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Protein Dynamics

Methods and Protocols

  • Book
  • © 2014

Overview

Editors:
  1. Dennis R. Livesay

    1. Department of Bioinformatics and Genomic, University of North Carolina at Charlott, Charlotte, USA

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  • Details both experimental and computational methods to interrogate molecular level fluctuations
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 1084)

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Table of contents (15 protocols)

  1. Front Matter

    Pages i-xiv
    Download chapter PDF

  2. Experimental Methods for Characterizing Protein Dynamics

    1. Front Matter

      Pages 1-1
      Download chapter PDF

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

      • Chad M. Petit, Andrew L. Lee
      Pages 3-27

    3. CPMG Relaxation Dispersion

      • Rieko Ishima
      Pages 29-49

    4. Confocal Single-Molecule FRET for Protein Conformational Dynamics

      • Yan-Wen Tan, Jeffrey A. Hanson, Jhih-Wei Chu, Haw Yang
      Pages 51-62

    5. Protein Structural Dynamics Revealed by Site-Directed Spin Labeling and Multifrequency EPR

      • Yuri E. Nesmelov
      Pages 63-79

    6. Probing Backbone Dynamics with Hydrogen/Deuterium Exchange Mass Spectrometry

      • Harsimran Singh, Laura S. Busenlehner
      Pages 81-99

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

      • Jörg Zimmermann, Floyd E. Romesberg
      Pages 101-119

  3. Computational Methods for Characterizing Protein Dynamics

    1. Front Matter

      Pages 121-121
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    2. Balancing Bond, Nonbond, and Gō-Like Terms in Coarse Grain Simulations of Conformational Dynamics

      • Ronald D. Hills Jr.
      Pages 123-140

    3. A Tutorial on Building Markov State Models with MSMBuilder and Coarse-Graining Them with BACE

      • Gregory R. Bowman
      Pages 141-158

    4. Analysis of Protein Conformational Transitions Using Elastic Network Model

      • Wenjun Zheng, Mustafa Tekpinar
      Pages 159-172

    5. Geometric Simulation of Flexible Motion in Proteins

      • Stephen A. Wells
      Pages 173-192

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

      • Charles C. David, Donald J. Jacobs
      Pages 193-226

    7. 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, Dennis R. Livesay
      Pages 227-238

    8. Towards Comprehensive Analysis of Protein Family Quantitative Stability–Flexibility Relationships Using Homology Models

      • Deeptak Verma, Jun-tao Guo, Donald J. Jacobs, Dennis R. Livesay
      Pages 239-254

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

      • Vincent J. Hilser, Steven T. Whitten
      Pages 255-269

    10. Morphing Methods to Visualize Coarse-Grained Protein Dynamics

      • Dahlia R. Weiss, Patrice Koehl
      Pages 271-282

  4. Back Matter

    Pages 283-285
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Keywords

About this book

In Protein Dynamics: Methods and Protocols, expert researchers in the field detail both experimental and computational methods to interrogate molecular 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.

 

Editors and Affiliations

  • Department of Bioinformatics and Genomic, University of North Carolina at Charlott, Charlotte, USA

    Dennis R. Livesay

Bibliographic Information

  • Book Title: Protein Dynamics

  • Book Subtitle: Methods and Protocols

  • Editors: Dennis R. Livesay

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-62703-658-0

  • Publisher: Humana Totowa, NJ

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media,New York 2014

  • Hardcover ISBN: 978-1-62703-657-3Published: 24 September 2013

  • Softcover ISBN: 978-1-4939-6307-2Published: 23 August 2016

  • eBook ISBN: 978-1-62703-658-0Published: 24 September 2013

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XIV, 285

  • Number of Illustrations: 26 b/w illustrations, 56 illustrations in colour

  • Topics: Protein Science, Computer Appl. in Life Sciences, Protein Structure

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