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Author : Silke Andrea Wieninger
Publisher :
ISBN 13 :
Total Pages : 206 pages
Book Rating : 4.:/5 (856 download)
Download or read book Coarse-grained Modeling of Protein Dynamics Using Elastic Network Models written by Silke Andrea Wieninger and published by . This book was released on 2013 with total page 206 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Ayşe Özge Kürkçüoğlu
Publisher :
ISBN 13 :
Total Pages : 124 pages
Book Rating : 4.:/5 (79 download)
Download or read book Mixed Coarse-graining of Large Proteins Using Elastic Network Model written by Ayşe Özge Kürkçüoğlu and published by . This book was released on 2003 with total page 124 pages. Available in PDF, EPUB and Kindle. Book excerpt: Mixed coarse-graining approach to elastic network model of proteins has been introduced to enable the modeling of a protein's native conformation with regions of low and high resolution. This method is applied to two large proteins, Influenza virus hemagglutinin and b-galactocidase, with 1509 and 4044 residues, respectively. In the mixed-resolution model, each node of the elastic network represents the center of mass of a single residue (high-resolution) or a group of residues (low-resolution), and close-neighbouring nodes are connected by springs. As a result, the dynamics of the interesting parts within a large protein are analyzed at high resolution, while the rest of the structure is represented at lower resolution, thus keeping the total number of nodes in the system at a reasonable level for computational efficiency. Two parameters of the model, the cutoff radius and the force constant are calculated for hierarchical levels of uniform coarse-graining and further used in the mixed coarse-graining simulations. The calculated mean-square fluctuations are in good agreement with the fluctuations obtained from experimental temperature factors for the high resolution parts. The first mode shapes and modes of motion are obtained with high correlations for different levels of mixed coarse-grained proteins. It is also shown that similar frequency distributions are obtained at the lower end of the spectrum for different proteins and at different levels of coarse-graining. The results indicate that the vibrational dynamics of specific components in a large multi-subunit protein are described at best by retaining all the components in the structure at least at a lower resolution.
Author : Nicoletta Ceres
Publisher :
ISBN 13 :
Total Pages : 0 pages
Book Rating : 4.:/5 (874 download)
Download or read book Coarse-grain Modeling of Proteins written by Nicoletta Ceres and published by . This book was released on 2012 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Proteins are flexible molecules, which accomplish a variety of cellular tasks through mechanical motions and conformational fluctuations encoded in their three-dimensional structure. Amongst the theoretical approaches contributing to a better understanding of the relationship between protein structure, mechanics, dynamics and function, coarse-grain models are a powerful tool. They can be used to integrate structural and dynamic information over broad time and size scales at a low computational cost, achieved by averaging out the less important degrees of freedom. In this work, fast comparative studies of protein flexibility and mechanics have been performed with the simple coarse-grain Elastic Network Model. However, the dependency of the results on the starting conformation, and the rather constrained backbone dynamics imposed by the harmonic approximation, motivated the development of a new approach, for a more extensive exploration of conformational space. These efforts led to the PaLaCe model, designed to allow significant changes in secondary structure, while maintaining residue specificity despite a lower-level resolution. Using PaLaCe, we were able to reproduce two processes involving protein plasticity: the mechanical unfolding of the I27 domain of the giant muscle protein titin and the near-native dynamics of two homologous enzymes adapted to work at different temperatures. Agreement with experimental data and results from published atomistic models demonstrate that PaLaCe is a reliable, sufficiently accurate, but computationally inexpensive approach. It therefore opens the doors for a systematic investigation of the link between protein dynamics/mechanics and function.
