Protein-substrate interactions

Protein-Substrate Interactions During the Proton Transfer... 

I was thinking particularly of electrostatic interactions between enzyme residues and substrate molecules. Let us compare the hydrophilic cytoplasmic phase (say, with dielectric constant e = 80) and the hydrophobic regions within membranes (say, with e = 2). Is it possible that protein-substrate interactions may be enhanced in certain membrane-associated enzyme schemes That is, might specific intermolecular forces play a more significant role in influencing the site-to-site migration of intermediate substrates, as compared to the same system in the hydrophilic phase [R. Coleman, Biochim. Biophys. Acta, 300, 1 (1973) P. A. Srere and K. Mosbach, Anti. Rev. Microbiol., 28, 61 (1974) and H. Frohlich, Proc. Nat. Acad. Sci. (U.S.), 72, 4211 (1975).]... 

In conclusion, TIRF promises to be exceedingly useful in the study of protein-substrate interactions. It gives in situ, possibly remote, real-time information about protein adsorption-desorption parameters, conformational changes upon adsorption and hopefully, nanosecond time-resolved fluorescence lifetime information about adsorbed proteins 156). 

M.J. Sippl, M. Jaritz, M. Hendlich, M. Ortner, and P. Lackner. Applications of knowledge based mean fields in the determination of protein structures. In Doniach, ed., Statistical Mechanics, Protein Structure and Protein-Substrate Interactions, 297-315. Plenum Press, 1994. 

Molecular recognition, defined as the favored binding of a molecule (i.e., a substrate) to a specific site in a receptor over other structurally and chemically related molecules, is at the forefront of science.1 s Long before man walked on this earth, nature had succeeded in the creation of a series of biologically based recognition elements with unmatched specificity antibodies, enzymes, and receptors. Perhaps the simplest well-known example of this concept is the lock and key hypothesis that has been used to describe protein-substrate interactions in biological systems.5-7... 

As well as simple ions that contribute to changes in osmotic pressure and may influence protein binding, we must also consider the impact of complex ionic systems. DNA and RNA are both polymeric anions as the individual nucleosides are linked by charged phosphate groups. Similarly many proteins have side chains that may be ionized, a process that in turn can affect secondary and tertiary structure as well as protein-protein or protein-substrate interactions. 

Sebastian Doniach, Statistical Mechanics, Protein Structure, and Protein Substrate Interactions. Proceedings of a NATO Advanced Research Workshop on Statistical Mechanics, Protein Structure, and Protein Substrate Interactions, held June 1-5,1993, in Cargese, Corsica, France, Plenum, New York, 1994. 

Li, H. Y., and Poulos,T. L. 1995. Modeling Protein Substrate Interactions in the Heme Domain of Cytochrome P450(Bm-3). Acta Crystallographies D-Biological Crystallography, 51, 21-32. 

N.m.r. and e.s.r. techniques similar to those used for the determination of the location and environment of solubilizates in micellar systems have also been employed in investigations of solubilization by lipid micelles and of protein-substrate interactions (McDonald and Phillips, 1967 Meadows et al., 1967 Spotswood et al., 1967 Chapman, 1968 Penkett et al., 1968 Mildvan and Weiner, 1969 Raftery et al., 1969 Roberts et al., 1969a, b Rosenberg et al., 1969 Small et al., 1969). 

Protein-substrate interaction. The substrate is shown in black and red, with the red representing the terminal amino acid. Blue indicates side chains from enzyme that help bind the substrate. 

I. Coluzza, D. Frenkel (2005) Designing specificity of protein-substrate interactions. Phys. Rev. E 70, p. 051917... 

Based on this knowledge, Fusetti et have modeled a substrate molecule in the catalytic site of 2,3QD (Figure 29). Quercetin possesses five hydroxyl groups that probably replace part of the water structure upon binding in the active site. The manual docking was guided by the position of solvent molecules present in the active site of four crystallographically independent molecules. The orientation of the quercetin molecule was adjusted to maximize the number of favorable protein—substrate interactions. 

The size and shape of the various substrates shown in Figure 3.16 are sufficiently diverse that the structural basis for what controls substrate specificity can, at least in part, be understood. As expected, all substrates are situated such that the atom to be hydroxylated is within 4-5 A of the heme iron. Thus, regio- and stereo-seleetive hydroxylation by the hypothetical Fe(IV)-0 species is achieved by specific protein-substrate interactions that hold the substrate in the correct position. The exception is P450BM3. The structure of the P450BM3 heme domain with palmi-toleic acid and N-pamitoylglycine show that the fatty acid substrate is ==7-8 A from the iron which is too far for hydroxylation. However, NMR results indicate that the substrate moves to be within 3 A of the iron upon reduction from Fe(III) to Fe(II) . Precisely how reduction is linked to such a large repositioning of the substrate remains unknown. 

Li, H. and XL. Poulos (1995). Modeling protein substrate interactions in the heme domain of cytochrome P450BM-3. Acta Crystallogr. D 51, 21-32. 

C Nmr investigations of proteins and/or polypeptide systems can be classified into three general categories (1) 1 3C chemical shifts and spin lattice relaxation times of native and specifically labelled or 13C-enriched proteins and subunits (2) helix-coil transitions of polypeptides and (3) binding studies, protein-substrate interactions and complex formation. 

A number of protein-substrate interactions and binding studies have also been examined using 1 3 C nmr spectroscopic techniques. Interactions of 1 3C enriched pyruvates with Mn(II), Mn(II)-pyruvate carboxylase and Mn(II)-pyruvate kinase have been studied using the... 

Despite the evident role of coulombic protein-substrate interactions, SEC calibration curves on derivatized silica do not always reveal expected differences among proteins in various charge states. Le Maire et al. (78) found... 

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