Pub Date : 2009-04-21DOI: 10.4208/cicp.2009.08.202
T. Weikl
The folding dynamics of small single-domain proteins is a current focus of simulations and experiments. Many of these proteins are 'two-state folders', i.e. proteins that fold rather directly from the denatured state to the native state, without populating metastable intermediate states. A central question is how to characterize the instable, partially folded conformations of two-state proteins, in particular the rate-limiting transition-state conformations between the denatured and the native state. These partially folded conformations are short-lived and cannot be observed directly in experiments. However, experimental data from detailed mutational analyses of the folding dynamics provide indirect access to transition states. The interpretation of these data, in particular the reconstruction of transition-state conformations, requires simulation and modeling. The traditional interpretation of the mutational data aims to reconstruct the degree of structure formation of individual residues in the transition state, while a novel interpretation aims at degrees of structure formation of cooperative substructures such as alpha-helices and beta-hairpins. By splitting up mutation-induced free energy changes into secondary and tertiary structural components, the novel interpretation resolves some of the inconsistencies of the traditional interpretation.
{"title":"Transition states in protein folding","authors":"T. Weikl","doi":"10.4208/cicp.2009.08.202","DOIUrl":"https://doi.org/10.4208/cicp.2009.08.202","url":null,"abstract":"The folding dynamics of small single-domain proteins is a current focus of simulations and experiments. Many of these proteins are 'two-state folders', i.e. proteins that fold rather directly from the denatured state to the native state, without populating metastable intermediate states. A central question is how to characterize the instable, partially folded conformations of two-state proteins, in particular the rate-limiting transition-state conformations between the denatured and the native state. These partially folded conformations are short-lived and cannot be observed directly in experiments. However, experimental data from detailed mutational analyses of the folding dynamics provide indirect access to transition states. The interpretation of these data, in particular the reconstruction of transition-state conformations, requires simulation and modeling. The traditional interpretation of the mutational data aims to reconstruct the degree of structure formation of individual residues in the transition state, while a novel interpretation aims at degrees of structure formation of cooperative substructures such as alpha-helices and beta-hairpins. By splitting up mutation-induced free energy changes into secondary and tertiary structural components, the novel interpretation resolves some of the inconsistencies of the traditional interpretation.","PeriodicalId":8447,"journal":{"name":"arXiv: Biomolecules","volume":"25 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2009-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81770215","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2008-07-04DOI: 10.1142/9789814261418_0005
R. Eisenberg
I believe an atomic biology is needed to supplement present day molecular biology, if we are to design and understand proteins, as well as define, make, and use them. Topics in the paper are molecular biology and atomic biology. Electrodiffusion in the open channel. Electrodiffusion in mixed electrolytes. Models of permeation. State Models of Permeation are Inconsistent with the Electric Field. Making models in atomic biology. Molecular dynamics. Temporal Limitations; Spatial Limitations; Periodic boundary conditions. Hierarchy of models of the open channel. Stochastic Motion of the Channel. Langevin Dynamics. Simulations of the Reaction Path: the Permion. Chemical reactions. What was wrong? Back to the hierarchy: Occam's razor can slit your throat. Poisson-Nernst-Planck PNP Models Flux Ratios; Pumping by Field Coupling. Gating in channels of one conformation. Gating by Field Switching; Gating Current; Gating in Branched Channels; Blocking. Back to the hierarchy: Linking levels. Is there a theory? At what level will the adaptation be found? Simplicity, evolution, and natural function.