Author : Gregory A. Voth
Publisher : CRC Press
ISBN 13 : 1420059564
Total Pages : 492 pages
Book Rating : 4.4/5 (2 download)
Download or read book Coarse-Graining of Condensed Phase and Biomolecular Systems written by Gregory A. Voth and published by CRC Press. This book was released on 2008-09-22 with total page 492 pages. Available in PDF, EPUB and Kindle. Book excerpt: Exploring recent developments in the field, Coarse-Graining of Condensed Phase and Biomolecular Systems examines systematic ways of constructing coarse-grained representations for complex systems. It explains how this approach can be used in the simulation and modeling of condensed phase and biomolecular systems. Assembling some of the most influential, world-renowned researchers in the field, this book covers the latest developments in the coarse-grained molecular dynamics simulation and modeling of condensed phase and biomolecular systems. Each chapter focuses on specific examples of evolving coarse-graining methodologies and presents results for a variety of complex systems. The contributors discuss the minimalist, inversion, and multiscale approaches to coarse-graining, along with the emerging challenges of coarse-graining. They also connect atomic-level information with new coarse-grained representations of complex systems, such as lipid bilayers, proteins, peptides, and DNA.
Author : Qiang Cui
Publisher : CRC Press
ISBN 13 : 142003507X
Total Pages : 448 pages
Book Rating : 4.4/5 (2 download)
Download or read book Normal Mode Analysis written by Qiang Cui and published by CRC Press. This book was released on 2005-12-12 with total page 448 pages. Available in PDF, EPUB and Kindle. Book excerpt: Rapid developments in experimental techniques continue to push back the limits in the resolution, size, and complexity of the chemical and biological systems that can be investigated. This challenges the theoretical community to develop innovative methods for better interpreting experimental results. Normal Mode Analysis (NMA) is one such technique
Author : Mustafa Tekpinar
Publisher :
ISBN 13 :
Total Pages : 96 pages
Book Rating : 4.:/5 (832 download)
Download or read book Investigating Conformational Transitions of Proteins by Coarse-grained Elastic Network Models written by Mustafa Tekpinar and published by . This book was released on 2012 with total page 96 pages. Available in PDF, EPUB and Kindle. Book excerpt: Proteins are large molecular machines. Many of these machines carry out conformationaltransitions to perform function. It is very difficult to determine all metastable proteinconformations experimentally. Therefore, computational methods have been developed toinvestigate metastable protein conformations and conformational transitions. For most ofproteins, atomistic molecular dynamics cannot reach the time scales of conformationaltransitions, which are typically beyond microseconds. The large size of proteins is anotherobstacle in atomistic molecular dynamics simulations. Coarse-grained elastic network modelscan provide an alternative to overcome the time scale and size problems. In this dissertation, we have investigated conformational transitions of proteins by using modified elasticnetwork models. These models can be applied in two ways. First, they allow us to analyzeconformational transition pathways and deduce the dynamic order of structural events. Second, they enable us to build models for unknown protein conformations by incorporatingexperimental data. For the first application, a transition pathway modeling method callediENM will be presented in Chapter 2. For the second application, a flexible fitting methodbased on small angle X-ray scattering (SAXS) data will be discussed in Chapter 3. Ourmethods will be compared to alternative methods and they will be validated by experimentaldata.
Author : Reza Soheilifard
Publisher :
ISBN 13 :
Total Pages : 240 pages
Book Rating : 4.:/5 (893 download)
Download or read book Mechanical Models of Proteins written by Reza Soheilifard and published by . This book was released on 2011 with total page 240 pages. Available in PDF, EPUB and Kindle. Book excerpt: In general, this dissertation is concerned with modeling of mechanical behavior of protein molecules. In particular, we focus on coarse-grained models, which bridge the gap in time and length scale between the atomistic simulation and biological processes. The dissertation presents three independent studies involving such models. The first study is concerned with a rigorous coarse-graining method for dynamics of linear systems. In this method, as usual, the conformational space of the original atomistic system is divided into master and slave degrees of freedom. Under the assumption that the characteristic timescales of the masters are slower than those of the slaves, the method results in Langevin-type equations of motion governed by an effective potential of mean force. In addition, coarse-graining introduces hydrodynamic-like coupling among the masters as well as non-trivial inertial effects. Application of our method to the long-timescale part of the relaxation spectra of proteins shows that such dynamic coupling is essential for reproducing their relaxation rates and modes. The second study is concerned with calibration of elastic network models based on the so-called B-factors, obtained from x-ray crystallographic measurements. We show that a proper calibration procedure must account for rigid-body motion and constraints imposed by the crystalline environment on the protein. These fundamental aspects of protein dynamics in crystals are often ignored in currently used elastic network models, leading to potentially erroneous network parameters. We develop an elastic network model that properly takes rigid-body motion and crystalline constraints into account. This model reveals that B-factors are dominated by rigid-body motion rather than deformation, and therefore B-factors are poorly suited for identifying elastic properties of protein molecules. Furthermore, it turns out that B-factors for a benchmark set of three hundred and thirty protein molecules can be well approximated by assuming that the protein molecules are rigid. The third study is concerned with the polymer mediated interaction between two planar surfaces. In particular, we consider the case where a thin polymer layer bridges two parallel plates. We consider two models of monodisperse and polydisperse for the polymer layer and obtain an analytical expression for the force-distance relationship of the two plates.
