Changes in protein dynamical parameters derived from quasi-elastic neutron scattering spectra induced by coherent scattering: A molecular dynamics simulation study

Abstract

AbstractProtein dynamics at the sub-nanosecond timescale and the Å length-scale has widely been studied using quasi-elastic neutron scattering (QENS). In almost all QENS studies on hydrogenated proteins in D2O buffers, analysis of the spectra after buffer subtraction is carried out under the assumption that the remaining spectra arise from incoherent scattering of proteins while the contribution of coherent scattering is negligible. On the contrary, a study using polarization analysis has shown that the coherent scattering accounts for more than 10% of the total scattering intensity of hydrogenated proteins (Gaspar et al., Biochim. Biophys. Acta 1804:76–82 (2010)). In addition, the effects of coherent scattering on the values of dynamical parameters of proteins obtained by analysis of QENS spectra remain unclear. Here, molecular dynamics (MD) simulation on hen egg white lysozyme was used to investigate this issue. QENS spectra containing only incoherent scattering and those containing both incoherent and coherent scattering were calculated from the MD trajectory. Dynamical parameters were then extracted from the two simulated QENS spectra. Comparison of the resultant dynamical parameters has shown that the error in the values of the dynamical parameters induced by coherent scattering is at most 6%. This error is unlikely to significantly affect the results of QENS studies that investigate the relative changes in protein dynamics caused by different physicochemical conditions such as temperature unless dynamical parameters need to be determined with high precision at the absolute scale.