Dynamics of Proteins and Nucleic Acids

This book is a self-contained introduction to the theory of atomic motion in proteins and nucleic acids.

Dynamics of Proteins and Nucleic Acids

This book is a self-contained introduction to the theory of atomic motion in proteins and nucleic acids. An understanding of such motion is essential because it plays a crucially important role in biological activity. The authors, both of whom are well known for their work in this field, describe in detail the major theoretical methods that are likely to be useful in the computer-aided design of drugs, enzymes and other molecules. A variety of theoretical and experimental studies is described and these are critically analyzed to provide a comprehensive picture of dynamic aspects of biomolecular structure and function. The book will be of interest to graduate students and research workers in structural biochemistry (X-ray diffraction and NMR), theoretical chemistry (liquids and polymers), biophysics, enzymology, molecular biology, pharmaceutical chemistry, genetic engineering and biotechnology.

Dynamics of Proteins and Nucleic Acids

DYNAMICS. OF. PROTEINS. AND. NUCLEIC. ACIDS. Tatyana Karabencheva-
Christova Department of Applied Sciences, Faculty of Health and Life Sciences,
Northumbria University, Newcastle upon Tyne, United Kingdom Proteins and ...

Dynamics of Proteins and Nucleic Acids

Published continuously since 1944, Advances in Protein Chemistry and Structural Biology has been a continuous, essential resource for protein chemists. Covering reviews of methodology and research in all aspects of protein chemistry, including purification/expression, proteomics, modeling and structural determination and design, each volume brings forth new information about protocols and analysis of proteins while presenting the most recent findings from leading experts in a broad range of protein-related topics. Covers reviews of methodology and research in all aspects of protein chemistry Brings forth new information about protocols and analysis of proteins while presenting the most recent findings from leading experts in a broad range of protein-related topics

Molecular Modeling at the Atomic Scale

In some complexes, the hydrophobic stacking force is unexpectedly prevalent
between the protein and nucleic acid bases. There have been an increasing
number of studies of protein–nucleic acid complexes that address the dynamics
of ...

Molecular Modeling at the Atomic Scale

Although molecular modeling has been around for a while, the groundbreaking advancement of massively parallel supercomputers and novel algorithms for parallelization is shaping this field into an exciting new area. Developments in molecular modeling from experimental and computational techniques have enabled a wide range of biological applications. Responding to this renaissance, Molecular Modeling at the Atomic Scale: Methods and Applications in Quantitative Biology includes discussions of advanced techniques of molecular modeling and the latest research advancements in biomolecular applications from leading experts. The book begins with a brief introduction of major methods and applications, then covers the development of cutting-edge methods/algorithms, new polarizable force fields, and massively parallel computing techniques, followed by descriptions of how these novel techniques can be applied in various research areas in molecular biology. It also examines the self-assembly of biomacromolecules, including protein folding, RNA folding, amyloid peptide aggregation, and membrane lipid bilayer formation. Additional topics highlight biomolecular interactions, including protein interactions with DNA/RNA, membrane, ligands, and nanoparticles. Discussion of emerging topics in biomolecular modeling such as DNA sequencing with solid-state nanopores and biological water under nanoconfinement round out the coverage. This timely summary contains the perspectives of leading experts on this transformation in molecular biology and includes state-of-the-art examples of how molecular modeling approaches are being applied to critical questions in modern quantitative biology. It pulls together the latest research and applications of molecular modeling and real-world expertise that can boost your research and development of applications in this rapidly changing field.

Structure Computation and Dynamics in Protein NMR

In the case ofnucleic acids, several three-bon coupling constant values involving
sugar protons are often estimated, ... This procedure has been succ applied to fit
2QF-COSY peaks of DNA duplexes and an RNAQDNA hybr et al., 1989; ...

Structure Computation and Dynamics in Protein NMR

Volume 17 is the second in a special topic series devoted to modern techniques in protein NMR, under the Biological Magnetic Resonance series. Volume 16, with the subtitle Modern Techniques in Protein NMR , is the first in this series. These two volumes present some of the recent, significant advances in the biomolecular NMR field with emphasis on developments during the last five years. We are honored to have brought together in these volume some of the world s foremost experts who have provided broad leadership in advancing this field. Volume 16 contains - vances in two broad categories: I. Large Proteins, Complexes, and Membrane Proteins and II. Pulse Methods. Volume 17 contains major advances in: I. Com- tational Methods and II. Structure and Dynamics. The opening chapter of volume 17 starts with a consideration of some important aspects of modeling from spectroscopic and diffraction data by Wilfred van Gunsteren and his colleagues. The next two chapters deal with combined automated assignments and protein structure determination, an area of intense research in many laboratories since the traditional manual methods are often inadequate or laborious in handling large volumes of NMR data on large proteins. First, Werner Braun and his associates describe their experience with the NOAH/DIAMOD protocol developed in their laboratory.