{"title":"Atomic Biology, Electrostatics, and Ionic Channels","authors":"R. Eisenberg","doi":"10.1142/9789814261418_0005","DOIUrl":"https://doi.org/10.1142/9789814261418_0005","url":null,"abstract":"I believe an atomic biology is needed to supplement present day molecular biology, if we are to design and understand proteins, as well as define, make, and use them. Topics in the paper are molecular biology and atomic biology. Electrodiffusion in the open channel. Electrodiffusion in mixed electrolytes. Models of permeation. State Models of Permeation are Inconsistent with the Electric Field. Making models in atomic biology. Molecular dynamics. Temporal Limitations; Spatial Limitations; Periodic boundary conditions. Hierarchy of models of the open channel. Stochastic Motion of the Channel. Langevin Dynamics. Simulations of the Reaction Path: the Permion. Chemical reactions. What was wrong? Back to the hierarchy: Occam's razor can slit your throat. Poisson-Nernst-Planck PNP Models Flux Ratios; Pumping by Field Coupling. Gating in channels of one conformation. Gating by Field Switching; Gating Current; Gating in Branched Channels; Blocking. Back to the hierarchy: Linking levels. Is there a theory? At what level will the adaptation be found? Simplicity, evolution, and natural function.","PeriodicalId":8447,"journal":{"name":"arXiv: Biomolecules","volume":"77 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2008-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79676837","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Although the importance of protein dynamics in protein function is generally recognized, the role of protein fluctuations in allosteric effects scarcely has been considered. To address this gap, the Kullback‐Leibler divergence (Dx) between protein conformational distributions before and after ligand binding was proposed as a means of quantifying allosteric effects in proteins. Here, previous applications of Dx to methods for analysis and simulation of proteins are first reviewed, and their implications for understanding aspects of protein function and protein evolution are discussed. Next, equations for Dx suggest that kBTDx should be interpreted as an allosteric free energy — the free energy associated with changing the ligand‐free protein conformational distribution to the ligand‐bound conformational distribution. This interpretation leads to a thermodynamic model of allosteric transitions that unifies existing perspectives on the relation between ligand binding and changes in protein conformational dis...
{"title":"Ligand Binding, Protein Fluctuations, And Allosteric Free Energy","authors":"M. Wall","doi":"10.1063/1.2345620","DOIUrl":"https://doi.org/10.1063/1.2345620","url":null,"abstract":"Although the importance of protein dynamics in protein function is generally recognized, the role of protein fluctuations in allosteric effects scarcely has been considered. To address this gap, the Kullback‐Leibler divergence (Dx) between protein conformational distributions before and after ligand binding was proposed as a means of quantifying allosteric effects in proteins. Here, previous applications of Dx to methods for analysis and simulation of proteins are first reviewed, and their implications for understanding aspects of protein function and protein evolution are discussed. Next, equations for Dx suggest that kBTDx should be interpreted as an allosteric free energy — the free energy associated with changing the ligand‐free protein conformational distribution to the ligand‐bound conformational distribution. This interpretation leads to a thermodynamic model of allosteric transitions that unifies existing perspectives on the relation between ligand binding and changes in protein conformational dis...","PeriodicalId":8447,"journal":{"name":"arXiv: Biomolecules","volume":"11 1","pages":"16-33"},"PeriodicalIF":0.0,"publicationDate":"2006-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81990301","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2006-01-14DOI: 10.1007/978-0-387-68372-0_6
Jie Liang
{"title":"Computation of protein geometry and its applications: Packing and function prediction","authors":"Jie Liang","doi":"10.1007/978-0-387-68372-0_6","DOIUrl":"https://doi.org/10.1007/978-0-387-68372-0_6","url":null,"abstract":"","PeriodicalId":8447,"journal":{"name":"arXiv: Biomolecules","volume":"1 1","pages":"181-206"},"PeriodicalIF":0.0,"publicationDate":"2006-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86707088","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2004-08-26DOI: 10.1201/9781420035070.ch15
H. Fujisaki, L. Bu, J. Straub
Vibrational energy relaxation (VER) of a selected mode in cytochrome c (hemeprotein) in vacuum is studied using two theoretical approaches: One is the equilibrium simulation approach with quantum correction factors, and the other is the reduced model approach which describes the protein as an ensemble of normal modes coupled with nonlinear coupling elements. Both methods result in estimates of VER time (sub ps) for a CD stretching mode in the protein at room temperature, that are in accord with the experimental data of Romesberg's group. The applicability of the two methods is examined through a discussion of the validity of Fermi's golden rule on which the two methods are based.
