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You searched for: Journal name Biochemistry Remove constraint Journal name: Biochemistry Subject term models Remove constraint Subject term: models
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1. (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

2. 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

3. 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

4. A Binary Arginine Methylation Switch on Histone H3 Arginine 2 Regulates Its Interaction with WDR5

Author:
Benjamin M. Lorton; Rajesh K. Harijan; Emmanuel S. Burgos; Jeffrey B. Bonanno; Steven C. Almo; David Shechter
Source:
Biochemistry 2020 v.59 no.39 pp. 3696-3708
ISSN:
1520-4995
Subject:
arginine; crystal structure; epigenetics; histones; methylation; models; peptides; protein arginine methyltransferases
Abstract:
... Histone H3 arginine 2 (H3R2) is post-translationally modified in three different states by “writers” of the protein arginine methyltransferase (PRMT) family. H3R2 methylarginine isoforms include PRMT5-catalyzed monomethylation (me1) and symmetric dimethylation (me2s) and PRMT6-catalyzed me1 and asymmetric dimethylation (me2a). WD-40 repeat-containing protein 5 (WDR5) is an epigenetic “reader” prot ...
DOI:
10.1021/acs.biochem.0c00035

5. A Biophysical Perspective on Enzyme Catalysis

Author:
Pratul K. Agarwal
Source:
Biochemistry 2018 v.58 no.6 pp. 438-449
ISSN:
1520-4995
Subject:
active sites; catalytic activity; energy transfer; enzymes; models; solvents
Abstract:
... Even after a century of investigation, our understanding of how enzymes work remains far from complete. In particular, several factors that enable enzymes to achieve high catalytic efficiencies remain only poorly understood. A number of theories have been developed, which propose or reaffirm that enzymes work as structural scaffolds, serving to bring together and properly orient the participants s ...
DOI:
10.1021/acs.biochem.8b01004
PubMed:
30507164
PubMed Central:
PMC6386455

6. A Central Region of NF-κB Essential Modulator Is Required for IKKβ-Induced Conformational Change and for Signal Propagation

Author:
Robert Shaffer; Anthony M. DeMaria; Larisa Kagermazova; Yuekun Liu; Milad Babaei; Suhaily Caban-Penix; Arisdelsy Cervantes; Stefan Jehle; Lee Makowski; Thomas D. Gilmore; Adrian Whitty; Karen N. Allen
Source:
Biochemistry 2019 v.58 no.26 pp. 2906-2920
ISSN:
1520-4995
Subject:
IKappaB kinase; amino acids; models; mutation; peptides; phosphorylation; scaffolding proteins; small-angle X-ray scattering; transcription factor NF-kappa B
Abstract:
... NF-κB essential modulator (NEMO) regulates NF-κB signaling by acting as a scaffold for the kinase IKKβ to direct its activity toward the NF-κB inhibitor, IκBα. Here, we show that a highly conserved central region of NEMO termed the intervening domain (IVD, amino acids 112–195) plays a key role in NEMO function. We determined a structural model of full-length NEMO by small-angle X-ray scattering an ...
DOI:
10.1021/acs.biochem.8b01316

7. A Chemical Chaperone Decouples TDP-43 Disordered Domain Phase Separation from Fibrillation

Author:
Kyoung-Jae Choi; Phoebe S. Tsoi; Mahdi Muhammad Moosa; Adriana Paulucci-Holthauzen; Shih-Chu Jeff Liao; Josephine C. Ferreon; Allan Chris M. Ferreon
Source:
Biochemistry 2018 v.57 no.50 pp. 6822-6826
ISSN:
1520-4995
Subject:
cytoplasmic granules; liquids; models; ribonucleoproteins; separation; therapeutics; trimethylamine
Abstract:
... Ribonucleoprotein (RNP) condensations through liquid–liquid phase separation play vital roles in the dynamic formation–dissolution of stress granules (SGs). These condensations are, however, usually assumed to be linked to pathologic fibrillation. Here, we show that physiologic condensation and pathologic fibrillation of RNPs are independent processes that can be unlinked with the chemical chapero ...
DOI:
10.1021/acs.biochem.8b01051
PubMed:
30520303
PubMed Central:
PMC6555487

