Multiscale Molecular Modeling Studies Of The Dynamics And Catalytic Mechanisms Of Ironii And Zincii Dependent Metalloenzymes

Download Multiscale Molecular Modeling Studies Of The Dynamics And Catalytic Mechanisms Of Ironii And Zincii Dependent Metalloenzymes full books in PDF, epub, and Kindle. Read online Multiscale Molecular Modeling Studies Of The Dynamics And Catalytic Mechanisms Of Ironii And Zincii Dependent Metalloenzymes ebook anywhere anytime directly on your device. Fast Download speed and no annoying ads. We cannot guarantee that every ebooks is available!

MULTISCALE MOLECULAR MODELING STUDIES OF THE DYNAMICS AND CATALYTIC MECHANISMS OF IRON(II)- AND ZINC(II)-DEPENDENT METALLOENZYMES

Author :
Publisher :
ISBN 13 :
Total Pages : 0 pages
Book Rating : 4.:/5 (138 download)

DOWNLOAD NOW!

Book Synopsis MULTISCALE MOLECULAR MODELING STUDIES OF THE DYNAMICS AND CATALYTIC MECHANISMS OF IRON(II)- AND ZINC(II)-DEPENDENT METALLOENZYMES by :

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.

Design and Evolution of Metalloenzymes Through Multi-scale Approaches

Author : Crystal Edie Valdez
Publisher :
ISBN 13 :
Total Pages : 226 pages
Book Rating : 4.:/5 (925 download)

DOWNLOAD NOW!

Book Synopsis Design and Evolution of Metalloenzymes Through Multi-scale Approaches by : Crystal Edie Valdez

Download or read book Design and Evolution of Metalloenzymes Through Multi-scale Approaches written by Crystal Edie Valdez and published by . This book was released on 2015 with total page 226 pages. Available in PDF, EPUB and Kindle. Book excerpt: Natural metalloenzymes are often the most proficient catalysts in terms of their activity, selectivity, and ability to operate at mild conditions. However, metalloenzymes are occasionally surprising in their choice of catalytic metals, and in their responses to metal substitution. Indeed, from the isolated standpoint of producing the best catalyst, a chemist designing from first principles would likely choose a different metal. Due to competing evolutionary pressures, many natural enzymes may not have evolved to be ideal catalysts and can be improved for the isolated purpose of catalysis in vitro when the competing factors are removed. To improve and, in due course, design metalloenzymes, extensive sampling and proper treatment of the electronic structure of the bound metal(s), is required, while seamlessly merging the required techniques to assess energies and entropies, or their changes, for the entire system. Approaching these challenges with a multi-scale approach, the Alexandrova group has developed an accurate and efficient quantum mechanical/molecular mechanics (QM/MM) hybrid dynamics method to model metalloproteins called quantum mechanics/discrete molecular mechanics (QM/DMD). QM/DMD operates through an iterative scheme between QM and MM machineries. DMD is a flavor of molecular dynamics (MD) that approximates the continuous interaction potentials in classical MD with square-well potentials, course-graining the potentials and overall reducing the number of calculations needed. Due to these discretized potentials, DMD is driven by collision events rather than physical forces as in traditional MM and MD. Therefore, the user saves a tremendous amount of time with DMD by solving ballistic equations of motions rather than Newtonian equations of motions. This fast and efficient hybrid dynamics tools has allowed us to investigate various metal-dependent phenomena in natural metalloenzymes such as: 1) exploring Nature's curious choices for specific metals using two amide hydrolases that contain different metals as a case study, 2) examining protein conformational responses to substrate binding and metal replacement as showcased by the role of a flexible loop [beta]-lactamase in binding antibiotic substrates and 3) investigating how the species of the metal dictates the reaction mechanism in a pair acireductone dioxygenases (ARD/ARD'). Extending outside the realm of naturally occurring enzymes, our tools have the ability to span across formidable challenges such as metalloenzyme design, where stabilization of a transition state of the catalyzed reaction in the specific binding pocket around the metal needs to be achieved. QM/DMD was used in the redesign of a well-studied Zn2+ peptidase, carboxypeptidase A (CPA), an enzyme involved in the breakdown of proteins, with a slight preference for bulky hydrophobic groups. More specifically, the enzyme and substrate system were modified to create specific-specific binding and subsequent experiments proved the mutant to be catalytically active. Additionally, another tool called Eris-QM/DMD was formulated to better gauge the effect of mutation on protein structure during the design process. Eris is a stand-alone package that evaluates protein stability upon mutagenesis. Coupling the software to QM/DMD gives us the distinct advantage of accounting for the effect of the metal during protein alternations. With this diverse set of tools, our future ambitious goals are to install catalytically potent non-physiological metals into proteins. While nature is limited to operating with bio-available elements, some metals such as Ir, Pd, Sc, and Rh, which have been shown to be excellent catalysts, even surpassing physiological metals. If the catalytic activity of these non-physiological metals can be combined with the superb selectivity and mild operational conditions characteristic of proteins, new proficient enzymes may emerge. Another advantage to enzymatic catalysis, done either in vitro, or in vivo, is that it can be cheaper, "greener", and more efficient than synthetic catalysis. An early endeavor in this frontier of metalloenzyme design involves installing Pd2+ into an existing protein scaffold, specifically for intramolecular hydroarylation of C-C triple bonds to form coumarins.

