Search results for: interfacial-enzyme-kinetics

Interfacial Enzyme Kinetics

Author : Otto G. Berg
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A vast number of biochemical reactions are catalysed by molecules fixed to the surface of membranes (or other biological structures) with molecules in the surrounding solution. The study of the mechanisms at these "Biointerfaces" are becoming increasingly important for the understanding of biological catalysts, such as enzymes. This project is the first book to deal with the physical and chemical principles of an emerging field of science, for which the authors have set the ground-work. * The first book to deal with this newly emerging area. * Concentrates on the chemical and physical foundation of enzyme catalysis * Key area for the deeper understanding of biocatalytic processes * Examples for proteins and nucleic acids, two central areas of biochemical and bioorganic research

Characterization of Interfacial Enzyme Kinetics and Phosphorylation dephosphorylation Cycle of Phosphoinositides on Model Lipid Membrane

Author : Chun Liu
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To answer the above questions, first we studied the binding affinity and specificity of sensor proteins to the phosphoinositides. YFP-PH-Grp1 and mCherry-PH-Grp1 are shown to bind PI(3,4,5)P3 specifically, while EGFP-PH-PLC[delta]1 is shown to bind PI(4,5)P2 specifically. Fluorescent protein-labeled Grp1 and PLC[delta]1 are then used to quantify and monitor PI(3,4,5)P3 and PI(4,5)P2 amounts in the presence of enzymes by either TIRF or confocal microscopy.

Enzyme Kinetics

Author : Alejandro G. Marangoni
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Practical Enzyme Kinetics provides a practical how-to guide for beginning students, technicians, and non-specialists for evaluating enzyme kinetics using common software packages to perform easy enzymatic analyses.

The Role of Water in the Control of Enzyme Functionality at Interfaces

Author : Chetan S. Rao
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Enzymology at the Membrane Interface Interfacial Enzymology and Protein Membrane Binding

Author :
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Enzymology at the Membrane Interface, the latest volume in the Methods in Enzymology series, covers a subset of enzymes that work in the environment of the biological cell membrane. This field, called interfacial enzymology, involves a special series of experimental approaches for the isolation and study of these enzymes. Covers a subset of enzymes that work in the environment of the biological cell membrane Offers a series of experimental approaches for the isolation and study of enzymes

Enzyme Kinetics

Author : Hans Bisswanger
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This new, expanded and updated edition of the user-friendly and comprehensive treatise on enzyme kinetics expertly balances theory and practice. This is an indispensable aid for advanced students and professionals working with enzymes, whether biochemists, biotechnologists, chemical biologists, pharmacologists or bioengineers in academia, industry and clinical research.

Enzyme Catalysis in Water organic Solvent Two phase Systems

Author : Rolf Andrew Ramelmeier
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Enzyme Kinetics Catalysis and Control

Author : Daniel L. Purich
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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

Enzymes and Coenzymes Advances in Research and Application 2012 Edition

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Enzymes and Coenzymes—Advances in Research and Application: 2012 Edition is a ScholarlyEditions™ eBook that delivers timely, authoritative, and comprehensive information about Enzymes and Coenzymes. The editors have built Enzymes and Coenzymes—Advances in Research and Application: 2012 Edition on the vast information databases of ScholarlyNews.™ You can expect the information about Enzymes and Coenzymes in this eBook to be deeper than what you can access anywhere else, as well as consistently reliable, authoritative, informed, and relevant. The content of Enzymes and Coenzymes—Advances in Research and Application: 2012 Edition has been produced by the world’s leading scientists, engineers, analysts, research institutions, and companies. All of the content is from peer-reviewed sources, and all of it is written, assembled, and edited by the editors at ScholarlyEditions™ and available exclusively from us. You now have a source you can cite with authority, confidence, and credibility. More information is available at http://www.ScholarlyEditions.com/.

