Download or read book Computational Approaches for Studying Enzyme Mechanism Part A written by and published by Academic Press. This book was released on 2016-08-04 with total page 560 pages. Available in PDF, EPUB and Kindle. Book excerpt: Computational Approaches for Studying Enzyme Mechanism Part A, is the first of two volumes in the Methods in Enzymology series, focusses on computational approaches for studying enzyme mechanism. The serial achieves the critically acclaimed gold standard of laboratory practices and remains one of the most highly respected publications in the molecular biosciences. Each volume is eagerly awaited, frequently consulted, and praised by researchers and reviewers alike. Now with over 550 volumes, the series remains a prominent and essential publication for researchers in all fields of life sciences and biotechnology, including biochemistry, chemical biology, microbiology, synthetic biology, cancer research, and genetics to name a few. Focuses on computational approaches for studying enzyme mechanism Continues the legacy of this premier serial with quality chapters authored by leaders in the field Covers research methods in intermediate filament associated proteins, and contains sections on such topics as lamin-associated proteins, intermediate filament-associated proteins and plakin, and other cytoskeletal cross-linkers

Download or read book Computational Approaches for Studying Enzyme Mechanism Part B written by and published by Academic Press. This book was released on 2016-08-03 with total page 538 pages. Available in PDF, EPUB and Kindle. Book excerpt: Computational Approaches for Studying Enzyme Mechanism, Part B is the first of two volumes in the Methods in Enzymology series that focuses on computational approaches for studying enzyme mechanism. The serial achieves the critically acclaimed gold standard of laboratory practices and remains one of the most highly respected publications in the molecular biosciences. Each volume is eagerly awaited, frequently consulted, and praised by researchers and reviewers alike. Now with over 550 volumes, the series remains a prominent and essential publication for researchers in all fields of the life sciences and biotechnology, including biochemistry, chemical biology, microbiology, synthetic biology, cancer research, genetics, and other fields of study. Focuses on computational approaches for studying enzyme mechanism Continues the legacy of this premier serial with quality chapters authored by leaders in the field Covers research methods in intermediate filament associated proteins, and contains sections on such topics as lamin-associated proteins, intermediate filament-associated proteins and plakin, and other cytoskeletal cross-linkers

Download or read book Computational Approaches for Studying Enzyme Mechanism written by Gregory Voth and published by Academic Press. This book was released on 2016-08-18 with total page 514 pages. Available in PDF, EPUB and Kindle. Book excerpt: "Computational Approaches for Studying Enzyme Mechanism, Part B" is the first of two volumes in the Methods in Enzymology series that focuses on computational approaches for studying enzyme mechanism. The serial achieves the critically acclaimed gold standard of laboratory practices and remains one of the most highly respected publications in the molecular biosciences. Each volume is eagerly awaited, frequently consulted, and praised by researchers and reviewers alike. Now with over 550 volumes, the series remains a prominent and essential publication for researchers in all fields of the life sciences and biotechnology, including biochemistry, chemical biology, microbiology, synthetic biology, cancer research, genetics, and other fields of study. Focuses on computational approaches for studying enzyme mechanismContinues the legacy of this premier serial with quality chapters authored by leaders in the field Covers research methods in intermediate filament associated proteins, and contains sections on such topics as lamin-associated proteins, intermediate filament-associated proteins and plakin, and other cytoskeletal cross-linkers

