Publication:
A multi-state coarse grained modeling approach for an intrinsically disordered peptide

dc.contributor.departmentDepartment of Chemical and Biological Engineering
dc.contributor.departmentGraduate School of Sciences and Engineering
dc.contributor.kuauthorDalgıçdır, Cahit
dc.contributor.kuauthorRamezanghorbani, Farhad
dc.contributor.kuauthorSayar, Mehmet
dc.contributor.schoolcollegeinstituteCollege of Engineering
dc.contributor.schoolcollegeinstituteGRADUATE SCHOOL OF SCIENCES AND ENGINEERING
dc.date.accessioned2024-11-09T12:28:15Z
dc.date.issued2017
dc.description.abstractMany 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.fulltextYES
dc.description.indexedbyWOS
dc.description.indexedbyScopus
dc.description.indexedbyPubMed
dc.description.issue9
dc.description.openaccessYES
dc.description.publisherscopeInternational
dc.description.sponsoredbyTubitakEuTÜBİTAK
dc.description.sponsorshipScientific and Technological Research Council of Turkey (TÜBİTAK)
dc.description.sponsorshipTurkish Academy of Sciences through the Young Scientist Award Program
dc.description.versionPublisher version
dc.description.volume147
dc.identifier.doi10.1063/1.5001087
dc.identifier.embargoNO
dc.identifier.filenameinventorynoIR01271
dc.identifier.issn0021-9606
dc.identifier.quartileQ1
dc.identifier.scopus2-s2.0-85029331750
dc.identifier.urihttps://hdl.handle.net/20.500.14288/1798
dc.identifier.wos409946200007
dc.keywordsResolution protein model
dc.keywordsLeucine-lysine peptide
dc.keywordsComputer simulations
dc.keywordsMolecular simulation
dc.keywordsForce-field
dc.keywordsTransferability
dc.keywordsConformation
dc.keywordsAggregation
dc.keywordsPotentials
dc.keywordsImplementation
dc.language.isoeng
dc.publisherAmerican Institute of Physics (AIP) Publishing
dc.relation.grantno212T184
dc.relation.grantnoTUBA GEBIP 2012
dc.relation.ispartofJournal of Chemical Physics
dc.relation.urihttp://cdm21054.contentdm.oclc.org/cdm/ref/collection/IR/id/7442
dc.subjectChemistry
dc.subjectPhysics
dc.titleA multi-state coarse grained modeling approach for an intrinsically disordered peptide
dc.typeJournal Article
dspace.entity.typePublication
local.contributor.kuauthorSayar, Mehmet
local.contributor.kuauthorDalgıçdır, Cahit
local.contributor.kuauthorRamezanghorbani, Farhad
local.publication.orgunit1College of Engineering
local.publication.orgunit1GRADUATE SCHOOL OF SCIENCES AND ENGINEERING
local.publication.orgunit2Department of Chemical and Biological Engineering
local.publication.orgunit2Graduate School of Sciences and Engineering
relation.isOrgUnitOfPublicationc747a256-6e0c-4969-b1bf-3b9f2f674289
relation.isOrgUnitOfPublication3fc31c89-e803-4eb1-af6b-6258bc42c3d8
relation.isOrgUnitOfPublication.latestForDiscoveryc747a256-6e0c-4969-b1bf-3b9f2f674289
relation.isParentOrgUnitOfPublication8e756b23-2d4a-4ce8-b1b3-62c794a8c164
relation.isParentOrgUnitOfPublication434c9663-2b11-4e66-9399-c863e2ebae43
relation.isParentOrgUnitOfPublication.latestForDiscovery8e756b23-2d4a-4ce8-b1b3-62c794a8c164

Files

Original bundle

Now showing 1 - 1 of 1
Thumbnail Image
Name:
7442.pdf
Size:
7.26 MB
Format:
Adobe Portable Document Format