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N-glycosylation of the I-like domain of beta1 integrin plays an essential role in integrin structure and function, and the altered sialylation of beta1 integrin regulates beta1 integrin binding to fibronectin. However, the structural basis underlying the effect of altered sialylation of the beta1 I-like domain on beta1 integrin binding to fibronectin remains largely unknown. In this study, we used a combination of molecular dynamics simulations and binding free energy analyses to investigate changes in binding thermodynamics and in conformation of the glycosylated beta1 I-like domain-FN-III(9-10) complex caused by altered sialylation of the beta1 I-like domain. Binding free energy analyses showed that desialylation of beta1 I-like domain increased beta1 integrin binding to fibronectin, consistent with experimental results. Interaction analyses showed that altered sialylation of the beta1 I-like domain resulted in significant changes in the interaction of the N-glycans of the I-like domain with both the I-like domain and fibronectin, and these changes could directly affect the allosteric regulation of the interaction between the I-like domain and fibronectin. Altered sialylation of the beta1 I-like domain caused significant conformational changes in key functional sites of both the beta1 I-like domain and fibronectin. In addition, altered sialylation of the beta1 I-like domain resulted in changes in the degree of correlated motions between residues in the I-like domain and residues in fibronectin, and in the degree of motion changes in fibronectin, which could affect beta1 integrin binding to fibronectin. We believe results from this study provide thermodynamic and structural evidence for a role of altered sialylation of beta1 integrin in regulating beta1 integrin binding to fibronectin and it's induced cellular activities., (Copyright 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.)