Computational Investigation of the Catalytic and Structural Roles of Metals in Metalloenzymes

Author : Rimsha Mehmood
Publisher :
ISBN 13 :
Total Pages : 0 pages
Book Rating : 4.:/5 (134 download)

DOWNLOAD NOW!

Book Synopsis Computational Investigation of the Catalytic and Structural Roles of Metals in Metalloenzymes by : Rimsha Mehmood

Download or read book Computational Investigation of the Catalytic and Structural Roles of Metals in Metalloenzymes written by Rimsha Mehmood and published by . This book was released on 2021 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Metalloenzymes capitalize on the unique roles of metal co-factors and protein scaffolds in catalyzing crucial chemical transformations at ambient conditions with exquisite selectivity. Some metalloenzymes exploit the redox properties of metal cofactors to catalyze challenging reactions, while others recruit metals for structural roles in stabilizing enzyme-substrate complexes. Although crystallography and spectroscopy provide foundational knowledge of the structure and reactivity of metalloenzymes, critical gaps remain in our understanding of the catalytic and structural role of metals in enzymes. Therefore, the use of novel computational tools to understand the role of metals and protein environment in dynamically promoting the reactivity and selectivity of metalloenzymes is of fundamental importance.

Multiscale Modeling of Metalloenzymes: Design and Evolution

Author : Michael Nechay
Publisher :
ISBN 13 :
Total Pages : 212 pages
Book Rating : 4.:/5 (14 download)

DOWNLOAD NOW!

Book Synopsis Multiscale Modeling of Metalloenzymes: Design and Evolution by : Michael Nechay

Download or read book Multiscale Modeling of Metalloenzymes: Design and Evolution written by Michael Nechay and published by . This book was released on 2017 with total page 212 pages. Available in PDF, EPUB and Kindle. Book excerpt: With just a simple alphabet of natural amino acids and common metals, enzymes perform a spectacular number of reactions necessary for life on earth with enviable ease - with neither the extreme conditions nor chemical waste seen from many industrial reactors in human-developed catalysis. Principally, protein structure and related function is not well understood beyond being decisive for its unique selectivity and efficiency. A reliable treatment of larger protein movements/sampling coupled with precise quantum mechanical treatment of metals and bonds breaking/forming (multiscale) is still an open problem in Computational Chemistry. Metalloenzymes can be particularly challenging to model so we present some of the latest in multiscale modeling techniques. We have developed methods sensitive enough to study "selection" of similar metals in enzymes such as HDAC8, where previous literature failed to conclude which metal is active during in vivo catalysis, while fast enough to study larger protein movements including fold stability. Eminently, multiscale modeling opens the discussion of engineering enzymes to cater to modern day needs in catalysis. Society has not only developed needs in catalysis outside the scope of natural evolution (e.g., drug synthesis, energy conversion) but also has access to more of the periodic table than nature has had a chance to explore. Thus, combining the efficacy of natural enzymes with modern catalytic processes has enormous potential. We have studied iridium, a rare metal with thermodynamic advantages over other metals in promoting catalysis of hydroamination and transfer hydrogenation. In the context of an enzyme we predict catalytic rates near and even exceeding existing organometallic catalysts with further design for specificity available. We are in collaboration with an experimental group in designing a protein fold which both directly accommodates and uses iridium in catalysis. We hope these foundations will support metalloenzyme design efforts towards novel chemical transformations performed as efficiently and environmentally soundly as nature has shown us is possible.

