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Advances in Protein Chemistry and Structural Biology

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https://www.readbyqxmd.com/read/29413002/preface
#1
EDITORIAL
Rossen Donev
No abstract text is available yet for this article.
2018: Advances in Protein Chemistry and Structural Biology
https://www.readbyqxmd.com/read/29413001/intrinsic-disorder-protein-protein-interactions-and-disease
#2
Vladimir N Uversky
It is recognized now that biologically active proteins without stable tertiary structure (known as intrinsically disordered proteins, IDPs) and hybrid proteins containing ordered domains and intrinsically disordered protein regions (IDPRs) are important players found in any given proteome. These IDPs/IDPRs possess functions that complement functional repertoire of their ordered counterparts, being commonly related to recognition, as well as control and regulation of various signaling pathways. They are interaction masters, being able to utilize a wide spectrum of interaction mechanisms, ranging from induced folding to formation of fuzzy complexes where significant levels of disorder are preserved, to polyvalent stochastic interactions playing crucial roles in the liquid-liquid phase transitions leading to the formation of proteinaceous membrane-less organelles...
2018: Advances in Protein Chemistry and Structural Biology
https://www.readbyqxmd.com/read/29413000/protein-protein-interaction-modulators-for-epigenetic-therapies
#3
Bárbara I Díaz-Eufracio, J Jesús Naveja, José L Medina-Franco
Targeting protein-protein interactions (PPIs) is becoming an attractive approach for drug discovery. This is particularly true for difficult or emerging targets, such as epitargets that may be elusive to drugs that fall into the traditional chemical space. The chemical nature of the PPIs makes attractive the use of peptides or peptidomimetics to selectively modulate such interactions. Despite the fact peptide-based drug discovery has been challenging, the use of peptides as leads compounds for drug discovery is still a valid strategy...
2018: Advances in Protein Chemistry and Structural Biology
https://www.readbyqxmd.com/read/29412999/using-tr-fret-to-investigate-protein-protein-interactions-a-case-study-of-pxr-coregulator-interaction
#4
Wenwei Lin, Taosheng Chen
Time-resolved fluorescence resonance energy transfer (TR-FRET) protein-protein interaction assays, especially in the format of receptor coregulator (coactivator and corepressor) recruitment/repression assays, have been widely used in nuclear receptor research to characterize the modes of action, efficacies, and binding affinities of ligands (including their properties as agonists, antagonists, and inverse agonists). However, there has been only limited progress in using this assay format for pregnane X receptor (PXR)...
2018: Advances in Protein Chemistry and Structural Biology
https://www.readbyqxmd.com/read/29412998/computational-resources-for-predicting-protein-protein-interactions
#5
Himani Tanwar, C George Priya Doss
Proteins are the essential building blocks and functional components of a cell. They account for the vital functions of an organism. Proteins interact with each other and form protein interaction networks. These protein interactions play a major role in all the biological processes and pathways. The previous methods of predicting protein interactions were experimental which focused on a small set of proteins or a particular protein. However, these experimental approaches are low-throughput as they are time-consuming and require a significant amount of human effort...
2018: Advances in Protein Chemistry and Structural Biology
https://www.readbyqxmd.com/read/29412997/structural-prediction-of-protein-protein-interactions-by-docking-application-to-biomedical-problems
#6
Didier Barradas-Bautista, Mireia Rosell, Chiara Pallara, Juan Fernández-Recio
A huge amount of genetic information is available thanks to the recent advances in sequencing technologies and the larger computational capabilities, but the interpretation of such genetic data at phenotypic level remains elusive. One of the reasons is that proteins are not acting alone, but are specifically interacting with other proteins and biomolecules, forming intricate interaction networks that are essential for the majority of cell processes and pathological conditions. Thus, characterizing such interaction networks is an important step in understanding how information flows from gene to phenotype...
2018: Advances in Protein Chemistry and Structural Biology
https://www.readbyqxmd.com/read/29412996/probing-the-protein-protein-interaction-network-of-proteins-causing-maturity-onset-diabetes-of-the-young
#7
P Sneha, D Thirumal Kumar, Jose Lijo, M Megha, R Siva, C George Priya Doss
Protein-protein interactions (PPIs) play vital roles in various cellular pathways. Most of the proteins perform their responsibilities by interacting with an enormous number of proteins. Understanding these interactions of the proteins and their interacting partners has shed light toward the field of drug discovery. Also, PPIs enable us to understand the functions of a protein by understanding their interacting partners. Consequently, in the current study, PPI network of the proteins causing MODY (Maturity Onset Diabetes of the Young) was drawn, and their correlation in causing a disease condition was marked...
