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Journal of Chemical Physics / Volume 135 / Issue 20 / ARTICLES / Biological Molecules, Biopolymers, and Biological Systems

J. Chem. Phys. 135, 205101 (2011); http://dx.doi.org/10.1063/1.3662490 (13 pages)

Amyloid-β peptide structure in aqueous solution varies with fragment size

Olivia Wise-Scira1, Liang Xu1, Taizo Kitahara1, George Perry2, and Orkid Coskuner1,2

1The University of Texas at San Antonio, Department of Chemistry, One UTSA Circle, San Antonio, Texas 78249, USA
2The University of Texas at San Antonio, Neurosciences Institute, One UTSA Circle, San Antonio, Texas 78249, USA

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(Received 11 July 2011; accepted 1 November 2011; published online 28 November 2011)

Various fragment sizes of the amyloid-β (Aβ) peptide have been utilized to mimic the properties of the full-length Aβ peptide in solution. Among these smaller fragments, Aβ16 and Aβ28 have been investigated extensively. In this work, we report the structural and thermodynamic properties of the Aβ16, Aβ28, and Aβ42 peptides in an aqueous solution environment. We performed replica exchange molecular dynamics simulations along with thermodynamic calculations for investigating the conformational free energies, secondary and tertiary structures of the Aβ16, Aβ28, and Aβ42 peptides. The results show that the thermodynamic properties vary from each other for these peptides. Furthermore, the secondary structures in the Asp1-Lys16 and Asp1-Lys28 regions of Aβ42 cannot be completely captured by the Aβ16 and Aβ28 fragments. For example, the β-sheet structures in the N-terminal region of Aβ16 and Aβ28 are either not present or the abundance is significantly decreased in Aβ42. The α-helix and β-sheet abundances in Aβ28 and Aβ42 show trends – to some extent – with the potential of mean forces but no such trend could be obtained for Aβ16. Interestingly, Arg5 forms salt bridges with large abundances in all three peptides. The formation of a salt bridge between Asp23-Lys28 is more preferred over the Glu22-Lys28 salt bridge in Aβ28 but this trend is vice versa for Aβ42. This study shows that the Asp1-Lys16 and Asp1-Lys28 regions of the full length Aβ42 peptide cannot be completely mimicked by studying the Aβ16 and Aβ28 peptides.

© 2011 American Institute of Physics

Article Outline

  1. INTRODUCTION
  2. METHODS
  3. RESULTS AND DISCUSSION
    1. Secondary structure properties
    2. Intra-molecular peptide interactions
  4. CONCLUSION

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KEYWORDS and PACS

Keywords

biochemistry, free energy, intramolecular forces, macromolecules, molecular biophysics, molecular configurations, molecular dynamics method, potential energy surfaces, proteins

PACS

ARTICLE DATA

Digital Object Identifier
http://dx.doi.org/10.1063/1.3662490

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.
    N. Mousseau, W. Chen, and P. Derreumaux, J. Chem. Phys. 125(8), 084911 (2006)JCPSA6000125000008084911000001.


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