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Author: Kilho Eom
Publisher:
ISBN:
Category : Proteins
Languages : en
Pages :
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Book Description
Author: Kilho Eom
Publisher:
ISBN:
Category : Proteins
Languages : en
Pages :
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Book Description
Author: Naomi K. Fox
Publisher:
ISBN:
Category : Molecules
Languages : en
Pages : 166
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Book Description
Through their motion, proteins perform essential functions in the living cell. Although we cannot observe protein motion directly, over 68,000 crystal structures are freely available from the Protein Data Bank. Computational protein rigidity analysis systems leverage this data, building a mechanical model from atoms and pairwise interactions determined from a static 3D structure. The rigid and flexible components of the model are then calculated with a pebble game algorithm, predicting a protein's flexibility with much more computational efficiency than physical simulation. In prior work with rigidity analysis systems, the available modeling options were hard-coded, and evaluation was limited to case studies. The focus of this thesis is improving accuracy and robustness of rigidity analysis systems. The first contribution is in new approaches to mechanical modeling of noncovalent interactions, namely hydrogen bonds and hydrophobic interactions. Unlike covalent bonds, the behavior of these interactions varies with their energies. I systematically investigate energy-refined modeling of these interactions. Included in this is a method to assign a score to a predicted cluster decomposition, adapted from the B-cubed score from information retrieval. Another contribution of this thesis is in new approaches to measuring the robustness of rigidity analysis results. The protein's fold is held in place by weak, noncovalent interactions, known to break and form during natural fluctuations. Rigidity analysis has been conventionally performed on only a single snapshot, rather than on an entire trajectory, and no information was made available on the sensitivity of the clusters to variations in the interaction network. I propose an approach to measure the robustness of rigidity results, by studying how detrimental the loss of a single interaction may be to a cluster's rigidity. The accompanying study shows that, when present, highly critical interactions are concentrated around the active site, indicating that nature has designed a very versatile system for transitioning between unique conformations. Over the course of this thesis, we develop the KINARI library for experimenting with extensions to rigidity analysis. The modular design of the software allows for easy extensions and tool development. A specific feature is the inclusion of several modeling options, allowing more freedom in exploring biological hypotheses and future benchmarking experiments.
Author: Andrew Gamble
Publisher: Springer
ISBN: 3319099760
Category : Science
Languages : en
Pages : 332
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Book Description
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: Andrzej Kolinski
Publisher: Springer Science & Business Media
ISBN: 144196889X
Category : Science
Languages : en
Pages : 360
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Book Description
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: Reza Soheilifard
Publisher:
ISBN:
Category :
Languages : en
Pages : 240
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Book Description
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: Ivet Bahar
Publisher: Garland Science
ISBN: 1351815016
Category : Science
Languages : en
Pages : 337
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Book Description
Protein Actions: Principles and Modeling is aimed at graduates, advanced undergraduates, and any professional who seeks an introduction to the biological, chemical, and physical properties of proteins. Broadly accessible to biophysicists and biochemists, it will be particularly useful to student and professional structural biologists and molecular biophysicists, bioinformaticians and computational biologists, biological chemists (particularly drug designers) and molecular bioengineers. The book begins by introducing the basic principles of protein structure and function. Some readers will be familiar with aspects of this, but the authors build up a more quantitative approach than their competitors. Emphasizing concepts and theory rather than experimental techniques, the book shows how proteins can be analyzed using the disciplines of elementary statistical mechanics, energetics, and kinetics. These chapters illuminate how proteins attain biologically active states and the properties of those states. The book ends with a synopsis the roles of computational biology and bioinformatics in protein science.
Author: George Locke
Publisher:
ISBN:
Category : DNA-binding proteins
Languages : en
Pages : 136
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Book Description
Author: Nicoletta Ceres
Publisher:
ISBN:
Category :
Languages : en
Pages : 0
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Book Description
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: Tatiana Koshlan
Publisher: Springer
ISBN: 3319983040
Category : Science
Languages : en
Pages : 378
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Book Description
This book is devoted to the physical and mathematical modeling of the formation of complexes of protein molecules. The models developed show remarkable sensitivity to the amino acid sequences of proteins, which facilitates experimental studies and allows one to reduce the associated costs by reducing the number of measurements required according to the developed criteria. These models make it possible to reach a conclusion about the interactions between different amino acid chains and to identify more stable sites on proteins. The models also take the phosphorylation of amino acid residues into account. At the end of the book, the authors present possible directions of application of their physical and mathematical models in clinical medicine.
Author: Valerie Daggett
Publisher: Elsevier
ISBN: 0080493785
Category : Medical
Languages : en
Pages : 477
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Book Description
Protein Simulation focuses on predicting how protein will act in vivo. These studies use computer analysis, computer modeling, and statistical probability to predict protein function. * Force Fields* Ligand Binding* Protein Membrane Simulation* Enzyme Dynamics* Protein Folding and unfolding simulations
