About this Journal Submit a Manuscript Table of Contents
BioMed Research International
Volume 2013 (2013), Article ID 752514, 12 pages
http://dx.doi.org/10.1155/2013/752514
Research Article

Increasing Affinity of Interferon- Receptor 1 to Interferon- by Computer-Aided Design

Institute of Biotechnology AS CR, v. v. i., Vídeňská 1083, 142 20 Prague, Czech Republic

Received 29 April 2013; Revised 6 August 2013; Accepted 13 August 2013

Academic Editor: David Stammers

Copyright © 2013 Pavel Mikulecký et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

We describe a computer-based protocol to design protein mutations increasing binding affinity between ligand and its receptor. The method was applied to mutate interferon- receptor 1 (IFN- -Rx) to increase its affinity to natural ligand IFN- , protein important for innate immunity. We analyzed all four available crystal structures of the IFN- -Rx/IFN- complex to identify 40 receptor residues forming the interface with IFN- . For these 40 residues, we performed computational mutation analysis by substituting each of the interface receptor residues by the remaining standard amino acids. The corresponding changes of the free energy were calculated by a protocol consisting of FoldX and molecular dynamics calculations. Based on the computed changes of the free energy and on sequence conservation criteria obtained by the analysis of 32 receptor sequences from 19 different species, we selected 14 receptor variants predicted to increase the receptor affinity to IFN- . These variants were expressed as recombinant proteins in Escherichia coli, and their affinities to IFN- were determined experimentally by surface plasmon resonance (SPR). The SPR measurements showed that the simple computational protocol succeeded in finding two receptor variants with affinity to IFN- increased about fivefold compared to the wild-type receptor.