Protein Dynamics: Methods and Protocols

ISBN-13: 9781627036573 / Angielski / Twarda / 2013 / 285 str.

Dennis R. Livesay

Opis

InProtein Dynamics: Methods and Protocols, expert researchers in the field detail both experimental and computational methods to interrogatemolecular level fluctuations. Chapters detail best-practice recipes covering both experimental and computational techniques, reflecting modern protein research. Written in the highly successfulMethods in Molecular Biology 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 Protocolsdescribes the most common and powerful methods used to characterize protein dynamics.

Spis treści

Part I: Experimental Methods for Characterizing Protein Dynamics

1. Monitoring Side-Chain Dynamics of Proteins Using ²H Relaxation

Chad M. Petit and Andrew L. Lee

 2. CPMG Relaxation Dispersion

Rieko Ishima

 3. Confocal Single-Molecule FRET for Protein Conformational DynamicsYan-Wen Tan, Jeffrey A. Hanson, Jhih-Wei Chu, and Haw Yang

 4. Protein Structural Dynamics Revealed by Site-directed Spin Labeling and Multifrequency EPR

Yuri E. Nesmelov

 

5. Probing Backbone Dynamics With Hydrogen/Deuterium Exchange Mass Spectrometry

Harsimran Singh and Laura S. Busenlehner

 

6. Carbon-Deuterium Bonds as Non-perturbative Infrared Probes of Protein Dynamics, Electrostatics, Heterogeneity, and Folding

Jörg Zimmermann and Floyd E. Romesberg

 

Part II: Computational Methods for Characterizing Protein Dynamics

7. Balancing Bond, Nonbond and Gō-like Terms in Coarse Grain Simulations of Conformational Dynamics

Ronald D. Hills Jr.

 

8. Tutorial on Building Markov State  Models with MSMBuilder and Coarse-graining them with BACE

Gregory R. Bowman

 9. Analysis of Protein Conformational Transitions Using Elastic Network Model

Wenjun Zheng and Mustafa Tekpinar

 

10. Geometric Simulation of Flexible Motion in Proteins

Stephen A. Wells

 

11. Principal Component Analysis: A Method for Determining the Essential Dynamics of Proteins

Charles C. David and Donald J. Jacobs

 

12. A Case Study Comparing Quantitative Stability/Flexibility Relationships Across Five Metallo-β-Lactamases Highlighting Differences within NDM-1

Matthew C. Brown, Deeptak Verma, Christian Russell, Donald J. Jacobs, and  Dennis R. Livesay

 13. Towards Comprehensive Analysis of Protein Family Quantitative Stability/Flexibility Relationships using Homology Models

Deeptak Verma, Jun-tao Guo, Donald J. Jacobs^, and Dennis R. Livesay

 

14. Using the COREX/BEST Server to Model the Native State Ensemble

Vincent J. Hilser and Steven T. Whitten

 

15. Morphing Methods to Visualize Coarse-grained Protein Dynamics

Dahlia R. Weiss and Patrice Koehl