Reorientations of aromatic amino acids and their side chain models: anisotropy measurements and molecular dynamics simulations.
We present a study of reorientation dynamics of the three aromatic amino acids and their side chain models in aqueous solution. Experimentally, anisotropy decay measurements with picosecond time resolution were performed for blocked tryptophan, tyrosine, and phenyalanine and model compounds p-cresol and 3-methylindole. Computationally, rotational diffusion was modeled by molecular dynamics simulations for the three aromatic residues and their side chain models: benzene, toluene, phenol, p-cresol, indole, and 3-methylindole in explicit water. Our simulations used the CHARMM protein force field and associated TIP3P water model and tend to underestimate the rotational correlation times. However, the simulations yield several interesting qualitative insights into reorientational motions that complement the experimental measurements. The effects of substituent and temperature on reorientations of the parent compounds are well reproduced computationally. Additionally, simulations indicate strongly anisotropic reorientations for most of the studied compounds and a separation of time scales between conformational dynamics and rotational diffusion. Comparison with continuum hydrodynamic models suggests that we may consider that the blocked amino acids move under stick boundary conditions, while the dynamics for most of the model compounds falls between stick and slip conditions. Our systematic treatment of blocked amino acids, starting from the parent compounds (benzene, phenol, and indole) provides a baseline for understanding the anisotropy decay signals of more complicated peptide systems.
Kuczera
Krzysztof
K
Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, USA.
Unruh
Jay
J
Johnson
Carey K
CK
Jas
Gouri S
GS
D024322:Amino Acids, Aromatic / Q000737:chemistry*; D016880:Anisotropy; D008956:Models, Chemical; D056004:Molecular Dynamics Simulation; D013696:Temperature
D024322:Amino Acids, Aromatic