Document Detail


Role of protein matrix rigidity and local polarization effects in the monovalent cation selectivity of crystallographic sites in the Na-coupled aspartate transporter Glt(Ph).
MedLine Citation:
PMID:  23301243     Owner:  NLM     Status:  Publisher    
Abstract/OtherAbstract:
We have studied Li(+)/Na(+)/K(+) selectivity of the bacterial aspartate transporter Glt(Ph) using all-atom molecular dynamics (MD) and free energy simulations (FES) to evaluate the role of different factors that control ion preferences of the binding sites identified in the crystallographic structure. The role of the bound ions in stabilizing the hairpin loop (HP2) by acting as an extracellular gate is discussed. Free energy simulations with classical and polarizable force-fields were used to characterize the role of the protein matrix, the site composition and the induced polarization in the stabilization of native and non-native cations, such as Li(+) and K(+), in the ion-binding sites of the transporter. The role of different factors that control the selectivity of the binding sites was highlighted with a number of reduced models using a scheme recently developed by Yu et al. (Proc. Natl. Acad. Sci. U. S. A., 2010, 107, 20329-20334 and J. Phys. Chem. B, 2009, 113, 8725).
Authors:
Bogdan Lev; Sergei Yu Noskov
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Publication Detail:
Type:  JOURNAL ARTICLE     Date:  2013-1-9
Journal Detail:
Title:  Physical chemistry chemical physics : PCCP     Volume:  -     ISSN:  1463-9084     ISO Abbreviation:  Phys Chem Chem Phys     Publication Date:  2013 Jan 
Date Detail:
Created Date:  2013-1-9     Completed Date:  -     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  100888160     Medline TA:  Phys Chem Chem Phys     Country:  -    
Other Details:
Languages:  ENG     Pagination:  -     Citation Subset:  -    
Affiliation:
Institute for Biocomplexity and Informatics and Department for Biological Sciences, 2500 University Drive, Calgary, Alberta, CanadaT2N1N4. snoskov@ucalgary.ca blev@ucalgary.ca.
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