Nanomedicine: Nanotechnology, Biology and Medicine
Volume 1, Issue 1 , Pages 41-46, March 2005

Clustering and diversity of fluctuations for proteins

  • Melik C. Demirel, PhD

      Affiliations

    • College of Engineering, Pennsylvania State University, University Park, Pennsylvania
    • Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
    • Corresponding Author InformationCorresponding author. 212 EES Bldg., School of Engineering, Pennsylvania State University, University Park, PA 16802.
    • ,
  • Dmitry Cherny, PhD

      Affiliations

    • Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany

Received 16 October 2004; accepted 25 November 2004.

Abstract 

Background

Protein topology plays a key role in various types of interactions. Topological constraints of a protein are defined by a contact map. We studied the fluctuations of proteins with use of a new approach based on contact map.

Methods

An annealing algorithm is used to generate a 3-dimensional protein structure from the contact map. First, we study the properties of structural elements based on fluctuations by adding individual structures (domains or subdomains). Thereafter, we focus on the building block of proteins in terms of fluctuations.

Results

To verify our hypothesis, we analyzed the pattern of fluctuations for chymotrypsin inhibitor-2 (CI2) by unstructuring (melting) of subregions. The data show different patterns of fluctuations for the unstructured CI2 relative to that calculated for the intact protein.

Conclusion

Our approach introduces a new concept for classifying building blocks of proteins based on thermal fluctuations.

Key words: Protein fluctuations, Elastic network model, Simulated annealing

To access this article, please choose from the options below

Login to an existing account or Register a new account.

  • Purchase this article for 10.00 USD (You must login/register to purchase this article)

    Online access for 24 hours. The PDF version can be downloaded as your permanent record.

  • Subscribe to this title

    Get unlimited online access to this article and all other articles in this title 24/7 for one year.

  • Claim access now

    For current subscribers with Society Membership or Account Number.

  • Visit SciVerse ScienceDirect to see if you have access via your institution.
 

PII: S1549-9634(05)00008-0

doi:10.1016/j.nano.2004.11.007

Nanomedicine: Nanotechnology, Biology and Medicine
Volume 1, Issue 1 , Pages 41-46, March 2005

Article Tools

* Image Usage & Resolution