{"title":"Probing vibrational energy relaxation in proteins using normal modes","authors":"H. Fujisaki, L. Bu, J. Straub","doi":"10.1201/9781420035070.ch15","DOIUrl":"https://doi.org/10.1201/9781420035070.ch15","url":null,"abstract":"Vibrational energy relaxation (VER) of a selected mode in cytochrome c (hemeprotein) in vacuum is studied using two theoretical approaches: One is the equilibrium simulation approach with quantum correction factors, and the other is the reduced model approach which describes the protein as an ensemble of normal modes coupled with nonlinear coupling elements. Both methods result in estimates of VER time (sub ps) for a CD stretching mode in the protein at room temperature, that are in accord with the experimental data of Romesberg's group. The applicability of the two methods is examined through a discussion of the validity of Fermi's golden rule on which the two methods are based.","PeriodicalId":8447,"journal":{"name":"arXiv: Biomolecules","volume":"91 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2004-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90356644","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
We first review how to determine the rate of vibrational energy relaxation (VER) using perturbation theory. We then apply those theoretical results to the problem of VER of a CD stretching mode in the protein cytochrome c. We model cytochrome c in vacuum as a normal mode system with the lowest-order anharmonic coupling elements. We find that, for the “lifetime” width parameter = 3 ∼ 30 cm 1 , the VER time is 0.2 ∼ 0.3 ps, which agrees rather well with the previous classical calculation using the quantum correction factor method, and is consistent with spectroscopic experiments by Romesberg’s group. We decompose the VER rate into separate contributions from two modes, and find that the most significant contribution, which depends on the “lifetime” width parameter, comes from those modes most resonant with the CD vibrational mode.
我们首先回顾了如何用微扰理论确定振动能量弛豫率。然后，我们将这些理论结果应用于蛋白质细胞色素c的CD拉伸模式的VER问题。我们将真空中的细胞色素c建模为具有最低阶非谐波耦合元素的正常模式系统。我们发现，当“寿命”宽度参数= 3 ~ 30 cm 1时，VER时间为0.2 ~ 0.3 ps，这与先前使用量子校正因子方法的经典计算结果相当吻合，并且与Romesberg小组的光谱实验结果一致。我们将VER率分解为两种模式的独立贡献，发现与CD振动模式最共振的模式对VER率的贡献最大，这取决于“寿命”宽度参数。
{"title":"Vibrational energy relaxation (VER) of a CD stretching mode in cytochrome c","authors":"H. Fujisaki, L. Bu, J. Straub","doi":"10.1002/0471712531.CH15","DOIUrl":"https://doi.org/10.1002/0471712531.CH15","url":null,"abstract":"We first review how to determine the rate of vibrational energy relaxation (VER) using perturbation theory. We then apply those theoretical results to the problem of VER of a CD stretching mode in the protein cytochrome c. We model cytochrome c in vacuum as a normal mode system with the lowest-order anharmonic coupling elements. We find that, for the “lifetime” width parameter = 3 ∼ 30 cm 1 , the VER time is 0.2 ∼ 0.3 ps, which agrees rather well with the previous classical calculation using the quantum correction factor method, and is consistent with spectroscopic experiments by Romesberg’s group. We decompose the VER rate into separate contributions from two modes, and find that the most significant contribution, which depends on the “lifetime” width parameter, comes from those modes most resonant with the CD vibrational mode.","PeriodicalId":8447,"journal":{"name":"arXiv: Biomolecules","volume":"20 1","pages":"179-203"},"PeriodicalIF":0.0,"publicationDate":"2004-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74499669","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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