Download or read book Computational Approaches to Understand the Atomistic Drivers of Enzyme Catalysis written by Natasha Seelam and published by . This book was released on 2021 with total page 213 pages. Available in PDF, EPUB and Kindle. Book excerpt: Enzymes readily perform chemical reactions several orders of magnitude faster than their uncatalyzed versions in ambient conditions with high specificity, making them attractive design targets for industrial purposes. Traditionally, enzyme reactivity has been contextualized through transition-state theory (TST), in which catalytic strategies are described by their ability to minimize the activation energy to cross the reaction barrier through a combination of ground-state destabilization (GSD) and transition-state stabilization (TSS). While excellent progress has been made to rationally design enzymes, the complexity of the design space and the highly optimized nature of enzymes make general application of these approaches difficult. This thesis presents a set of computational methods and applications in order to investigate the larger perspective of enzyme-assisted kinetic processes. For the first part of the thesis, we analyzed the energetics and dynamics of proficient catalyst orotidine 5'-monophosphate decarboxylase (OMPDC), an enzyme that catalyzes decarboxylation nearly 17 orders of magnitude more proficiently than the uncatalyzed reaction in aqueous solvent. Potential-of-mean-force (PMF) calculations on wild type (WT) and two catalytically hindered mutants, S127A and V155D (representing TSS and GSD, respectively), characterized the energy barriers associated with decarboxylation as a function of two parameters: the distance between the breaking C–C bond and a proton-transfer coordinate from the nearby side chain of K72, a conserved lysine in the active site. Coupling PMF analyses with transition path sampling (TPS) approaches revealed two distinct decarboxylation strategies: a simultaneous, K72-assisted pathway and a stepwise, relatively K72-independent pathway. Both PMF and TPS rate calculations reasonably reproduced the empirical differences in relative rates between WT and mutant systems, suggesting these approaches can enable in silico inquiry into both pathway and mechanism identification in enzyme kinetics. For the second study, we investigated the electronic determinants of reactivity, using the enzyme ketol-acid reductoisomerase (KARI). KARI catalyzes first a methyl isomerization and then reduction with an active site comprised of several polar residues, two magnesium divalent cations, and NADPH. This study focused on isomerization, which is rate limiting, with two objectives: characterization of chemical mechanism in successful catalytic events (“reactive”) versus failed attempts to cross the barrier ("non-reactive"), and the interplay between atomic positions, electronic descriptors, and reactivity. Natural bonding orbital (NBO) analyses provided detailed electronic description of the dynamics through the reaction and revealed that successful catalytic events crossed the reaction barrier through a 3-center-2-electron (3C) bond, concurrent to isomerization of hydroxyl/carbonyls on the substrate. Interestingly, the non-reactive ensemble adopted a similar electronic pathway as the reactive ensemble, but its members were generally unable to form and sustain the 3C bond. Supervised machine learning classifiers then identified small subsets of geometric and electronic descriptors, “features”, that predicted reactivity; our results indicated that fewer electronic features were able to predict reactivity as effectively as a larger set of geometric features. Of these electronic features, the models selected diverse descriptors representing several facets of the chemical mechanism (charge, breaking–bond order, atomic orbital hybridization states, etc.). We then inquired how geometric features reported on electronic features with classifiers that leveraged pairs of geometric features to predict the relative magnitude of each electronic feature. Our findings indicated that the geometric, pair-feature models predicted electronic structure with comparable performance as cumulative geometric models, suggesting small subsets of features were capable of reporting on electronic descriptors, and that different subsets could be leveraged to describe various aspects of a chemical mechanism. Lastly, we revisited OMPDC in order to learn the key geometric features that distinguished between the simultaneous and stepwise pathways of decarboxylation, aggregating and labeling pathways drawn from WT and mutant systems ensembles. We leveraged classifiers that predicted between reactive pathways by selecting small subsets of structural features from 620 geometric features comprised of atoms from the active site. The classifiers performed comparably, with greater than 80% testing accuracy and AUC, between times starting from in the reactant basin to 30 fs into crossing the reaction barrier. Remarkably, model-selected features reported on chemically meaningful interactions despite no explicit prior knowledge of the mechanism in training. To illustrate this, we focused analyses on two particular features shown to be predictive while in the reactant basin, prior to crossing the barrier: a potential hydrogen-bond between D75*, an aspartate in the active site, and the 2'-hydroxyl of OMP, and electrostatic repulsion through the proximity of a different aspartate, D70, to the leaving group carboxylate of OMP. Analysis between the simultaneous and stepwise ensembles demonstrated that the simultaneous ensemble adopted shorter distances for both features, generally suggesting stronger interactions. Both features were additionally shown to be associated with the ability to distort the planarity of the orotidyl ring, where shorter distances for either feature were correlated with larger degrees of distortion. Taken together, this suggested the simultaneous ensemble was more effective at distorting the ground state structure prior to crossing the reaction barrier.

