Journal article
Energy Landscapes Associated with the Self-Aggregation of an Alanine-Based Oligopeptide (AAKA)(4)
The journal of physical chemistry. B, v 113(17), pp 6054-6061
30 Apr 2009
PMID: 19385693
Featured in Collection : UN Sustainable Development Goals @ Drexel
Abstract
The alanine-based 16-mer peptide (AAKA)(4) has recently been shown to aggregate into a hydrogel at centimolar concentrations and high ionic strength (Measey, T. J.; Schweitzer-Stenner, R. J. Ani. Chem. Soc. 2006, 128, 13324.). This is a surprising result since the current understanding of peptide self-aggregation would lead one to expect that the positively charged lysine residues inhibit the formation of beta-sheet structures. The present study was aimed at shedding some light on the mechanism governing the initial phase of the self-aggregation process. To this end we measured CD and FTIR spectra of the (AAKA)(n) at millimolar concentration and low ionic strength and found that the peptide forms soluble aggregates rather than a hydrogel under these conditions. To analyze the initial phase of this aggregation process, we carried out simulations on the dimerization and trimerization of (AAKA)(4) Using replica exchange molecular dynamics (MD) methods based on an implicit solvent model. The results indicate that the peptide aggregates into stable antiparallel beta-sheet structures under conditions comparable to experiments. Furthermore, the existence of trimers is a very sensitive function of the peptide concentration and temperature; no significant amount of trimers is formed at low concentration and the trimer population drops sharply as temperature increases above about 320 K. These results on oligomers are consistent with the trend observed in our experiments (reported elsewhere). We have also obtained the free energy landscapes of the trimers as a function of reaction coordinates, which reveal a few basins of minimal free energy. Associated with them, six major types of stable conformers were identified and the structures of transition states between them were also determined. We suggest a possible transition mechanism between these conformers based on the landscape and structural analysis of the aggregates.
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Details
- Title
- Energy Landscapes Associated with the Self-Aggregation of an Alanine-Based Oligopeptide (AAKA)(4)
- Creators
- Soonmin Jang - Sejong UniversityJian-Min Yuan - National Chung Hsing UniversityJungho Shin - Sejong Univ, Dept Chem, Seoul 143747, South KoreaThomas J. Measey - National Chung Hsing UniversityReinhard Schweitzer-Stenner - National Chung Hsing UniversityFeng-Yin Li - National Chung Hsing University
- Publication Details
- The journal of physical chemistry. B, v 113(17), pp 6054-6061
- Publisher
- American Chemical Society; Washington, DC
- Number of pages
- 8
- Grant note
- C00369-102969 / Korea Research Foundation CHEM 0804492 / NSF; National Science Foundation (NSF)
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- Physics; Chemistry
- Web of Science ID
- WOS:000265529900048
- Scopus ID
- 2-s2.0-66349125942
- Other Identifier
- 991019168393304721
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- Collaboration types
- Domestic collaboration
- International collaboration
- Web of Science research areas
- Chemistry, Physical