Conformational changes of the protein

Fi re 12.6 Schematic diagram Illustrating the proton movements in the photocycle of bacteriorhodopsin. The protein adopts two main conformational states, tense (T) and relaxed (R). The T state binds trans-tetinal tightly and the R state binds c/s-retinal. (a) Stmcture of bacteriorhodopsin in the T state with hflus-retinal bound to Lys 216 via a Schiff base, (b) A proton is transferred from the Schiff base to Asp 85 following isomerization of retinal and a conformational change of the protein. 

Fig. 2.5.5 A study examining the conformational changes of the protein ubiquitin, showing the population ratio of the A-state to the native-state as a function of time, (a) The reaction from 0 to 120 s. (b) The reaction for the first 40 s, including curves fit to a single exponential. Reprinted with permission from Ref. [37]. Copyright (2003) American Chemical Society.

The CP MAS NMR spectroscopy has been also extensively used for studies of proteins containing retinylidene chromophore like proteorhodopsin or bacteriorhodopsin. Bacteriorhodopsin is a protein component of purple membrane of Halobacterium salinarium.71 7 This protein contains 248 amino acids residues, forming a 7-helix bundle and a retinal chromophore covalently bound to Lys-216 via a Schiff base linkage. It is a light-driven proton pump that translocates protons from the inside to the outside of the cell. After photoisomerization of retinal, the reaction cycle is described by several intermediate states (J, K, L, M, N, O). Between L and M intermediate states, a proton transfer takes place from the protonated Schiff base to the anionic Asp85 at the central part of the protein. In the M and/or N intermediate states, the global conformational changes of the protein backbone take place. 

Heimburg, T, HUdebrandt, P., and Marsh, D., 1991, Cytochrome c-hpid interactions studied by resonance Raman and P NMR spectroscopy. Correlation between the conformational changes of the protein and the lipid bUayer Biochemistry 30 9084-9089. 

Prediction of the conformational change of the protein under binding is a challenge. New structural parameters based on high resolution X-Ray structures have been presented recently (69). Such studies open the door to a more extended analysis of conformational changes of protein cavity when binding with different ligands. 

The situation in the calcium-binding protein aequorin is that there is a store of energy built into a special organic molecule and into the fold of the protein. On binding calcium the protein emits lights at around 500 nm and there is a conformational change of the protein. It is not easy to write... 

Z- E configurational change of the chromophore and the subsequent conformational changes of the protein [63]. However, in view of the considerable uncertainties about the size of the orientation angles and about the conformations of the Pr and Pfr chromophores, definitive conclusions on this point would be premature at the present. 

Evidence indicates that microwaves affect the kinetics of conformation changes of proteins such as P-lactoglobulin (Bohr and Bohr, 2000). It is thought that even approximately a few GHz can excite protein molecules. Consequently, the kinetics of conformational changes of the protein molecule are enhanced, and this denaturing effect is... 

Raman difference spectroscopy has also been used to understand the molecular mechanism of viral core assemblies yielding information on viral subunits from precursor and mature states. Benevides et al. employed Raman difference spectroscopy to investigate conformational changes of the protein building blocks of the icosahedral core of a double-stranded RNA (p6 virus during viral procapsid and capsid assembly [18],... 

The crystal structure of S100A7 revealed that this protein, in contrast to other S100 proteins, probably binds only one calcium ion per monomer and this binding does not induce large conformational changes of the protein (Boeshans et al 2006 Brodersen et al 1998). 

To follow the dynamics of protein folding, the conformational changes of the protein must be measured as a function of time. Moreover, it would be advantageous to be able, simultaneously and independently, to detect the different conformers rather than to obtain a measured value that reflects the average state of all the conformers in solution. ESI-MS is suitable for this kind of a study. 

The effect of diethylamine (DEA) on the conductance of a single Na channel is depicted in Figure 5.5a. In the control trace, the channel can be seen to oscillate between two states of conductance, with currents of 0 and 1 pA, respectively. A conductance of 0 would be expected for the closed and the inactivated states, respectively, whereas the conductance of 1 pA would represent the open state. This illustrates a very neat feature of the single channel recording techniques - they let us observe the discrete and stochastic nature of conformational changes of the proteins in a much more direct fashion than typically possible with other allosteric proteins (e.g., enzymes or hormone receptors). In the presence of DEA, open and closed state still alternate, but the conductance of the open state is reduced by about 40%, indicating a partial blockade of the channel. 

---