Protein Association Reactions

Huber, G.A. Kim, S., Weighted-ensemble Brownian dynamics simulations for protein association reactions, Biophys. 7. 1996, 70, 97-110... 

Prior to the availability of time-resolved measurements, such so-called Perrin plots were used extensively to determine the apparent hydrodynamic volume of proteins [129—131]. Since protein association reactions usually affect the rotational correlation time of the protein label, such reactions have been characterized by steady state anisotropy measurements [132, 133]. 

Equations (IV-76), (IV-77), and (IV-78) provide additional means for the determination of Ki, K2, and Kij for the side-chain hydrogen bonds involved in denaturation. While no accurate data are available to test these equations for the rupture of side-chain hydrogen bonds, they have been applied to the reverse process (the formation of hydrogen bonds in a protein association reaction), which will be considered in Chapter V. 

The cross relation has proven valuable to estimate ET rates of interest from data tliat might be more readily available for individual reaction partners. Simple application of tire cross-relation is, of course, limited if tire electronic coupling interactions associated with tire self exchange processes are drastically different from tliose for tire cross reaction. This is a particular concern in protein/protein ET reactions where tire coupling may vary drastically as a function of docking geometry. 

Steinberg, I. Z., Scheraga, H. A. Entropy changes accompanying association reactions of proteins. J. Biol. Chem. 238 (1963)172-181. 

J. J. Robinson, Roles of Ca(2 + ), Mg (2 + ) and NaCl in modulating the self association reaction of hyalin, a major protein component of the sea urchin extra-embryonic hyaline layer, Biochem J., 256(1), 225 (1988). 

Both the protein and the ligand are solvated by water when they are separated. As the two surfaces interact, water is excluded, hydrogen bonds are broken and formed, hydrophobic interactions occur, and the protein and ligand stick to each other. As in protein folding and for the same reasons, the hydrophobic interaction provides much of the free energy for the association reaction, but polar groups that are removed... 

The major reasons for using intrinsic fluorescence and phosphorescence to study conformation are that these spectroscopies are extremely sensitive, they provide many specific parameters to correlate with physical structure, and they cover a wide time range, from picoseconds to seconds, which allows the study of a variety of different processes. The time scale of tyrosine fluorescence extends from picoseconds to a few nanoseconds, which is a good time window to obtain information about rotational diffusion, intermolecular association reactions, and conformational relaxation in the presence and absence of cofactors and substrates. Moreover, the time dependence of the fluorescence intensity and anisotropy decay can be used to test predictions from molecular dynamics.(167) In using tyrosine to study the dynamics of protein structure, it is particularly important that we begin to understand the basis for the anisotropy decay of tyrosine in terms of the potential motions of the phenol ring.(221) For example, the frequency of flips about the C -C bond of tyrosine appears to cover a time range from milliseconds to nanoseconds.(222)... 

The binding of a small molecule ligand to a protein receptor follows a bimolecu-lar association reaction with second-order kinetics. For the reversible reaction of a ligand L and a protein P to form a non-covalendy bound complex C at equilibrium, Eq. (1) applies where kon and kgS represent the forward and reverse mass transfer rate constants. 

Fluorescence spectroscopy Binding of substrates, association reactions between species, denaturation of proteins and other macromolecules ... 

A biochemical system is at the center of the cell cycle, of which the most important players are Ser/Thr-specific protein kinases and regulatory proteins associated with these. The activity of this central cell cycle apparatus regulates processes downstream that help to carry out the many phase-specific biochemical reactions of the cell cycle in a defined order. 

IIS and 7S proteins dissociate into subunits at ionic strength below O.IM and 0.5M, respectively (11, 12). This is, therefore, a plausible explanation oT" tKe observed solubility behavior. The sharp minimum at O.IM salt concentration in the case of the NPI might correspond to the cooperative association reactions involving IIS subunits. Even though there has been no experimental demonstration, it would not be unreasonable to postulate that random association reactions also occur for denatured soy proteins. The broader minimum between 0.1 and 0.2M salt concentration might be indicative of less cooperative association reactions. 

The rate constants for the association of proteins with one another and with other macromolecules are profoundly influenced by the geometry of the interaction and by electrostatic factors. Only a small part of each protein may be involved in the formation of a protein-protein complex, which imposes a bad steric factor on the reaction. Accordingly, protein-protein association rate constants may be as low as 104 s 1 M x (Table 4.1). But there is very fast association at > 5 X 109 s-1 AT 1 at low ionic strength for proteins that have complementary charged surfaces, such as bamase with its polypeptide inhibitor barstarfwhose, properties are discussed in Chapter 19), thrombin with its polypeptide inhibitor hirudin, and ferricytochrome c with ferrocytochrome b5. 

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