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Journal of Chemical Physics / Volume 135 / Issue 23 / ARTICLES / Biological Molecules, Biopolymers, and Biological Systems

J. Chem. Phys. 135, 235103 (2011); http://dx.doi.org/10.1063/1.3665930 (10 pages)

Denaturation of proteins near polar surfaces

Anna Starzyk and Marek Cieplak

Institute of Physics, Polish Academy of Sciences, Aleja Lotników 32/46, 02-668 Warsaw, Poland

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(Received 24 May 2011; accepted 14 November 2011; published online 20 December 2011)

All-atom molecular dynamics simulations for proteins placed near a model mica surface indicate existence of two types of evolution. One type leads to the surface-induced unfolding and the other just to a deformation. The two behaviors are characterized by distinct properties of the radius of gyration and of a novel distortion parameter that distinguishes between elongated, globular, and planar shapes. They also differ in the nature of their single site diffusion and two-site distance fluctuations. The four proteins chosen for the studies, the tryptophan cage, protein G, hydrophobin and lyzozyme, are small to allow for a fair determination of the forces generated by the surface as the effects of finite cutoffs in the Coulombic interactions are thus minimized. When the net charge on the surface is set to zero artificially, infliction of deformation is seen to persists but no unfolding takes place. Unfolding may also be prevented by a cluster of disulfide bonds, as we observe in simulations of hydrophobin.

© 2011 American Institute of Physics

Article Outline

  1. INTRODUCTION
  2. METHODS
  3. TRYPTOPHANE CAGE IN THE VICINITY OF MICA
  4. PROTEIN G IN THE VICINITY OF MICA
  5. TRYPTOPHANE CAGE NEAR A NON-POLAR SURFACE
  6. SURFACE AFFECTED CONFORMATIONS OF THE HEN EGG-WHITE LYZOZYME AND HYDROPHOBIN HFBII PROTEINS
  7. FINAL COMMENTS

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KEYWORDS and PACS

Keywords

biochemistry, biodiffusion, biomechanics, bonds (chemical), deformation, distortion, enzymes, fluctuations, molecular biophysics, molecular configurations, molecular dynamics method

PACS

ARTICLE DATA

Digital Object Identifier
http://dx.doi.org/10.1063/1.3665930

PUBLICATION DATA

ISSN

0021-9606 (print)  
1089-7690 (online)

Publisher

$abstract.society.value is a Member of CrossRef American Institute of Physics

For access to fully linked references, you need to log in.
    M. Cieplak and S. Niewieczerzal, J. Chem. Phys. 130, 124906, (2009)JCPSA6000130000012124906000001.


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