Methyl dynamics in crystalline amino acids: MD and NMR

• Published in: Journal of computational chemistry 2003-07, Vol.24 (9), p.1052-1058
• Main Authors: Chatfield, David C., Augsten, Alberto, D'Cunha, Cassian, Wong, Sergio E.
• Format: Article
• Language: English
• Subjects: Algorithms; Amino Acids - chemistry; Computer Simulation; correlation time; crystalline amino acids; Crystallography, X-Ray; Leucine - chemistry; MD simulation; MD/NMR; Methane - chemistry; methyl rotation; Nuclear Magnetic Resonance, Biomolecular; Peptides, Cyclic - chemistry; Protein Conformation; Thermodynamics; Valine - chemistry
• ISSN: 0192-8651; 1096-987X
• DOI: 10.1002/jcc.10263

Correlation times for rotation of deuterated methyls in crystalline leucine, valine, and cyclo‐L‐alanyl‐L‐alanine are calculated with molecular dynamics and compared with NMR data. The simulations distinguish between methyls having different steric environments in the crystal, yielding correlation times differing by a factor of up to 30 for methyls within a given crystal. MD and NMR correlation times agree to within a factor of 2. However, averaging over nonequivalent methyls can yield correlation functions that, although actually multiexponential, are well fit by single exponentials. This may have significance for interpreting NMR data; previous NMR data did not distinguish between the methyls in these crystals. Adiabatic rotational barriers calculated with the X‐ray structure differ from effective barriers during simulation by up to ±1 kcal/mol; the difference indicates that dynamical effects have a significant role in determining rotational correlation times. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1052–1058, 2003