Nirthanan Selvanayagam; Gopalakrishnakone Ponnampalam; Tytgat Jan; Sato Kazuki
Source:
Biochemistry 2016 v.55 no.21 pp. 2927-2935
ISSN:
1520-4995
Subject:
Heterometrus; active sites; alanine; crosslinking; diagnostic techniques; disulfide bonds; inhibitory concentration 50; neoplasms; neurotoxins; potassium channels; structure-activity relationships; therapeutics; venoms
Abstract:
... Peptide toxins from scorpion venoms constitute the largest group of toxins that target the voltage-gated potassium channel (Kv). Spinoxin (SPX) isolated from the venom of scorpion Heterometrus spinifer is a 34-residue peptide neurotoxin cross-linked by four disulfide bridges. SPX is a potent inhibitor of Kv1.3 potassium channels (IC₅₀ = 63 nM), which are considered to be valid molecular targets in ...
DOI:
10.1021/acs.biochem.6b00139

85. Active and resting states of the O2-evolving complex of photosystem II

Author:
Beck, W.F.; De Paula, J.C.; Brudvig, G.W.
Source:
Biochemistry 1985 v.24 no.12 pp. 3035-3043
ISSN:
0006-2960
Subject:
Spinacia oleracea; photosystem II; oxygen consumption; dark adaptation
DOI:
10.1021/bi00333a035
PubMed:
2990539

86. An Active, Ligand-Responsive Pulling Geometry Reports on Internal Signaling between Subdomains of the DnaK Nucleotide-Binding Domain in Single-Molecule Mechanical Experiments

Author:
Sarah Meinhold; Daniela Bauer; Jonas Huber; Ulrich Merkel; Andreas Weißl; Gabriel Žoldák; Matthias Rief
Source:
Biochemistry 2019 v.58 no.47 pp. 4744-4750
ISSN:
1520-4995
Subject:
forces; geometry; mutation; paper; proteins
Abstract:
... Single-molecule mechanical experiments have proven to be ideal tools for probing the energetics and mechanics of large proteins and domains. In this paper, we investigate the nucleotide-dependent unfolding mechanics of the nucleotide-binding domain (NBD) of the Hsp70 chaperone DnaK. The NBD binds ADP or ATP in the binding cleft formed by lobe I and lobe II, which consists of two subdomains each. W ...
DOI:
10.1021/acs.biochem.9b00155

87. Active-site binding of glycosides by Thermomonospora fusca endocellulase E2

Author:
Barr, B.K.; Wolfgang, D.E.; Piens, K.; Claeyssens, M.; Wilson, D.B.
Source:
Biochemistry 1998 v.37 no.26 pp. 9220-9229
ISSN:
0006-2960
Subject:
Thermobifida fusca; Trichoderma reesei; active sites; binding capacity; calorimetry; cellobiose; endo-1,4-beta-glucanase; fluorescence; glycosides; hydrolysis; ligands; mutagenesis; polymerase chain reaction; structure-activity relationships; titration
Abstract:
... The determination of the high-resolution structure of the Thermomonospora fusca endocellulase E2 catalytic domain makes it ideal for exploring cellulase structure-function relationships. Here we present binding parameters (K(d) delta H degree, and delta S degree) describing the interaction of E2 with 4-methylumbelliferyl glycosides, determined by titrating the quenching of ligand fluorescence in e ...
DOI:
10.1021/bi980063i
PubMed:
9649302

88. Activities and interfacial properties of Rhizopus delemar and porcine pancreatic lipases after treatment with phospholipids

Author:
Sugihara, A.; Gargouri, Y.; Pieroni, G.; Riviere, C.; Sarda, L.; Verger, R.
Source:
Biochemistry 1986 v.25 no.11 pp. 3430-3434
ISSN:
0006-2960
Subject:
swine; pancreas; enzyme activity; triacylglycerol lipase; Rhizopus; phospholipids
DOI:
10.1021/bi00359a050

