Conformational substates in proteins

Frauenfelder, H., Parak, R, and Young, R. D. 1988. Conformational substates in proteins. Annu. Rev. Biophys. Biophys. Chem. 17 451-79. 

Conformational maps 60 Conformational substates in proteins 496 Conidia 20 Conjugate bases 486 Connective tissue 72, 431 Connexons 29... 

Peleg G, Ghanouni P, Kobilka BK, Zare RN. Single-molecule spectroscopy of the P2 adrenergic receptor observation of conformational substates in a membrane protein. Proc Natl Acad Sci USA2001 98 8469-8474. 

There is direct evidence of conformational substates in a protein, and some of the substates have extremely low energy barriers so that the... 

Figure 8 shows a one-dimensional sketch of a small fraction of that energy landscape (bold line) including one conformational substate (minimum) as well as, to the right, one out of the typically huge number of barriers separating this local minimum from other ones. Keeping this picture in mind the conformational dynamics of a protein can be characterized as jumps between these local minima. At the MD time scale below nanoseconds only very low barriers can be overcome, so that the studied protein remains in or close to its initial conformational substate and no predictions of slower conformational transitions can be made. 

Step 1 A short conventional MD simulation (typically extending over a few lOOps) is performed to generate an ensemble of protein structures x 6 71 (each described by N atomic positions), which characterizes the initial conformational substate. The 2-dimensional sketch in Fig. 9 shows such an ensemble as a cloud of dots, each dot x representing one snapshot of the protein. 

Schamagl C, Raupp-Kossmann R, Fischer SF (1999) Molecular basis for pH sensitivity and proton transfer in green fluorescent protein protonation and conformational substates from electrostatic calculations. Biophys J 77 1839-1857... 

In physical terms the site inhomogeneous component may be conceived of either as slightly different protein binding sites for chromophores or as a distribution of protein conformational substates [127] at any one site. In operational terms the spectral forms are represented by the sub-bands of a gaussian or lorentzian decomposition analysis of absorption or fluorescence spectra. 

Ye, X., lonascu, D., Gruia, R, Yu, A., Benabbas, A., and Champion, P. M. 2007. Temperature-dependent heme kinetics with nonexponential binding and barrier relaxation in the absence of protein conformational substates. Proc. Nat. Acad. Sci. USA 104 14682-87. 

Miscellaneous bRC. - The bRC of R. sphaeroides contains one accessible cysteine at the H subunit (His H-156). Poluektov et al.m have bound a specific nitroxide spin label to this Cys and used temperature-dependent multifrequency (9 and 130 GHz) EPR to determine the motion of the protein. It was found that the restricted dynamics can be described as fast libration in a cone with a correlation time of >10 9 s. Several dynamically nonequivalent sites were observed that indicate conformational substates of local protein structure. 

In summary then, over the past five years, since the last NMR chemical shift meeting in Maryland (57), progress with protein NMR shift (and EFG) calculations has been very exciting. At the time of the last US meeting, our view was that electric fields played a major role in the shielding differences seen due to folding for most nuclei. This now only seems likely for 19F in fluoroaromatic amino-acids and for the CO-heme conformational substates. This is particularly fortunate, however, since chemical shifts are now seen to be primarily probes of < >, / and %, the backbone and... 

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