In numerous biological processes, the ensuing protein structural changes accompanying a reaction at a specific site must spatially extend to the mesoscopic dimensions of the protein to achieve a biological function. The molecular mechanism of cooperativity in oxygen binding of hemoglobin is one of the classical problems in this aspect. This review describes our recent works on protein dynamics of myoglobin and hemoglobin by using time-resolved resonance Raman spectroscopy.
A precision microwave dielectric spectroscopic technique has been developed. This technique enables us to analyze hydration properties of ions, proteins, and other biomolecules. φ-scan method gives an image of the information of spatial distribution of dielectric property of water surrounding protein molecules. Fixed φ analysis gives a direct comparison of hydration properties of different proteins. With this technique we analyzed the state change of F-actin hydration upon binding with myosin, and found that hyper-mobile water (HMW) is induced around F-actin and increased upon binding with myosin S1. Thus, we may obtain further information of collective properties of water surrounding proteins and biomolecules.
Various dynamics observed for proteins and water structures are explained from experimental results obtained from broadband dielectric spectroscopy (BDS) and complementary techniques. Dielectric measuring techniques make it possible to observe molecular dynamics in whole span of the time/frequency range: 200 ks-0.2 ps/1 μHz-1 THz, and are still developed to offer more precise and stable measuring systems. A recent approach with universal treatments of aqueous complex systems is also explained. Topics shown here are based on a recent concept of dynamic behaviors of complex systems.
AcrB is a major multidrug efflux transporter in Escherichia coli cooperating with an outer membrane channel TolC and a membrane fusion protein AcrA. Here, I describe crystal structures of AcrB with and without substrates. The AcrB-drug complex consists of three protomers, each of which has different conformation corresponding to one of the three functional states of the transport cycle. Bound substrate was found in the periplasmic domain of one of the three protomers. The voluminous binding pocket is aromatic and allows multi-site binding. The structures show that drugs are presumably exported by a three-step functionally rotating mechanism in which drugs undergo ordered binding change.
Major facilitator superfamily (MFS) is the largest family of secondary transporters. MFS includes uniporter, antiporter and symporter. The structure of oxalate transporter reported by electron crystallography showed a “closed” conformation and it revealed remarkably symmetric architecture with twelve helices surrounding a central cavity. Some of the structures reported by X-ray crystallography showed “open” conformation. Comparing these structures, a transport mechanism based on the simple domain movement has been proposed.