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Structural Modeling Extends QSAR Analysis of Antibody-Lysozyme Interactions to 3D-QSAR

Eva K. Freyhult^*,, Karl Andersson^,* and Mats G. Gustafsson

^*The Linnaeus Centre for Bioinformatics, Uppsala University and the Swedish University of Agricultural Sciences, Sweden; Biacore AB, Uppsala, Sweden; and Signals and Systems, Uppsala University, Sweden

Correspondence: Address reprint requests to Eva K. Freyhult, The Linnaeus Center for Bioinformatics, Box 598, Uppsala, Sweden 75124. Tel.: +46-18-4716688; E-mail: eva.freyhult{at}lcb.uu.se.

This work shows that quantitative multivariate modeling is an emerging possibility for unraveling protein-protein interactions using a combination of designed mutations with sequence and structure information. Using this approach, it is possible to stereochemically determine which residue properties contribute most to the interaction. This is illustrated by results from modeling of the interaction of the wild-type and 17 single and double mutants of a camel antibody specific for lysozyme. Linear multivariate models describing association and dissociation rates as well as affinity were developed. Sequence information in the form of amino acid property scales was combined with 3D structure information (obtained using molecular mechanics calculations) in the form of coordinates of the -carbons and the center of the side chains. The results show that in addition to the amino acid properties of the mutated residues 101 and 105, the dissociation rate is controlled by the side-chain coordinate of residue 105, whereas the association is determined by the coordinates of residues 99, 100, 105 (side chain), 111, and 112. The great difference between the models for association and dissociation rates illustrates that the event of molecular recognition and the property of binding stability rely on different physical processes.

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