Peptide Isomerization Induced by pH Change Regulates the S1 Binding Site in Ficolins
Lifeng Yang A B , Jing Zhang B C and Jeak Ling Ding A B D
+ Author Affiliations
- Author Affiliations
A Computational and Systems Biology, Singapore-MIT Alliance, 4 Engineering Drive 3, Singapore 117576.
B Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543.
C NUS Graduate School for Integrative Science and Engineering, National University of Singapore, 28 Medical Drive, Singapore 117543.
D Corresponding author. Email: dbsdjl@nus.edu.sg
Australian Journal of Chemistry 64(7) 887-893 https://doi.org/10.1071/CH11050
Submitted: 28 January 2011 Accepted: 1 April 2011 Published: 19 July 2011
Abstract
Infection-inflammation mediated interactions between human ficolin and the pathogen GlcNAc is associated with local acidosis, leading to antimicrobial action. Therefore, revealing the precise molecular conformation induced by pH-shift is crucial in understanding the immune response. Here, we performed constant-pH molecular dynamics simulations on the L-ficolin fibrinogen-like domain over pH 4.5–9. An unusual cis-Asn244-Cys245 peptide bond prevailed over the pH range in the S1 binding site. Analysis of the hydrogen-bond network at S1 suggested Asn244 to be indispensible for maintaining the cis form of Asn244-Cys245, and the absence of the hydroxyl group on Phe262 accounts for the lack of GlcNAc binding.
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