Exploring the Unfolding Pathway of Maltose Binding Proteins: An Integrated Computational Approach

Handle URI:
http://hdl.handle.net/10754/598294
Title:
Exploring the Unfolding Pathway of Maltose Binding Proteins: An Integrated Computational Approach
Authors:
Guardiani, Carlo; Marino, Daniele Di; Tramontano, Anna; Chinappi, Mauro; Cecconi, Fabio
Abstract:
© 2014 American Chemical Society. Recent single-molecule force spectroscopy experiments on the Maltose Binding Proteins (MBPs) identified four stable structural units, termed unfoldons, that resist mechanical stress and determine the intermediates of the unfolding pathway. In this work, we analyze the topological origin and the dynamical role of the unfoldons using an integrated approach which combines a graph-theoretical analysis of the interaction network of the MBP native-state with steered molecular dynamics simulations. The topological analysis of the native state, while revealing the structural nature of the unfoldons, provides a framework to interpret the MBP mechanical unfolding pathway. Indeed, the experimental pathway can be effectively predicted by means of molecular dynamics simulations with a simple topology-based and low-resolution model of the MBP. The results obtained from the coarse-grained approach are confirmed and further refined by all-atom molecular dynamics.
Citation:
Guardiani C, Marino DD, Tramontano A, Chinappi M, Cecconi F (2014) Exploring the Unfolding Pathway of Maltose Binding Proteins: An Integrated Computational Approach. Journal of Chemical Theory and Computation 10: 3589–3597. Available: http://dx.doi.org/10.1021/ct500283s.
Publisher:
American Chemical Society (ACS)
Journal:
Journal of Chemical Theory and Computation
Issue Date:
9-Sep-2014
DOI:
10.1021/ct500283s
PubMed ID:
26588503
Type:
Article
ISSN:
1549-9618; 1549-9626
Sponsors:
We acknowledge the CINECA (ISCRA project NAPS) for the availability of high performance computing resources and support. This research used the resources of the Supercomputing Laboratory at King Abdullah University of Science & Technology (KAUST) in Thuwal, Saudi Arabia.
Appears in Collections:
Publications Acknowledging KAUST Support

Full metadata record

DC FieldValue Language
dc.contributor.authorGuardiani, Carloen
dc.contributor.authorMarino, Daniele Dien
dc.contributor.authorTramontano, Annaen
dc.contributor.authorChinappi, Mauroen
dc.contributor.authorCecconi, Fabioen
dc.date.accessioned2016-02-25T13:18:09Zen
dc.date.available2016-02-25T13:18:09Zen
dc.date.issued2014-09-09en
dc.identifier.citationGuardiani C, Marino DD, Tramontano A, Chinappi M, Cecconi F (2014) Exploring the Unfolding Pathway of Maltose Binding Proteins: An Integrated Computational Approach. Journal of Chemical Theory and Computation 10: 3589–3597. Available: http://dx.doi.org/10.1021/ct500283s.en
dc.identifier.issn1549-9618en
dc.identifier.issn1549-9626en
dc.identifier.pmid26588503en
dc.identifier.doi10.1021/ct500283sen
dc.identifier.urihttp://hdl.handle.net/10754/598294en
dc.description.abstract© 2014 American Chemical Society. Recent single-molecule force spectroscopy experiments on the Maltose Binding Proteins (MBPs) identified four stable structural units, termed unfoldons, that resist mechanical stress and determine the intermediates of the unfolding pathway. In this work, we analyze the topological origin and the dynamical role of the unfoldons using an integrated approach which combines a graph-theoretical analysis of the interaction network of the MBP native-state with steered molecular dynamics simulations. The topological analysis of the native state, while revealing the structural nature of the unfoldons, provides a framework to interpret the MBP mechanical unfolding pathway. Indeed, the experimental pathway can be effectively predicted by means of molecular dynamics simulations with a simple topology-based and low-resolution model of the MBP. The results obtained from the coarse-grained approach are confirmed and further refined by all-atom molecular dynamics.en
dc.description.sponsorshipWe acknowledge the CINECA (ISCRA project NAPS) for the availability of high performance computing resources and support. This research used the resources of the Supercomputing Laboratory at King Abdullah University of Science & Technology (KAUST) in Thuwal, Saudi Arabia.en
dc.publisherAmerican Chemical Society (ACS)en
dc.titleExploring the Unfolding Pathway of Maltose Binding Proteins: An Integrated Computational Approachen
dc.typeArticleen
dc.identifier.journalJournal of Chemical Theory and Computationen
dc.contributor.institutionUniversita degli Studi di Roma La Sapienza, Rome, Italyen
dc.contributor.institutionIstituto Italiano di Tecnologia, Genoa, Italyen
dc.contributor.institutionCNR-Istituto Dei Sistemi Complessi (ISC), Rome, Italyen
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