Journal
BIOPHYSICAL JOURNAL
Volume 103, Issue 10, Pages 2167-2176Publisher
CELL PRESS
DOI: 10.1016/j.bpj.2012.10.013
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Funding
- National Science Foundation [MCB-0842871, TG-MCA08X032]
- National Energy Research Scientific Computing Center [M906]
- Austrian Science Fund (FWF) [M906] Funding Source: Austrian Science Fund (FWF)
- Direct For Biological Sciences
- Div Of Molecular and Cellular Bioscience [0842871] Funding Source: National Science Foundation
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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.
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