Publication:
Assembly of triblock amphiphilic peptides into one-dimensional aggregates and network formation

dc.contributor.coauthorN/A
dc.contributor.departmentDepartment of Mechanical Engineering
dc.contributor.departmentGraduate School of Sciences and Engineering
dc.contributor.kuauthorÖzgür, Beytullah
dc.contributor.kuauthorSayar, Mehmet
dc.contributor.schoolcollegeinstituteCollege of Engineering
dc.contributor.schoolcollegeinstituteGRADUATE SCHOOL OF SCIENCES AND ENGINEERING
dc.date.accessioned2024-11-09T22:57:46Z
dc.date.issued2016
dc.description.abstractPeptide assembly plays a key role in both neurological diseases and development of novel biomaterials with well-defined nanostructures. Synthetic model peptides provide a unique platform to explore the role of intermolecular interactions in the assembly process. a triblock peptide architecture designed by the Hartgerink group is a versatile system which relies on Coulomb interactions, hydrogen bonding, and hydrophobicity to guide these peptides' assembly at three different length scales: beta-sheets, double-wall ribbon-like aggregates, and finally a highly porous network structure which can support gels with <= 1% by weight peptide concentration. in this study, by using molecular dynamics simulations of a structure based implicit solvent coarse grained model, we analyzed this hierarchical assembly process. Parametrization of our CG model is based on multiple-state points from atomistic simulations, which enables this model to represent the conformational adaptability of the triblock peptide molecule based on the surrounding medium. Our results indicate that emergence of the double-wall beta-sheet packing mechanism, proposed in light of the experimental evidence, strongly depends on the subtle balance of the intermolecular forces. We demonstrate that, even though backbone hydrogen bonding dominates the early nucleation stages, depending on the strength of the hydrophobic and Coulomb forces, Alternative structures such as zero-dimensional aggregates with two beta-sheets oriented orthogonally (which we refer to as a cross-packed structure) and beta-sheets with misoriented hydrophobic side chains are also feasible. We discuss the implications of these competing structures for the three different length scales of assembly by systematically investigating the influence of density, counterion valency, and hydrophobicity.
dc.description.indexedbyWOS
dc.description.indexedbyScopus
dc.description.indexedbyPubMed
dc.description.issue39
dc.description.openaccessNO
dc.description.publisherscopeInternational
dc.description.sponsoredbyTubitakEuTÜBİTAK
dc.description.sponsorshipTUBITAK[112T496]
dc.description.sponsorshipTUBa Distinguished Young Scientist award M.S. thanks TUBITAK(Grant No. 112T496) and TUBa Distinguished Young Scientist award (2012 awardee) for financial support. We would like to thank Dr. Ozge Sensoy for a critical reading of our manuscript and scientific discussions.
dc.description.volume120
dc.identifier.doi10.1021/acs.jpcb.6b07545
dc.identifier.eissn1520-5207
dc.identifier.issn1520-6106
dc.identifier.quartileQ3
dc.identifier.scopus2-s2.0-84990851651
dc.identifier.urihttps://doi.org/10.1021/acs.jpcb.6b07545
dc.identifier.urihttps://hdl.handle.net/20.500.14288/7601
dc.identifier.wos384959200008
dc.keywordsMolecular-dynamics simulations
dc.keywordsResolution protein model
dc.keywordsAmyloid fibril formation
dc.keywordsSide-chain interactions
dc.keywordsCoarse-grained models
dc.keywordsBeta-sheet structure
dc.keywordsYeast prion sup35
dc.keywordsforce-field
dc.keywordsComputer-simulations
dc.keywordsSequence dependence
dc.language.isoeng
dc.publisheramer Chemical Soc
dc.relation.ispartofJournal of Physical Chemistry B
dc.subjectChemistry
dc.subjectPhysical chemistry
dc.titleAssembly of triblock amphiphilic peptides into one-dimensional aggregates and network formation
dc.typeJournal Article
dspace.entity.typePublication
local.contributor.kuauthorÖzgür, Beytullah
local.contributor.kuauthorSayar, Mehmet
local.publication.orgunit1GRADUATE SCHOOL OF SCIENCES AND ENGINEERING
local.publication.orgunit1College of Engineering
local.publication.orgunit2Department of Mechanical Engineering
local.publication.orgunit2Graduate School of Sciences and Engineering
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