Download or read book Cell Wide Identification of Metabolite Protein Interactions written by Aleksandra Skirycz and published by Springer Nature. This book was released on 2022-09-30 with total page 261 pages. Available in PDF, EPUB and Kindle. Book excerpt: This thorough volume explores protocols of proteome- and metabolome-wide strategies for the identification of protein-small molecule complexes in different organisms, in order to shed light on these important regulatory interactions. Experimental and computational strategies to characterize protein-metabolite interactions are discussed, and recent advances in enabling technologies are featured as well. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of detail and expert implementation advice to ensure success in future research. Authoritative and practical, Cell-Wide Identification of Metabolite-Protein Interactions will aid researchers seeking a better understanding of the mechanisms of signal transduction occurring in the cell and assessing the effect of complex formation on cell physiology.

Download or read book Computational Approaches to Biochemical Reactivity written by Gábor Náray-Szabó and published by Springer Science & Business Media. This book was released on 2006-04-11 with total page 386 pages. Available in PDF, EPUB and Kindle. Book excerpt: A quantitative description of the action of enzymes and other biological systems is both a challenge and a fundamental requirement for further progress in our und- standing of biochemical processes. This can help in practical design of new drugs and in the development of artificial enzymes as well as in fundamental understanding of the factors that control the activity of biological systems. Structural and biochemical st- ies have yielded major insights about the action of biological molecules and the mechanism of enzymatic reactions. However it is not entirely clear how to use this - portant information in a consistent and quantitative analysis of the factors that are - sponsible for rate acceleration in enzyme active sites. The problem is associated with the fact that reaction rates are determined by energetics (i. e. activation energies) and the available experimental methods by themselves cannot provide a correlation - tween structure and energy. Even mutations of specific active site residues, which are extremely useful, cannot tell us about the totality of the interaction between the active site and the substrate. In fact, short of inventing experiments that allow one to measure the forces in enzyme active sites it is hard to see how can one use a direct experimental approach to unambiguously correlate the structure and function of enzymes. In fact, in view of the complexity of biological systems it seems that only computers can handle the task of providing a quantitative structure-function correlation.

Download or read book A Multiscale Computational Approach to Study RNase A Catalysis written by Thakshila D. Dissanayake Rallage and published by . This book was released on 2016 with total page 124 pages. Available in PDF, EPUB and Kindle. Book excerpt: Enzyme catalysis is an extremely important and complex process that is fundamental to biology. Experiments provide a wealth of valuable information about the function of enzymes; however, this information requires the use of computational models to establish a meaningful interpretation that can be used to guide design. Multiscale computational models, which integrate a hierarchy of theoretical methods to address complex biomolecular problems that span large spatial and temporal ranges, afford powerful tools to provide a detailed molecular level interpretation of a wide range of experimental data from which a consensus view of catalytic mechanism may emerge. In this dissertation, I detail my efforts to develop and apply multiscale methods to study the mechanisms of RNA backbone cleavage catalyzed by Ribonuclease A, an important archetype enzyme system, and the factors that regulate its activity. In the first phase of this research, I use molecular dynamics simulations to characterize the structure and dynamics of the active enzyme in solution at different stages along the reaction path. In this work, I demonstrate that the crystallographic structure represents an inactive, catalytically non-relevant state, and make predictions that a conformational change involving the flipping of the side chain of a conserved histidine residue (His12) is required to adopt a catalytically competent conformation. In the second phase of this research, I apply ''constant pH molecular dynamics simulations'' (CpHMD) to characterize the conditional probability of finding key active site residues in a protonation state that supports general acid-base catalysis. This allowed the prediction of pKa shifts for His12, His119 and Lys41, and, for the first time, activity-pH profiles for an enzyme system that can be compared directly with those measured in kinetic experiments. In the third phase of this research, I use combined quantum mechanical/molecular mechanical methods to study the catalytic chemical steps of transphosphorylation. Results of this work predict a free energy landscape for the reaction, from which the minimum free energy pathway that connects reactants and products allows a detailed molecular-level picture of mechanism. In the fourth phase of this research, I extend the CpHMD method to nucleic acid systems, to benchmark the method for the study of ribozymes that catalyze the same reaction as RNase A.

