Protein catalytic, conformational

This idea also helps to explain some of the mystery surrounding the enormous catalytic power of enzymes In enzyme catalysis, precise orientation of catalytic residues comprising the active site is necessary for the reaction to occur substrate binding induces this precise orientation by the changes it causes in the protein s conformation. 

Several thermodynamic and kinetic behaviors of enzyme-catalyzed reactions performed in ILs, with respect to enzymatic reactions carried out in conventional solvents, could lead to an improvement in the process performance [34—37]. ILs showed an over-stabilization effect on biocatalysts [38] on the basis of the double role played by these neoteric solvents ILs could provide an adequate microenvironment for the catalytic action of the enzyme (mass transfer phenomena and active catalytic conformation) and if they act as a solvent, ILs may be regarded as liquid immobilization supports, since multipoint enzyme-1L interactions (hydrogen. Van der Waals, ionic, etc.) may occur, resulting in a flexible supramolecular not able to maintain the active protein conformation [39]. Their polar and non-coordinating properties hold considerable potential for enantioselective reactions since profound effects on reactivities and selectivities are expected [40]. In recent years attention has been focused on the appUcation of ILs as reaction media for enantioselective processes [41—43]. 

As lipases are proteins, their conformation can be affected by the temperature and pH and, hence, their catalytic activity is expected to have an optimum for these two parameters as happens with most enzymes. The optimum pH for lipase-catalyzed reactions is slightly shifted toward a more alkaline range after immobilization... 

Nature, in her desire to design proteins to serve as smart and versatile machines, has used a system poised near a phase transition to exploit this sensitivity. Indeed, it is well-known that proteins utilize conformational flexibility [40] to achieve optimal catalytic properties [6]. That protein structures are poised near a phase transition provides the versatility and the flexibility needed for the amazing range of functions that proteins perform. 

Numerous experimental and theoretical studies have documented the direct correlation between internal motions of an enzyme and its activity. For example, the catalytic activities of many enzymes are closely associated with loop motions, which open and close the active site and also position key residues into contact with the substrate [7, 8]. X-ray crystal structmes of hgand-bound and fi-ee enzymes show that substantial conformational changes can be induced by ligand binding and by chemical transformation during an enzymatic reaction [9, 10]. The reaction catalyzed by thymidylate synthase has been shown to couple directly with the protein s conformation-... 

A systematic approach to induce new catalytic activities in proteins has been developed in our laboratory.quj- method consists of perturbing the native conformation of the protein and subsequent binding of an analog to the active site of an enzyme whose activity is to be generated. The product of this method is known as a catalytic conformationally modified protein (CCMP). Although the mechanism of the conformational modification method remains unknown, the flexibility of protein structure, and ligand-induced conformational modifications, probably play a role in the... 

Surprisingly this simple procedure has been shown to yield catalytic enzyme-like materials for several reactions. These materials can be purified in the same way as natural proteins are extracted from a crude biological fluid. In addition the properties of these catalysts are in many cases different than their natural enzyme counterpart. The pH optimum is often changed, the cofactor requirement of the native enzyme may not be present, and the substrate specificity is usually quite different. Of course, these materials when prepared from readily available protein can easily be produced in large quantities. Several examples of catalytic conformationally modified proteins (CCMP) are described below. 

We have previously calculated conformational free energy differences for a well-suited model system, the catalytic subunit of cAMP-dependent protein kinase (cAPK), which is the best characterized member of the protein kinase family. It has been crystallized in three different conformations and our main focus was on how ligand binding shifts the equilibrium among these ([Helms and McCammon 1997]). As an example using state-of-the-art computational techniques, we summarize the main conclusions of this study and discuss a variety of methods that may be used to extend this study into the dynamic regime of protein domain motion. 

The catalytic subunit of cAPK contains two domains connected by a peptide linker. ATP binds in a deep cleft between the two domains. Presently, crystal structures showed cAPK in three different conformations, (1) in a closed conformation in the ternary complex with ATP or other tight-binding ligands and a peptide inhibitor PKI(5-24), (2) in an intermediate conformation in the binary complex with adenosine, and (3) in an open conformation in the binary complex of mammalian cAPK with PKI(5-24). Fig.l shows a superposition of the three protein kinase configurations to visualize the type of conformational movement. 

Karlsson, R., Zheng, J., Zheng, N.-H., Taylor, S. S., Sowadski, J. M. Structure of the mamalian catalytic subunit of cAMP-dependent protein kinase and an inhibitor peptide displays an open conformation. Acta Cryst. D 49 (1993) 381-388. 

A prior distribution for sequence profiles can be derived from mixtures of Dirichlet distributions [16,51-54]. The idea is simple Each position in a multiple alignment represents one of a limited number of possible distributions that reflect the important physical forces that determine protein structure and function. In certain core positions, we expect to get a distribution restricted to Val, He, Met, and Leu. Other core positions may include these amino acids plus the large hydrophobic aromatic amino acids Phe and Trp. There will also be positions that are completely conserved, including catalytic residues (often Lys, GIu, Asp, Arg, Ser, and other polar amino acids) and Gly and Pro residues that are important in achieving certain backbone conformations in coil regions. Cys residues that form disulfide bonds or coordinate metal ions are also usually well conserved. 

RNA structures, compared to the helical motifs that dominate DNA, are quite diverse, assuming various loop conformations in addition to helical structures. This diversity allows RNA molecules to assume a wide variety of tertiary structures with many biological functions beyond the storage and propagation of the genetic code. Examples include transfer RNA, which is involved in the translation of mRNA into proteins, the RNA components of ribosomes, the translation machinery, and catalytic RNA molecules. In addition, it is now known that secondary and tertiary elements of mRNA can act to regulate the translation of its own primary sequence. Such diversity makes RNA a prime area for the study of structure-function relationships to which computational approaches can make a significant contribution. 

In free CDK2 the active site cleft is blocked by the T-loop and Thr 160 is buried (Figure 6.20a). Substrates cannot bind and Thr 160 cannot be phosphorylated consequently free CDK2 is inactive. The conformational changes induced by cyclin A binding not only expose the active site cleft so that ATP and protein substrates can bind but also rearrange essential active site residues to make the enzyme catalytically competent (Figure 6.20b). In addition Thr... 

Figure 13.32 Regulation of the catalytic activity of members of the Src family of tyrosine kinases, (a) The inactive form based on structure determinations. Helix aC is in a position and orientation where the catalytically important Glu residue is facing away from the active site. The activation segment has a conformation that through steric contacts blocks the catalytically competent positioning of helix aC. (b) A hypothetical active conformation based on comparisons with the active forms of other similar protein kinases. The linker region is released from SH3, and the activation segment changes its structure to allow helix aC to move and bring the Glu residue into the active site in contact with an important Lys residue.

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