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
