Molecular dynamics simulations for a series of cis- and trans- N-acethyl-N'-methylamide of Xaa-Pro = 트랜스와 시스의 N-아세틸-N'-메틸아미이드 Xaa-Pro에 대한 분자동역학 시뮬레이션

It has been commonly accepted that the occurrence of cis amide bonds in proteins is quite rare due to the unfavorable contacts between adjacent amino acid residues in cis isomeric form, but the occurrence of cis imide bonds in proteins is relatively high because the trans isomeric form is unstable by steric clash between $\delta$-carbon of proline and $\beta$-carbon of the residue preceding proline. To examine the relationship between this occurrence of cis imide bonds and the residue preceding proline, we perform molecular dynamics simulations for a series of trans-and cis-N-acethyl-N``-methylamides of Xaa-Pro dipeptides. We investigate the conformational energies and structures of trans-and cis-blocked dipeptides for each amino acid, in both vacuum and solutions state. It is found that the occurrence of cis imide bonds is strongly affected by the residue preceding proline and the dihedral angles ($\varphi$, $\Psi$) of backbone in Ac-Xaa-Pro-NHMe are influenced by the configuration of imide bond. We also findthat the equilibrium properties of Xaa-Pro in solution state are more similar to X-ray crystallographic data analysis than those in vacuum.
Advisors
Jhon, Mu-Shikresearcher전무식researcher
Publisher
한국과학기술원
Issue Date
1993
Identifier
68379/325007 / 000911593
Language
eng
Description

학위논문(석사) - 한국과학기술원 : 화학과, 1993.2, [ v, 33 p. ]

URI
http://hdl.handle.net/10203/32649
Link
http://library.kaist.ac.kr/search/detail/view.do?bibCtrlNo=68379&flag=t
Appears in Collection
CH-Theses_Master(석사논문)
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