Author : Andrzej Kolinski
Publisher : Springer Science & Business Media
ISBN 13 : 144196889X
Total Pages : 360 pages
Book Rating : 4.4/5 (419 download)
Download or read book Multiscale Approaches to Protein Modeling written by Andrzej Kolinski and published by Springer Science & Business Media. This book was released on 2010-10-13 with total page 360 pages. Available in PDF, EPUB and Kindle. Book excerpt: The book gives a comprehensive review of the most advanced multiscale methods for protein structure prediction, computational studies of protein dynamics, folding mechanisms and macromolecular interactions. It approaches span a wide range of the levels of coarse-grained representations, various sampling techniques and variety of applications to biomedical and biophysical problems. This book is intended to be used as a reference book for those who are just beginning their adventure with biomacromolecular modeling but also as a valuable source of detailed information for those who are already experts in the field of biomacromolecular modeling and in related areas of computational biology or biophysics.
Author : Sidney A. Simon
Publisher : Academic Press
ISBN 13 : 0080925855
Total Pages : 606 pages
Book Rating : 4.0/5 (89 download)
Download or read book Peptide-Lipid Interactions written by Sidney A. Simon and published by Academic Press. This book was released on 2002-11-13 with total page 606 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume contains a comprehensive overview of peptide-lipid interactions by leading researchers. The first part covers theoretical concepts, experimental considerations, and thermodynamics. The second part presents new results obtained through site-directed EPR, electron microscopy, NMR, isothermal calorimetry, and fluorescence quenching. The final part covers problems of biological interest, including signal transduction, membrane transport, fusion, and adhesion. Key Features * world-renowned experts * state-of-the-art experimental methods * monolayers, bilayers, biological membranes * theoretical aspects and computer simulations * rafts * synaptic transmission * membrane fusion * signal transduction
Author : Garegin A. Papoian
Publisher : CRC Press
ISBN 13 : 1315356708
Total Pages : 399 pages
Book Rating : 4.3/5 (153 download)
Download or read book Coarse-Grained Modeling of Biomolecules written by Garegin A. Papoian and published by CRC Press. This book was released on 2017-10-30 with total page 399 pages. Available in PDF, EPUB and Kindle. Book excerpt: "The chapters in this book survey the progress in simulating biomolecular dynamics.... The images conjured up by this work are not yet universally loved, but are beginning to bring new insights into the study of biological structure and function. The future will decide whether this scientific movement can bring forth its Picasso or Modigliani." –from the Foreword by Peter G. Wolynes, Bullard-Welch Foundation Professor of Science, Rice University This book highlights the state-of-art in coarse-grained modeling of biomolecules, covering both fundamentals as well as various cutting edge applications. Coarse-graining of biomolecules is an area of rapid advances, with numerous new force fields having appeared recently and significant progress made in developing a systematic theory of coarse-graining. The contents start with first fundamental principles based on physics, then survey specific state-of-art coarse-grained force fields of proteins and nucleic acids, and provide examples of exciting biological problems that are at large scale, and hence, only amenable to coarse-grained modeling. Introduces coarse-grained models of proteins and nucleic acids. Showcases applications such as genome packaging in nuclei and understanding ribosome dynamics Gives the physical foundations of coarse-graining Demonstrates use of models for large-scale assemblies in modern studies Garegin A. Papoian is the first Monroe Martin Associate Professor with appointments in the Department of Chemistry and Biochemistry and the Institute for Physical Science and Technology at the University of Maryland.