MULTILEVEL COMPUTATIONAL INVESTIGATION INTO THE DYNAMICS AND REACTION MECHANISMS OF NON-HEME IRON AND 2-OXOGLUTARATE DEPENDENT ENZYMES

Download MULTILEVEL COMPUTATIONAL INVESTIGATION INTO THE DYNAMICS AND REACTION MECHANISMS OF NON-HEME IRON AND 2-OXOGLUTARATE DEPENDENT ENZYMES PDF Online Free

Author :
Publisher :
ISBN 13 :
Total Pages : 0 pages
Book Rating : 4.:/5 (137 download)

DOWNLOAD NOW!

Book Synopsis MULTILEVEL COMPUTATIONAL INVESTIGATION INTO THE DYNAMICS AND REACTION MECHANISMS OF NON-HEME IRON AND 2-OXOGLUTARATE DEPENDENT ENZYMES by :

Download or read book MULTILEVEL COMPUTATIONAL INVESTIGATION INTO THE DYNAMICS AND REACTION MECHANISMS OF NON-HEME IRON AND 2-OXOGLUTARATE DEPENDENT ENZYMES written by and published by . This book was released on 2022 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Abstract : Computational chemistry methods have been extensively applied to investigate biological systems. This dissertation utilizes a multilevel computational approach to explore the dynamics and reaction mechanisms of two groups of enzymes belonging to non-heme Fe(II) and 2-oxoglutarate (2OG) dependent superfamily - histone lysine demethylases from class 7 and ethylene forming enzyme (EFE). Chapter 2 uncovers the role of conformational dynamics in the substrate selectivity of histone lysine demethylases 7A and 7B. The molecular dynamics (MD) simulations of the two enzymes revealed the importance of linker flexibility and dynamics in relative orientations of the reader (PHD) and the catalytic (JmjC) domains. Chapter 3 describes the use of combined quantum mechanics/molecular mechanics (QM/MM) and MD simulations to explore the reaction mechanism of histone lysine demethylases 7B (PHF8), including dioxygen activation, 2OG binding modes, and substrate demethylation steps. Importantly, the calculations imply the rearrangement of the 2OG C-1 carboxylate prior to dioxygen binding at a five-coordination stage in catalysis, highlighting the dynamic nature of the non-heme Fe-center. Chapter 4 develops a computational framework for identifying second coordination sphere (SCS) and especially long range (LR) residues relevant for catalysis through dynamic cross correlation analysis (DCCA) using the PHF8 as a model oxygenase and explores their effects on the rate determining hydrogen atom transfer step. The results from the QM/MM calculations suggest that DCCA can identify non-active site residues relevant to catalysis. Chapter 5 explores the unique catalytic mechanism of EFE. In particular, the study elucidates the atomic and electronic structure determinants that distinguish between ethylene formation and L-Arg hydroxylation reaction mechanisms in the EFE. The results indicated that synergy between the conformation of L-Arg and the coordination mode of 2OG directs the reaction toward ethylene formation or L-Arg hydroxylation. Chapter 6 demonstrates that applying an external electric field (EEF) along the Fe-O bond in the EFE·Fe(III)·OO.-·2OG·L-Arg complex can switch the EFE reactivity between L-Arg hydroxylation and ethylene generation. Overall, applying an EEF on EFE indicates that making the intrinsic electric field of EFE less negative and stabilizing the off-line binding of 2OG might increase ethylene generation while reducing L-Arg hydroxylation. Chapter 7 probes the role of the protein environment in modulating the dioxygen diffusion and binding and thus ultimately contributing to the diverging reactivities of PHF8 and EFE. Overall, the results of this dissertation together highlight the several catalytic strategies utilized by the non-heme Fe(II) and 2OG dependent enzymes for achieving their reaction outcomes. In the longer term, the results can be used to modulate the activities of these enzymes either through enzyme redesign or the generation of enzyme-selective inhibitors.

Multiscale Modeling of Metalloproteins and Protonation Equilibria in Biomolecular Systems

Author : Patrick G. Blachly
Publisher :
ISBN 13 : 9781321138009
Total Pages : 176 pages
Book Rating : 4.1/5 (38 download)

DOWNLOAD NOW!

