Protein catalytic function

Many enzymes carry out their catalytic function relying solely on their protein structure. Many others require nonprotein components, called cofactors (Table 14.2). Cofactors may be metal ions or organic molecules referred to as coenzymes. Cofactors, because they are structurally less complex than proteins, tend to be stable to heat (incubation in a boiling water bath). Typically, proteins are denatured under such conditions. Many coenzymes are vitamins or contain vitamins as part of their structure. Usually coenzymes are actively involved in the catalytic reaction of the enzyme, often serving as intermediate carriers of functional groups in the conversion of substrates to products. In most cases, a coenzyme is firmly associated with its enzyme, perhaps even by covalent bonds, and it is difficult to... 

Watson, J. D., ed., 1987. Evolution of catalytic function. Cold Spring Harbor Symposium on Quantitative Biology 52 1- 955. Publications from a symposium on tlie nature and evolution of catalytic biomolecules (proteins and RNA) prompted by tlie discovery that RNA could act catalytically. 

Proteins may be classified on the basis of the solubility, shape, or function or of the presence of a prosthetic group such as heme. Proteins perform complex physical and catalytic functions by positioning specific chemical groups in a precise three-dimensional arrangement that is both functionally efficient and physically strong. 

Proteins either strengthen the membrane structure (building proteins) or fulfil various transport or catalytic functions (functional proteins). They are often only electrostatically bound to the membrane surface (extrinsic proteins) or are covalently bound to the lipoprotein complexes (intrinsic or integral proteins). They are usually present in the form of an or-helix or random coil. Some integral proteins penetrate through the membrane (see Section 6.4.2). 

A variety of formats for protein arrays are possible. For example, a set of antibodies can be gridded on a filter or slide and used to detect protein expression levels (Pandey and Mann, 2000). Another type of array consists of proteins from an organism arrayed directly on to a glass slide, nylon filter or in microtiter wells (MacBeath and Schreiber, 2000). This format could be used to map protein-protein interactions or to associate a catalytic function with a protein. 

The understanding of the catalytic function of enzymes is a prime objective in biomolecular science. In the last decade, significant developments in computational approaches have made quantum chemistry a powerful tool for the study of enzymatic mechanisms. In all applications of quantum chemistry to proteins, a key concept is the active site, i.e. a local region where the chemical reactivity takes place. The concept of the active site makes it possible to scale down large enzymatic systems to models small enough to be handled by accurate quantum chemistry methods. 

The crystallographic structure of rubredoxin from Clostridium pasteurianum at 2.5 A, a resolution sufficient to reveal the sequence of several of the bulky amino acid side chains, shows the iron coordinated to two pairs of cysteine residues located rather near the termini of the polypeptide chain (Fig. 1). A related rubredoxin, with a three times larger molecular weight, from Pseudomonas oleovorans is believed to bind iron in a similar fashion. This conclusion is based on physical probes, especially electron paramagnetic resonance spectroscopy, all of which indicate that the iron is in each case situated in a highly similar environment however, the proteins display some specificity in catalytic function. 

The cytoplasmic domain primarily consists of the catalytic domain and various autophosphorylation sites that regulate catalytic function and serve as docking sites for SH2 do main-containing proteins. The protein kinase catalytic domains of RPTKs are highly conserved and similar in structure to those of the NRPTK (see above). 

The PDHC catalyzes the irreversible conversion of pyruvate to acetyl-CoA (Fig. 42-3) and is dependent on thiamine and lipoic acid as cofactors (see Ch. 35). The complex has five enzymes three subserving a catalytic function and two subserving a regulatory role. The catalytic components include PDH, El dihydrolipoyl trans-acetylase, E2 and dihydrolipoyl dehydrogenase, E3. The two regulatory enzymes include PDH-specific kinase and phospho-PDH-specific phosphatase. The multienzyme complex contains nine protein subunits, including... 

To understand the basic role served by vitamins in human health, we need to retreat to chapter 9 for a moment. We discussed there the nature of an amazing group of proteins, the catalysts of living systems, enzymes. Many enzymes are perfectly happy to work by themselves and they do work by themselves. Others, in contrast, require a partner for their catalytic functions. These partners are known by the generic name of coenzymes. Basically, they cooperate with enzymes in getting the catalytic job accomplished. Although his name implies that he worked... 

Of the five snRNAs, U2 and U6 interact with the reaction site (the 5 splice site and the branch point) in the first chemical step. These two snRNAs are known to anneal together to form a stable-based paired structure in the absence of proteins and in the presence of ions as shown in Fig. 13, with U2 acting as an inducer molecule that displaces the U4 (that is an antisense molecule that regulates the catalytic function of U6 RNA) from the initially formed U4-U6 duplex. The secondary (or higher ordered) structure of the U2-U6 complex consists of the active site of the spliceosome. Recent data suggests that these two snRNAs function as the catalytic domain of the spliceosome that catalyzes the first step of the splicing reaction [145]. 

Any protein exhibiting more than one catalytic function as a result of distinct parts of a polypeptide chain ( domains ) or distinct subunits, or both. 

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