8. A Comparison of DNA Compaction by Arginine and Lysine Peptides: A Physical Basis for Arginine Rich Protamines

Author:
DeRouchey Jason; Hoover Brandon; Rau Donald C.
Source:
Biochemistry 2013 v.52 no.17 pp. 3000-3009
ISSN:
1520-4995
Subject:
DNA; DNA damage; X-radiation; arginine; lysine; models; mutagenicity; neutralization; ornithine; osmotic stress; peptides; protamines; spermatozoa
Abstract:
... Protamines are small, highly positively charged peptides used to package DNA at very high densities in sperm nuclei. Tight DNA packing is considered essential for the minimization of DNA damage by mutagens and reactive oxidizing species. A striking and general feature of protamines is the almost exclusive use of arginine over lysine for the positive charge to neutralize DNA. We have investigated w ...
DOI:
10.1021/bi4001408
PubMed:
23540557
PubMed Central:
PMC3648981

9. A Complicated Relationship: Glycosylation, Ca(II), and Primary Sequence Affect the Interactions and Kinetics between Two Model Mollusk Shell Intracrystalline Nacre Proteins

Author:
Jose Juan-Colas; Yong Seob Jung; Steven Johnson; John Spencer Evans
Source:
Biochemistry 2019 v.59 no.4 pp. 346-350
ISSN:
1520-4995
Subject:
Haliotis rufescens; amino acid sequences; glycoproteins; glycosylation; hydrogels; kinetics; models; molluscs; nacre; particles; physical properties; shell (molluscs)
Abstract:
... The formation of the mollusk shell requires the participation of proteins, many of which may be interactive with one another. We examined a model protein pair system from the mollusk Haliotis rufescens, wherein we probed the interactions between recombinant forms of two major nacre layer proteins, AP7, and the glycoprotein, AP24. Here, the focus was on the impact that the AP24 glycosylation and pr ...
DOI:
10.1021/acs.biochem.9b00867

10. A Conserved Amphipathic Ligand Binding Region Influences K-Path-Dependent Activity of Cytochrome c Oxidase

Author:
Hiser Carrie; Buhrow Leann; Liu Jian; Kuhn Leslie; Ferguson-Miller Shelagh
Source:
Biochemistry 2013 v.52 no.8 pp. 1385-1396
ISSN:
1520-4995
Subject:
Rhodobacter sphaeroides; bilirubin; binding sites; cattle; cytochrome-c oxidase; deoxycholic acid; detergents; electron transfer; fatty acids; heme; ligands; models; mutants; protoporphyrin; spectral analysis; steroids
Abstract:
... A conserved, crystallographically defined bile acid binding site was originally identified in the membrane domain of mammalian and bacterial cytochrome c oxidase (CcO). Current studies show other amphipathic molecules including detergents, fatty acids, steroids, and porphyrins bind to this site and affect the already 50% inhibited activity of the E101A mutant of Rhodobacter sphaeroides CcO as well ...
DOI:
10.1021/bi3014505
PubMed:
23351100
PubMed Central:
PMC3622084

11. A Disulfide-Stabilized Aβ that Forms Dimers but Does Not Form Fibrils

Author:
Sheng Zhang; Stan Yoo; Dalton T. Snyder; Benjamin B. Katz; Amy Henrickson; Borries Demeler; Vicki H. Wysocki; Adam G. Kreutzer; James S. Nowick
Source:
Biochemistry 2022 v.61 no.4 pp. 252-264
ISSN:
1520-4995
Subject:
Escherichia coli; amyloid; bacterial culture; circular dichroism spectroscopy; detergents; disulfide bonds; fluorescence; hydrogen; lipids; mass spectrometry; models; neurotoxicity; peptides; polyacrylamide gel electrophoresis; reversed-phase high performance liquid chromatography; transmission electron microscopy
Abstract:
... Aβ dimers are a basic building block of many larger Aβ oligomers and are among the most neurotoxic and pathologically relevant species in Alzheimer’s disease. Homogeneous Aβ dimers are difficult to prepare, characterize, and study because Aβ forms heterogeneous mixtures of oligomers that vary in size and can rapidly aggregate into more stable fibrils. This paper introduces AβC₁₈C₃₃ as a disulfide- ...
DOI:
10.1021/acs.biochem.1c00739

