Residue length and solvation model dependency of elastinlike polypeptides.
We have performed exhaustive multicanonical Monte Carlo simulations of elastinlike polypeptides with a chain including amino acids (valine-proline-glycine-valine-glycine)n or in short (VPGVG)n, where n changes from 1 to 4, in order to investigate the thermodynamic and structural properties. To predict the characteristic secondary structure motifs of the molecules, Ramachandran plots were prepared and analyzed as well. In these studies, we utilized a realistic model where the interactions between all types of atoms were taken into account. Effects of solvation were also simulated by using an implicit-solvent model with two commonly used solvation parameter sets and compared with the vacuum case.
Bilsel
Mustafa
M
Department of Physics Engineering, Ankara University, Tandoğan, Ankara 06100, Turkey. mfbilsel@gmail.com
Arkin
Handan
H
D000596:Amino Acids / Q000737:chemistry; D000818:Animals; D001703:Biophysics / Q000379:methods*; D004549:Elastin / Q000737:chemistry*; D005998:Glycine / Q000737:chemistry; D006801:Humans; D009010:Monte Carlo Method; D010455:Peptides / Q000737:chemistry*; D011392:Proline / Q000737:chemistry; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry; D012997:Solvents / Q000737:chemistry; D013816:Thermodynamics; D014633:Valine / Q000737:chemistry
D000596:Amino Acids; D010455:Peptides; D011506:Proteins; D012997:Solvents; D004549:Elastin; D011392:Proline; D014633:Valine; D005998:Glycine