
Proceedings Paper
Estimation of atomic hydrophobicities using molecular dynamics simulation of peptidesFormat | Member Price | Non-Member Price |
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Paper Abstract
The hydrophobic force is one of the main driving forces in protein folding and binding. However, its nature is not yet
well understood and consequently there are more than 80 different scales published trying to quantify it. Most of the
hydrophobicity scales are amino acid-based, but the interaction between the molecular surface of the proteins (and DNA)
and surfaces they are immobilized on, e.g., on biomedical micro/nanodevices, occurs on fractions of, rather than whole
amino acids. This fragmented structure of the biomolecular surface requires the derivation of atom-level hydrophobicity.
Most attempts for the evaluation of atomic hydrophobicities are derived from amino acid-based values, which ignore
dynamic and steric factors. This contribution reports on the Molecular Dynamics simulations that aim to overcome this
simplification. The calculations examine various tripeptides in an aqueous solution and the analysis focuses on the
distance of the nearest water molecules to the individual atoms in the peptides. Different environments result in a
variation of average distances for similar atoms in different tripeptides. Comparison with the atomic hydrophobicities
derived from the amino acid-based hydrophobicity obtained from peptide partition in water-octanol (Dgoct) and
transport through the membrane interface (Dgwif) shows a similar trend to the calculated distances. The variations are
likely due to the steric differences of similar types of atoms in different geometric contexts. Therefore, Molecular
Dynamics simulations proved convenient for the evaluation of atomic hydrophobicities and open new research avenues.
The atomic hydrophobicities can be used to design surfaces that mimic the biomolecular surfaces and therefore elicit an
expected biomolecular activity from the immobilized biomolecules.
Paper Details
Date Published: 27 December 2007
PDF: 7 pages
Proc. SPIE 6799, BioMEMS and Nanotechnology III, 679916 (27 December 2007); doi: 10.1117/12.759385
Published in SPIE Proceedings Vol. 6799:
BioMEMS and Nanotechnology III
Dan V. Nicolau; Derek Abbott; Kourosh Kalantar-Zadeh; Tiziana Di Matteo; Sergey M. Bezrukov, Editor(s)
PDF: 7 pages
Proc. SPIE 6799, BioMEMS and Nanotechnology III, 679916 (27 December 2007); doi: 10.1117/12.759385
Show Author Affiliations
Marie Held, Liverpool Univ. (United Kingdom)
Dan V. Nicolau, Liverpool Univ. (United Kingdom)
Published in SPIE Proceedings Vol. 6799:
BioMEMS and Nanotechnology III
Dan V. Nicolau; Derek Abbott; Kourosh Kalantar-Zadeh; Tiziana Di Matteo; Sergey M. Bezrukov, Editor(s)
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