Protein conformational dynamics

The first experimental evidences that electron transfer from QA to P+ and from QA to Qb in reaction centers are controlled by the protein conformational dynamics, was obtained in the late 1970 s (Berg 1978a,b Likhtenshtein et al., 1979 a, b) This conclusion was confirmed in subsequent experimental studies in which molecular dynamics of RC and the photsynthetic membrane were determined with a whole set of physical labels. (Kotelnikov et al., 1983, Kochetkov et al., 1984 Parak et al., 1983). It was shown that the electron transfer from reduced primary acceptor QA to secondary acceptor Qb takes place only under conditions in which the labels record the mobility of the protein moiety in the membrane with the correlation frequency u0 > 107 s-1 (Fig. 3.16). 

The latter point to a conformational transition of the protein at Tin. The time-resolved fluorescence studies indicated that the intrinsic Trp fluorescence emission of the protein was represented by a bimodal distribution with Lorential shape and was strongly affected by the protein conformational dynamics (Bismuto et al., 1999 D Auria et al.,1999). Parameters of the temperature dependence of the bimodal lifetime distribution, such as fraction relative intensity, the position of centres, and the distribution line widths,... 

Single-Molecule Protein Conformational Dynamics in Enzymatic Reactions... 

Apart from the unusual temperature dependence of the Fe Mossbauer quadrupole splitting, which can be rationalized on the basis of heme/protein conformational dynamics, the diamagnetism of oxyMb/Hb originally reported by Pauling and Coryell in 1936 has held up to scrutiny remarkably well. The reported O—O distances of bound O2 in oxyHb and oxyMb range from... 

Best RB, Chen YG, Hummer G. 2005. Slow protein conformational dynamics from multiple experimental structures The hehx/sheet transition of arc repressor. Structure 13 1755. 

Figure 1.1 Location of protein backbone amide hydrogens in Factor Vila (PDB I DAN [I]). HX of the protein backbone amides (gray circles) occur spontaneously in a solution containing DJD. The rates of exchange are highly dependent on hydrogen bonding and to a lesser extent solvent accessibility and thus report on protein conformation, dynamics, and intermolecular interactions. Adapted from Ref [2], (See insert for color representation of the figure.)...

Currently available HX-MS software provides users with various options to visualize HX results (reviewed in Section 3.3.5). Some common options include deuterium uptake kinetic curves, heat maps [56], and butterfly plots [59]. The latter two present information such as the protein conformational dynamics and the differential deuterium uptake comparisons of full-length proteins in a single graph, making data interpretation more efficient. Anotha- informative way to interpret the HX results is to map the changes of deuterium uptake onto a known X-ray stracture of the antigen [41]. 

HX-MS for proteins in lyophilized powders has developed over the past 5 years. Recent studies suggest that the method can provide detailed information on protein conformation, dynamics, and interactions with excipients in lyophilized solids and that HX with mass spectral peak width analysis can be used to screen protein formulations for the presence of nonnative subpopulations. Though the utility of the method for developing lyophilized protein formulations has not been fully tested, early results promote the wider development and application of the method. 

R. B. Gregory and A. Rosenberg, Methods Enzymol, 131, 448 (1986). Protein Conformational Dynamics Measured by Hydrogen Isotope Exchange Techniques. 

Min W, Xie XS, Bagchi B (2008) Two-dimensional reaction free eneigy surfaces of catalytic reaction effects of protein conformational dynamics on enzyme catalysis. J Phys Chem B 112(2) 454 66... 

Following these methodological improvements, HDX and ESI-MS have been used in numerous studies for analysis of protein-protein, protein-ligand," and protein-membrane interactions." HDX and ESI-MS have also been used for the smdy of protein conformational dynamics. In a study performed in the Gross group, four different conformations of insulin were detected using HDX and ESI-MS. "... 

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