Proteins function observation

More detailed aspects of protein function can be obtained also by force-field based approaches. Whereas protein function requires protein dynamics, no experimental technique can observe it directly on an atomic scale, and motions have to be simulated by molecular dynamics (MD) simulations. Also free energy differences (e.g. between binding energies of different protein ligands) can be characterised by MD simulations. Molecular mechanics or molecular dynamics based approaches are also necessary for homology modelling and for structure refinement in X-ray crystallography and NMR structure determination. 

There are four levels of sUucture observed in proteins [9] and it is important that once the molecular weight of a protein has been determined that these are also elucidated in order that the way in which the protein functions may be understood. 

Polymorphism A common (i.e., at least 1% prevalence of the minor allele in the population) sequence variation observed in an individual at a polymorphic site. Polymorphisms include nucleotide substitutions, insertions, deletions and microsatellites. They may be functional or silent, i.e., they do not result in detectable differences in gene expression or protein function. 

The ligand binding or catalytic sites are the most relevant parts of a protein domain for the development of small molecules as modulators of protein function. There is evidence that proteins with conserved folds often also have their functional sites on the same topological location. In some cases a remarkable conservatism in functional sites can be observed. This is true for the example described later in this review on similarity of Cdc25A phosphatase, acetylcholinesterase (AChE) and 1 Ifl-hydroxysteroid dehydrogenases (1 l HSD) (Fig. 9). Nevertheless, it should be stressed that the correlation patterns of amino acid sequence, protein fold and protein function remain a matter of debate. Moreover, a vast number of specific functions can be carried out by the limited number of protein domains due to the high amino acid diversity of proteins with similar folds. " ... 

The Ras GTP-mediated activation of P13-kinase links the Ras pathway with fimcti-ons of the Rho/Rac proteins. Members of this protein family within the Ras superfamily control formation of the cytoskeleton. The exact nature of the linkage with the Ras/PI3-kinase signal conduction to the Rac proteins is unknown. There is evidence that the product of the P13-kinase, Ptd-lns(3,4,5)P3, binds to the PH domain of the Vav protein and activates the latter. The Vav protein functions as a nucleotide exchange factor for the Rac GTPase (Han et al., 1998). The observation that activation of the Ras pathway is accompanied by reorganization of the cytoskeleton is in agreement with these findings. 

The p53 protein is central to a control function that imderlies progress in the cell cycle when DNA damage or other faults in the cell cycle are present. If cells are exposed to damage such as UV irradiation, an increase in the concentration of p53 protein is observed and the p53 protein is activated. One of the signals that has been identified as leading to activation of the p53 protein is a DNA strand break. Conditions that favor a strand break are the effect of UV irradiation, incomplete repair processes or a pause in DNA replication due to a damaged DNA template. 

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