Download or read book Dynamics of Proteins and Nucleic Acids written by J. Andrew McCammon and published by Cambridge University Press. This book was released on 1988-04-29 with total page 256 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Download or read book Structure and Dynamics of Nucleic Acids Proteins and Membranes written by E. Clementi and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 454 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume collects a number of the invited lectures and a few selected contrib utions presented at the International Symposium on Structure and Dynamics of Nucleic Acids, Proteins and Membranes held August 31st through September 5th, 1986, in Riva del Garda, Italy. The title of the conference as well as a number of the topics covered represent a continuation of two previous conferences, the first held in 1982 at the University of California in San Diego, and the second in 1984 in Rome at the Accademia dei Lincei. These two earlier conferences have been documented in Structure and Dynamics: Nucleic Acids and Proteins, edited by E. Clementi and R. H. Sarma, Adenine Press, New York, 1983, and Structure and Motion: Membranes, Nucleic Acids and Proteins, edited by E. Clementi, G. Corongiu, M. H. Sarma and R. H. Sarma, Adenine Press, New York, 1985. At this conference in Riva del Garda we were very hesitant to keep the name of the conference the same as the two previous ones. Indeed, a number of topics discussed in this conference were not included in the previous ones and even the emphasis of this gathering is only partly reflected in the conference title. An alternative title would have been Structure and Dynamics of Nucleic Acids, Proteins, and Higher Functions, or, possibly, "higher components" rather than "higher functions.

Download or read book Dynamics of Proteins and Nucleic Acids written by and published by Elsevier. This book was released on 2013-08-14 with total page 368 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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

Download or read book Structure and Dynamics Nucleic Acids and Proteins written by Enrico Clementi and published by . This book was released on 1983 with total page 520 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Dynamics and the Problem of Recognition in Biological Macromolecules written by Oleg Jardetzky and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 308 pages. Available in PDF, EPUB and Kindle. Book excerpt: From within complex structures of organisms and cells down to the molecular level, biological processes all involve movement. Muscular fibers slide on each other to activate the muscle, as polymerases do along nucleic acids for replicating and transcribing the genetic material. Cells move and organize themselves into organs by recognizing each other through macromolecular surface-specific interactions. These recognition processes involve the mu tual adaptation of structures that rely on their flexibility. All sorts of conformational changes occur in proteins involved in through-membrane signal transmission, showing another aspect of the flexibility of these macromolecules. The movement and flexibility are inscribed in the polymeric nature of essential biological macromolecules such as proteins and nucleic acids. For instance, the well-defined structures formed by the long protein chain are held together by weak noncovalent interac tions that design a complex potential well in which the protein floats, permanently fluctuating between several micro- or macroconformations in a wide range of frequencies and ampli tudes. The inherent mobility of biomolecular edifices may be crucial to the adaptation of their structures to particular functions. Progress in methods for investigating macromolecular structures and dynamics make this hypothesis not only attractive but more and more testable.

Download or read book Structure and Dynamics of Nucleic Acids and Proteins by NMR written by Marco Tonelli and published by . This book was released on 2003 with total page 380 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Protein and Nucleic Acid Structure and Dynamics written by Jonathan King and published by Benjamin-Cummings Publishing Company. This book was released on 1985 with total page 608 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Biomolecular Structure and Dynamics written by G. Vergoten and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 327 pages. Available in PDF, EPUB and Kindle. Book excerpt: Biomolecular Structure and Dynamics describes recent fundamental advances in the experimental and theoretical study of molecular dynamics and stochastic dynamic simulations, X-ray crystallography and NMR of biomolecules, the structure of proteins and its prediction, time resolved Fourier transform IR spectroscopy of biomolecules, the computation of free energy, applications of vibrational CD of nucleic acids, and solid state NMR. Further presentations include recent advances in UV resonance Raman spectroscopy of biomolecules, semiempirical MO methods, empirical force fields, quantitative studies of the structure of proteins in water by Fourier transform IR, and density functional theory. Metal-ligand interactions, DFT treatment of organometallic and biological systems, and simulation vs. X-ray and far IR experiments are also discussed in some detail. The book provides a broad perspective of the current theoretical aspects and recent experimental findings in the field of biomolecular dynamics, revealing future research trends, especially in areas where theoreticians and experimentalists could fruitfully collaborate.