The Role of Interfacial and entropic Enzymes in Transitory Starch Degeradation

Author : Önder Kartal
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Plants and some unicellular algae store carbon in the form of transitory starch on a diurnal basis. The turnover of this glucose polymer is tightly regulated and timely synthesis as well as mobilization is essential to provide energy for heterotrophic growth. Especially for starch degradation, novel enzymes and mechanisms have been proposed recently. However, the catalytic properties of these enzymes and their coordination with metabolic regulation are still to be discovered.This thesis develops theoretical methods in order to interpret and analyze enzymes and their role in starch degradation. In the first part, a novel description of interfacial enzyme catalysis is proposed. Since the initial steps of starch degradation involve reactions at the starch-stroma interface it is necessary to have a framework which allows the derivation of interfacial enzyme rate laws. A cornerstone of the method is the introduction of the available area function - a concept from surface physics - to describe the adsorption step in the catalytic cycle. The method is applied to derive rate laws for two hydrolases, the Beta-amylase (BAM3) and the Isoamylase (DBE/ISA3), as well as to the Glucan, water dikinase (GWD) and a Phosphoglucan phosphatase (DSP/SEX4). The second part uses the interfacial rate laws to formulate a kinetic model of starch degradation. It aims at reproducing the stimulatory effect of reversible phosphorylation by GWD and DSP on the breakdown of the granule. The model can describe the dynamics of interfacial properties during degradation and suggests that interfacial amylopectin side-chains undergo spontaneous helix-coil transitions. Reversible phosphorylation has a synergistic effect on glucan release especially in the early phase dropping off during degradation. Based on the model, the hypothesis is formulated that interfacial phosphorylation is important for the rapid switch from starch synthesis to starch degradation. The third part takes a broader perspective on carbohydrate-active enzymes (CAZymes) but is motivated by the organization of the downstream pathway of starch breakdown. This comprises Alpha-1,4-glucanotransferases (DPE1 and DPE2) and Alpha-glucan-phosphorylases (Pho or PHS) both in the stroma and in the cytosol. CAZymes accept many different substrates and catalyze numerous reactions and therefore cannot be characterized in classical enzymological terms. A concise characterization is provided by conceptually linking statistical thermodynamics and polymer biochemistry. Each reactant is interpreted as an energy level, transitions between which are constrained by the enzymatic mechanisms. Combinations of in vitro assays of polymer-active CAZymes essential for carbon metabolism in plants confirmed the dominance of entropic gradients. The principle of entropy maximization provides a generalization of the equilibrium constant. Stochastic simulations confirm the results and suggest that randomization of metabolites in the cytosolic pool of soluble heteroglycans (SHG) may contribute to a robust integration of fluctuating carbon fluxes coming from chloroplasts.

Understanding Enzymes

Author : Allan Svendsen
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Understanding Enzymes: Function, Design, Engineering, and Analysis focuses on the understanding of enzyme function and optimization gained in the past decade, past enzyme function analysis, enzyme engineering, and growing insights from the simulation work and nanotechnology measurement of enzymes in action in vitro or in silico. The book also presents new insights into the mechanistic function and understanding of enzyme reactions, as well as touching upon structural characteristics, including X-ray and nuclear magnetic resonance (NMR) structural methods. A major focus of the book is enzyme molecules’ dependency on dynamic and biophysical environmental impacts on their function in ensembles as well as single molecules. A wide range of readers, including academics, professionals, PhD and master’s students, industry experts, and chemists, will immensely benefit from this exclusive book.

Stability and Kinetics of Interfacial Protein Films

Author : Luis Gustavo Cascao Pereira
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Multiscale Simulations

