Protein Conformational Dynamics

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Protein Conformational Dynamics

Author : Ke-li Han
Publisher : Springer Science & Business Media
ISBN 13 : 3319029703
Total Pages : 488 pages
Book Rating : 4.3/5 (19 download)

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Book Synopsis Protein Conformational Dynamics by : Ke-li Han

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.

Protein Conformational Dynamics: a Computational Study

Author : Ferruccio Palazzesi
Publisher :
ISBN 13 :
Total Pages : pages
Book Rating : 4.:/5 (935 download)

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Book Synopsis Protein Conformational Dynamics: a Computational Study by : Ferruccio Palazzesi

Download or read book Protein Conformational Dynamics: a Computational Study written by Ferruccio Palazzesi and published by . This book was released on 2015 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:

Modeling Protein Conformational Dynamics Using Kinetic Network Models

Author : Zhaoning Cui
Publisher :
ISBN 13 :
Total Pages : 151 pages
Book Rating : 4.:/5 (881 download)

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Book Synopsis Modeling Protein Conformational Dynamics Using Kinetic Network Models by : Zhaoning Cui

Download or read book Modeling Protein Conformational Dynamics Using Kinetic Network Models written by Zhaoning Cui and published by . This book was released on 2013 with total page 151 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Bridging the Gap Between Protein Structure and Dynamics

Author : Jeffrey Alan Hanson
Publisher :
ISBN 13 :
Total Pages : 488 pages
Book Rating : 4.:/5 (35 download)

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Book Synopsis Bridging the Gap Between Protein Structure and Dynamics by : Jeffrey Alan Hanson

Download or read book Bridging the Gap Between Protein Structure and Dynamics written by Jeffrey Alan Hanson and published by . This book was released on 2009 with total page 488 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Infrared Measurements of Protein Conformational Dynamics

Author : Robert M. Culik
Publisher :
ISBN 13 :
Total Pages : 183 pages
Book Rating : 4.:/5 (89 download)

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Book Synopsis Infrared Measurements of Protein Conformational Dynamics by : Robert M. Culik

Download or read book Infrared Measurements of Protein Conformational Dynamics written by Robert M. Culik and published by . This book was released on 2014 with total page 183 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Protein Conformational Dynamics in a Two-component Signal Transduction System

Author : Rahul Banerjee
Publisher :
ISBN 13 : 9781321153163
Total Pages : 217 pages
Book Rating : 4.1/5 (531 download)

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Book Synopsis Protein Conformational Dynamics in a Two-component Signal Transduction System by : Rahul Banerjee

Download or read book Protein Conformational Dynamics in a Two-component Signal Transduction System written by Rahul Banerjee and published by . This book was released on 2014 with total page 217 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Protein Dynamics

Author : Dennis R. Livesay
Publisher : Humana
ISBN 13 : 9781493963072
Total Pages : 0 pages
Book Rating : 4.9/5 (63 download)

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Book Synopsis Protein Dynamics by : Dennis R. Livesay

Download or read book Protein Dynamics written by Dennis R. Livesay and published by Humana. This book was released on 2016-08-23 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: In Protein Dynamics: Methods and Protocols, expert researchers in the field detail both experimental and computational methods to interrogate molecular level fluctuations. Chapters detail best-practice recipes covering both experimental and computational techniques, reflecting modern protein research. Written in the highly successful Methods in Molecular BiologyTM series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Protein Dynamics: Methods and Protocols describes the most common and powerful methods used to characterize protein dynamics.

Conformational Dynamics of Proteins by Fluorescence Fluctuation Spectroscopy

Author : Robel Birru Yirdaw
Publisher :
ISBN 13 :
Total Pages : 151 pages
Book Rating : 4.:/5 (798 download)

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Book Synopsis Conformational Dynamics of Proteins by Fluorescence Fluctuation Spectroscopy by : Robel Birru Yirdaw

Download or read book Conformational Dynamics of Proteins by Fluorescence Fluctuation Spectroscopy written by Robel Birru Yirdaw and published by . This book was released on 2012 with total page 151 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Shedding a New Light on Protein Conformational Dynamics