Enzyme Functionality

51. 52. 53. 54. 55. 56. 57. ligand, protein–protein, and protein-nucleic acid
noncovalent interactions. ... Potential energy function and parameters for
simulations of the molecular dynamics of proteins and nucleic acids in solution.
Comp Phys ...

Enzyme Functionality

Enzyme Functionality serves as a conduit for trailblazing research in enzyme engineering-relating current understanding of sequence families, the new notion of enzyme structure classes, and modern methods in protein engineering, design, and directed evolution to accelerate the development of novel enzyme functionalities. This reference gathers the

Linking Protein Dynamics to Protein Function

( 16 ) McCammon , J. A. ( 1987 ) Dynamics of Proteins and Nucleic Acids .
Mccammon , J. a . and S. C. Harvey . Dynamics of Proteins and Nucleic Acids . Xii
+ 234p . Cambridge University Press : Cambridge , England , Uk ; New York ,
New ...

Linking Protein Dynamics to Protein Function


Proteins

A Theoretical Perspective of Dynamics, Structure, and Thermodynamics Charles
L. Brooks, Martin Karplus, ... An introductory description of the dynamics of
proteins and nucleic acid has been presented by McCammon and Harvey.*
CHAPTER ...

Proteins

Presenting a wide-ranging view of current developments in protein research, the papers in this collection, each written by highly regarded experts in the field, examine various aspects of protein structure, functions, dynamics, and experimentation. Topics include dynamical simulation methods, the biological role of atom fluctuations, protein folding, influences on protein dynamics, and a variety of analytical techniques, such as X-ray diffraction, vibrational spectroscopy, photodissociation and rebinding kinetics. This is part of a series devoted to providing general information on a wide variety of topics in chemical physics in order to stimulate new research and to serve as a text for beginners in a particular area of chemical physics.

ESR Spectroscopy in Membrane Biophysics

DYNAMICS. STUDIED. BY ... emerged as a powerful method for studying the
structure and conformational dynamics of proteins and nucleic acids under
conditions relevant to function (for reviews see, e.g., Feix and Klug 1998; Hubbell
et al.

ESR Spectroscopy in Membrane Biophysics

Starting from a comprehensive quantum mechanical description, this book introduces the optical (IR, Raman, UV/Vis, CD, fluorescence and laser spectroscopy) and magnetic resonance (1D and 2D-NMR, ESR) techniques. The book offers a timely review of the increasing interest in using spin-label ESR as an alternative structural technique for NMR or X-ray diffraction. Future aspects are treated as well, but only as an illustration of the progress of ESR in this field.

NMR for Chemists and Biologists

We shall describe in this chapter the use of NMR in the biomolecular field,
especially its contribution to the structural elucidation of proteins and nucleic
acids. An introduction to the analysis of biomolecular dynamics by NMR will also
be ...

NMR for Chemists and Biologists

This book intends to be an easy and concise introduction to the field of nuclear magnetic resonance or NMR, which has revolutionized life sciences in the last twenty years. A significant part of the progress observed in scientific areas like Chemistry, Biology or Medicine can be ascribed to the development experienced by NMR in recent times. Many of the books currently available on NMR deal with the theoretical basis and some of its main applications, but they generally demand a strong background in Physics and Mathematics for a full understanding. This book is aimed to a wide scientific audience, trying to introduce NMR by making all possible effort to remove, without losing any formality and rigor, most of the theoretical jargon that is present in other NMR books. Furthermore, illustrations are provided that show all the basic concepts using a naive vector formalism, or using a simplified approach to the particular NMR-technique described. The intention has been to show simply the foundations and main concepts of NMR, rather than seeking thorough mathematical expressions.

Biological NMR Spectroscopy

Its potential as a method for determining structures and describing the dynamics
of proteins and nucleic acids in aqueous solution has been realized in recent
years, and the approach has become an essential part of structural biology.

