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Solution study of engineered quartz binding peptides using replica exchange molecular dynamics
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Notman, Rebecca, Oren, E. Emre, Tamerler, Candan, Sarikaya, Mehmet, Samudrala, Ram and Walsh, Tiffany R.. (2010) Solution study of engineered quartz binding peptides using replica exchange molecular dynamics. Biomacromolecules, Vol.11 (No.12). pp. 3266-3274. ISSN 1525-7797
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Official URL: http://dx.doi.org/10.1021/bm100646z
Abstract
We use replica-exchange molecular dynamics (REMD) to interrogate molecular structures and properties of four engineered dodecapeptides (in solution, in the absence of a surface) that have been shown to bind to quartz with different propensities. We find that all of the strong-binding peptides feature some polyproline type II secondary structure, have less conformational freedom, and feature fewer intrapeptide hydrogen bonds compared with the weak binder. The regions of contiguous proline content in a given sequence appear to play a role in fostering some of these properties of the strong binders. For preliminary insights into quartz binding, we perform lattice-matching studies between a grid corresponding with the quartz (100) surface and the strong-binding peptide REMD structures. Our findings indicate a commonality among the putative contact residues, even for peptide structures with very different backbone conformations. Furthermore, interpeptide interactions in solution are studied. Our preliminary findings indicate that the strong-binder interpeptide contacts are dominated by weak, nonspecific hydrophobic interactions, while the weak-binding peptide shows more variable behavior due to the distribution of charged residues. In summary, the solution structures of peptides appear to be significant. We propose that these differences in their intra- and interpeptide interactions can influence their propensity to bind onto a solid substrate.
| Item Type: | Journal Article | ||||
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| Subjects: | Q Science > QA Mathematics > QA76 Electronic computers. Computer science. Computer software Q Science > QD Chemistry Q Science > QP Physiology |
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| Divisions: | Faculty of Science > Chemistry Faculty of Science > Centre for Scientific Computing |
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| Library of Congress Subject Headings (LCSH): | Molecular dynamics, Peptides, Biomolecules, Adsorption, Bioinformatics, Computer simulation | ||||
| Journal or Publication Title: | Biomacromolecules | ||||
| Publisher: | American Chemical Society | ||||
| ISSN: | 1525-7797 | ||||
| Official Date: | December 2010 | ||||
| Dates: |
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| Volume: | Vol.11 | ||||
| Number: | No.12 | ||||
| Number of Pages: | 9 | ||||
| Page Range: | pp. 3266-3274 | ||||
| Identification Number: | 10.1021/bm100646z | ||||
| Status: | Peer Reviewed | ||||
| Publication Status: | Published | ||||
| Access rights to Published version: | Restricted or Subscription Access | ||||
| Funder: | National Science Foundation (U.S.). Materials Research Science and Engineering Centers (Program), Engineering and Physical Sciences Research Council (EPSRC) | ||||
| Grant number: | EP/E02095X/1 (EPSRC) | ||||
| URI: | http://wrap.warwick.ac.uk/id/eprint/4627 |
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