Download or read book Structure and Motion written by Enrico Clementi and published by . This book was released on 1985 with total page 600 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 Hydrogen Exchange and Structural Dynamics of Proteins and Nucleic Acids written by S. Walter Englander and published by . This book was released on 1983 with total page 135 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Mobility and Function in Proteins and Nucleic Acids written by Ruth Porter and published by John Wiley & Sons. This book was released on 2009-09-14 with total page 192 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Novartis Foundation Series is a popular collection of the proceedings from Novartis Foundation Symposia, in which groups of leading scientists from a range of topics across biology, chemistry and medicine assembled to present papers and discuss results. The Novartis Foundation, originally known as the Ciba Foundation, is well known to scientists and clinicians around the world.

Download or read book Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes written by Adam Liwo and published by Springer. This book was released on 2018-12-19 with total page 851 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides a comprehensive overview of modern computer-based techniques for analyzing the structure, properties and dynamics of biomolecules and biomolecular processes. It is organized in four main parts; the first one deals with methodology of molecular simulations; the second one with applications of molecular simulations; the third one introduces bioinformatics methods and the use of experimental information in molecular simulations; the last part reports on selected applications of molecular quantum mechanics. This second edition has been thoroughly revised and updated to include the latest progresses made in the respective field of research.

Download or read book Molecular Biology of the Cell written by and published by . This book was released on 2002 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Training Foreign Language Teachers written by Michael J. Wallace and published by Cambridge University Press. This book was released on 1991-04-18 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Training Foreign Language Teachers is aimed at anyone in the area of foreign language teaching who is engaged in designing, running or taking part in teacher education programmes. It begins by examining some current models of teacher education. It goes on to describe the notion of the teacher as 'reflective practitioner' - someone who reflects on the practice of their profession as a way of developing their expertise in it. Training Foreign Language Teachers explores ways in which a reflective approach can be applied to many areas of the teacher education programme, including: * classroom observation * microteaching * design and assesment of teacher education programmes. It contains many suggestions for practical work and discussion, and numerous applications to actual situations, including an extended case-study.