Author : Rory Sleno
Publisher :
ISBN 13 :
Total Pages : pages
Book Rating : 4.:/5 (11 download)

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Book Synopsis Shedding a New Light on Protein Conformational Dynamics by : Rory Sleno

Download or read book Shedding a New Light on Protein Conformational Dynamics written by Rory Sleno and published by . This book was released on 2017 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: "As key effector units of the cell, understanding structure and function relationships of proteins are integral to explaining physiology and, in turn, pathophysiology. With the cost of drug development soaring and success dwindling, new ways to probe protein function will be at the forefront of innovation. A protein's function is the product of its conformational dynamics, where distinct 3-dimensional conformations of a protein dictate its various effects on the cell. Though highly valuable technologies capable of reporting on protein conformation currently exist, X-ray crystallography and nuclear magnetic resonance among others, their capacity to report on dynamic events and/or in physiologically relevant assay conditions are limited.This thesis describes the development and application of biosensors capable of reporting on protein conformation in live human cells. Biosensors were developed for two classes of protein targets, ion channels - Kir3, and G protein-coupled receptors (GPCR) - FP and AT1R, together representing the targets of a majority of current prescription drugs. The biosensor design was based on bioluminescence resonance energy transfer (BRET) and required the insertion of a bioluminescent protein and a short peptide sequences within the protein of interest. Due to the specific affinity for the peptide sequence of an organic fluorophore, fluorescein biarsenical hairpin binder (FlAsH), the latter could be used as a resonance energy transfer acceptor to probe the different conformations of the protein of interest without disrupting its function.Both panels of biosensors successfully reported on ligand-induced conformational rearrangements in the target proteins and correlated with functional effects. The GPCR biosensors were further applied to enrich our understanding of receptor dimerization and allosteric communication between proteins, in this case, the FP/AT1R heterodimer." --

Protein Conformation

Author : Derek J. Chadwick
Publisher : John Wiley & Sons
ISBN 13 : 0470514159
Total Pages : 282 pages
Book Rating : 4.4/5 (75 download)

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Book Synopsis Protein Conformation by : Derek J. Chadwick

Download or read book Protein Conformation written by Derek J. Chadwick and published by John Wiley & Sons. This book was released on 2008-04-30 with total page 282 pages. Available in PDF, EPUB and Kindle. Book excerpt: How the amino acid sequence of a protein determines its three-dimensional structure is a major problem in biology and chemistry. Leading experts in the fields of NMR spectroscopy, X-ray crystallography, protein engineering and molecular modeling offer provocative insights into current views on the protein folding problem and various aspects for future progress.

Protein Conformational Dynamics In Genomic Analysis

Author : Brandon Mac Butler
Publisher :
ISBN 13 :
Total Pages : 135 pages
Book Rating : 4.:/5 (1 download)

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Book Synopsis Protein Conformational Dynamics In Genomic Analysis by : Brandon Mac Butler

Download or read book Protein Conformational Dynamics In Genomic Analysis written by Brandon Mac Butler and published by . This book was released on 2016 with total page 135 pages. Available in PDF, EPUB and Kindle. Book excerpt: Proteins are essential for most biological processes that constitute life. The function of a protein is encoded within its 3D folded structure, which is determined by its sequence of amino acids. A variation of a single nucleotide in the DNA during transcription (nSNV) can alter the amino acid sequence (i.e., a mutation in the protein sequence), which can adversely impact protein function and sometimes cause disease. These mutations are the most prevalent form of variations in humans, and each individual genome harbors tens of thousands of nSNVs that can be benign (neutral) or lead to disease. The primary way to assess the impact of nSNVs on function is through evolutionary approaches based on positional amino acid conservation. These approaches are largely inadequate in the regime where positions evolve at a fast rate. We developed a method called dynamic flexibility index (DFI) that measures site-specific conformational dynamics of a protein, which is paramount in exploring mechanisms of the impact of nSNVs on function. In this thesis, we demonstrate that DFI can distinguish the disease-associated and neutral nSNVs, particularly for fast evolving positions where evolutionary approaches lack predictive power. We also describe an additional dynamics-based metric, dynamic coupling index (DCI), which measures the dynamic allosteric residue coupling of distal sites on the protein with the functionally critical (i.e., active) sites. Through DCI, we analyzed 200 disease mutations of a specific enzyme called GCase, and a proteome-wide analysis of 75 human enzymes containing 323 neutral and 362 disease mutations. In both cases we observed that sites with high dynamic allosteric residue coupling with the functional sites (i.e., DARC spots) have an increased susceptibility to harboring disease nSNVs. Overall, our comprehensive proteome-wide analysis suggests that incorporating these novel position-specific conformational dynamics based metrics into genomics can complement current approaches to increase the accuracy of diagnosing disease nSNVs. Furthermore, they provide mechanistic insights about disease development. Lastly, we introduce a new, purely sequence-based model that can estimate the dynamics profile of a protein by only utilizing coevolution information, eliminating the requirement of the 3D structure for determining dynamics.

