Identification of amino acid residues of a designed ankyrin repeat protein potentially involved in intermolecular interactions with CD4: analysis by molecular dynamics simulations.
作者： Piyarat Nimmanpipug , Chalermpon Khampa , Vannajan Sanghiran Lee , Sawitree Nangola , Chatchai Tayapiwatana
DOI: 10.1016/J.JMGM.2011.09.003
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摘要: Abstract We applied molecular dynamics simulations to investigate the binding properties of a designed ankyrin repeat protein, DARPin–CD4 complex. DARPin 23.2 has been reported disturb human immunodeficiency virus (HIV) viral entry process by Schweizer et al. The protein docking simulation was analysed comparing specific binder (DARPin 23.2) an irrelevant control (2JAB) in forming composite with CD4. To determine free energy both ankyrins, MM/PBSA and MM/GBSA protocols were used. decomposition complexes explore role certain amino acid residues complex configuration. Interestingly, analysis revealed similar CD4 interaction regarding gp120 theoretical anchoring motif. In contrast, occurred at different location. This observation suggests that there is advantage modification 23.2, enhanced affinity for
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