Hydrogen exchange kinetics

C. K. Woodward and B. D. Hilton, Hydrogen exchange kinetics and internal motions in proteins, Annu. Rev. Biophys. Bioeng. 8, 99-128 (1979). 

O. Kircher, M. Fichtner, Hydrogen exchange kinetics in NaAlH catalyzed in different decomposition states , J. Appl. Phys. 95 (2004) 7748-7753. 

Rosenberg, A. and Somogyi, B. (1986) Conformational fluctuations, thermal stability and hydration of proteins, studies by hydrogen exchange kinetics. n Dynamic of Biochemical systems, edited by S. Damjanovich, T.Keleti and L.Tron, pp. 101-112. Amsterdam Elsevier. 

The nmr data for this type of motion are direct and the motion clearly involves rotation about bonds in the millisecond time scale range. However. less direct evidence for motion comes from other techniques such as fluorescence depolarization, 02 diffusion, hydrogen exchange kinetics, and nmr relaxation times (see Ref. 4). The extent of this motion is not yet easy to define, but this evidence points to motion in the nanosecond time scale range. It is tempting to see the motion in this time scale as bond oscillations rather than rotations. To put it in a different way, on this time scale the side chains have some freedom to move with respect to each other but not normally to undergo substantial bond rotation. Table IV summarizes some references for motion of different types. Additionally, nmr relaxation studies suggest that the backbone or main chain of a protein is more restricted than that of the side chains. 

Comparison of the data on hydrogen exchange kinetics in naphthalene and biphenyl (Shatenshtein, 1958, 1960b) clearly shows that there is a difference in the electron mechanism of transmission of the influence of one benzene ring on another in the above two compounds (cf. Section XV, A). 

Mechanism p-Hydrogen Exchange Kinetic S Faster Than Order Elimination General or Specific Base Catalysis Electron Withdrawal atCP Electron release atCa Leaving- Group Isotope Effect or Element Effect... 

Table 6.1 System parameters and derived rate data for sodium-hydrogen exchange kinetics on a styrene sulfonate resin (12% DVB) - finite volume. (Data from C. E. Harland, Ph.D. Thesis, University of Leeds, 1972)... 

In summary, what in the deferripeptides is manifested as conformational differences among the analogues (40), in the chelates is evidenced as stability differences dramatically expressed in their different hydrogen exchange kinetics and only slightly reflected in the PMR spectra. 

The reaction stages and species involved may be expected to be similar on the feed and permeate sides of a hydrogen membrane. If the flux is driven by reaction with oxygen on the permeate side, this side may naturally be quite different, both in terms of ionic species and electronic (holes versus electrons). The formation or presence of water vapor may also play a significant role in hydrogen exchange kinetics. 

The surface kinetics is crucial for a membrane in operation. For oxygen separation membranes, it has proven to be rate limiting in many cases, and has been studied extensively. For proton-conducting materials and membranes, much less has been done, partly because surface kinetics has been less of a problem up to now. Still, we believe membrane materials will be better and thinner, until the surfaces eventually become rate limiting. We, therefore, mention a couple of techniques for studying hydrogen exchange kinetics. 

The last assumption that is required for the time correction process to be reliable is that the reaction is approximately first order with an effective rate constant that is a linear function of the chemical exchange rate constant. As discussed in Section 17.3.1, the assumption of first-order kinetics with an approximately EX2-like mechanism for disordered proteins may not be accurate. The reliability of the time correction method is only as good as the extent to which the hydrogen exchange kinetics follow an EX2-like mechanism. Taking all of these factors into account, it is clear that the use of low pH labeling to reach msec HX must be approached with some measure of caution. 

The hydrogen exchange kinetics of the free and bound forms of the proteins are often well described by empirical stretched exponential or biexponential fits, as developed by the Englanda- lab [69] (see Section 7.3.3) ... 

Figure 17.7 Hydrogen exchange kinetics of free ACTR and CBP and their complex. Representative spectra (a) and uptake curves (b) from peptides in CBP and ACTR that become a-helical in the complex. Secondary structure elements shown In diagram indicate a-helical (boxes), loop (lines), and unstructured (dotted lines) that ACTR adopts in complex with CBP [29]. The vertical dashed lines in the spectra denote the centroids of the undeuterated and fully deuterated states. The dashed lines in the uptake curves denote data fitting using Equation 17.20. (c) The kinetic analysis provides estimates of peptide-averaged protection, depicted as different colored bars mapped onto the sequence and secondary structure found in the complex. Adapted from Ref [81] with permission, 2011 American Chemical Society. (See insert for color representation of the figure.)...

Qian, H., Chan, S.I. (1999) Hydrogen exchange kinetics of proteins in denaturants A generalized two-process model. J Mol Biol, 286 (2), 607-616. 

Ohta S, Tsuboi M, Yoshida M and Kagawa Y (1980) Inter subunit interaction in proton translocating adenosine triphosphatase as revealed by hydrogen exchange kinetics. Biochemistry 19t 2160-2164. Pullman ME and Monroy GC (1963) A naturally occuring inhibitor of mitochondrial adenosine triphosphtase, J. Biol. Chem. 238, 3762-3769. Rott R and Nelson N (1981) Purification and immunological properties of proton ATPase complexes from yeast and rat liver mitochondria, J. Biol. Chem. 256, 9224-9228. 

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