应《网络安全法》要求，自2017年10月1日起，未进行实名认证将不得使用互联网跟帖服务。为保障您的帐号能够正常使用，请尽快对帐号进行手机号验证，感谢您的理解与支持！

24小时热门版块排行榜    

小木虫论坛-学术科研互动平台 » 材料区 » 材料综合 » 综合资源 » Theory of Phase Transitions in Polypeptides and Proteins (Springer Theses)2011
191/1返回列表
查看: 1291  |  回复: 18
只看楼主 @他人 存档 新回复提醒 (忽略) 收藏    在APP中查看
【奖励】 本帖被评价16次，作者wenke1526增加金币 12.4 个

wenke1526

荣誉版主 (著名写手)

[资源] Theory of Phase Transitions in Polypeptides and Proteins (Springer Theses)2011

There are nearly 100 000 different protein sequences encoded in the human genome, each with its own specific fold. Understanding how a newly formed polypeptide sequence finds its way to the correct fold is one of the greatest challenges in the modern structural biology. The aim of this thesis is to provide novel insights into protein folding by considering the problem from the point of view of statistical mechanics. The thesis starts by investigating the fundamental degrees of freedom in polypeptides that are responsible for the conformational transitions. This knowledge is then applied in the statistical mechanics description of helix?coil transitions in polypeptides. Finally, the theoretical formalism is generalized to the case of proteins in an aqueous environment. The major novelty of this work lies in comabining (a) a formalism based on fundamental physical properties of the system and (b) the resulting possibility of describing the folding?unfolding transitions quantitatively. The clear physical nature of the formalism opens the way to further applications in a large variety of systems and processes.

Common terms and phrases:
amino acids degrees of freedom dihedral angles heat capacity molecular dynamics partition function potential energy surface protein folding random coil