Biological NMR Spectroscopy

This book presents a critical assessment of progress on the use of nuclear magnetic resonance spectroscopy to determine the structure of proteins, including brief reviews of the history of the field along with coverage of current clinical and in vivo applications. The book, in honor of Oleg Jardetsky, one of the pioneers of the field, is edited by two of the most highly respected investigators using NMR, and features contributions by most of the leading workers in the field. It will be valued as a landmark publication that presents the state-of-the-art perspectives regarding one of today's most important technologies.

Neutron Scattering in Biology

21.6 Conclusions and Future Prospects The dynamics of proteins and nucleic
acids have been the subject of intense study with a variety of experimental
methods and computational modeling . Neutron spectroscopy occupies a special
 ...

Neutron Scattering in Biology

The advent of new neutron facilities and the improvement of existing sources and instruments world wide supply the biological community with many new opportunities in the areas of structural biology and biological physics. The present volume offers a clear description of the various neutron-scattering techniques currently being used to answer biologically relevant questions. Their utility is illustrated through examples by some of the leading researchers in the field of neutron scattering. This volume will be a reference for researchers and a step-by-step guide for young scientists entering the field and the advanced graduate student.

Molecular Electrostatic Potentials

INTRODUCTION Electrostatic forces and interactions constitute one of the main
classes of physical effects that govern the structure, function and dynamics of
proteins and nucleic acids. Because of this it is essential to provide a reliable and
, ...

Molecular Electrostatic Potentials

Over the past 25 years, the molecular electrostatic potential has become firmly established as an effective guide to molecular interactions. With the recent advances in computational technology, it is currently being applied to a variety of important chemical and biological systems. Its range of applicability has expanded from primarily a focus on sites for electrophilic and nucleophilic attack to now include solvent effects, studies of zeolite, molecular cluster and crystal behavior, and the correlation and prediction of a wide range of macroscopic properties. Moreover, the increasing prominence of density functional theory has raised the molecular electrostatic potential to a new stature on a more fundamental conceptual level. It is rigorously defined in terms of the electron density, and has very interesting topological characteristics since it explicitly reflects opposing contributions from the nuclei and the electrons. This volume opens with a survey chapter by one of the original pioneers of the use of the electrostatic potential in studies of chemical reactivity, Jacopo Tomasi. Though the flow of the succeeding chapters is not stringently defined, the overall trend is that the emphasis changes gradually from methodology to applications. Chapters discussing more theoretical topics are placed near the end. Readers will find the wide variety of topics provided by an international group of authors both convincing and useful.

Molecular Dynamics and Protein Structure

I would contend , however , that this class of macromolecules , the small DNA
binding proteins , is particularly amenable to such techniques . The
macromolecules involved , protein and single stranded DNA , are well defined
and their dynamic ...

Molecular Dynamics and Protein Structure


Supramolecular Structure and Function 8

... of site-directed spin labelled biomolecules (site-directed spin labelling, SDSL)
has emerged as a powerful method for studying the structure and conformational
dynamics of proteins and nucleic acids under conditions relevant to function”.

Supramolecular Structure and Function 8

This volume covers some powerful biophysical methods, such as analytical centrifugation, mass spectrometry, fluorescence spectroscopy, electron spin resonance and nuclear magnetic resonance, for the study of complex biological structures, and discusses useful physical concepts as applied to biological and biochemical systems. Case-orientated studies concentrating on particular methodologies are presented and examples are given, addressing some of the most important aspects of structure-function relationship in biological assemblies. Biophysics nowadays collaborates closely with molecular biology and bioinformatics and this is also demonstrated in this book. The book will be of interest both to experienced researchers wishing to widen their insight into molecular structure and function, and to younger scientists at the doctoral and postdoctoral level interested in the molecular nature of fundamental biological entities and phenomena.

Protein and Nucleic Acid Structure and Dynamics

Jonathan King. 375 03 Protein and Nucleic Acid Structure and Dynamics Protein
and Nucleic.

Protein and Nucleic Acid Structure and Dynamics


Numerical Simulation in Molecular Dynamics

... the general dynamics of proteins and their conformations, the formation of
membrane structures, the determination of inhibitor-ligand binding energies, and
the study of the folding and unfolding of peptides, proteins, and nucleic acids.

