Yamashita S, Mizuno M, Takemura K, Kitao A, Mizutani Y. Dependence of Vibrational Energy Transfer on Distance in a Four-Helix Bundle Protein: Equidistant Increments with the Periodicity of α Helices.
J Phys Chem B 2022;
126:3283-3290. [PMID:
35467860 DOI:
10.1021/acs.jpcb.2c00956]
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Abstract
Vibrational energy exchanges between various degrees of freedom are critical to barrier-crossing processes in proteins. Heme proteins are highly suitable for studies of the vibrational energy exchanges in proteins. The migration of excess energy released by heme in a protein moiety can be observed using time-resolved anti-Stokes ultraviolet resonance Raman spectroscopy. The anti-Stokes resonance Raman intensity of a tryptophan residue is an excellent probe for the excess energy and the spatial resolution of a single amino acid residue can be achieved. Here, we studied dependence of vibrational energy transfer on the distance in cytochrome b562, which is a heme-containing, four-helix bundle protein. The vibrational energy transfer from the heme group to a single tryptophan residue introduced by site-directed mutagenesis was examined for different heme-tryptophan distances by a quasi-constant length with the periodicity of α helices. Taken together with structural data obtained by molecular dynamics simulations, the energy transfer could be well described by the model of classical thermal diffusion, which suggests that continuum media provide a good approximation of the protein interior, of which the atomic packing density is very high.
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