12. A Dynamic Protein–Protein Coupling between the TonB-Dependent Transporter FhuA and TonB

Author:
Jessica L. Sarver; Michael Zhang; Lishan Liu; David Nyenhuis; David S. Cafiso
Source:
Biochemistry 2018 v.57 no.6 pp. 1045-1053
ISSN:
1520-4995
Subject:
Escherichia coli; citrates; crystal structure; electron paramagnetic resonance spectroscopy; ferrichrome; models; transporters; vitamin B12
Abstract:
... Bacterial outer membrane TonB-dependent transporters function by executing cycles of binding and unbinding to the inner membrane protein TonB. In the vitamin B₁₂ transporter BtuB and the ferric citrate transporter FecA, substrate binding increases the periplasmic exposure of the Ton box, an energy-coupling segment. This increased exposure appears to enhance the affinity of the transporter for TonB ...
DOI:
10.1021/acs.biochem.7b01223
PubMed:
29338257
PubMed Central:
PMC5811355

13. A Fold-Independent Interface Residue Is Crucial for Complex Formation and Allosteric Signaling in Class I Glutamine Amidotransferases

Author:
Florian Semmelmann; Enrico Hupfeld; Leonhard Heizinger; Rainer Merkl; Reinhard Sterner
Source:
Biochemistry 2019 v.58 no.22 pp. 2584-2588
ISSN:
1520-4995
Subject:
alanine; aminodeoxychorismate synthase; ammonia; aspartic acid; biochemical pathways; catalytic activity; databases; enzyme activity; enzyme kinetics; gel chromatography; glutamic acid; glutaminase; glutamine; glycerol; hydrolysis; imidazole; models; mutants; phosphates
Abstract:
... The members of the glutamine amidotransferase (GATase) family catalyze the incorporation of ammonia within numerous metabolic pathways and can be categorized in two classes. Here, we concentrated on class I GATases, which are heteromeric enzyme complexes consisting of synthase subunits and glutaminase subunits with a catalytic Cys-His-Glu triad. Glutamine hydrolysis at the glutaminase subunit is ( ...
DOI:
10.1021/acs.biochem.9b00286

14. A Fusion Protein of the p53 Transaction Domain and the p53-Binding Domain of the Oncoprotein MdmX as an Efficient System for High-Throughput Screening of MdmX Inhibitors

Author:
Chen Rong; Zhou Jingjing; Qin Lingyun; Chen Yao; Huang Yongqi; Liu Huili; Su Zhengding
Source:
Biochemistry 2017 v.56 no.25 pp. 3273-3282
ISSN:
1520-4995
Subject:
amino acids; antineoplastic activity; drugs; fluorescence; fluorescence emission spectroscopy; ligands; models; neoplasms; oncogene proteins; screening; therapeutics
Abstract:
... In nearly half of cancers, the anticancer activity of p53 protein is often impaired by the overexpressed oncoprotein Mdm2 and its homologue, MdmX, demanding efficient therapeutics to disrupt the aberrant p53–MdmX/Mdm2 interactions to restore the p53 activity. While many potent Mdm2-specific inhibitors have already undergone clinical investigations, searching for MdmX-specific inhibitors has become ...
DOI:
10.1021/acs.biochem.7b00085

15. A General Mechanism for the Propagation of Mutational Effects in Proteins

Author:
Rajasekaran Nandakumar; Suresh Swaathiratna; Gopi Soundhararajan; Raman Karthik; Naganathan Athi N.
Source:
Biochemistry 2017 v.56 no.1 pp. 294-305
ISSN:
1520-4995
Subject:
energy; hydrophobicity; models; molecular dynamics; mutants; network theory; nuclear magnetic resonance spectroscopy; point mutation; prediction; thermodynamics; ubiquitin
Abstract:
... Mutations in the hydrophobic interior of proteins are generally thought to weaken the interactions only in their immediate neighborhood. This forms the basis of protein engineering-based studies of folding mechanism and function. However, mutational work on diverse proteins has shown that distant residues are thermodynamically coupled, with the network of interactions within the protein acting as ...
DOI:
10.1021/acs.biochem.6b00798

16. A General in Vitro Assay for Studying Enzymatic Activities of the Ubiquitin System

Author:
Yukun Zuo; Boon Keat Chong; Kun Jiang; Daniel Finley; David Klenerman; Yu Ye
Source:
Biochemistry 2020 v.59 no.7 pp. 851-861
ISSN:
1520-4995
Subject:
artificial intelligence; assays; energy transfer; enzyme activity; enzymes; kinetics; models; signal transduction; ubiquitin; ubiquitination
Abstract:
... The ubiquitin (Ub) system regulates a wide range of cellular signaling pathways. Several hundred E1, E2, and E3 enzymes are together responsible for protein ubiquitination, thereby controlling cellular activities. Due to the numerous enzymes and processes involved, studies of ubiquitination activities have been challenging. We here report a novel Förster resonance energy transfer (FRET)-based ass ...
DOI:
10.1021/acs.biochem.9b00602

