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Author: Jiabin Xu
Publisher:
ISBN:
Category :
Languages : en
Pages :
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Book Description
Computer simulations for investigating protein folding and evolution are presented. In chapter 1, an all-atom model with a knowledge-based potential is used to study the folding kinetics of Formin-Binding protein. We study the folding kinetics by performing Monte Carlo simulations. We examine the order of formation of two beta-hairpins, the folding mechanism of each individual beta-hairpin, and transition state ensemble (TSE) and compare our results with experimental data and previous computational studies. Further, a rigorous Pfold analysis is used to obtain representative samples of the TSEs showing good quantitative agreement between experimental and simulated phi values.
Author: Jiabin Xu
Publisher:
ISBN:
Category :
Languages : en
Pages :
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Book Description
Computer simulations for investigating protein folding and evolution are presented. In chapter 1, an all-atom model with a knowledge-based potential is used to study the folding kinetics of Formin-Binding protein. We study the folding kinetics by performing Monte Carlo simulations. We examine the order of formation of two beta-hairpins, the folding mechanism of each individual beta-hairpin, and transition state ensemble (TSE) and compare our results with experimental data and previous computational studies. Further, a rigorous Pfold analysis is used to obtain representative samples of the TSEs showing good quantitative agreement between experimental and simulated phi values.
Author: Serafin Fraga
Publisher: Springer Science & Business Media
ISBN: 3642514995
Category : Science
Languages : en
Pages : 296
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Book Description
Protein engineering endeavors to design new peptides and proteins or to change the structural and/or functional characteristics of existing ones for specific purposes, opening the way for the development of new drugs. This work develops in a comprehensive way the theoretical formulation for the methods used in computer-assisted modeling and predictions, starting from the basic concepts and proceeding to the more sophisticated methods, such as Monte Carlo and molecular dynamics. An evaluation of the approximations inherent to the simulations will allow the reader to obtain a perspective of the possible deficiencies and difficulties and approach the task with realistic expectations. Examples from the authors laboratories, as well as from the literature provide useful information.
Author: Haydn Wyn Williams
Publisher:
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Category :
Languages : en
Pages :
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Book Description
Computer simulations of biological systems provide novel data while both supporting and challenging traditional experimental methods. However, continued innovation is required to ensure that these technologies are able to work with increasingly complex systems. Coarse-grained approximations of protein structure have been studied using a lattice model designed to find low-energy conformations. A hydrogen-bonding term has been introduced. The ability to form [beta]-sheet has been demonstrated, and the intricacies of reproducing the more complex [alpha]-helix on a lattice have been considered. An alternative strategy, that of better utilising computing power through the technique of milestoning, has shown good agreement with previous experimental and computational work. The increased efficiency allows significantly less extreme simulation conditions to be applied than those used in alternative simulation methods, and allows more simulation repeats. Finally, the principles of Least Action Dynamics have been employed to combine the two approaches described above. By splitting a simulation trajectory into a number of smaller components, and using the lattice model to optimise the path from a start structure to an end structure, it has been possible to efficiently generate dynamical information using an alternative method to traditional molecular dynamics.
Author: Atipat Rojnuckarin
Publisher:
ISBN:
Category :
Languages : en
Pages : 432
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Book Description
Author: Victor Muñoz
Publisher: Royal Society of Chemistry
ISBN: 0854042571
Category : Science
Languages : en
Pages : 290
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Book Description
Protein folding and aggregation is the process by which newly synthesized proteins fold into the specific three-dimensional structures defining their biologically active states. It has always been a major focus of research in biochemistry and has often been seen as the unsolved second part of the genetic code. In the last 10 years we have witnessed a quantum leap in the research in this exciting area. Computational methods have improved to the extent of making possible to simulate the complete folding process of small proteins and the early stages of protein aggregation. Experimental methods h.
Author: R. A. Broglia
Publisher: IOS Press
ISBN: 9781586031664
Category : Science
Languages : en
Pages : 378
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Book Description
This text presents the results of broad interdisciplinary effort to study proteins in physical and evolutionary prospectives. Among the authors are physicists, chemists, crystallographers, and evolutionary biologists. Experimental and theoretical developments from molecules to cells are presented providing a broad picture of modern biophysical chemistry.
Author: Hung Duc Nguyen
Publisher:
ISBN:
Category :
Languages : en
Pages : 285
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Book Description
Keywords: fibril formation, protein folding, protein aggregation, polyalanine, amyloid, computer simulation, molecular dynamics.
Author:
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Category :
Languages : en
Pages :
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Book Description
Computer simulation is used to study the competition between protein folding and aggregation, especially the formation of ordered structures that are also known as amyloid fibrils. Employing simplified protein models, we simulate multi-protein systems at a greater level of detail than has previously been possible, probe the fundamental physics that govern protein folding and aggregation, and explore the energetic and structural characteristics of amorphous and fibrillar protein aggregates. We first tackle the aggregation problem by using a low-resolution model called the lattice HP model developed by Lau and Dill. Dynamic Monte Carlo simulations are conducted on a system of simple, two-dimensional lattice protein molecules. We investigate how changing the rate of chemical or thermal renaturation affects the folding and aggregation behavior of the model protein molecule by simulating three renaturation methods: infinitely slow cooling, slow but finite cooling, and quenching. We find that the infinitely slow cooling method provides the highest refolding yields. We then study how the variation of protein concentration affects the refolding yield by simulating the pulse renaturation method, in which denatured proteins are slowly added to the refolding simulation box in a stepwise manner. We observe that the pulse renaturation method provides refolding yields that are substantially higher than those observed in the other three methods even at high packing fractions. We then investigate the folding of a polyalanine peptide with the sequence Ac-KA14K-NH2 using a novel off-lattice, intermediate-resolution protein model originally developed by Smith and Hall. The thermodynamics of a system containing a single Ac-KA14K-NH2 molecule is explored by employing the replica exchange simulation method to map out the conformational transitions as a function of temperature. We also explore the influence of solvent type on the folding process by varying the relative strength of the sid.
Author: Peter Eastman
Publisher:
ISBN:
Category :
Languages : en
Pages : 248
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Author: Kuo Hao Lee
Publisher:
ISBN:
Category : Proteins
Languages : en
Pages : 164
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Book Description
In this dissertation, computer simulations were used to study protein evolution in simple viruses and peptide-nanoparticle interactions. Understanding protein evolution in viruses is important because a single amino acid mutation can cause a previously effective vaccine to be ineffective. Understanding peptide-nanoparticle interactions is important to improve the efficiency of using nanoparticle conjugates for drug delivery. To study protein evolution, bacteriophage (phage) ID11 and [phi] X174 were used as model systems. The central hypothesis is that beneficial mutations that arise in a phage population exposed to elevated temperature stabilize the protein-protein interactions. This hypothesis was tested by calculating how amino acid mutations change the binding affinity between proteins in ID11. Results suggest that most mutations stabilized protein stability, consistent with the hypothesis. The effect of random mutations on protein folding stability and protein-protein binding stability was tested for different protein sequences and system temperatures for [phi] X174. Results show that random mutations always tend to destabilize protein folding, but can tend to stabilize or destabilize protein binding depending on the system. Peptide-nanoparticle interactions were studied by comparing structural and dynamic features of unbound peptides to peptides bound to a gold-nanoparticle. The hypothesis is that binding the peptides to the nanoparticle will change peptide structure and dynamics. Results show that bound peptides are typically less dynamic than unbound peptides, but for some sequences it is possible for bound peptides to be more flexible than unbound.