Book Synopsis Multiscale Modeling of Metalloproteins and Protonation Equilibria in Biomolecular Systems by : Patrick G. Blachly

Download or read book Multiscale Modeling of Metalloproteins and Protonation Equilibria in Biomolecular Systems written by Patrick G. Blachly and published by . This book was released on 2014 with total page 176 pages. Available in PDF, EPUB and Kindle. Book excerpt: A combination of classical and quantum mechanical approaches are described in Chapter 1 and utilized in this dissertation to study catalysis and allostery in the metalloprotein IspH, as well as to probe protonation equilibria in a variety of macromolecules. Chapters 2 and 3 are dedicated to characterizing the oxidized [4Fe-4S] IspH protein, which is biologically important as an antimicrobial drug target. In Chapter 2, the protonation states of active site residues in substrate-bound IspH are characterized using broken-symmetry density functional theory to provide a foundation for exploring IspH catalysis. Subsequently, a more coarse-grained approach is used in Chapter 3 to assess the internal motions of IspH, both with and without its substrate bound, using classical molecular dynamics. Both these studies reveal rational approaches for the design of novel IspH inhibitors. Chapters 4 and 5 deviate from the metalloprotein theme established in Chapters 2 and 3 to consider classical approaches for treating proton binding and unbinding in the context of molecular dynamics simulations. The ability of the constant pH molecular dynamics method to predict protein pKa values is assessed in Chapter 4 using an experimental test set comprising Staphylococcal nuclease variants. Building on this work, Chapter 5 provides proof of concept for the constant pH molecular dynamics method to obtain pH-dependent binding free energies in conjunction with Wyman's binding polynomial formalism.

Computational Study of Enzymes and Molecular Machines

Author : Song Yang
Publisher :
ISBN 13 :
Total Pages : 214 pages
Book Rating : 4.:/5 (14 download)

DOWNLOAD NOW!

Book Synopsis Computational Study of Enzymes and Molecular Machines by : Song Yang

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.

2-Oxoglutarate-Dependent Oxygenases

Author : Christopher J Schofield
Publisher : Royal Society of Chemistry
ISBN 13 : 1849739501
Total Pages : 508 pages
Book Rating : 4.8/5 (497 download)

DOWNLOAD NOW!

Book Synopsis 2-Oxoglutarate-Dependent Oxygenases by : Christopher J Schofield

Download or read book 2-Oxoglutarate-Dependent Oxygenases written by Christopher J Schofield and published by Royal Society of Chemistry. This book was released on 2015-05-06 with total page 508 pages. Available in PDF, EPUB and Kindle. Book excerpt: Since the discovery of the first examples of 2-oxoglutarate-dependent oxygenase-catalysed reactions in the 1960s, a remarkably broad diversity of alternate reactions and substrates has been revealed, and extensive advances have been achieved in our understanding of the structures and catalytic mechanisms. These enzymes are important agrochemical targets and are being pursued as therapeutic targets for a wide range of diseases including cancer and anemia. This book provides a central source of information that summarizes the key features of the essential group of 2-oxoglutarate-dependent dioxygenases and related enzymes. Given the numerous recent advances and biomedical interest in the field, this book aims to unite the latest research for those already working in the field as well as to provide an introduction for those newly approaching the topic, and for those interested in translating the basic science into medicinal and agricultural benefits. The book begins with four broad chapters that highlight critical aspects, including an overview of possible catalytic reactions, structures and mechanisms. The following seventeen chapters focus on carefully selected topics, each written by leading experts in the area. Readers will find explanations of rapidly evolving research, from the chemistry of isopenicillin N synthase to the oxidation mechanism of 5-methylcytosine in DNA by ten-eleven-translocase oxygenases.

Free Energy Calculations

Author : Christophe Chipot
Publisher : Springer Science & Business Media
ISBN 13 : 3540384472
Total Pages : 528 pages
Book Rating : 4.5/5 (43 download)

DOWNLOAD NOW!

Book Synopsis Free Energy Calculations by : Christophe Chipot

Download or read book Free Energy Calculations written by Christophe Chipot and published by Springer Science & Business Media. This book was released on 2007-01-08 with total page 528 pages. Available in PDF, EPUB and Kindle. Book excerpt: Free energy constitutes the most important thermodynamic quantity to understand how chemical species recognize each other, associate or react. Examples of problems in which knowledge of the underlying free energy behaviour is required, include conformational equilibria and molecular association, partitioning between immiscible liquids, receptor-drug interaction, protein-protein and protein-DNA association, and protein stability. This volume sets out to present a coherent and comprehensive account of the concepts that underlie different approaches devised for the determination of free energies. The reader will gain the necessary insight into the theoretical and computational foundations of the subject and will be presented with relevant applications from molecular-level modelling and simulations of chemical and biological systems. Both formally accurate and approximate methods are covered using both classical and quantum mechanical descriptions. A central theme of the book is that the wide variety of free energy calculation techniques available today can be understood as different implementations of a few basic principles. The book is aimed at a broad readership of graduate students and researchers having a background in chemistry, physics, engineering and physical biology.

