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Peptide models. XIV. Ab initio study on the role of side‐chain backbone interaction stabilizing the building unit of right‐ and left‐handed helices in peptides and proteins
Author(s) -
Perczel András,
Farkas Ödön,
Marcoccia John F.,
Csizmadia Imre G.
Publication year - 1997
Publication title -
international journal of quantum chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.484
H-Index - 105
eISSN - 1097-461X
pISSN - 0020-7608
DOI - 10.1002/(sici)1097-461x(1997)61:5<797::aid-qua6>3.0.co;2-r
Subject(s) - chemistry , ramachandran plot , ab initio , side chain , crystallography , energy minimization , helix (gastropod) , monomer , chain (unit) , stereochemistry , computational chemistry , protein structure , physics , ecology , biochemistry , organic chemistry , astronomy , snail , biology , polymer
Previous ab initio computations revealed that the conformational building unit of the right‐handed helix (ϕ ≈ −54°, ψ ≈ −45°) is not an energy minimum on two‐dimensional‐type Ramachandran potential energy surfaces ( E = E {ϕ, ψ}). Theoretical investigations were performed on several single‐amino‐acid diamides such as For‐Gly‐NH 2 , For‐L‐Ala‐NH 2 , Ac‐L‐Ala‐NHMe, and For‐L‐Val‐NH 2 containing amino acid residues (e.g., Ala) which can often be found in helices as shown by X‐ray data analysis of globular proteins. The current ab initio [self‐consistent field (SCF)] results (based on four different basis sets [3‐21G, 4‐21G, 4‐21G * , and 6‐31G * ]) presented point toward an intrinsic (i.e., non‐environmental‐assisted) stability of the right‐handed helical subconformation of a simple amino acid diamide if the residue contains a polar side chain. Such is the case for a serine derivative when its (SINGLE BOND)CH 2 OH side chain is favorably oriented. For the For‐L‐Ser‐NH 2 model compound two slightly different right‐handed helical backbone conformations were determined. Depending on the relative orientation of the side chain, the conformational monomer of the 3 10 helix (a sharper helical structure with an [ i, i + 3]‐type H‐bond network) as well as the building block of the “standard” α‐helix (the regular helical structure with an [ i, i + 4]‐type H‐bond network) were determined computationally by geometry optimization. © 1997 John Wiley & Sons, Inc.