Specificity of Heparin/Heparan sulphate binding to proteins


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Heparin/heparan sulphate? Protein interactions modulate a number of physiological processes such as coagulation, immune response, angiogenesis, and morphogenesis and pathogen infection. A majority of these interactions involve allosteric regulation of the target protein and are poorly understood. We have developed a genetic algorithm-based combinatorial virtual screening approach to understand the nature of interaction of heparin/heparan sulphate with proteins. A dual-filter strategy employing an ?affinity? filter followed by a ?specificity? Filter rapidly sorts the combinatorial library into distinct groups of sequences. Application of this strategy on a library of ~46,000 sequences resulted in identification of only five sequences that recognize heparin cofactor II with ?high-affinity and high-specificity?. Comparative analysis of ant thrombin? heparin and thrombin? Heparin crystal structures using a variety of structural biology tools reveals major differences between the heparin binding pockets of the two proteins. The strategy presents a general approach for understanding specificity features of heparin/heparan sulphate interactions, which are crucial for the development of novel allosteric heparin/heparan sulphate sequences as agonists or antagonists of proteins.

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