Coupled Flexibility Change in Cytochrome P450cam Substrate Binding Determined by Neutron Scattering, NMR, and Molecular Dynamics Simulation

• Published in: Biophysical journal Vol. 103; no. 10; pp. 2167 - 2176
• Main Authors: Miao, Yinglong, Yi, Zheng, Cantrell, Carey, Glass, Dennis C., Baudry, Jerome, Jain, Nitin, Smith, Jeremy C.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 21.11.2012; Biophysical Society; The Biophysical Society
• Subjects: Binding; binding proteins; Binding sites; camphor; Camphor 5-Monooxygenase - chemistry; Crystallography, X-Ray; Cytochromes; Flexibility; Hydrogen Bonding; Hydrogen bonds; Hydrophobic and Hydrophilic Interactions; hydrophobic bonding; Magnetic Resonance Spectroscopy; Molecular dynamics; Molecular Dynamics Simulation; Molecules; Neutron Diffraction; Neutron scattering; Nuclear magnetic resonance; nuclear magnetic resonance spectroscopy; Proteins; Proteins and Nucleic Acids; Pseudomonas putida - enzymology; Scattering; Simulation; Substrate Specificity
• ISSN: 0006-3495; 1542-0086
• DOI: 10.1016/j.bpj.2012.10.013

Neutron scattering and nuclear magnetic resonance relaxation experiments are combined with molecular dynamics (MD) simulations in a novel, to our knowledge, approach to investigate the change in internal dynamics on substrate (camphor) binding to a protein (cytochrome P450cam). The MD simulations agree well with both the neutron scattering, which furnishes information on global flexibility, and the nuclear magnetic resonance data, which provides residue-specific order parameters. Decreased fluctuations are seen in the camphor-bound form using all three techniques, dominated by changes in specific regions of the protein. The combined experimental and simulation results permit a detailed description of the dynamical change, which involves modifications in the coupling between the dominant regions and concomitant substrate access channel closing, via specific salt-bridge, hydrogen-bonding, and hydrophobic interactions. The work demonstrates how the combination of complementary experimental spectroscopies with MD simulation can provide an in-depth description of functional dynamical protein changes.