2018: Advances in Protein Chemistry and Structural Biology
https://www.readbyqxmd.com/read/29412995/targeting-protein-protein-interactions-in-the-ubiquitin-proteasome-pathway
#8
Maria Gaczynska, Pawel A Osmulski
The ubiquitin-proteasome pathway (UPP) is a major venue for controlled intracellular protein degradation in Eukaryota. The machinery of several hundred proteins is involved in recognizing, tagging, transporting, and cleaving proteins, all in a highly regulated manner. Short-lived transcription factors, misfolded translation products, stress-damaged polypeptides, or worn-out long-lived proteins, all can be found among the substrates of UPP. Carefully choreographed protein-protein interactions (PPI) are involved in each step of the pathway...
2018: Advances in Protein Chemistry and Structural Biology
https://www.readbyqxmd.com/read/29412994/analysis-of-protein-interactions-by-surface-plasmon-resonance
#9
Dennis G Drescher, Dakshnamurthy Selvakumar, Marian J Drescher
Surface plasmon resonance is an optical technique that is utilized for detecting molecular interactions, such as interactions that occur between proteins or other classes of molecules. Binding of a mobile molecule (analyte) to a molecule immobilized on a thin metal film (ligand) changes the refractive index of the film. The angle of extinction of light that is completely reflected after polarized light impinges upon the film, is altered and monitored as a change in detector position for a dip in reflected intensity (the surface plasmon resonance phenomenon)...
2018: Advances in Protein Chemistry and Structural Biology
https://www.readbyqxmd.com/read/28683924/preface
#10
EDITORIAL
Tatyana Karabencheva-Christova
No abstract text is available yet for this article.
2017: Advances in Protein Chemistry and Structural Biology
https://www.readbyqxmd.com/read/28683923/computational-biochemistry-enzyme-mechanisms-explored
#11
REVIEW
Martin Culka, Florian J Gisdon, G Matthias Ullmann
Understanding enzyme mechanisms is a major task to achieve in order to comprehend how living cells work. Recent advances in biomolecular research provide huge amount of data on enzyme kinetics and structure. The analysis of diverse experimental results and their combination into an overall picture is, however, often challenging. Microscopic details of the enzymatic processes are often anticipated based on several hints from macroscopic experimental data. Computational biochemistry aims at creation of a computational model of an enzyme in order to explain microscopic details of the catalytic process and reproduce or predict macroscopic experimental findings...
2017: Advances in Protein Chemistry and Structural Biology
https://www.readbyqxmd.com/read/28683922/mechanistic-insights-into-catalytic-rna-protein-complexes-involved-in-translation-of-the-genetic-code
#12
REVIEW
Satya B Routh, Rajan Sankaranarayanan
The contemporary world is an "RNA-protein world" rather than a "protein world" and tracing its evolutionary origins is of great interest and importance. The different RNAs that function in close collaboration with proteins are involved in several key physiological processes, including catalysis. Ribosome-the complex megadalton cellular machinery that translates genetic information encoded in nucleotide sequence to amino acid sequence-epitomizes such an association between RNA and protein. RNAs that can catalyze biochemical reactions are known as ribozymes...
2017: Advances in Protein Chemistry and Structural Biology
https://www.readbyqxmd.com/read/28683921/biology-mechanism-and-structure-of-enzymes-in-the-%C3%AE-d-phosphohexomutase-superfamily
#13
Kyle M Stiers, Andrew G Muenks, Lesa J Beamer
Enzymes in the α-d-phosphohexomutases superfamily catalyze the reversible conversion of phosphosugars, such as glucose 1-phosphate and glucose 6-phosphate. These reactions are fundamental to primary metabolism across the kingdoms of life and are required for a myriad of cellular processes, ranging from exopolysaccharide production to protein glycosylation. The subject of extensive mechanistic characterization during the latter half of the 20th century, these enzymes have recently benefitted from biophysical characterization, including X-ray crystallography, NMR, and hydrogen-deuterium exchange studies...
2017: Advances in Protein Chemistry and Structural Biology
https://www.readbyqxmd.com/read/28683920/computational-glycobiology-mechanistic-studies-of-carbohydrate-active-enzymes-and-implication-for-inhibitor-design
#14
REVIEW
Andrew P Montgomery, Kela Xiao, Xingyong Wang, Danielle Skropeta, Haibo Yu
Carbohydrate-active enzymes (CAZymes) are families of essential and structurally related enzymes, which catalyze the creation, modification, and degradation of glycosidic bonds in carbohydrates to maintain essentially all kingdoms of life. CAZymes play a key role in many biological processes underpinning human health and diseases (e.g., cancer, diabetes, Alzheimer's diseases, AIDS) and have thus emerged as important drug targets in the fight against pathogenesis. The realization of the full potential of CAZymes remains a significant challenge, relying on a deeper understanding of the molecular mechanisms of catalysis...
