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Protein Folding Protocols

  • Book
  • © 2006

Overview

Editors:
  1. Yawen Bai

    1. Laboratory of Biochemistry, National Cancer Institute, National Institutes of Health, Bethesda

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  2. Ruth Nussinov

    1. Center for Cancer Research Nanobiology Program SAIC, National Cancer Institute-Frederick, Frederick
      Department of Human Genetics, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel

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    You can also search for this editor in PubMed   Google Scholar

Part of the book series: Methods in Molecular Biology (MIMB, volume 350)

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Table of contents (16 protocols)

  1. Front Matter

    Pages i-xiii
    Download chapter PDF

  2. Infrared Temperature-Jump Study of the Folding Dynamics of α-Helices and β-Hairpins

    • Feng Gai, Deguo Du, Yao Xu
    Pages 1-20

  3. The Use of High-Pressure Nuclear Magnetic Resonance to Study Protein Folding

    • Michael W. Lassalle, Kazuyuki Akasaka
    Pages 21-38

  4. Characterization of Denatured Proteins Using Residual Dipolar Couplings

    • Erika B. Gebel, David Shortle
    Pages 39-48

  5. Characterizing Residual Structure in Disordered Protein States Using Nuclear Magnetic Resonance

    • David Eliezer
    Pages 49-67

  6. Population and Structure Determination of Hidden Folding Intermediates by Native-State Hydrogen Exchange-Directed Protein Engineering and Nuclear Magnetic Resonance

    • Yawen Bai, Hanqiao Feng, Zheng Zhou
    Pages 69-81

  7. Characterizing Protein Folding Transition States Using Ψ-Analysis

    • Adarsh D. Pandit, Bryan A. Krantz, Robin S. Dothager, Tobin R. Sosnick
    Pages 83-104

  8. Advances in the Analysis of Conformational Transitions in Peptides Using Differential Scanning Calorimetry

    • Werner W. Streicher, George I. Makhatadze
    Pages 105-113

  9. Application of Single Molecule Förster Resonance Energy Transfer to Protein Folding

    • Benjamin Schuler
    Pages 115-138

  10. Single Molecule Studies of Protein Folding Using Atomic Force Microscopy

    • Sean P. Ng, Lucy G. Randles, Jane Clarke
    Pages 139-167

  11. Using Triplet-Triplet Energy Transfer to Measure Conformational Dynamics in Polypeptide Chains

    • Beat Fierz, Karin Joder, Florian Krieger, Thomas Kiefhaber
    Pages 169-187

  12. A Hierarchical Protein Folding Scheme Based on the Building Block Folding Model

    • Nurit Haspel, Gilad Wainreb, Yuval Inbar, Hui-Hsu (Gavin) Tsai, Chung-Jung Tsai, Haim J. Wolfson et al.
    Pages 189-204

  13. Replica Exchange Molecular Dynamics Method for Protein Folding Simulation

    • Ruhong Zhou
    Pages 205-223

  14. Estimation of Folding Probabilities and Φ Values From Molecular Dynamics Simulations of Reversible Peptide Folding

    • Francesco Rao, Giovanni Settanni, Amedeo Caflisch
    Pages 225-249

  15. Packing Regularities in Biological Structures Relate to Their Dynamics

    • Robert L. Jernigan, Andrzej Kloczkowski
    Pages 251-276

  16. Intermediates and Transition States in Protein Folding

    • D. Thirumalai, Dmitri K. Klimov
    Pages 277-303

  17. Thinking the Impossible

    • Rita Casadio, Piero Fariselli, Pier Luigi Martelli, Gianluca Tasco
    Pages 305-320

  18. Back Matter

    Pages 321-327
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Keywords

About this book

Protein Folding Protocols presents protocols for studying and characterizing steps and conformational ensembles populating pathways in protein folding from the unfolded to the folded state. It further presents a sample of approaches toward the prediction of protein structure starting from the amino acid sequence, in the absence of overall homologous sequences. Protein folding is a crucial step in the transfer of genetic information from the DNA to the protein. The Genome Project has led to a huge number of available DNA sequences and, therefore, protein sequences. The Structural Genomics initiative largely aims to obtain “new” folds not currently present in the Protein Data Bank. Yet, the number of available structures inevitably lags behind the number of sequences. At the same time, an equally important problem is to find out the types and scope of dissimilar (nonhomologous) protein sequences that adopt a similar fold. Assembling data and comprehension of the sequence space of protein folds should be very useful in computational protein structure prediction. This would enhance the scope of homology modeling, which currently is the method of choice. Thus, experimental and theoretical studies on the relationship between sequence and structure are critical. Figuring out the relationship between sequence and structure would further assist in the prediction of fibril structures observed in protein misfolding diseases, and in figuring out the conformational changes and dynamics resulting from mutations. Protein folding is one of the most important and challenging problems in current molecular and chemical biology.

Reviews

"...great value to graduate students and researchers who would like to learn about modern techniques to probe protein folding events." -Journal of American Chemical Society

Editors and Affiliations

  • Laboratory of Biochemistry, National Cancer Institute, National Institutes of Health, Bethesda

    Yawen Bai

  • Center for Cancer Research Nanobiology Program SAIC, National Cancer Institute-Frederick, Frederick

    Ruth Nussinov

  • Department of Human Genetics, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel

    Ruth Nussinov

Bibliographic Information

  • Book Title: Protein Folding Protocols

  • Editors: Yawen Bai, Ruth Nussinov

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1385/1597451894

  • Publisher: Humana Totowa, NJ

  • eBook Packages: Springer Protocols

  • Copyright Information: Humana Press 2006

  • Hardcover ISBN: 978-1-58829-622-1Published: 24 July 2006

  • Softcover ISBN: 978-1-61737-676-4Published: 19 November 2010

  • eBook ISBN: 978-1-59745-189-5Published: 04 February 2008

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XIV, 328

  • Number of Illustrations: 111 b/w illustrations

  • Topics: Cell Biology

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