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Identification of Functionally Important Residues in Proteins Using Comparative Models

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Rational design in protein engineering leads to significant progresses in medicinal chemistry research.It alleviates the difficulty of exploring unreasonable biological functions.Combining with analysis of biophysical-chemical properties,a three-dimensional (3D)structure provides fruitful information for rational design by revealing functionally important residues.Comparative (homology)modeling,one of the 3D structural prediction techniques,takes advantage of that homologous proteins share similarity in their 3D structures despite the lack of sequence similarity.Of the most value,3D models provide functional clues even though the function may have been modified during evolution.

We illustrate here two applications to medicinal chemistry research where comparative models made a significant improvement on the understanding of relevant biological functions of two proteins.These multiple collaborative projects involve the identification of solvent-exposed residues in a membrane anchoring domain of human coagulation factor V,and revealing critical residues in the interfaces of an antibody and a polynuclear aromatic hydrocarbon ligand.Since the protocol of comparative modeling technique we employed is essential to proposing useful hypotheses for experimental testing,we also present our methodology underlying our modeling programs.Our results show that inaccuracies in comparative models do not hamper functional evaluation as long as an in depth analysis of 3D structures is performed.
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Keywords: antibody; coagulation cascade; crystal structure; factor v; homology modeling; pah; polynuclear aromatic hydrocarbons; three-dimensional structure

Document Type: Review Article

Affiliations: CEA Valrho -Centre de Marcoule,DSV / / DIEP / SBTN,BP17171,30207 Bagnols sur Ceze Cedex, France.

Publication date: 2004-03-01

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  • Current Medicinal Chemistry covers all the latest and outstanding developments in medicinal chemistry and rational drug design. Each issue contains a series of timely in-depth reviews written by leaders in the field covering a range of the current topics in medicinal chemistry. Current Medicinal Chemistry is an essential journal for every medicinal chemist who wishes to be kept informed and up-to-date with the latest and most important developments.
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