Characterization of the conformational domains of bradykinin by computational methods

✍ Scribed by Juan J. Perez; Yolanda M. Sanchez; Nuria B. Centeno

• Publisher: John Wiley and Sons
• Year: 1995
• Tongue: English
• Weight: 665 KB
• Volume: 1
• Category: Article
• ISSN: 1075-2617
• DOI: 10.1002/psc.310010403

✦ Synopsis

Abstract

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.