Author :
Publisher : Marco Giulini
ISBN 13 :
Total Pages : 174 pages
Book Rating : 4./5 ( download)
Download or read book The mapping problem in coarse-grained modelling of biomolecules written by and published by Marco Giulini. This book was released on 2022-05-16 with total page 174 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Andrew Gamble
Publisher : Springer
ISBN 13 : 3319099760
Total Pages : 332 pages
Book Rating : 4.3/5 (19 download)
Download or read book Protein Modelling written by Andrew Gamble and published by Springer. This book was released on 2014-11-13 with total page 332 pages. Available in PDF, EPUB and Kindle. Book excerpt: In this volume, a detailed description of cutting-edge computational methods applied to protein modeling as well as specific applications are presented. Chapters include: the application of Car-Parrinello techniques to enzyme mechanisms, the outline and application of QM/MM methods, polarizable force fields, recent methods of ligand docking, molecular dynamics related to NMR spectroscopy, computer optimization of absorption, distribution, metabolism and excretion extended by toxicity for drugs, enzyme design and bioinformatics applied to protein structure prediction. A keen emphasis is laid on the clear presentation of complex concepts, since the book is primarily aimed at Ph.D. students, who need an insight in up-to-date protein modeling. The inclusion of descriptive, color figures will allow the reader to get a pictorial representation of complicated structural issues.
Author : Guang Hu
Publisher : Frontiers Media SA
ISBN 13 : 2889668487
Total Pages : 276 pages
Book Rating : 4.8/5 (896 download)
Download or read book Understanding Protein Dynamics, Binding and Allostery for Drug Design written by Guang Hu and published by Frontiers Media SA. This book was released on 2021-06-08 with total page 276 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Monika Fuxreiter
Publisher : CRC Press
ISBN 13 : 1482297868
Total Pages : 458 pages
Book Rating : 4.4/5 (822 download)
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
Author : Bruce J Berne
Publisher : World Scientific
ISBN 13 : 9814496057
Total Pages : 881 pages
Book Rating : 4.8/5 (144 download)
Download or read book Classical And Quantum Dynamics In Condensed Phase Simulations: Proceedings Of The International School Of Physics written by Bruce J Berne and published by World Scientific. This book was released on 1998-06-17 with total page 881 pages. Available in PDF, EPUB and Kindle. Book excerpt: The school held at Villa Marigola, Lerici, Italy, in July 1997 was very much an educational experiment aimed not just at teaching a new generation of students the latest developments in computer simulation methods and theory, but also at bringing together researchers from the condensed matter computer simulation community, the biophysical chemistry community and the quantum dynamics community to confront the shared problem: the development of methods to treat the dynamics of quantum condensed phase systems.This volume collects the lectures delivered there. Due to the focus of the school, the contributions divide along natural lines into two broad groups: (1) the most sophisticated forms of the art of computer simulation, including biased phase space sampling schemes, methods which address the multiplicity of time scales in condensed phase problems, and static equilibrium methods for treating quantum systems; (2) the contributions on quantum dynamics, including methods for mixing quantum and classical dynamics in condensed phase simulations and methods capable of treating all degrees of freedom quantum-mechanically.
Author : Joshua Lev Adelman
Publisher :
ISBN 13 :
Total Pages : 232 pages
Book Rating : 4.:/5 (35 download)
Download or read book Elucidating the Mechanics and Mechanism of Two Prototypical Ring Shaped Proteins Using Modeling and Simulation written by Joshua Lev Adelman and published by . This book was released on 2009 with total page 232 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Ke-li Han
Publisher : Springer Science & Business Media
ISBN 13 : 3319029703
Total Pages : 488 pages
Book Rating : 4.3/5 (19 download)
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.
