Publication: A multi-state coarse grained modeling approach for an intrinsically disordered peptide
dc.contributor.department | Department of Chemical and Biological Engineering | |
dc.contributor.department | Graduate School of Sciences and Engineering | |
dc.contributor.kuauthor | Dalgıçdır, Cahit | |
dc.contributor.kuauthor | Ramezanghorbani, Farhad | |
dc.contributor.kuauthor | Sayar, Mehmet | |
dc.contributor.schoolcollegeinstitute | College of Engineering | |
dc.contributor.schoolcollegeinstitute | GRADUATE SCHOOL OF SCIENCES AND ENGINEERING | |
dc.date.accessioned | 2024-11-09T12:28:15Z | |
dc.date.issued | 2017 | |
dc.description.abstract | Many proteins display a marginally stable tertiary structure, which can be altered via external stimuli. Since a majority of coarse grained (CG) models are aimed at structure prediction, their success for an intrinsically disordered peptide's conformational space with marginal stability and sensitivity to external stimuli cannot be taken for granted. In this study, by using the LK alpha 14 peptide as a test system, we demonstrate a bottom-up approach for constructing a multi-state CG model, which can capture the conformational behavior of this peptide in three distinct environments with a unique set of interaction parameters. LK alpha 14 is disordered in dilute solutions; however, it strictly adopts the alpha-helix conformation upon aggregation or when in contact with a hydrophobic/hydrophilic interface. Our bottom-up approach combines a generic base model, that is unbiased for any particular secondary structure, with nonbonded interactions which represent hydrogen bonds, electrostatics, and hydrophobic forces. We demonstrate that by using carefully designed all atom potential of mean force calculations from all three states of interest, one can get a balanced representation of the nonbonded interactions. Our CG model behaves intrinsically disordered in bulk water, folds into an alpha-helix in the presence of an interface or a neighboring peptide, and is stable as a tetrameric unit, successfully reproducing the all atom molecular dynamics simulations and experimental results. | |
dc.description.fulltext | YES | |
dc.description.indexedby | WOS | |
dc.description.indexedby | Scopus | |
dc.description.indexedby | PubMed | |
dc.description.issue | 9 | |
dc.description.openaccess | YES | |
dc.description.publisherscope | International | |
dc.description.sponsoredbyTubitakEu | TÜBİTAK | |
dc.description.sponsorship | Scientific and Technological Research Council of Turkey (TÜBİTAK) | |
dc.description.sponsorship | Turkish Academy of Sciences through the Young Scientist Award Program | |
dc.description.version | Publisher version | |
dc.description.volume | 147 | |
dc.identifier.doi | 10.1063/1.5001087 | |
dc.identifier.embargo | NO | |
dc.identifier.filenameinventoryno | IR01271 | |
dc.identifier.issn | 0021-9606 | |
dc.identifier.quartile | Q1 | |
dc.identifier.scopus | 2-s2.0-85029331750 | |
dc.identifier.uri | https://hdl.handle.net/20.500.14288/1798 | |
dc.identifier.wos | 409946200007 | |
dc.keywords | Resolution protein model | |
dc.keywords | Leucine-lysine peptide | |
dc.keywords | Computer simulations | |
dc.keywords | Molecular simulation | |
dc.keywords | Force-field | |
dc.keywords | Transferability | |
dc.keywords | Conformation | |
dc.keywords | Aggregation | |
dc.keywords | Potentials | |
dc.keywords | Implementation | |
dc.language.iso | eng | |
dc.publisher | American Institute of Physics (AIP) Publishing | |
dc.relation.grantno | 212T184 | |
dc.relation.grantno | TUBA GEBIP 2012 | |
dc.relation.ispartof | Journal of Chemical Physics | |
dc.relation.uri | http://cdm21054.contentdm.oclc.org/cdm/ref/collection/IR/id/7442 | |
dc.subject | Chemistry | |
dc.subject | Physics | |
dc.title | A multi-state coarse grained modeling approach for an intrinsically disordered peptide | |
dc.type | Journal Article | |
dspace.entity.type | Publication | |
local.contributor.kuauthor | Sayar, Mehmet | |
local.contributor.kuauthor | Dalgıçdır, Cahit | |
local.contributor.kuauthor | Ramezanghorbani, Farhad | |
local.publication.orgunit1 | College of Engineering | |
local.publication.orgunit1 | GRADUATE SCHOOL OF SCIENCES AND ENGINEERING | |
local.publication.orgunit2 | Department of Chemical and Biological Engineering | |
local.publication.orgunit2 | Graduate School of Sciences and Engineering | |
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relation.isOrgUnitOfPublication | 3fc31c89-e803-4eb1-af6b-6258bc42c3d8 | |
relation.isOrgUnitOfPublication.latestForDiscovery | c747a256-6e0c-4969-b1bf-3b9f2f674289 | |
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