Amide, hydrogen exchange

When 2D-NMR techniques are used, hydrogen exchange rates are determined, e.g., by fitting normalized peak volume versus time to Eq. [77]  

The relative contribution from direct exchange with water decreases rapidly as the pH is shifted from pH,j,in. 

The rate of hydrogen exchange in native proteins can be slowed by many orders of magnitude. The most popular kinetic model for slowed hydrogen exchange at any given NH is based on the notion that fluctuations in protein conformation are required to permit access of the solvent. 

If k i, the exchange is a first-order process and the rate constant is given by (k s = op) process). 

the exchange is a second-order process and the rate constant is 

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Zhang, Z. Smith, D.L. Determination of amide hydrogen exchange by mass spectrometry a new tool for protein structure elucidation. Protein Sd. 1993, 2, 522-531. 

Smith, D.L. Dharmasiri, K. Protein-ligand binding studied by amide hydrogen exchange and mass spectrometry. NATO ASI Ser. C 1998, 510, 45-58. 

Several features affect the rate of amide hydrogen exchange, which reflect the protein s structure and dynamic properties. These include an amide s participation in hydrogen bonding [36], its distance from the protein surface [3], and the... 

Formalisms to relate the observed rates of amide hydrogen exchange to thermodynamic stabilization of proteins have been developed [38]. Amide hydrogens of proteins in the native, folded state are proposed to exchange according to the following equation ... 

Kaltashov I.A., Eyles S.J. Crossing the phase boundary to study protein dynamics and function combination of amide hydrogen exchange in solution and ion fragmentation in the gas phase. J. Mass Spectrom. 2002, 37, 557-565. 

Zhang Z., Post C.B., Smith D.L. Amide hydrogen exchange determined by mass spectrometry application to rabbit muscle aldolase. Biochemistry 1996, 35, 779—791. 

Sivaraman T., Arrington C.B., Robertson A.D. Kinetics of unfolding and folding from amide hydrogen exchange in native ubiqutin. Nat. Struct. Biol. 2001, 8, 331-333. 

Woods V.L. Jr Method for characterization of the fine structure of protein binding sites employing amide hydrogen exchange. U.S. 

Amide hydrogen exchange is usually discussed in terms of a model proposed by Linderstrc )m-Lang in 1955.554/556 He suggested that portions of protein molecules unfold sporadically to allow rapid exchange which can be catalyzed by H+, HO, or other acids or... 

Fig. 2.8. Histograms showing the distribution of protection factors from amide hydrogen exchange for (a) the authentic form and (b) the recombinant form of goat a-lactalbumin in the MG-state at pHobs 1.7 and 25°C (Nakamura et al., unpublished)...

Fig. 22. Hydration dependence of amide hydrogen exchange in lysozyme powder at pH 5. Individual samples of pH 5 fully labeled (with H O) lysozyme were equilibrated at 25°C for 24 hr at various water contents obtained by isopiestic equilibration ( ) or by the addition and mixing of solvent (A). The samples were then dissolved to a concentration of 20 mg/ml and 100-/U.1 aliquots were analyzed by gel filtration. The arrow indicates the 24-hr solution H . end point. H, represents the number of hydrogens remaining unexchanged. From Schinkel el al. (1985).

Fig. 23. Dependence on log water activity of log ratio of powder to solution amide hydrogen exchange rate for lysozyme. Log rate ratio data for pH 2 (bottom) to pH 10 (top) are given as a function of log(/ /Po). The slopes of the lines give the order of the protein exchange reaction with respect to water. The slopes from least-squares linear regression are the following pH 2, 2.57 pH 3, 2.90 pH 5, 3.14 pH 7, 3.14 and pH 10, 2.53. Displacement along the log rate ratio axis is arbitrary. Numbers indicate some of the H m values for which rate ratios were determined. From Schinkel et at. (1985).

Amide hydrogen exchange in protein powders depends weakly on water activity, and its hydration dependence is complete within the low-hydration region (0.15 A). Apparently, the rate-determining step for the exchange of buried hydrogens is not much influenced by the protein surface. This is unexplained. 

Experimental approaches for monitoring the amide hydrogen exchange 486... 

Figure 14.5. HX reveals a temperature-dependent transition in mobility, (a) Arrhenius plot for the oxidation of protonated (circles) or deuterated (squares) benzyl alcohol by htADH. The discontinuity at 30 °C indicates a transition in activation energy for the reaction, (b) Weighted averaged HX rate constant ( HX(wA)) fot peptides from htADH plotted versus 1 /T show/s discontinuities at 30 °C in five peptides. The w/eighted averaged kHX is defined as (A(ti + 6(t2 + Ck )/NH where NH is the total number of amide hydrogens in the peptide, and A, B, and C are the number of amide hydrogens exchanging with rate...

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