89. Activities of Topoisomerase I in Its Complex with SRSF1

Author:
Ishikawa Takao; Krzysko Krystiana A.; Kowalska-Loth Barbara; Skrajna Aleksandra M.; Czubaty Alicja; Girstun Agnieszka; Cieplak Maja K.; Lesyng Bogdan; Staron Krzysztof
Source:
Biochemistry 2012 v.51 no.8 pp. 1803-1816
ISSN:
1520-4995
Subject:
DNA; DNA topoisomerase; binding sites; humans; models; mutants; phosphorylation
Abstract:
... Human DNA topoisomerase I (topo I) catalyzes DNA relaxation and phosphorylates SRSF1. Whereas the structure of topo I complexed with DNA has been resolved, the structure of topo I in the complex with SRSF1 and structural determinants of topo I activities in this complex are not known. The main obstacle to resolving the structure is a contribution of unfolded domains of topo I and SRSF1 in formatio ...
DOI:
10.1021/bi300043t

90. Activity Enhancement of the Synthetic Syrbactin Proteasome Inhibitor Hybrid and Biological Evaluation in Tumor Cells

Author:
Archer Crystal R.; Groll Michael; Stein Martin L.; Schellenberg Barbara; Clerc Jérôme; Kaiser Markus; Kondratyuk Tamara P.; Pezzuto John M.; Dudler Robert; Bachmann André S.
Source:
Biochemistry 2012 v.51 no.34 pp. 6880-6888
ISSN:
1520-4995
Subject:
active sites; animal ovaries; antineoplastic agents; cell growth; chemical elements; eukaryotic cells; myeloma; neoplasm cells; ovarian neoplasms; proteasome endopeptidase complex; structure-activity relationships; transcription factor NF-kappa B
Abstract:
... Syrbactins belong to a recently emergent class of bacterial natural product inhibitors that irreversibly inhibit the proteasome of eukaryotes by a novel mechanism. The total syntheses of the syrbactin molecules syringolin A, syringolin B, and glidobactin A have been achieved, which allowed the preparation of syrbactin-inspired derivatives, such as the syringolin A–glidobactin A hybrid molecule (Sy ...
DOI:
10.1021/bi300841r

91. Activity Mapping the Acyl Carrier Protein: Elongating Ketosynthase Interaction in Fatty Acid Biosynthesis

Author:
Jeffrey T. Mindrebo; Laetitia E. Misson; Caitlin Johnson; Joseph P. Noel; Michael D. Burkart
Source:
Biochemistry 2020 v.59 no.38 pp. 3626-3638
ISSN:
1520-4995
Subject:
Escherichia coli; active sites; acyl carrier protein; biochemical pathways; biosynthesis; engineering; fatty acids; fatty-acid synthase; mutants; polyketide synthases; sequence analysis; site-directed mutagenesis; surfaces
Abstract:
... Elongating ketosynthases (KSs) catalyze carbon–carbon bond-forming reactions during the committed step for each round of chain extension in both fatty acid synthases (FASs) and polyketide synthases (PKSs). A small α-helical acyl carrier protein (ACP) shuttles fatty acyl intermediates between enzyme active sites. To accomplish this task, the ACP relies on a series of dynamic interactions with multi ...
DOI:
10.1021/acs.biochem.0c00605

92. Activity of Antimicrobial Peptide Aggregates Decreases with Increased Cell Membrane Embedding Free Energy Cost

Author:
Rongfeng Zou; Xiaomin Zhu; Yaoquan Tu; Junchen Wu; Markita P. Landry
Source:
Biochemistry 2018 v.57 no.18 pp. 2606-2610
ISSN:
1520-4995
Subject:
Gibbs free energy; Gram-negative bacteria; adenosine monophosphate; antibacterial properties; antibiotic resistance; antibiotics; antimicrobial peptides; bacterial infections; cell membranes; energy costs; hydrogen bonding; hydrophobicity; molecular dynamics; prediction; simulation models
Abstract:
... Antimicrobial peptides (AMPs) are a promising alternative to antibiotics for mitigating bacterial infections, in light of increasing bacterial resistance to antibiotics. However, predicting, understanding, and controlling the antibacterial activity of AMPs remain a significant challenge. While peptide intramolecular interactions are known to modulate AMP antimicrobial activity, peptide intermolecu ...
DOI:
10.1021/acs.biochem.8b00052

