Coarse-grained Modeling of Protein Dynamics Using Elastic Network Models PDF Download
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Author: Silke Andrea Wieninger
Publisher:
ISBN:
Category :
Languages : en
Pages : 206
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Book Description
Author: Silke Andrea Wieninger
Publisher:
ISBN:
Category :
Languages : en
Pages : 206
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Book Description
Author: Ayşe Özge Kürkçüoğlu
Publisher:
ISBN:
Category : Anisotropy
Languages : en
Pages : 124
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Book Description
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:
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: Gregory A. Voth
Publisher: CRC Press
ISBN: 1420059564
Category : Science
Languages : en
Pages : 492
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Book Description
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: 142003507X
Category : Mathematics
Languages : en
Pages : 448
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Book Description
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:
Category :
Languages : en
Pages : 96
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Book Description
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:
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: 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: Sidney A. Simon
Publisher: Academic Press
ISBN: 0080925855
Category : Science
Languages : en
Pages : 606
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Book Description
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: 1315356708
Category : Science
Languages : en
Pages : 399
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Book Description
"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.