Insights Into Protein Function from Evolutionary and Conformational Dynamics

Author : Philip W. Bransford
Publisher :
ISBN 13 :
Total Pages : 145 pages
Book Rating : 4.:/5 (82 download)

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Book Synopsis Insights Into Protein Function from Evolutionary and Conformational Dynamics by : Philip W. Bransford

Download or read book Insights Into Protein Function from Evolutionary and Conformational Dynamics written by Philip W. Bransford and published by . This book was released on 2011 with total page 145 pages. Available in PDF, EPUB and Kindle. Book excerpt: The volume of protein structure data has grown rapidly over the past 30 years, leaving a wake of facts that still require explanation. We endeavored to answer a few open questions on the structure-function relationship of intriguing mechanochemical protein systems. To this end this thesis work contains five studies that offer novel insights into molecular biomechanical systems that may guide future basic research or applications development. The first study concerns the biophysics of cadherin-mediated cell sorting observed in developing solid tissue. We investigated the evolutionary dynamics of the cadherin superfamily of cell-cell adhesion proteins to infer a structural basis for their paradoxical mixture of pairwise binding specificity and promiscuity. Our analysis predicts a small set of specificity-determining residues located within the protomer-protomer binding interface. The putative specificity-determinants form a design space with potential for engineering novel cell-cell adhesive interactions. The second study addresses the open question of how to automatically identify regions within a protein that engage in allosteric communication. To identify allostery we developed and tested two computational tools that operate on protein conformational dynamics data. These tools are useful for generating testable hypotheses about proteins with multiple functional sites for the design of non-competitive protein inhibitors. The third study asks, "What is the consequence of allosteric cooperation between the tandem binding sites in a class of proteins that bundle filamentous actin (F-actin)?" Through simulation we demonstrate that cooperative F-actin bundling tends to strengthen bundles by driving the formation of cross-links between neighboring filaments while depleting F-actin binding sites that are occupied but not cross-linked. We hence propose that allostery may be a natural feature of ABPs with tandem F-actin binding sites if nature indeed selects for sturdy F-actin bundles. The final two studies examine the impact of two structural perturbations to Factin on its mechanics. Using structure-based computer modeling we develop a simple explanation for the mechanism by which the structure of actin's polymorphic subdomain 2 mediates 4-fold changes in F-actin's flexibility. We further demonstrate that two calponin homology domains stabilize F-actin by binding in a configuration that tends to relax the stress concentration at actin-actin interfaces.

A Study of Protein Conformational Dynamics in Antigen

Author : David Collin Williams
Publisher :
ISBN 13 :
Total Pages : 460 pages
Book Rating : 4.:/5 (385 download)

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Book Synopsis A Study of Protein Conformational Dynamics in Antigen by : David Collin Williams

Download or read book A Study of Protein Conformational Dynamics in Antigen written by David Collin Williams and published by . This book was released on 1997 with total page 460 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Evaluating Experimental and Theoretical Measures of Protein Conformational Dynamics

Author : Benjamin Stone
Publisher :
ISBN 13 :
Total Pages : pages
Book Rating : 4.:/5 (16 download)

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Book Synopsis Evaluating Experimental and Theoretical Measures of Protein Conformational Dynamics by : Benjamin Stone

