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Characterization of the conformational domains of bradykinin by computational methods
Author(s) -
Perez Juan J.,
Sanchez Yolanda M.,
Centeno Nuria B.
Publication year - 1995
Publication title -
journal of peptide science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.475
H-Index - 66
eISSN - 1099-1387
pISSN - 1075-2617
DOI - 10.1002/psc.310010403
Subject(s) - dihedral angle , molecular dynamics , force field (fiction) , maxima and minima , chemistry , root mean square , crystallography , peptide , characterization (materials science) , stereochemistry , computational chemistry , molecule , materials science , physics , mathematics , biochemistry , nanotechnology , organic chemistry , hydrogen bond , mathematical analysis , quantum mechanics
The AMBER 4.0 force field was used to perform a characterization of the conformational profile of the nonapeptide bradykinin. A thorough conformational search was carried out using molecular dynamics as sampling technique, by computing cycles of high (900 K) and low (300 K) temperature trajectories. A total of 2400 minima were generated and subsequently clustered using the root‐mean‐square of the backbone dihedral angles as criterium. After the use of a tolerance value of 20deg;, the conformations were clustered in 233 unique conformations with energies up to 40 kcal/mol above the lowest minimum. The analysis of the low‐energy conformations indicate that the peptide exhibits a high tendency to adopt a β‐turn at the C‐terminus and a propensity to adopt a bent structure at the N‐terminus. These results are in agreement with the experimental evidence reported in the literature and provide detailed information necessary to understand the conformational preferences of the peptide.