Sensors in Water Pollutants Monitoring: Role of Material

Author : D. Pooja
Publisher : Springer Nature
ISBN 13 : 981150671X
Total Pages : 319 pages
Book Rating : 4.8/5 (115 download)

DOWNLOAD NOW!

Book Synopsis Sensors in Water Pollutants Monitoring: Role of Material by : D. Pooja

Download or read book Sensors in Water Pollutants Monitoring: Role of Material written by D. Pooja and published by Springer Nature. This book was released on 2019-10-24 with total page 319 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book discusses the sensitivity, selectivity, and response times of different sensor materials and their potential application in the design of portable sensor systems for monitoring water pollutants and remediation systems. Beginning with an overview on water pollutants and analytical methods for their detection, the book then moves on to describing the advances in sensor materials research, and the scope for their use in different types of sensors. The book lays emphasis on techniques such as colorimetric, fluorescence, electrochemical, and biological sensing of conventional and emerging pollutants. This book will serve as a handy guide for students, researchers, and professional engineers working in the field of sensor systems for monitoring water pollutants to address various challenges.

Quadruplex Nucleic Acids

Author : Stephen Neidle
Publisher : Royal Society of Chemistry
ISBN 13 : 1847555292
Total Pages : 317 pages
Book Rating : 4.8/5 (475 download)

DOWNLOAD NOW!

Book Synopsis Quadruplex Nucleic Acids by : Stephen Neidle

Download or read book Quadruplex Nucleic Acids written by Stephen Neidle and published by Royal Society of Chemistry. This book was released on 2007-10-31 with total page 317 pages. Available in PDF, EPUB and Kindle. Book excerpt: Guanine rich DNA has been known for decades to form unusual structures, although their biological relevance was little understood. Recent advances have demonstrated that quadruplex structures can play a role in gene expression and provide opportunities for a new class of anticancer therapeutics. A number of quadruplex-specific proteins have also been discovered. Quadruplex Nucleic Acids discusses all aspects of the fundamentals of quadruplex structures, including their structure in solution and the crystalline state, the kinetics of quadruplex folding, and the role of cations in structure and stability. The biology of quadruplexes and G-rich genomic regions and G-quartets in supramolecular chemistry and nanoscience are also considered. Surveying the current state of knowledge, and with contributions from leading experts, this is the first comprehensive review of this rapidly growing area. Quadruplex Nucleic Acids is ideal for researchers interested in areas related to chemistry, chemical biology, medicinal chemistry, molecular pharmacology, and structural and molecular biology.

Biocatalysis for Green Chemistry and Chemical Process Development

Author : Junhua (Alex) Tao
Publisher : John Wiley & Sons
ISBN 13 : 1118028295
Total Pages : 494 pages
Book Rating : 4.1/5 (18 download)

DOWNLOAD NOW!

Book Synopsis Biocatalysis for Green Chemistry and Chemical Process Development by : Junhua (Alex) Tao

Download or read book Biocatalysis for Green Chemistry and Chemical Process Development written by Junhua (Alex) Tao and published by John Wiley & Sons. This book was released on 2011-06-09 with total page 494 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book describes recent progress in enzyme-driven green syntheses of industrially important molecules. The first three introductory chapters overview recent technological advances in enzymes and cell-based transformations, and green chemistry metrics for synthetic efficiency. The remaining chapters are directed to case studies in biotechnological production of pharmaceuticals (small molecules, natural products and biologics), flavors, fragrance and cosmetics, fine chemicals, value-added chemicals from glucose and biomass, and polymeric materials. The book is aimed to facilitate the industrial applications of this powerful and emerging green technology, and catalyze the advancement of the technology itself.

Globins and Other Nitric Oxide-Reactive Proteins, Part A

Author : Robert K. Poole
Publisher : Academic Press
ISBN 13 : 9780123742773
Total Pages : 672 pages
Book Rating : 4.7/5 (427 download)

DOWNLOAD NOW!