Download or read book Computational Approaches to Study the Impact of Mutations on Disease and Drug Resistance written by Nir Ben-Tal and published by Frontiers Media SA. This book was released on 2022-01-27 with total page 139 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Computational Approaches to Protein Dynamics written by Monika Fuxreiter and published by CRC Press. This book was released on 2014-12-24 with total page 458 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Latest Developments on the Role of Dynamics in Protein FunctionsComputational Approaches to Protein Dynamics: From Quantum to Coarse-Grained Methods presents modern biomolecular computational techniques that address protein flexibility/dynamics at all levels of theory. An international contingent of leading researchers in chemistry, physics, an

Download or read book Enzyme Kinetics and Mechanisms Part E Energetics of Enzyme Catalysis written by and published by Elsevier. This book was released on 1999-09-06 with total page 494 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume supplements Volumes 63, 64, 87, and 249 of Methods in Enzymology. These volumes provide a basic source for the quantitative interpretation of enzyme rate data and the analysis of enzyme catalysis. Among the major topics covered are Engergetic Coupling in Enzymatic Reactions, Intermediates and Complexes in Catalysis, Detection and Properties of Low Barrier Hydrogen Bonds, Transition State Determination, and Inhibitors. The critically acclaimed laboratory standard for more than forty years, Methods in Enzymology is one of the most highly respected publications in the field of biochemistry. Since 1955, each volume has been eagerly awaited, frequently consulted, and praised by researchers and reviewers alike. Now with more than 300 volumes (all of them still in print), the series contains much material still relevant today--truly an essential publication for researchers in all fields of life sciences.