93. Activity of Topotecan toward the DNA/Topoisomerase I Complex: A Theoretical Rationalization

Author:
Semiha Kevser Bali; Antoine Marion; Ilke Ugur; Ayse Kumru Dikmenli; Saron Catak; Viktorya Aviyente
Source:
Biochemistry 2018 v.57 no.9 pp. 1542-1551
ISSN:
1520-4995
Subject:
DNA; DNA topoisomerase; active sites; antineoplastic agents; asparagine; binding capacity; hydrogen bonding; lysine; nucleobases; pH; quantum mechanics; topology
Abstract:
... Topotecan (TPT) is a nontoxic anticancer drug characterized by a pH-dependent lactone/carboxyl equilibrium. TPT acts on the covalently bonded DNA/topoisomerase I (DNA/TopoI) complex by intercalating between two DNA bases at the active site. This turns TopoI into a DNA-damaging agent and inhibits supercoil relaxation. Although only the lactone form of the drug is active and effectively inhibits Top ...
DOI:
10.1021/acs.biochem.7b01297

94. Activity-Based Protein Profiling of the Escherichia coli GlpG Rhomboid Protein Delineates the Catalytic Core

Author:
Sherratt Allison R.; Blais David R.; Ghasriani Houman; Pezacki John Paul; Goto Natalie K.
Source:
Biochemistry 2012 v.51 no.39 pp. 7794-7803
ISSN:
1520-4995
Subject:
Escherichia coli; active sites; bacteria; catalytic activity; enzyme activity; functional status; humans; hydrolysis; lipid bilayers; mutation; nuclear magnetic resonance spectroscopy; proteinases; proteins; proteolysis; proteomics
Abstract:
... Rhomboid proteins comprise the largest class of intramembrane protease known, being conserved from bacteria to humans. The functional status of these proteases is typically assessed through direct or indirect detection of peptide cleavage products. Although these assays can report on the ability of a rhomboid to catalyze peptide bond cleavage, differences in measured hydrolysis rates can reflect c ...
DOI:
10.1021/bi301087c

95. Activity-Dependent Phosphorylation of Dynamin 1 at Serine 857

Author:
Xie Wen; Adayev Tatyana; Zhu Huiyuan; Wegiel Jerzy; Wieraszko Andrzej; Hwang Yu-Wen
Source:
Biochemistry 2012 v.51 no.34 pp. 6786-6796
ISSN:
1520-4995
Subject:
Down syndrome; axons; chromosomes; dendrites; dephosphorylation; dynamins; fluorescent antibody technique; hippocampus; nerve tissue; protein phosphorylation; receptors; serine; staining; synapse; synaptic transmission
Abstract:
... Dynamin 1 is thought to mediate synaptic transmission through interactions with multiple endocytic accessory proteins in a phosphorylation-dependent manner. Previously, we have shown that DYRK1A, a chromosome 21-encoded kinase implicated in the mental retardation of Down syndrome, phosphorylates primarily serine 857 (S857) in the proline-rich domain, found only in 1xa, one of the alternative C-ter ...
DOI:
10.1021/bi2017798

96. The Acyl-CoA Specificity of Human Lysine Acetyltransferase KAT2A

Author:
Ananya Anmangandla; Yuxiang Ren; Qin Fu; Sheng Zhang; Hening Lin
Source:
Biochemistry 2022 v.61 no.17 pp. 1874-1882
ISSN:
1520-4995
Subject:
acetylation; histone acetyltransferase; histone deacetylase; histones; humans; lysine; lysine N-acetyltransferase; malonyl coenzyme A; metabolism; signal transduction; substrate specificity
Abstract:
... Protein post-translational modifications serve to regulate a broad range of cellular functions including signal transduction, transcription, and metabolism. Protein lysine residues undergo many post-translational acylations and are regulated by a range of enzymes, such as histone acetyl transferases (HATs) and histone deacetylases (HDACs). KAT2A, well characterized as a lysine acetyltransferase fo ...
DOI:
10.1021/acs.biochem.2c00308