Numerical Simulation in Molecular Dynamics

This book details the necessary numerical methods, the theoretical background and foundations and the techniques involved in creating computer particle models, including linked-cell method, SPME-method, tree codes, amd multipol technique. It illustrates modeling, discretization, algorithms and their parallel implementation with MPI on computer systems with distributed memory. The text offers step-by-step explanations of numerical simulation, providing illustrative code examples. With the description of the algorithms and the presentation of the results of various simulations from fields such as material science, nanotechnology, biochemistry and astrophysics, the reader of this book will learn how to write programs capable of running successful experiments for molecular dynamics.

Molecular Biophysics for the Life Sciences

These advances enable us to visualize the structures and dynamics of proteins
and nucleic acids at atomic resolution, observe single molecules in real time,
monitor processes within living cells at high resolution, identify and determine the
 ...

Molecular Biophysics for the Life Sciences

This volume provides an overview of the development and scope of molecular biophysics and in-depth discussions of the major experimental methods that enable biological macromolecules to be studied at atomic resolution. It also reviews the physical chemical concepts that are needed to interpret the experimental results and to understand how the structure, dynamics, and physical properties of biological macromolecules enable them to perform their biological functions. Reviews of research on three disparate biomolecular machines—DNA helicases, ATP synthases, and myosin--illustrate how the combination of theory and experiment leads to new insights and new questions.

Nuclear Magnetic Resonance

proteins. and. nucleic. acids. P. J. Simpson DOI: 10.1039/b704485m 1.
Introduction This chapter highlights a number of key ... Section 3, with the
deliberately nebulous title ''Studies of dynamic processes'', this year focuses on
protein-ligand ...

Nuclear Magnetic Resonance

As a spectroscopic method, nuclear magnetic resonance (NMR) has seen spectacular growth over the past two decades, both as a technique and in its applications. Today the applications of NMR span a wide range of scientific disciplines, from physics to biology to medicine. Each volume of Nuclear Magnetic Resonance comprises a combination of annual and biennial reports which together provide comprehensive coverage of the literature on this topic. This Specialist Periodical Report reflects the growing volume of published work involving NMR techniques and applications, in particular NMR of natural macromolecules which is covered in two reports: ""NMR of Proteins and Nucleic Acids"" and ""NMR of Carbohydrates, Lipids and Membranes"". For those wanting to become rapidly acquainted with specific areas of NMR, this title provides unrivalled scope of coverage. Seasoned practitioners of NMR will find this an invaluable source of current methods and applications.

Protein Conformational Dynamics

The other type belongs to ringshaped NTPase motors that also move or transport
nucleic acid or protein substrate in a directional manner, such as for genome
packaging or protein degradation. The central issue in this review is on how the ...

Protein Conformational Dynamics

This book discusses how biological molecules exert their function and regulate biological processes, with a clear focus on how conformational dynamics of proteins are critical in this respect. In the last decade, the advancements in computational biology, nuclear magnetic resonance including paramagnetic relaxation enhancement, and fluorescence-based ensemble/single-molecule techniques have shown that biological molecules (proteins, DNAs and RNAs) fluctuate under equilibrium conditions. The conformational and energetic spaces that these fluctuations explore likely contain active conformations that are critical for their function. More interestingly, these fluctuations can respond actively to external cues, which introduces layers of tight regulation on the biological processes that they dictate. A growing number of studies have suggested that conformational dynamics of proteins govern their role in regulating biological functions, examples of this regulation can be found in signal transduction, molecular recognition, apoptosis, protein / ion / other molecules translocation and gene expression. On the experimental side, the technical advances have offered deep insights into the conformational motions of a number of proteins. These studies greatly enrich our knowledge of the interplay between structure and function. On the theoretical side, novel approaches and detailed computational simulations have provided powerful tools in the study of enzyme catalysis, protein / drug design, protein / ion / other molecule translocation and protein folding/aggregation, to name but a few. This work contains detailed information, not only on the conformational motions of biological systems, but also on the potential governing forces of conformational dynamics (transient interactions, chemical and physical origins, thermodynamic properties). New developments in computational simulations will greatly enhance our understanding of how these molecules function in various biological events.

Modern Techniques in Computational Chemistry MOTECC 91

To describe the protein dynamics in the nano seconds and microseconds time
domain and beyond, we have to seek new ... chapter we discuss Langevin
dynamic simulations of complex macromolecules such as proteins and nucleic
acids.

Modern Techniques in Computational Chemistry  MOTECC 91