Download or read book Advancements in Biomass Feedstock Preprocessing Conversion Ready Feedstocks Volume II written by Timothy G. Rials and published by Frontiers Media SA. This book was released on 2022-11-11 with total page 219 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Computational Study of Enzymes and Molecular Machines written by Song Yang and published by . This book was released on 2018 with total page 214 pages. Available in PDF, EPUB and Kindle. Book excerpt: Chapters 1-6 describe studies of enzymes and their applications in biocatalysis. Biocatalysis, the use of natural enzymes or engineered enzymes to produce molecules of interest, has been an emerging and favorable approach to supplement or replace traditional organic synthesis. Enzymes are very efficient and selective in catalysis, and enzyme catalysis is also environmentally friendly. The first portion of this dissertation reports the theoretical study of several enzymes that catalyze very different reactions, including oxidation, halogenation as well as Diels-Alder reactions. The study reveals the mechanism behind each enzyme-catalyzed reaction in terms of efficiency, substrate specificity and regio-/stereo selectivity. In addition to the understanding of each enzyme, mutations are proposed based on the mechanism of the enzyme reactions to improve the natural enzymes for better catalysis. Chapter 1 introduces a general strategy for synthesis of macrolactones using nickel catalyzed C-C coupling and a site-selective P450 C-H oxidations carried out at Michigan by the groups of Montgomery and Sherman. Quantum mechanical (QM) computations show the intrinsic energy barriers at different hydrogen atoms at different sites in a single substrate. Molecular dynamic (MD) simulations reproduce the site selectivity and stereoselectivity in the biocatalytic oxidations with the aid of QM results. Our results suggest the linker length and its interaction with the enzyme determines the reaction yield. Chapter 2 presents a study of the first natural Diels-Alderase (DAase) and its mechanism for catalyzing a DA reaction. QM calculations suggest the reaction goes through an ambimodal TS leading to both [4+2] and [6+4] adducts. MD simulations show that trajectories pass through the TS and go to [4+2] adduct more in the enzyme than in gas phase or water. The enzyme influences the outcome of bifurcation dramatically, mainly through hydrophobic contact. The energy barrier of the enzymatic reaction is also reproduced accurately with our newly developed method: Environment Perturbed TS Sampling (EPTSS). Chapter 3 studies the Cope rearrangement and cyclization in hapalindole biogenesis. The X-ray crystal structure of HpiC1 is reported in this study. Mutagenesis study as well as computational computations uncover the key residues for the enzymatic reaction. QM computations show the reaction goes through an acid-catalyzed [3,3]-sigmatropic rearrangement. The switch from hapalindole to fischerindole is explained by the position change of the terminal electrophilic aromatic substitution in MD simulations. Chapter 4 describes the mechanism of Diels-Alderase PyrI4 in pyrroindomycins biosynthesis. Density functional theory (DFT) calculations and EPTSS calculations compare the energy barriers of the reaction in the gas phase, theozyme model, and in the enzyme. Hydrogen bonding has limited contribution to the TS stabilization in the enzyme. MD simulations show that hydrophobic interactions dominate in the catalysis of the enzyme catalyzed Diels-Alder reaction by fitting with the exo TS better than other TSs or the reactants. Chapter 5 presents the study of a multifunctional P450 MycG and its substrate specificity. QM computations reveal the mechanism behind the MycG biopathway. MD simulations show that a hydrophobic cavity in MycG differentiates the three different substrates favors the binding of the natural substrate. Based on MD simulations, potential beneficial mutations are proposed and tested by the Sherman group at Michigan, and are proven to improve the enzyme performance in experiment. Chapter 6 studies flavin dependent halogenase and its regioselectivity in directed evolution. The flavin dependent halogenase RebH was engineered to catalyze chlorination at different regioselective sites of tryptamine. QM calculations reveal that the intrinsic energy barriers at different sites are similar to each other. Docking and MD simulations show the different binding poses are favorable in WT and the mutants. Key mutations are identified through MD simulations and reverse mutations. Chapters 7-9 are projects about molecular machines in solid state as well as solvent phase, studied experimentally by the Garcia-Garibay group. Ever since Prof. Feynman's famous talk "There is plenty of room at the bottom", nanotechnology has witnessed tremendous progress in the synthesis and design of molecular machines capable of mechanical movements. The early stage of molecular machine development was simply to mimic macroscopic designs. However, to succeed in building nanoscale versions of the mechanical world, more understanding is required, rather than simple mimicry. In these chapters, I have studied the dynamics of molecular rotation in dendrimetric materials, MOFs crystal and organic solvents. With computational study, the rotational process is revealed at nanosecond time scale. New designs of molecular machine are proposed to improve their performance in different environments. Chapter 7 studies the rotation of phenyl rings at different parts in a dendrimeric material. Molecular dynamics study reveals the different dynamics of molecular rotations at the core, branches and peripheral ends. The energy surfaces of molecular rotation are scanned using umbrella sampling, and the energy barriers are computed. In Chapter 8, the rotational dynamics of molecular rotors in amphidynamic crystals are studied. The energy barriers of the rotation are computed by QM study to be ~0.2 kcal/mol, consistent with the ultrafast rotation in the rigid BODCA-MOF crystals. MD simulations reveal the ultrafast rotation at different temperatures and find it to be diffusion-like at high temperature. Chapter 9 compares and studies the gearing performance of different molecular spur gears. The gearing efficiency is affected by the distance between the two rotors in molecular gears. Solvent molecules are shown to interfere with the rotation of the molecular rotors and promote slippage rather than gearing. A new design of molecular spur gear is proposed and tested by MD simulations. With a macrocyclic structure, the solvent effect is eliminated and the molecular spur gear is able to gear in solvent phase.