97. Adapter Proteins for Opposing Motors Interact Simultaneously with Nuclear Pore Protein Nup358

Author:
Heying Cui; Crystal R. Noell; Rachael P. Behler; Jacqueline B. Zahn; Lynn R. Terry; Blaine B. Russ; Sozanne R. Solmaz
Source:
Biochemistry 2019 v.58 no.50 pp. 5085-5097
ISSN:
1520-4995
Subject:
binding sites; brain; chromosome segregation; dynein ATPase; insects; light; microtubules; mitotic spindle apparatus; motors; mutation; nuclear pore; oligomerization; protein subunits; proteins; vertebrates
Abstract:
... Nup358 is a protein subunit of the nuclear pore complex that recruits the opposing microtubule motors kinesin-1 and dynein [via the dynein adaptor Bicaudal D2 (BicD2)] to the nuclear envelope. This pathway is important for positioning of the nucleus during the early steps of mitotic spindle assembly and also essential for an important process in brain development. It is unknown whether dynein and ...
DOI:
10.1021/acs.biochem.9b00907

98. An Additional Role for the Brønsted Acid–Base Catalysts of Mandelate Racemase in Transition State Stabilization

Author:
Nagar Mitesh; Bearne Stephen L.
Source:
Biochemistry 2015 v.54 no.44 pp. 6743-6752
ISSN:
1520-4995
Subject:
aromatic compounds; binding capacity; biochemistry; calorimetry; carbon; catalysts; catalytic activity; enantiomers; hydrophobic bonding; ligands; mutants; site-directed mutagenesis; titration
Abstract:
... Mandelate racemase (MR) catalyzes the interconversion of the enantiomers of mandelate and serves as a paradigm for understanding the enzyme-catalyzed abstraction of an α-proton from a carbon acid substrate with a high pKₐ. The enzyme utilizes a two-base mechanism with Lys 166 and His 297 acting as Brønsted acid and base catalysts, respectively, in the R → S reaction direction. In the S → R reactio ...
DOI:
10.1021/acs.biochem.5b00982

99. Adenine Phosphoribosyltransferase from Sulfolobus solfataricus Is an Enzyme with Unusual Kinetic Properties and a Crystal Structure that Suggests It Evolved from a 6-Oxopurine Phosphoribosyltransferase

Author:
Jensen Kaj Frank; Hansen Michael Riis; Jensen Kristine Steen; Christoffersen Stig; Poulsen Jens-Christian Navarro; Mølgaard Anne; Kadziola Anders
Source:
Biochemistry 2015 v.54 no.14 pp. 2323-2334
ISSN:
1520-4995
Subject:
Sulfolobus solfataricus; active sites; adenine; adenine phosphoribosyltransferase; adenosine diphosphate; adenosine monophosphate; binding properties; binding sites; buffers; crystal structure; crystals; hydrolysis; open reading frames; pH; phosphates; polypeptides
Abstract:
... The adenine phosphoribosyltransferase (APRTase) encoded by the open reading frame SSO2342 of Sulfolobus solfataricus P2 was subjected to crystallographic, kinetic, and ligand binding analyses. The enzyme forms dimers in solution and in the crystals, and binds one molecule of the reactants 5-phosphoribosyl-α-1-pyrophosphate (PRPP) and adenine or the product adenosine monophosphate (AMP) or the inhi ...
DOI:
10.1021/bi501334m

100. Adenylate Kinase-Catalyzed Reaction of AMP in Pieces: Enzyme Activation for Phosphoryl Transfer to Phosphite Dianion

Author:
Patrick L. Fernandez; John P. Richard
Source:
Biochemistry 2021 v.60 no.35 pp. 2672-2676
ISSN:
1520-4995
Subject:
adenine; adenosine; adenylate kinase; catalytic activity; energy; enzyme activation
Abstract:
... The binding of adenosine 5′-triphosphate (ATP) and adenosine 5′-monophosphate (AMP) to adenylate kinase (AdK) drives closure of lids over the substrate adenosyl groups. We test the hypothesis that this conformational change activates AdK for catalysis. The rate constants for Homo sapiens adenylate kinase 1 (HsAdK1)-catalyzed phosphoryl group transfer to AMP, kcₐₜ/Kₘ = 7.0 × 10⁶ M–¹ s–¹, and phosph ...
DOI:
10.1021/acs.biochem.1c00535