Protein rates

Intramolecular Ru(II) to Cu(II) ET rates have been measured in two other blue copper proteins, stellacyanin [42, 43] and azurin [9, 13, 28]. Pseudomonas aeruginosa azurin has been ruthenated at His83 [13] (Fig. 5). The intramolecular Ru(II) to Cu(II) ET rate of 1.9 s was found to be independent of temperature [28]. The Cu reorganization enthalpy was estimated to be < 7 kcal/mol [13, 28], a value confirming that blue copper is structured for efficient ET. Again, a blue copper ET rate is low in comparison with heme protein rates over similar distances (at similar driving forces) (Table 1). 

Racemization rates (Table I) clearly differ among these seven amino acids. To compare results from the four proteins, rate constants were calculated from these data. For casein, D/L ratios were measured at 0, 1, 3, 8 and 24 hours. These results are plotted in Figure 2. The curves have two regions of different racemization rates. Rapid initial rates observable up to about 3 hours are followed by slower rates up to 24 hours. The amino acids apparently have not reached equilibrium by 24 hours of incubation. Theoretically for amino acids having one asymmetric center, the equilibrium D/L ratio is 1.0. This value has been observed in fossil bone protein (see 13) and in dry roasted proteins (10), but not in calcareous marine sediments (17) nor in fossil mollusc shell (18). 

The Ru-protein data points are scattered around the Ru azurin fi = 1.1 A exponential distance decay. More than three-fourths of the Ru protein ET rates fall in a 1.0 to 1.3 A y3-value zone. The data in Figure 5 suggest that a canonical distance decay constant will not describe long-range electron tunneling in proteins. Rates at a single distance can differ by as much as a factor of 10 and D/A distances that differ by as much as 5 A can produce identical rates. The... 

Protein rate processes are strongly affected by hydration. The dry protein shows greatly reduced internal motions, measured by Moss-liauer spectroscopy, neutron scattering, fluorescence spectroscopy, and other methods. Surface motions, monitored by spin probes or spin or Mossbauer labels, are similarly frozen in the dry protein. The following paragraphs comment on the appearance of motion characteristic of the hydrated protein and on the coupling between protein and solvent motions. 

TABLE 7. Amino Acids and Proteins Rate Constants of Quenching Processes... 

Methyl oleate concentration (mAf) Lipid uptake (nmol/mg protein) Rate of Ca uptake (percentage of control)"... 

The most familiar type of electrokinetic experiment consists of setting up a potential gradient in a solution containing charged particles and determining their rate of motion. If the particles are small molecular ions, the phenomenon is called ionic conductance, if they are larger units, such as protein molecules, or colloidal particles, it is called electrophoresis. 

Rate effects may not be chemical kinetic ones. Benson and co-worker [84], in a study of the rate of adsorption of water on lyophilized proteins, comment that the empirical rates of adsorption were very markedly complicated by the fact that the samples were appreciably heated by the heat evolved on adsorption. In fact, it appeared that the actual adsorption rates were very fast and that the time dependence of the adsorbate pressure above the adsorbent was simply due to the time variation of the temperature of the sample as it cooled after the initial heating when adsorbate was first introduced. 

Most reactions in cells are carried out by enzymes [1], In many instances the rates of enzyme-catalysed reactions are enhanced by a factor of a million. A significantly large fraction of all known enzymes are proteins which are made from twenty naturally occurring amino acids. The amino acids are linked by peptide bonds to fonn polypeptide chains. The primary sequence of a protein specifies the linear order in which the amino acids are linked. To carry out the catalytic activity the linear sequence has to fold to a well defined tliree-dimensional (3D) stmcture. In cells only a relatively small fraction of proteins require assistance from chaperones (helper proteins) [2]. Even in the complicated cellular environment most proteins fold spontaneously upon synthesis. The detennination of the 3D folded stmcture from the one-dimensional primary sequence is the most popular protein folding problem. 

The key question we want to answer is what are the intrinsic sequence dependent factors tliat not only detennine tire folding rates but also tire stability of tire native state It turns out tliat many of tire global aspects of tire folding kinetics of proteins can be understood in tenns of tire equilibrium transition temperatures. In particular, we will show tliat tire key factor tliat governs tire foldability of sequences is tire single parameter... 

Gutman M 1986 Application of the laser-induced proton pulse for measuring the protonation rate constants of specific sites on proteins and membranes Methods Enzymol. 127 522-38... 

The pathway model makes a number of key predictions, including (a) a substantial role for hydrogen bond mediation of tunnelling, (b) a difference in mediation characteristics as a function of secondary and tertiary stmcture, (c) an intrinsically nonexponential decay of rate witlr distance, and (d) patlrway specific Trot and cold spots for electron transfer. These predictions have been tested extensively. The most systematic and critical tests are provided witlr mtlrenium-modified proteins, where a syntlretic ET active group cair be attached to the protein aird tire rate of ET via a specific medium stmcture cair be probed (figure C3.2.5). 

The predictive power of patlrway airalysis is well illustrated with two of tire Ru-nrodified systems of Gray aird coworkers [29]. Consider, tire His 72 aird His 39 mtlrenium-modified cytoclrromes c [281. The ET rates in tlrese proteins are about tire same, despite tire fact tlrat tire trairsfer distairce is fully 5 A shorter in the His 72 derivative. 

A large body of rate data in native aird modified proteins was airalysed recently in tire context of tire patlrway... 

Figure C3.2.6. Zones associated witlr the distinctive decay of electronic coupling tlrrough a-helical against p-sheet stmctures in proteins. Points shown refer to specific rates in mtlrenium-modified proteins aird in tire photosyntlretic reaction centre. From Gray H B aird Wiirkler J R 1996 Electron trairsfer in proteins A . Rev. Biochem. 65 537.

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