Download or read book Protein Conformational Dynamics written by Ke-li Han and published by Springer Science & Business Media. This book was released on 2014-01-20 with total page 488 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Download or read book Information Transfer and Dynamics of Nucleic Acids Studied by Theoretical Approaches written by Alexandra Balaceanu and published by . This book was released on 2019 with total page 425 pages. Available in PDF, EPUB and Kindle. Book excerpt: 1.The Force Field Accuracy Problem. The utility and applicability of MD simulations to model biomolecular systems goes only as far as its ability to sufficiently sample the conformational space and the correct description of the potential in terms of the force field functional form and parameter set. Clearly, the force field defines the shape of the conformational space for a given set of atomic positions and also the accessibility of energy minima. When simulating systems at equilibrium, especially quite stable systems such as DNA, the force fields strive to generate ensembles that reproduce well real systems and this does not have to come as a big trade-off with sampling power. In recent years it has become the business of computer engineers and software developers to address the issue of achieving long and biologically relevant time scales. Convergence and reproducibility of atomistic DNA simulations with state-of-the-art force fields such as our parmbsc1 has been convincingly demonstrated. It also seems that until a significant revolution, where milliseconds of simulation become routine, current sampling ranges completely cover the internal structures and dynamics of B-DNAs at this time scale. The growing confidence has allowed many researchers to use MD for very detailed studies on the sequence-dependent nature of DNA oligomers and on the complex arsenal of mechanisms that govern its behavior. In any such studies careful validation of results is necessary since it is not yet entirely clear how well and to what degree are sequence effects reproduced in MD. The fact that the latest-generation of force fields agree very well between themselves and that they fit with the sparse experimental data is surely very encouraging, but it will be some time until small differences in sequence geometries can be validated. Our own extensive validation of the parmbsc1 force field, as well as a large number of other works that have, since its publication, either specifically set out to assess its performance, or have just applied it with success, speak of a very stable parametrization able to deal with a wide range of DNAs. It is worth to mention that in special conditions small improvements might be necessary, which could be achieved with the inclusion of polarization terms. However, up to date, no force field has been able to model polarization without eventually destabilizing the system and this at a huge cost (a factor of 10) to calculation speed. To sum up, based on the remarkable performance of parmbsc1, we and other groups can employ it with confidence in the detailed study of DNA dynamics and we expect that the number of supporting results will only increase. 2. 2.Sequence-dependence and polymorphisms of B-DNA. So what is it that we actually learn from analyzing the conformation variability of DNA over its sequence space at the tetramer level? It is well established that different bps have different preferences regarding their internal geometries, and to some extent, Calladine's set of heuristic rules is able to make sense of these differences. At the bps level, some sequences are extremely stable, such as ApT, and some sequences, such as CpG, have a bi-stable equilibrium and they convert between different arrangements of their internal geometries. There are cases where this frustration can be explained by their charge distribution, bulkiness or the strength of their stacking and h-bonding interactions, but in many cases in requires a more holistic view, taking higher-level sequence effects into account. In multi-microsecond MD simulations, intra-base-pair parameters are always unimodal since alternative states that might be accessed through base opening are not sampled in at this time scale. However, their ensemble averages show sizeable differences according to the change in sequence. Inter- base-pair parameters can be bimodal, but only in certain tetranulceotide combinations that make up about 5% of cases. This can be explained considering that the central bps of a particular combination of four nucleotides has a structural preference that is in conflict with those of its neighboring steps. In order to minimize the energy cost and satisfy as best as possible all conformational requirements, a more flexible bps will populate several states, usually a maximum of two. Optimization of geometries between several bps generally involve backbone rearrangements, with the sugar-phosphate acting as a hinge that allows consecutive bps to coordinate in a complex choreography often involving other factors, such as subtle changes in the solvent environment environment. In B-DNA the most important backbone transition is the BI/BII, which can be related to the base chemistry through the sequence-dependent relative strength of unconventional h-bonds that stabilize BII conformations. In a tetramer model of B-DNA, the backbone transitions of different tetramers are translated into motions along different internal degrees of freedom, depending on the sequence. Therefore, we are able now to build a picture of the interconnected conformational space of DNA as an overlap of tetranucleotide sequences with transferable structural descriptors. It is still a matter of speculation how these properties might be exploited by proteins and other binders for biological function. 3.Information transfer through the DNA. There are however a few special cases where the tetramer model does not seem to be sufficient. The CTAG is one such case that demonstrates that for a highly flexible and polymorphic tetramer, long-range sequence composition can have a notable effect on the structural properties of the central bps. Analyzing the mechanism behind this long-range communication through the DNA has meant more than anything else an opportunity to understand rare events of sequence modulation that might be a lot more general in cases of larger, induced distortions on the helix. In CTAG we could observe sequence influence not only from the hexamer level, but even from beyond, and the data points to a complex mechanism of information transfer across DNA through coordinated backbone movements. In performing biological function, DNA is often mistakenly viewed as an inert lattice onto which proteins assemble to replicate or transcribe genes. However, experiments demonstrate that information transfer in the DNA can happen even over long distances and can produce allosteric effects upon ligand binding. Without question, the binding of proteins or small molecules to the DNA can produce coupled conformational changes that may affect a neighboring binding site and increase its affinity for the secondary binding protein. Such changes need not alter ensemble averages and only potentiate modifications in the shape of the energy well at the secondary binding site. As seen from the dynamic information provided by an MD trajectory, maybe in more than one case of protein couples, DNA acts as a wire transmitting pulses of information originated at the primary binding site that travel to distant regions. We show that MD methods can provide reasonable explanations for cooperative binding phenomena on the DNA and open for the first time the possibility of the "allostery without conformational change" in the recruitment of proteins of the DNA scaffold. From a thermodynamic point of view, this type of cooperative binding seems to be entropy-driven. Thus, the first binding event freezes some of the degrees of freedom around it's own binding region, but also reduces the entropy cost associated to the second binding.