Validation of nitroxyl spin-label force-field parameters through molecular dynamics simulations

✍ Scribed by Christopher J. Van Zele; Mark A. Cunningham; Marvin W. Makinen

• Publisher: John Wiley and Sons
• Year: 2001
• Tongue: English
• Weight: 186 KB
• Volume: 22
• Category: Article
• ISSN: 0192-8651
• DOI: 10.1002/jcc.1071

✦ Synopsis

Abstract

A molecular mechanics parameter set for the nitroxyl spin‐label 3‐formyl‐2,2,5,5‐tetramethyl‐1‐oxypyrroline was developed by application of Gaussian94 at the HF/6‐31G(d) level suitable for use in molecular dynamics simulations. The parameter set was validated through molecular dynamics calculations for the methyl ester of N‐(2,2,5,5‐tetramethyl‐1‐oxypyrrolinyl‐3‐carboxyl)‐L‐tryptophan to simulate its conformation and structure in methanol and in chloroform at 300 K with use of the program package CHARMM. Excellent agreement of structural parameters derived by molecular dynamics simulations of the solute in both solvent systems was observed with the structure and conformation of the solute defined through electron nuclear double resonance studies [Wells, G. B. et al., J Am Chem Soc 1990, 112, 2566]. Although rotation about the C(2)C(15) bond connecting the oxypyrrolinyl ring system to the carbonyl group in the pseudopeptide linkage of the tryptophanyl moiety was governed by a potential energy function having two symmetrically placed minima separated by ±42° and a barrier height equivalent to only 2.5 kJ/mol, the spin label exhibited preferred occupancy of the −42° conformer, in direct agreement with spectroscopic studies. The excellent agreement observed between molecular dynamics and spectroscopically derived results provides a firm base for further applications of the force‐field parameter set of this spin label for investigation of macromolecular structure and conformational flexibility through electron magnetic resonance methods. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1113–1123, 2001