2010/06/07 by Yunfen He, Jing-Yin Chen, J.-Y. Chen +5 · 64 citations
Biochemistry, Genetics and Molecular Biology · Neuroscience · Physics and Astronomy · #Biology #Biophysics #Chemical physics #Optics #Photoreceptor and optogenetics research #Physics #Picosecond #Protein Structure and Dynamics #Spectroscopy and Quantum Chemical Studies #Statistical physics #physics.chem-ph #q-bio.BM
paper · pdf · doi:10.1016/j.bpj.2010.12.3731
published in Biophysical Journal 100(4), 1058-1065 (Elsevier BV)
arxiv created 2010/06/07 · openalex publication_date 2011/02/01 · arxiv updated 2015/05/19 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/06
We investigate the presence of structural collective motions on a picosecond time scale for the heme protein, cytochrome c, as a function of oxidation and hydration, using terahertz (THz) time-domain spectroscopy and molecular dynamics simulations. The THz response dramatically increases with oxidation, with the largest increase for lowest hydrations and highest frequencies. For both oxidation states the THz response rapidly increases with hydration saturating above ~25% (g H2O/g protein). Quasi-harmonic vibrational modes and dipole-dipole correlation functions are calculated from molecular dynamics trajectories. The collective mode density of states alone reproduces the measured hydration dependence providing strong evidence of the existence of these motions. The large oxidation dependence is reproduced only by the dipole-dipole correlation function, indicating the contrast arises from diffusive motions consistent with structural changes occurring in the vicinity of a buried internal water molecule.