17. A High-Throughput Assay for Collagen Secretion Suggests an Unanticipated Role for Hsp90 in Collagen Production

Author:
Madeline Y. Wong; Ngoc Duc Doan; Andrew S. DiChiara; Louis J. Papa; Jaime H. Cheah; Christian K. Soule; Nicki Watson; John D. Hulleman; Matthew D. Shoulders
Source:
Biochemistry 2018 v.57 no.19 pp. 2814-2827
ISSN:
1520-4995
Subject:
biosynthesis; bone formation; cell lines; collagen; endoplasmic reticulum; extracellular matrix; fibrosis; genetic disorders; humans; luminescence; models; neoplasms; secretion; therapeutics; type I secretion system
Abstract:
... Collagen overproduction is a feature of fibrosis and cancer, while insufficient deposition of functional collagen molecules and/or the secretion of malformed collagen is common in genetic disorders like osteogenesis imperfecta. Collagen secretion is an appealing therapeutic target in these and other diseases, as secretion directly connects intracellular biosynthesis to collagen deposition and biol ...
DOI:
10.1021/acs.biochem.8b00378
PubMed:
29676157
PubMed Central:
PMC6231715

18. A Key Glycine in Bacterial Steroid-Degrading Acyl-CoA Dehydrogenases Allows Flavin-Ring Repositioning and Modulates Substrate Side Chain Specificity

Author:
Alexander J. Stirling; Stephanie E. Gilbert; Megan Conner; Evan Mallette; Matthew S. Kimber; Stephen Y. K. Seah
Source:
Biochemistry 2020 v.59 no.42 pp. 4081-4092
ISSN:
1520-4995
Subject:
Mycobacterium tuberculosis; Thermomonospora curvata; active sites; acyl coenzyme A; bacteria; cholesterol; degradation; enzymes; eukaryotic cells; genes; metabolites; models; oxidation; saprophytes
Abstract:
... A wide variety of steroid metabolites synthesized by eukaryotes are all ultimately catabolized by bacteria; while generally saprophytic, pathogenic Mycobacteria have repurposed these pathways to utilize host intracellular cholesterol pools. Steroid degradation is complex, but a recurring theme is that cycles of β-oxidation are used to iteratively remove acetyl- or propanoyl-CoA groups. These β-oxi ...
DOI:
10.1021/acs.biochem.0c00568

19. A Kinetic Model of Nonenzymatic RNA Polymerization by Cytidine-5′-phosphoro-2-aminoimidazolide

Author:
Walton Travis; Szostak Jack W.
Source:
Biochemistry 2017 v.56 no.43 pp. 5739-5747
ISSN:
1520-4995
Subject:
RNA; kinetics; models; polymerization
Abstract:
... The nonenzymatic polymerization of RNA may have enabled copying of functional sequences during the origin of life. Recent progress utilizing 5′-phosphoro-2-aminoimidazole activation has reinvigorated the possibility of using nonenzymatic RNA polymerization for copying arbitrary sequences. However, the reasons why 2-aminoimidazole (AI) is a superior activation group remain unclear. Here we report t ...
DOI:
10.1021/acs.biochem.7b00792
PubMed:
29022704
PubMed Central:
PMC6340129

20. A Liposomal Platform for Delivery of a Protein Antigen to Langerin-Expressing Cells

Author:
Jessica Schulze; Mareike Rentzsch; Dongyoon Kim; Lydia Bellmann; Patrizia Stoitzner; Christoph Rademacher
Source:
Biochemistry 2019 v.58 no.21 pp. 2576-2580
ISSN:
1520-4995
Subject:
Langerhans cells; T-lymphocytes; antigens; cell lines; encapsulation; endosomes; flow cytometry; humans; image analysis; lectins; ligands; lysosomes; models; vaccination; vaccines
Abstract:
... The skin is an attractive site for vaccination and harbors a dense network of Langerhans cells that are the prime target for antigen delivery approaches in the epidermis. While specific targeting of Langerhans cells has been shown to elicit the necessary T-cell response using antibody-based delivery approaches, the targeted administration of particulate antigens in the form of nanoparticle-based v ...
DOI:
10.1021/acs.biochem.9b00402
PubMed:
31062587
PubMed Central:
PMC6541893