Author : Barry Zhongqi Shang
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The development of multiscale methods for computational simulation of biophysical systems represents a significant challenge. Effective computational models that bridge physical insights obtained from atomistic simulations and experimental findings are lacking. An accurate passing of information between these scales would enable: (1) an improved physical understanding of structure-function relationships, and (2) enhanced rational strategies for molecular engineering and materials design. Two approaches are described in this dissertation to facilitate these multiscale goals. In Part I, we develop a lattice kinetic Monte Carlo model to simulate cellulose decomposition by cellulase enzymes and to understand the effects of spatial confinement on enzyme kinetics. An enhanced mechanistic understanding of this reaction system could enhance the design of cellulose bioconversion technologies for renewable and sustainable energy. Using our model, we simulate the reaction up to experimental conversion times of days, while simultaneously capturing the microscopic kinetic behaviors. Therefore, the influence of molecular-scale kinetics on the macroscopic conversion rate is made transparent. The inclusion of spatial constraints in the kinetic model represents a significant advance over classical mass-action models commonly used to describe this reaction system. We find that restrictions due to enzyme jamming and substrate heterogeneity at the molecular level play a dominate role in limiting cellulose conversion. We identify that the key rate limitations are the slow rates of enzyme complexation with glucan chains and the competition between enzyme processivity and jamming. We show that the kinetics of complexation, which involves extraction of a glucan chain end from the cellulose surface and threading through the enzyme active site, occurs slowly on the order of hours, while intrinsic hydrolytic bond cleavage occurs on the order of seconds. We also elucidate the subtle trade-off between processivity and jamming. Highly processive enzymes cleave a large fraction of a glucan chain during each processive run but are prone to jamming at obstacles. Less processive enzymes avoid jamming but cleave only a small fraction of a chain. Optimizing this trade-off maximizes the cellulose conversion rate. We also elucidate the molecular-scale kinetic origins for synergy among cellulases in enzyme mixtures. In contrast to the currently accepted theory, we show that the ability of an endoglucanase to increase the concentration of chain ends for exoglucanases is insufficient for synergy to occur. Rather, endoglucanases must enhance the rate of complexation between exoglucanases and the newly created chain ends. This enhancement occurs when the endoglucanase is able to partially decrystallize the cellulose surface. We show generally that the driving forces for complexation and jamming, which govern the kinetics of pure exoglucanases, also control the degree of synergy in endo-exo mixtures. In Part II, we focus our attention on a different multiscale problem. This challenge is the development of coarse-grained models from atomistic models to access larger length- and time-scales in a simulation. This problem is difficult because it requires a delicate balance between maintaining (1) physical simplicity in the coarse-grained model and (2) physical consistency with the atomistic model. To achieve these goals, we develop a scheme to coarse-grain an atomistic fluid model into a fluctuating hydrodynamics (FHD) model. The FHD model describes the solvent as a field of fluctuating mass, momentum, and energy densities. The dynamics of the fluid are governed by continuum balance equations and fluctuation-dissipation relations based on the constitutive transport laws. The incorporation of both macroscopic transport and microscopic fluctuation phenomena could provide richer physical insight into the behaviors of biophysical systems driven by hydrodynamic fluctuations, such as hydrophobic assembly and crystal nucleation. To develop the FHD model, we map all-atom molecular dynamics trajectories onto mass, momentum, and energy density grids to generate a corresponding field trajectory. From the field statistics, the response functions and transport coefficients of the atomistic model are computed. These thermophysical properties are then used to parameterize an FHD model for the fluid that reproduces the hydrodynamic correlations underlying the atomistic model. We show that an FHD description of the fluid is preserved down to length scales of 5 Å, enabling application of this coarse-graining approach to molecular systems. We further extend our coarse-graining method by developing an interfacial FHD model using information obtained from simulations of an atomistic liquid-vapor interface. We illustrate that a phenomenological Ginzburg-Landau free energy employed in the FHD model can effectively represent the attractive molecular interactions of the atomistic model, which give rise to phase separation. For argon and water, we show that the interfacial FHD model can reproduce the compressibility, surface tension, and capillary wave spectrum of the atomistic model. Via this approach, simulations that explore the coupling between hydrodynamic fluctuations and phase equilibria with molecular-scale consistency are now possible. In both Parts I and II, the emerging theme is that the combination of bottom-up coarse graining and top-down phenomenology is essential for enabling a multiscale approach to remain physically consistent with molecular-scale interactions while simultaneously capturing the collective macroscopic behaviors. This hybrid strategy enables the resulting computational models to be both physically insightful and practically meaningful.

Characterization of Interfacial Structure and Properties of Colloidal Liquid Aphrons for Biocatalysis

Author : Prashant Srivastava
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Phosphatases

Author :
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Methods in Enzymology, Volume 607: Phosphatases, the latest release in this ongoing series, highlights new advances in the field as detailed by an international board of authors. This latest release includes chapters on Empirical Valence Bond Simulations of the Evolution of Enzyme Function, QM/MM Free Energy and Kinetic Isotope Analysis of Phosphoryl Transfer in Enzymes, the Structural, Mechanism and Evolution of Phosphatases, How to Define Rapid Motions in Pumping Pyrophosphatases, The Evolution of K+-Independence in Pyrophosphatases, the Crystallization of Michaelis, Intermediate and Inhibited Complexes in Phosphatases, and an Investigation of Nucleotide Loading and Effector Binding of K-Ras. Provides the authority and expertise of leading contributors from an international board of authors Presents the latest release in the Methods in Enzymology series Updated release includes the latest information on phosphatases

CELLULAR ANTIOXIDANT DEFENSE MECHANISM

Author : Ching K. Chow
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Physical Chemistry of Biological Interfaces

Author : Adam Baszkin
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An introduction to the most important fundamental concepts of physicochemical interface science and a description of experimental techniques and applications of surface science in relation to biological systems. It explores artificial assemblies of lipids, proteins and polysaccharides that perform novel functions that living systems cannot duplicat

Journal of the Chinese Chemical Society

Author : Chinese Chemical Society
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Book of Abstracts

Author :
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Encyclopedia of Interfacial Chemistry

Author :
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Encyclopedia of Interfacial Chemistry: Surface Science and Electrochemistry summarizes current, fundamental knowledge of interfacial chemistry, bringing readers the latest developments in the field. As the chemical and physical properties and processes at solid and liquid interfaces are the scientific basis of so many technologies which enhance our lives and create new opportunities, its important to highlight how these technologies enable the design and optimization of functional materials for heterogeneous and electro-catalysts in food production, pollution control, energy conversion and storage, medical applications requiring biocompatibility, drug delivery, and more. This book provides an interdisciplinary view that lies at the intersection of these fields. Presents fundamental knowledge of interfacial chemistry, surface science and electrochemistry and provides cutting-edge research from academics and practitioners across various fields and global regions