Identification of Functionally Important Residues in Proteins Using Comparative Models

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.

Structural basis for preferential binding of non-ortho-substituted polychlorinated biphenyls by the monoclonal antibody S2B1

“…First, non-identical amino acids in this chimeric structure were replaced with those of S2B1. The side chains were then oriented with a program developed by the authors (Chen and Pellequer, 2004). The peptide backbone conformations of S2B1 CDRs L1, L2, L3, H1 and H2 were the same as those in the respective template antibodies.…”

“…First, the root-mean-square deviation (RMSD) between coordinates of the C atoms of S2B1, excluding CDR H3, and both template antibodies 48G7 and N1G9 was computed using a cartesian superposition algorithm (Chen and Pellequer, 2004). The RMSD between S2B1 and 48G7 was 0.7 Å , and the RMSD between S2B1 and N1G9 was 1.1 Å .…”

Two Distinct Binding Sites for High Potential Iron-Sulfur Protein and Cytochrome c on the Reaction Center-bound Cytochrome of Rubrivivax gelatinosus

“…Alteration of backbone atomic positions was permitted only within inserted and deleted regions (indels). Side chains were replaced according to the corresponding protein sequence, and their atomic coordinates were minimized using our in-house program (28). Indels were built with computational graphics using the programs Turbo-Frodo (29) and Xfit (30).…”

“…It has fewer indels (four regions) and higher sequence identity (53%) to our molecular construction than B. viridis (Protein Data Bank code 1PRC (33)), which introduces eight indels and has lower sequence identity (49%). We used our superposition program, Sup3D, to perform superposition of 3D structures (28).…”

Mathematical Models of Blood Coagulation and Platelet Adhesion: Clinical Applications

“…their mechanisms; 3) planning rational therapeutic strategy and selecting targets for drug design; 4) development of biomaterials with non-thrombogenic properties for the design and clinical use of artificial organs and implantable devices. Molecular *Address correspondence to this author at the Center for Vascular & Inflammatory Diseases and Department of Biochemistry & Molecular Biology, University of Maryland School of Medicine, 800 W. Baltimore Street, Baltimore MD 21201, USA; E-mail: esaenko@som.umaryland.edu modeling in the design of coagulation drugs has been recently reviewed [3][4][5][6]. We avoid discussing mathematical details and modeling approaches as our purpose is to evaluate usefulness of the existing models for practical applications and to summarize the most promising findings in this field.…”