2017: Advances in Protein Chemistry and Structural Biology
https://www.readbyqxmd.com/read/28683919/sortase-transpeptidases-structural-biology-and-catalytic-mechanism
#15
REVIEW
Alex W Jacobitz, Michele D Kattke, Jeff Wereszczynski, Robert T Clubb
Gram-positive bacteria use sortase cysteine transpeptidase enzymes to covalently attach proteins to their cell wall and to assemble pili. In pathogenic bacteria sortases are potential drug targets, as many of the proteins that they display on the microbial surface play key roles in the infection process. Moreover, the Staphylococcus aureus Sortase A (SaSrtA) enzyme has been developed into a valuable biochemical reagent because of its ability to ligate biomolecules together in vitro via a covalent peptide bond...
2017: Advances in Protein Chemistry and Structural Biology
https://www.readbyqxmd.com/read/28683918/enzymology-of-microbial-dimethylsulfoniopropionate-catabolism
#16
REVIEW
Mishtu Dey
The biochemistry of dimethylsulfoniopropionate (DMSP) catabolism is reviewed. The microbes that catalyze the reactions central to DMSP catabolic pathways are described, and the focus is on the enzymology of the process. Approximately 10(9)tons of DMSP is released annually by marine eukaryotes as an osmolyte. A vast majority of DMSP is assimilated by bacteria through either a demethylation or lyase pathways, producing either the methane thiol or the volatile dimethylsulfide (DMS), respectively. Enzymatic breakdown of DMSP generates ~10(7)tons of DMS annually, which may have impact on global climate...
2017: Advances in Protein Chemistry and Structural Biology
https://www.readbyqxmd.com/read/28683917/striking-diversity-in-holoenzyme-architecture-and-extensive-conformational-variability-in-biotin-dependent-carboxylases
#17
REVIEW
Liang Tong
Biotin-dependent carboxylases are widely distributed in nature and have central roles in the metabolism of fatty acids, amino acids, carbohydrates, and other compounds. The last decade has seen the accumulation of structural information on most of these large holoenzymes, including the 500-kDa dimeric yeast acetyl-CoA carboxylase, the 750-kDa α6β6 dodecameric bacterial propionyl-CoA carboxylase, 3-methylcrotonyl-CoA carboxylase, and geranyl-CoA carboxylase, the 720-kDa hexameric bacterial long-chain acyl-CoA carboxylase, the 500-kDa tetrameric bacterial single-chain pyruvate carboxylase, the 370-kDa α2β4 bacterial two-subunit pyruvate carboxylase, and the 130-kDa monomeric eukaryotic urea carboxylase...
2017: Advances in Protein Chemistry and Structural Biology
https://www.readbyqxmd.com/read/28683916/a-paradigm-for-ch-bond-cleavage-structural-and-functional-aspects-of-transition-state-stabilization-by-mandelate-racemase
#18
REVIEW
Stephen L Bearne, Martin St Maurice
Mandelate racemase (MR) from Pseudomonas putida catalyzes the Mg(2+)-dependent, 1,1-proton transfer reaction that racemizes (R)- and (S)-mandelate. MR shares a partial reaction (i.e., the metal ion-assisted, Brønsted base-catalyzed proton abstraction of the α-proton of carboxylic acid substrates) and structural features ((β/α)7β-barrel and N-terminal α + β capping domains) with a vast group of homologous, yet functionally diverse, enzymes in the enolase superfamily. Mechanistic and structural studies have developed this enzyme into a paradigm for understanding how enzymes such as those of the enolase superfamily overcome kinetic and thermodynamic barriers to catalyze the abstraction of an α-proton from a carbon acid substrate with a relatively high pKa value...
2017: Advances in Protein Chemistry and Structural Biology
https://www.readbyqxmd.com/read/28683915/collagenolytic-matrix-metalloproteinase-structure-function-relationships-insights-from-molecular-dynamics-studies
#19
Tatyana G Karabencheva-Christova, Christo Z Christov, Gregg B Fields
Several members of the zinc-dependent matrix metalloproteinase (MMP) family catalyze collagen degradation. Experimental data reveal a collaboration between different MMP domains in order to achieve efficient collagenolysis. Molecular dynamics (MD) simulations have been utilized to provide atomistic details of the collagenolytic process. The triple-helical structure of collagen exhibits local regions of flexibility, with modulation of interchain salt bridges and water bridges contributing to accessibility of individual chains by the enzyme...
2017: Advances in Protein Chemistry and Structural Biology
https://www.readbyqxmd.com/read/28427566/preface
#20
EDITORIAL
Rossen Donev
No abstract text is available yet for this article.
2017: Advances in Protein Chemistry and Structural Biology
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