Protein Dynamics: Methods and Protocols (Paperback, Softcover Repri)

Part I: Experimental Methods for Characterizing Protein Dynamics 1. Monitoring Side-Chain Dynamics of Proteins Using 2 H 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 Jorg Zimmermann and Floyd E. Romesberg Part II: Computational Methods for Characterizing Protein Dynamics 7. Balancing Bond, Nonbond and G -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-beta-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