Download or read book Evaluating Experimental and Theoretical Measures of Protein Conformational Dynamics written by Benjamin Stone and published by . This book was released on 2016 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:

Statistical Models of Protein Conformational Dynamics

Author : Robert T. McGibbon
Publisher :
ISBN 13 :
Total Pages : pages
Book Rating : 4.:/5 (944 download)

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Book Synopsis Statistical Models of Protein Conformational Dynamics by : Robert T. McGibbon

Download or read book Statistical Models of Protein Conformational Dynamics written by Robert T. McGibbon and published by . This book was released on 2016 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Understanding the conformational dynamics of biological macromolecules at atomic resolution remains a grand challenge at the intersection of biology, chemistry, and physics. Molecular dynamics (MD) -- which refers to computational simulations of the atomic-level interactions and equations of motions that give rise to these dynamics -- is a powerful approach that now produces immense quantities of time series data on the dynamics of these systems. Here, I describe a variety of new methodologies for analyzing the rare events in these MD data sets in an automatic, statically-sound manner, and constructing the appropriate simplified models of these processes. These techniques are rooted in the theory of reversible Markov chains. They include new classes of Markov state models, hidden Markov models, and reaction coordinate finding algorithms, with applications to protein folding and conformational change. A particular focus herein is on methods for model selection and model comparison, and computationally efficient algorithms.

Computational Approaches to Protein Dynamics

Author : Monika Fuxreiter
Publisher : CRC Press
ISBN 13 : 1482297868
Total Pages : 458 pages
Book Rating : 4.4/5 (822 download)

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Book Synopsis Computational Approaches to Protein Dynamics by : Monika Fuxreiter

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

Sensing Conformational Dynamics of Single Trapped Proteins in Solution

Author : Samuel David Bockenhauer
Publisher :
ISBN 13 :
Total Pages : pages
Book Rating : 4.:/5 (858 download)

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Book Synopsis Sensing Conformational Dynamics of Single Trapped Proteins in Solution by : Samuel David Bockenhauer

Download or read book Sensing Conformational Dynamics of Single Trapped Proteins in Solution written by Samuel David Bockenhauer and published by . This book was released on 2013 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Proteins are macromolecular nanomachines that perform a wide variety of essential functions in living organisms. Distinct types of proteins in the cell serve as molecular sensors and signalers, sunlight-harvesting antennas and transducers, molecular motors for transport and metabolic energy storage, and oxidizers and reducers of physiological metal ions, to name a few. To achieve these complex functions, proteins are not static building blocks, but instead adopt multiple conformations in distinct functional states. These functions are inherently dynamic, meaning that methods capable of resolving dynamic behavior are necessary to fully elucidate protein function. Many bulk fluorescence methods have been used to study proteins by averaging together the signals from many copies of the same protein. However, such methods fail to capture distributions in protein conformations (e.g. mixtures of active and inactive states) and unsynchronized dynamics among these conformations (e.g. transition rates from inactive to active states under various conditions). Single-molecule fluorescence spectroscopy of proteins, on the other hand, allows direct observation of distributions and dynamics by watching only one protein at a time. In particular, a special device known as the Anti-Brownian ELectrokinetic (ABEL) trap can hold single fluorescently labeled proteins in solution for several seconds of spectroscopic observation without surface attachment, encapsulation, or the use of large beads. The ABEL trap combines fluorescence-based position estimation obtained by scanning a laser spot with the application of electrokinetic feedback forces to counter the Brownian motion of single proteins, one at a time. In this Dissertation I will describe my use of the ABEL trap technique to study dynamics of a variety of biomolecules, with emphasis on two proteins: the [beta]2-adrenergic receptor ([beta]2AR), an essential cellular signaling protein, and the peridinin-chlorophyll-protein (PCP), a sunlight-harvesting pigment-protein complex found in algae. In [beta]2AR, I observed a shift in protein conformation and in time scales of protein dynamics upon binding of an activating drug. In PCP, I observed two distinct classes of conformational change, indicating light-induced conformational flexibility, which may play a physiological role. Ongoing projects include resolving conformational substeps in FoF1 ATP synthase and measuring electron transfer kinetics of the multicopper oxidase Fet3p.