Download or read book Applying Computational Methods in the Study of Biomolecular Systems written by and published by . This book was released on 2007 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book MULTISCALE MOLECULAR MODELING STUDIES OF THE DYNAMICS AND CATALYTIC MECHANISMS OF IRON II AND ZINC II DEPENDENT METALLOENZYMES written by and published by . This book was released on 2023 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Abstract : Enzymes are biological systems that aid in specific biochemical reactions. They lower the reaction barrier, thus speeding up the reaction rate. A detailed knowledge of enzymes will not be achievable without computational modeling as it offers insight into atomistic details and catalytic species, which are crucial to designing enzyme-specific inhibitors and impossible to gain experimentally. This dissertation employs advanced multiscale computational approaches to study the dynamics and reaction mechanisms of non-heme Fe(II) and 2-oxoglutarate (2OG) dependent oxygenases, including AlkB, AlkBH2, TET2, and KDM4E, involved in DNA and histone demethylation. It also focuses on Zn(II) dependent matrix metalloproteinase-1 (MMP-1), which helps collagen degradation. Chapter 2 investigates the substrate selectivity and dynamics on the enzyme-substrate complexes of DNA repair enzymes, AlkB and FTO. Chapter 3 unravels the mechanisms and effects of dynamics on the demethylation of 3-methylcytosine substrate by AlkB and AlkBH2 enzymes. The results imply that the nature of DNA and conformational dynamics influence the electronic structure of the iron center during demethylation. Chapter 4 delineates how second-coordination and long-range residue mutations affect the oxidation of 5-methylcytosine substrate to 5-hydroxymethylcytosine by TET2 enzyme. The results reveal that mutations affect DNA binding/interactions and the energetic contributions of residues stabilizing key catalytic species. Chapter 5 describes the reparation of unnatural alkylated substrates by TET2, their effects on second-coordination interactions and long-range correlated motions in TET2. The study reveals that post-hydroxylation reactions occur in aqueous solution outside the enzyme environment. Chapter 6 establishes how applying external electric fields (EEFs) enhances specificity of KDM4E for C-H over N-H activation during dimethylated arginine substrate demethylation. The results reveal that applying positive EEFs parallel to Fe=O bond enhances C-H activation rate, while inhibiting the N-H one. Chapter 7 addresses the formation of catalytically competent MMP-1·THP complex of MMP-1. The studies reveal the role of MMP-1's catalytic domain a-helices, the linker, and changes in coordination states of catalytic Zn(II) during the transition. Overall, the presented results contribute to the in-depth understanding of the fundamental mechanisms of the studied enzymes and provide a background for developing enzyme-specific inhibitors against the associated disorders and diseases.

Download or read book Computational Catalysis written by Aravind Asthagiri and published by Royal Society of Chemistry. This book was released on 2014 with total page 277 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents a comprehensive review of the methods and approaches being adopted to push forward the boundaries of computational catalysis.

Download or read book Enzyme Kinetics Catalysis and Control written by Daniel L. Purich and published by Elsevier. This book was released on 2010-06-16 with total page 915 pages. Available in PDF, EPUB and Kindle. Book excerpt: Far more than a comprehensive treatise on initial-rate and fast-reaction kinetics, this one-of-a-kind desk reference places enzyme science in the fuller context of the organic, inorganic, and physical chemical processes occurring within enzyme active sites. Drawing on 2600 references, Enzyme Kinetics: Catalysis & Control develops all the kinetic tools needed to define enzyme catalysis, spanning the entire spectrum (from the basics of chemical kinetics and practical advice on rate measurement, to the very latest work on single-molecule kinetics and mechanoenzyme force generation), while also focusing on the persuasive power of kinetic isotope effects, the design of high-potency drugs, and the behavior of regulatory enzymes. Historical analysis of kinetic principles including advanced enzyme science Provides both theoretical and practical measurements tools Coverage of single molecular kinetics Examination of force generation mechanisms Discussion of organic and inorganic enzyme reactions

Download or read book Catalysis in Chemistry and Enzymology written by William P. Jencks and published by Courier Corporation. This book was released on 1987-01-01 with total page 866 pages. Available in PDF, EPUB and Kindle. Book excerpt: Exceptionally clear coverage of mechanisms for catalysis, forces in aqueous solution, carbonyl- and acyl-group reactions, practical kinetics, more.