Book Synopsis Globins and Other Nitric Oxide-Reactive Proteins, Part A by : Robert K. Poole

Download or read book Globins and Other Nitric Oxide-Reactive Proteins, Part A written by Robert K. Poole and published by Academic Press. This book was released on 2008-02-19 with total page 672 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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 over 400 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. Methods in Enzymology is now available online at ScienceDirect - full-text online of volumes 1 onwards. For more information about the Elsevier Book Series on ScienceDirect Program, please visit: http://www.info.sciencedirect.com/bookseries/ This volume features methods for the study of globin and other nitric oxide-reactive proteins.

Redox-Active Therapeutics

Author : Ines Batinić-Haberle
Publisher : Springer
ISBN 13 : 3319307053
Total Pages : 709 pages
Book Rating : 4.3/5 (193 download)

DOWNLOAD NOW!

Book Synopsis Redox-Active Therapeutics by : Ines Batinić-Haberle

Download or read book Redox-Active Therapeutics written by Ines Batinić-Haberle and published by Springer. This book was released on 2016-10-13 with total page 709 pages. Available in PDF, EPUB and Kindle. Book excerpt: This essential volume comprehensively discusses redox-active therapeutics, focusing particularly on their molecular design, mechanistic, pharmacological and medicinal aspects. The first section of the book describes the basic aspects of the chemistry and biology of redox-active drugs and includes a brief overview of the redox-based pathways involved in cancer and the medical aspects of redox-active drugs, assuming little in the way of prior knowledge. Subsequent sections and chapters describe more specialized aspects of central nervous system injuries, neurodegenerative diseases, pain, radiation injury and radioprotection (such as of brain, lungs, head and neck and erectile function) and neglected diseases (e.g., leishmaniasis). It encompasses several major classes of redox-active experimental therapeutics, which include porphyrins, salens, nitrones, and most notably metal-containing (e.g., Mn, Fe, Cu, Zn, Sb) drugs as either single compounds or formulations with nanomaterials and quantum dots. Numerous illustrations, tables and figures enhance and complement the text; extensive references to relevant literature are also included. Redox-Active Therapeutics is an invaluable addition to Springer’s Oxidative Stress in Applied Basic Research and Clinical Practice series. It is essential reading for researchers, clinicians and graduate students interested in understanding and exploring the Redoxome—the organism redox network—as an emerging frontier in drug design, redox biology and medicine.

Molecular Architectonics and Nanoarchitectonics

Author : Thimmaiah Govindaraju
Publisher :
ISBN 13 : 9789811641909
Total Pages : 0 pages
Book Rating : 4.6/5 (419 download)

DOWNLOAD NOW!

Book Synopsis Molecular Architectonics and Nanoarchitectonics by : Thimmaiah Govindaraju

Download or read book Molecular Architectonics and Nanoarchitectonics written by Thimmaiah Govindaraju and published by . This book was released on 2022 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is the ultimate assembly of recent research activities on molecular architectonics and nanoarchitectonics by authors who are worldwide experts. The book proposes new ways of creating functional materials at the nano level using the concepts of molecular architectonics and nanoarchitectonics, which are expected to be the next-generation approaches beyond conventional nanotechnology. All the contents are categorized by types of materials, organic materials, biomaterials, and nanomaterials. For that reason, non-specialists including graduate and undergraduate students can start reading the book from any points they would like. Cutting-edge trends in nanotechnology and material sciences are easily visible in the contents of the book, which is highly useful for both students and experimental materials scientists. .

Cytochrome Oxidase

Author : Mårten Wikström
Publisher :
ISBN 13 :
Total Pages : 216 pages
Book Rating : 4.:/5 (319 download)

DOWNLOAD NOW!

Book Synopsis Cytochrome Oxidase by : Mårten Wikström

Download or read book Cytochrome Oxidase written by Mårten Wikström and published by . This book was released on 1981 with total page 216 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Iron-containing Enzymes

Author : Sam P. De Visser
Publisher : Royal Society of Chemistry
ISBN 13 : 1849731810
Total Pages : 463 pages
Book Rating : 4.8/5 (497 download)

DOWNLOAD NOW!

Book Synopsis Iron-containing Enzymes by : Sam P. De Visser

Download or read book Iron-containing Enzymes written by Sam P. De Visser and published by Royal Society of Chemistry. This book was released on 2011 with total page 463 pages. Available in PDF, EPUB and Kindle. Book excerpt: Mononuclear iron containing enzymes are important intermediates in bioprocesses and have potential in the industrial biosynthesis of specific products. This book features topical review chapters by leaders in this field and its various sub-disciplines.