Dennis R Livesay

Protein Dynamics: Methods and Protocols - Methods in Molecular Biology Dennis R Livesay 2014 edition

Marc Notes: Includes bibliographic references and index. Table of Contents: Part I: Experimental Methods for Characterizing Protein Dynamics1. Monitoring Side-Chain Dynamics of Proteins Using 2H RelaxationChad M. Petit and Andrew L. Lee2. CPMG Relaxation Dispersion Rieko Ishima 3. Confocal Single-Molecule FRET for Protein Conformational DynamicsYan-Wen Tan, Jeffrey A. Hanson, Jhih-Wei Chu, and Haw Yang4. Protein Structural Dynamics Revealed by Site-directed Spin Labeling and Multifrequency EPRYuri E. Nesmelov 5. Probing Backbone Dynamics With Hydrogen/Deuterium Exchange Mass SpectrometryHarsimran Singh and Laura S. Busenlehner 6. Carbon-Deuterium Bonds as Non-perturbative Infrared Probes of Protein Dynamics, Electrostatics, Heterogeneity, and FoldingJorg Zimmermann and Floyd E. Romesberg Part II: Computational Methods for Characterizing Protein Dynamics7. Balancing Bond, Nonbond and G -like Terms in Coarse Grain Simulations of Conformational DynamicsRonald D. Hills Jr. 8. Tutorial on Building Markov State Models with MSMBuilder and Coarse-graining them with BACEGregory R. Bowman9. Analysis of Protein Conformational Transitions Using Elastic Network ModelWenjun Zheng and Mustafa Tekpinar 10. Geometric Simulation of Flexible Motion in ProteinsStephen A. Wells 11. Principal Component Analysis: A Method for Determining the Essential Dynamics of ProteinsCharles C. David and Donald J. Jacobs 12. A Case Study Comparing Quantitative Stability/Flexibility Relationships Across Five Metallo- -Lactamases Highlighting Differences within NDM-1Matthew C. Brown, Deeptak Verma, Christian Russell, Donald J. Jacobs, and Dennis R. Livesay13. Towards Comprehensive Analysis of Protein Family Quantitative Stability/Flexibility Relationships using Homology ModelsDeeptak Verma, Jun-tao Guo, Donald J. Jacobs, and Dennis R. Livesay 14. Using the COREX/BEST Server to Model the Native State EnsembleVincent J. Hilser and Steven T. Whitten 15. Morphing Methods to Visualize Coarse-grained Protein DynamicsDahlia R. Weiss and Patrice Koehl"Jacket Description/Back: In"Protein 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 successful"Methods 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 Protocols"describes the most common and powerful methods used to characterize protein dynamics."