Proteins conformational substates

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. 

Abstract An energy decomposition scheme is presented to elucidate the importance of the change of protein conformation substates to the reduction of activation barrier in an enzyme-catalyzed reaction. The analysis is illustrated by the reaction of orotidine 5 -monophosphate decarboxylase (ODCase), in which the catalyzed reaction is at least 10 faster than the spontaneous reaction. Analysis reveals that the enzyme conformation is more distorted in the reactant state than in the transition state. The energy released from conformational relaxation of the protein is the main source of the rate enhancement. The proposed mechanism is consistent with results from site-directed mutagenesis where mutations remote from the reaction center affect kcat but not Kyi. 

Nadler and Schulten, 1984] Nadler, W., and Schulten, K. Theory of Mossbauer spectra of proteins fluctuating between conformational substates. Proc. Natl. Acad. Sci. USA. 81 (1984) 5719-5723... 

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. 

H. Grubmueller and P. Tavan. Molecular dynamics of conformational substates for a simplified protein model. J. Chem. Phys. 101 (1994)... 

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... 

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

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. 

One example of this possible existence of a hierarchy of receptor states has been discussed by Frauenfelder (1988). He reviewed studies on the binding of substrates and ligands to myoglobin. The process follows a power law, characterizing the protein as a complex system. Nuclear magnetic resonance (NMR) analyses revealed a number of conformational substates. 

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

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... 

It must be noted that the molecular dynamics simulations of acetylcholinesterase mentioned above are far too short to sample transitions over barriers that separate many conformational substates of the protein. But, for acetylcholinesterase similar behavior is observed for the two subunits of the... 

Parak and collaborators (Hartmann et al., 1987 Parak et al., 1987) carried out X-ray structure analyses for metmyoglobin at temperatures of 80—300 K. One hundred sixty water molecules, more than one-third of the water in the crystals, were included in the refinement. The disorder is higher for water that for protein atoms (Fig. 31). Reduction in temperature partially freezes out the disorder for the water, as for the protein. The residual disorder at low temperature has been understood to represent conformational substates or a distribution of conformations, frozen in at low temperature and in mobile equilibrium at high temperature. 

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