Journal
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
Volume 113, Issue 38, Pages 10565-10570Publisher
NATL ACAD SCIENCES
DOI: 10.1073/pnas.1603539113
Keywords
time-resolved SAXS/WAXS; free-electron laser; molecular dynamics
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Funding
- Deutsche Forschungsgemeinschaft [HU 1971-1/1]
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Protein quake denotes the dissipation of excess energy across a protein, in response to a local perturbation such as the breaking of a chemical bond or the absorption of a photon. Femtosecond time-resolved small-and wide-angle X-ray scattering (TR-SWAXS) is capable of tracking such ultrafast protein dynamics. However, because the structural interpretation of the experiments is complicated, a molecular picture of protein quakes has remained elusive. In addition, new questions arose from recent TR-SWAXS data that were interpreted as underdamped oscillations of an entire protein, thus challenging the long-standing concept of overdamped global protein dynamics. Based on molecular-dynamics simulations, we present a detailed molecular movie of the protein quake after carbon monoxide (CO) photodissociation in myoglobin. The simulations suggest that the protein quake is characterized by a single pressure peak that propagates anisotropically within 500 fs across the protein and further into the solvent. By computing TR-SWAXS patterns from the simulations, we could interpret features in the reciprocal-space SWAXS signals as specific real-space dynamics, such as CO displacement and pressure wave propagation. Remarkably, we found that the small-angle data primarily detect modulations of the solvent density but not oscillations of the bare protein, thereby reconciling recent TR-SWAXS experiments with the notion of overdamped global protein dynamics.
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