Abstract
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.
Keywords: homology modeling, three-dimensional structure, crystal structure, coagulation cascade, factor v, antibody, polynuclear aromatic hydrocarbons, pah
Current Medicinal Chemistry
Title: Identification of Functionally Important Residues in Proteins Using Comparative Models
Volume: 11 Issue: 5
Author(s): Shu-wen W. Chen and Jean -Luc Pellequer
Affiliation:
Keywords: homology modeling, three-dimensional structure, crystal structure, coagulation cascade, factor v, antibody, polynuclear aromatic hydrocarbons, pah
Abstract: 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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Cite this article as:
Chen W. Shu-wen and Pellequer -Luc Jean, Identification of Functionally Important Residues in Proteins Using Comparative Models, Current Medicinal Chemistry 2004; 11 (5) . https://dx.doi.org/10.2174/0929867043455891
DOI https://dx.doi.org/10.2174/0929867043455891 |
Print ISSN 0929-8673 |
Publisher Name Bentham Science Publisher |
Online ISSN 1875-533X |
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