Elucidating differences in the conformational dynamics of K-Ras isoforms

Simple item page
dc.contributor.advisorCummings, Patrick
dc.contributor.committeeMemberNussinov, Ruth
dc.contributor.committeeMemberFitch, Carolyn A.
dc.creatorChakrabarti, Mayukh
dc.date.accessioned2016-12-15T06:27:41Z
dc.date.available2016-12-15T06:27:41Z
dc.date.created2015-05
dc.date.issued2015-05-15
dc.date.submittedMay 2015
dc.date.updated2016-12-15T06:27:41Z
dc.description.abstractHumans ubiquitously express three genes (HRAS, KRAS, and NRAS) that encode four different isoforms of Ras, an integral p21 GTPase acting as an effector of cell surface receptors and regulating cell survival, proliferation, and differentiation. Mutations in KRAS account for the majority of all RAS-mediated cancers, and are amongst the most frequently observed in epithelial carcinomas. Nearly all observed Ras isoform mutations are found at codons 12, 13 and 61, and affect both splice variants of KRAS, K-Ras4A and K-Ras4B. The K-Ras isoforms share significant sequence identity, and differ only in their 23 residue C- terminal hypervariable region (HVR) and in four catalytic domain residues. However, little is known about how these residue differences correlate to K-Ras conformational dynamics, and consequently, their effects on Ras functional behavior and effector interactions. In this investigation, the functional consequences of residue differences between K-Ras4A and K- Ras4B were probed through all-atom molecular dynamics (MD) simulations to elucidate the effects of isoform-specific differences on K-Ras conformational dynamics. These simulations, utilizing the CHARMM programming package and NAMD code, aimed to (1) study the conformational fluctuations of the K-Ras4A catalytic domain, (2) study the dynamics of the full-length K-Ras4A isoform, and (3) characterize potential HVR interactions with the catalytic domain of the protein. These studies suggest that: (1) GDP-bound K-Ras4A exhibits a more exposed nucleotide binding pocket than K-Ras4B, which may facilitate enhanced nucleotide dissociation in this isoform, (2) GDP-bound K-Ras4A exhibits dynamic fluctuations in Switch I and II that differ from GDP-bound K-Ras4B, implying additional conformational states that may influence its interactions with guanine- nucleotide exchange factors (GEFs), (3) residues Q165 and Y166 in K-Ras4A may allosterically modulate the observed dynamic Switch region fluctuations, (4) full-length K-Ras4A exhibits nucleotide-dependent HVR fluctuations, and (5) the HVR of GDP and GTP-bound K-Ras4A confers additional flexibility to the intrinsic fluctuations of its Switch I and Switch II regions. These results provide a basis for further studies examining the functional consequences of K-Ras4A dynamics.
dc.format.mimetypeapplication/pdf
dc.identifier.urihttp://jhir.library.jhu.edu/handle/1774.2/39254
dc.languageen
dc.publisherJohns Hopkins University
dc.publisher.countryUSA
dc.subjectRas
dc.subjectisoforms
dc.subjectMolecular Dynamics
dc.subjectsimulation
dc.subjectCHARMM
dc.subjectBiophysics
dc.subjectcancer
dc.subjectoncogenic
dc.subjectsignaling
dc.subjectGTPases
dc.subjectRTK
dc.subjectGEF
dc.subjectGAP
dc.subjectallosteric
dc.titleElucidating differences in the conformational dynamics of K-Ras isoforms
dc.typeThesis
dc.type.materialtext
thesis.degree.departmentnot listed
thesis.degree.disciplineBioinformatics
thesis.degree.grantorJohns Hopkins University
thesis.degree.grantorAdvanced Academic Programs
thesis.degree.levelMasters
thesis.degree.nameM.S.
Files
Original bundle
Now showing 1 - 1 of 1
Thumbnail Image
Name:
CHAKRABARTI-THESIS-2015.pdf
Size:
4.93 MB
Format:
Adobe Portable Document Format
Download
License bundle
Now showing 1 - 1 of 1
No Thumbnail Available
Name:
LICENSE.txt
Size:
2.68 KB
Format:
Plain Text
Description:
Download
Collections
ETD -- Graduate theses