Folding of Pig Gastric Mucin Non-glycosylated Domains: A Discrete Molecular Dynamics Study
| Autor: | Urbanc, Brigita, Turner, Bradley S., Bansil, Rama |
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| Rok vydání: | 2009 |
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| Druh dokumentu: | Working Paper |
| Popis: | Mucin glycoprotein consist of tandem repeating glycosylated regions flanked by non-repetitive protein domains with little glycosylation. These non-repetitive domains are involved in the pH dependent gelation of gastric mucin, which is essential to protecting the stomach from autodigestion. We have examined the folding of the non-repetitive sequence of von Willebrand factor vWF-C1 domain (67 amino acids) and PGM 2X (242 amino acids) at neutral and low pH using Discrete Molecular Dynamics. A four-bead protein model with hydrogen bonding and amino acid-specific hydrophobic/hydrophilic and electrostatic interactions of side chains) was used. The simulations reveal that the distant N- and C-terminal regions form salt-bridges at neutral pH giving a relatively compact folded structure. At low pH, the salt bridges break giving a more open and extended structure. The calculated average value of the beta-strand increases from 0.23 at neutral pH to 0.36 at low pH in very good agreement with CD data. Simulations of vWF C1 show 4-6 beta strands separated by turns/loops and we found that pH did not affect significantly the folded structure. The average beta-strand structure of 0.32 was again in very good agreement with the CD results. Comment: This paper has been withdrawn by the authors. This paper has been withdrawn due to the policies of many journals which will not consider a preprint posted on an e-print server for publication |
| Databáze: | arXiv |
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