Cover

Springer Theses

Theory of Phase Transitions in Polypeptides and Proteins

ISBN 9783642227318

Supervisor’s Foreword

Acknowledgments

Contents

1 Introduction

     1.1 Problems Addressed in the Thesis

     References

2 Theoretical Methods of Quantum Mechanics

     2.1 Introduction

     2.2 The Schrödinger Equation

     2.3 The Born--Oppenheimer Approximation

     2.4 Properties of the Wavefunction

     2.5 Hartree--Fock Theory

     2.6 Density Functional Theory

     2.7 Molecular Mechanics Approach: a Way to Overcome  the Complexity of Quantum Mechanics

     References

3 Degrees of Freedom in Polypeptides  and Proteins

     3.1 Introduction

     3.2 Conformational Properties of Alanine  and Glycine Chains

          3.2.1 Determination of the Polypeptides Twisting  Degrees of Freedom

          3.2.2 Optimized Geometries of Alanine Polypeptides

          3.2.3 Polypeptide Energy Dependance On the Dihedral  Angle   .

          3.2.4 Potential Energy Surface for Alanine Tripeptide

          3.2.5 Potential Energy Surface for Alanine Hexapeptide  with the Sheet and the Helix Secondary Structure

          3.2.6 Comparison of Calculation Results  with Experimental Data

     3.3 Conformational Changes in Glycine Tri- and Hexa-Peptide

          3.3.1 Optimized Geometries of Glycine Polypeptides

          3.3.2 Potential Energy Surface for Glycine Tripeptide

          3.3.3 Potential Energy Surface for Glycine Hexapeptide  with the Sheet and the Helix Secondary Structure

          3.3.4 Comparison of Calculation Results  with Experimental Data

     References

4 Partition Function of a Polypeptide

     4.1 Introduction

     4.2 Molecular Mechanics Potential

     4.3 Hamiltonial of a Polypeptide Chain

     4.4 Construction of the Partition Function

     4.5 Thermodynamical Characteristics of a Polypeptide Chain

     References

5 Phase Transitions in Polypeptides

     5.1 Introduction

     5.2 Molecular Dynamics Simulations

     5.3   a-HelixRandom  Coil Phase Transition in Polyalanine

          5.3.1 Accuracy of the Molecular Mechanics Potential

          5.3.2 Potential Energy Surface of Alanine Polypeptide

          5.3.3 Internal Energy of Alanine Polypeptide

          5.3.4 Heat Capacity of Alanine Polypeptide

          5.3.5 Calculation of the Zimm--Bragg Parameters

          5.3.6 Helicity of Alanine Polypeptides

          5.3.7 Correlation of Different Amino Acids in the Polypeptide

     5.4 Phase Transitions in Polypeptides:  Analysis of Energy Fluctuations

          5.4.1 Fluctuations of Internal Energy and Heat Capacity

          5.4.2   a-Helix Random  Coil Transition in Alanine Polypeptide

          5.4.3   p-Helix Random  Coil Transition in Valine Polypeptide

          5.4.4   p-Helix Random  Coil Transition in Leucine Polypeptide

          5.4.5 Appendix: Parameters of MD Simulation

     References

6 Folding of Proteins in Aqueous Environment

     6.1 Introduction

     6.2 Theoretical Methods

          6.2.1 Partition Function of a Protein

          6.2.2 Partition Function of a Protein in Water Environment

     6.3 Results and Discussion

          6.3.1 Heat Capacity of Staphylococcal Nuclease

          6.3.2 Heat Capacity of Metmyoglobin

     References

7 Summary and Conclusions

     References

u08eZUThffEC



[ Last edited by wenke1526 on 2011-12-14 at 11:13 ]
回复此楼

» 本帖附件资源列表

» 收录本帖的淘帖专辑推荐

锂电收藏 国外专业电子书

» 猜你喜欢

» 本主题相关价值贴推荐，对您同样有帮助:
1楼 2011-12-14 11:11:56
已阅   回复此楼   关注TA 给TA发消息 送TA红花 TA的回帖
简单回复
wenke15262楼
2011-12-14 11:14   回复  
vaughn3楼
2011-12-14 11:38   回复  
三星好评  顶一下，感谢分享！
kevinming4楼
2011-12-14 11:50   回复  
三星好评  顶一下，感谢分享！
zhke5235楼
2011-12-14 15:56   回复  
五星好评  顶一下，感谢分享！
fangyongxinxi6楼
2011-12-14 16:28   回复  
五星好评  顶一下，感谢分享！
dzb164097楼
2011-12-15 08:59   回复  
五星好评  顶一下，感谢分享！
lanxzh8楼
2012-05-12 06:24   回复  
五星好评  顶一下，感谢分享！
杨寻9楼
2012-11-17 10:05   回复  
五星好评  顶一下，感谢分享！
liusheng631110楼
2012-11-22 22:34   回复  
五星好评  顶一下，感谢分享！
wwj198277077111楼
2012-12-29 16:43   回复  
五星好评  顶一下，感谢分享！
wwj198277077112楼
2012-12-29 17:22   回复  
顶一下，感谢分享！
xiefenxiefen13楼
2013-01-23 20:10   回复  
五星好评  顶一下，感谢分享！
jhoo14楼
2013-08-30 16:02   回复  
五星好评  顶一下，感谢分享！
一泓山人15楼
2013-09-07 17:01   回复  
五星好评  顶一下，感谢分享！
geniuswq16楼
2013-09-24 18:11   回复  
五星好评  顶一下，感谢分享！
迷失的羊羔17楼
2013-12-14 08:44   回复  
五星好评  顶一下，感谢分享！
ypghnust6118楼
2013-12-20 14:41   回复  
五星好评  顶一下，感谢分享！
lerel1234519楼
2019-02-20 17:29   回复  
五星好评  顶一下，感谢分享！
相关版块跳转 我要订阅楼主 wenke1526 的主题更新
191/1返回列表
☆ 无星级 ★ 一星级 ★★★ 三星级 ★★★★★ 五星级
普通表情 龙 兔 虎 猫 高级回复 (可上传附件)
信息提示
关闭
请填处理意见
关闭