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Advances in Protein Chemistry and Structural Biology

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https://www.readbyqxmd.com/read/28683924/preface
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
EDITORIAL
Rossen Donev
No abstract text is available yet for this article.
2017: Advances in Protein Chemistry and Structural Biology
https://www.readbyqxmd.com/read/28427565/analyzing-the-effect-of-v66m-mutation-in-bdnf-in-causing-mood-disorders-a-computational-approach
#12
P Sneha, D Thirumal Kumar, Sugandhi Saini, Kreeti Kajal, R Magesh, R Siva, C George Priya Doss
Mental disorders or mood disorders are prevalent globally irrespective of region, race, and ethnic groups. Of the types of mood disorders, major depressive disorder (MDD) and bipolar disorder (BPD) are the most prevalent forms of psychiatric condition. A number of preclinical studies emphasize the essential role of brain-derived neurotrophic factor (BDNF) in the pathophysiology of mood disorders. Additionally, BDNF is the most common growth factor in the central nervous system along with their essential role during the neural development and the synaptic elasticity...
2017: Advances in Protein Chemistry and Structural Biology
https://www.readbyqxmd.com/read/28427564/inflammation-in-epileptic-encephalopathies
#13
Oleksii Shandra, Solomon L Moshé, Aristea S Galanopoulou
West syndrome (WS) is an infantile epileptic encephalopathy that manifests with infantile spasms (IS), hypsarrhythmia (in ~60% of infants), and poor neurodevelopmental outcomes. The etiologies of WS can be structural-metabolic pathologies (~60%), genetic (12%-15%), or of unknown origin. The current treatment options include hormonal treatment (adrenocorticotropic hormone and high-dose steroids) and the GABA aminotransferase inhibitor vigabatrin, while ketogenic diet can be given as add-on treatment in refractory IS...
2017: Advances in Protein Chemistry and Structural Biology
https://www.readbyqxmd.com/read/28427563/neuroinflammation-in-alzheimer-s-disease-the-preventive-and-therapeutic-potential-of-polyphenolic-nutraceuticals
#14
Yousef Sawikr, Nagendra Sastry Yarla, Ilaria Peluso, Mohammad Amjad Kamal, Gjumrakch Aliev, Anupam Bishayee
Brain inflammation, characterized by increased microglia and astrocyte activation, increases during aging and is a key feature of neurodegenerative diseases, such as Alzheimer's disease (AD). In AD, neuronal death and synaptic impairment, induced by amyloid-β (Aβ) peptide, are at least in part mediated by microglia and astrocyte activation. Glial activation results in the sustained production of proinflammatory cytokines and reactive oxygen species, giving rise to a chronic inflammatory process. Astrocytes are the most abundant glial cells in the central nervous system and are involved in the neuroinflammation...
2017: Advances in Protein Chemistry and Structural Biology
https://www.readbyqxmd.com/read/28427562/cardiokines-as-modulators-of-stress-induced-cardiac-disorders
#15
Anna Planavila, Joaquim Fernández-Solà, Francesc Villarroya
Almost 30 years ago, the protein, atrial natriuretic peptide, was identified as a heart-secreted hormone that provides a peripheral signal from the myocardium that communicates to the rest of the organism to modify blood pressure and volume under conditions of heart failure. Since then, additional peripheral factors secreted by the heart, termed cardiokines, have been identified and shown to coordinate this interorgan cross talk. In addition to this interorgan communication, cardiokines also act in an autocrine/paracrine manner to play a role in intercellular communication within the myocardium...
2017: Advances in Protein Chemistry and Structural Biology
https://www.readbyqxmd.com/read/28427561/molecular-targets-of-ascochlorin-and-its-derivatives-for-cancer-therapy
#16
Jason Chua Min-Wen, Benjamin Chua Yan-Jiang, Srishti Mishra, Xiaoyun Dai, Junji Magae, Ng Shyh-Chang, Alan Prem Kumar, Gautam Sethi
Cancer is an extremely complex disease comprising of a multitude of characteristic hallmarks that continue to evolve with time. At the genomic level, random mutations leading to deregulation of diverse oncogenic signal transduction cascades and polymorphisms coupled with environmental as well as life style-related factors are major causative agent contributing to chemoresistance and the failure of conventional therapies as well as molecular targeted agents. Hence, there is an urgent need to identify novel alternative therapies based on alternative medicines to combat this dreaded disease...
