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Exploring Peptide-Solvent Interactions: A Computational Study.
- Source :
- Molecules; Sep2018, Vol. 23 Issue 9, p2355, 14p, 2 Diagrams, 2 Charts, 4 Graphs
- Publication Year :
- 2018
-
Abstract
- The dilemma of reconciling the contradictory evidence regarding the conformation of long solvated peptide chains is the so-called "reconciliation problem". Clues regarding the stability of certain conformations likely lie in the electronic structure at the peptide-solvent interface, but the peptide-solvent interaction is not fully understood. Here, we study the influence of aqueous solvent on peptide conformations by using classical molecular dynamics (MD) and quantum mechanical/molecular mechanical (QM/MM) energy calculations. The model systems include an 11-residue peptide, X<subscript>2</subscript>A<subscript>7</subscript>O<subscript>2</subscript> (XAO), where X, A, and O denote diaminobutyric acid, alanine, and ornithine, respectively, and a 9-mer (Arg-Pro-Pro-Gly-Phe-Ser-Ala-Phe-Lys). Spectroscopic and MD data present conflicting evidence regarding the structure of XAO in water; some results indicate that XAO adopts a polyproline II (P<subscript>II</subscript>) conformation, whereas other findings suggest that XAO explores a range of conformations. To investigate this contradiction, we present here the results of MD simulations of XAO and the 9-mer in aqueous solution, combined with QM/MM energy calculations. [ABSTRACT FROM AUTHOR]
- Subjects :
- MOLECULAR dynamics
MOLECULAR physics
QUANTUM amplifier
POLYPROLINE
ORNITHINE
Subjects
Details
- Language :
- English
- ISSN :
- 14203049
- Volume :
- 23
- Issue :
- 9
- Database :
- Complementary Index
- Journal :
- Molecules
- Publication Type :
- Academic Journal
- Accession number :
- 131974717
- Full Text :
- https://doi.org/10.3390/molecules23092355