2017: Advances in Protein Chemistry and Structural Biology
https://www.readbyqxmd.com/read/28427560/stress-adaptive-response-in-ovarian-cancer-drug-resistance-role-of-trap1-in-oxidative-metabolism-driven-inflammation
#17
Maria Rosaria Amoroso, Danilo Swann Matassa, Ilenia Agliarulo, Rosario Avolio, Francesca Maddalena, Valentina Condelli, Matteo Landriscina, Franca Esposito
Metabolic reprogramming is one of the most frequent stress-adaptive response of cancer cells to survive environmental changes and meet increasing nutrient requirements during their growth. These modifications involve cellular bioenergetics and cross talk with surrounding microenvironment, in a dynamic network that connect different molecular processes, such as energy production, inflammatory response, and drug resistance. Even though the Warburg effect has long been considered the main metabolic feature of cancer cells, recent reports identify mitochondrial oxidative metabolism as a driving force for tumor growth in an increasing number of cellular contexts...
2017: Advances in Protein Chemistry and Structural Biology
https://www.readbyqxmd.com/read/28427559/stress-induced-nlrp3-inflammasome-in-human-diseases
#18
Elísabet Alcocer-Gómez, Beatriz Castejón-Vega, Mario D Cordero
Stress is a complex event that induces disturbances to physiological and psychological homeostasis, and it may have a detrimental impact on certain brain and physiological functions. In the last years, a dual role of the stress effect has been studied in order to elucidate the molecular mechanism by which can induce physiological symptoms after psychological stress exposition and vice versa. In this sense, inflammation has been proposed as an important starring. And in the same line, the inflammasome complex has emerged to give responses because of its role of stress sensor...
2017: Advances in Protein Chemistry and Structural Biology
https://www.readbyqxmd.com/read/28427558/a-computational-approach-to-identify-the-biophysical-and-structural-aspects-of-methylenetetrahydrofolate-reductase-mthfr-mutations-a222v-e429a-and-r594q-leading-to-schizophrenia
#19
Himani Tanwar, P Sneha, D Thirumal Kumar, R Siva, Charles Emmanuel Jebaraj Walter, C George Priya Doss
The association between depression and methylenetetrahydrofolate reductase (MTHFR) has been continually demonstrated in clinical studies, yet there are sparse resources available to build a relationship between the mutations associated with MTHFR and depression. The common mutations found to be associated with schizophrenia and MTHFR are A222V, E429A, and R594Q. Although abundant research on structural and functional effects caused by A222V mutation is available, very less amount of studies have been done on the other two mutants (E429A and R594Q)...
2017: Advances in Protein Chemistry and Structural Biology
https://www.readbyqxmd.com/read/28427557/oxidative-stress-love-and-hate-history-in-central-nervous-system
#20
Genaro Gabriel Ortiz, Fermín P Pacheco Moisés, Mario Mireles-Ramírez, Luis J Flores-Alvarado, Héctor González-Usigli, Víctor J Sánchez-González, Angélica L Sánchez-López, Lorenzo Sánchez-Romero, Eduardo I Díaz-Barba, J Francisco Santoscoy-Gutiérrez, Paloma Rivero-Moragrega
Molecular oxygen is essential for aerobic organisms in order to synthesize large amounts of energy during the process of oxidative phosphorylation and it is harnessed in the form of adenosine triphosphate, the chemical energy of the cell. Oxygen is toxic for anaerobic organisms but it is also less obvious that oxygen is poisonous to aerobic organisms at higher concentrations of oxygen. For instance, oxygen toxicity is a condition resulting from the harmful effects of breathing molecular oxygen at increased partial pressures...
2017: Advances in Protein Chemistry and Structural Biology
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