R
Rebika Shrestha
Researcher at University of Texas at Austin
Publications - 9
Citations - 121
Rebika Shrestha is an academic researcher from University of Texas at Austin. The author has contributed to research in topics: Membrane & Lipid bilayer. The author has an hindex of 3, co-authored 5 publications receiving 72 citations.
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Journal ArticleDOI
Membrane Permeation of a Peptide: It is Better to be Positive
TL;DR: The permeation mechanism, which is revealed by molecular dynamics simulations, is of a translocation assisted by a local defect and suggests that the fastest permeation is when the tryptophan is positively charged.
Posted ContentDOI
Machine Learning-driven Multiscale Modeling Reveals Lipid-Dependent Dynamics of RAS Signaling Proteins
Helgi I. Ingólfsson,Chris Neale,Timothy S. Carpenter,Rebika Shrestha,Cesar A. Lopez,Timothy H. Tran,Tomas Oppelstrup,Harsh Bhatia,Liam Stanton,Xiaohua Zhang,Shiv Sundram,Francesco Di Natale,Animesh Agarwal,Gautham Dharuman,Sara Kokkila Schumacher,Thomas J. Turbyville,Gulcin Gulten,Que Van,Debanjan Goswami,Frantz Jean-Francios,Constance Agamasu,De Chen,Jeevapani J. Hettige,Timothy Travers,Sumantra Sarkar,Michael P. Surh,Yue Yang,Adam Moody,Shusen Liu,Brian Van Essen,Arthur F. Voter,Arvind Ramanathan,Nicolas W. Hengartner,Dhirendra K. Simanshu,Andrew G. Stephen,Peer-Timo Bremer,Sandrasegaram Gnanakaran,James N. Glosli,Felice C. Lightstone,Frank McCormick,Dwight V. Nissley,Frederick H. Streitz +41 more
TL;DR: A multiscale simulation infrastructure is demonstrated that uses machine learning to create a scale-bridging ensemble of over 100,000 simulations of active wild-type KRAS on a complex, asymmetric membrane that reports distinctive patterns of local lipid composition that correlate with interfacially promiscuous RAS multimerization.
Journal ArticleDOI
Measurement of the membrane dipole electric field in DMPC vesicles using vibrational shifts of p-cyanophenylalanine and molecular dynamics simulations.
TL;DR: The magnitude of the membrane dipole field was measured using vibrational Stark effect (VSE) shifts of nitrile oscillators placed on the unnatural amino acid p-cyanophenylalanine (p-CN-Phe) added to a peptide sequence at four unique positions.
Journal ArticleDOI
Direct Measurement of the Effect of Cholesterol and 6-Ketocholestanol on the Membrane Dipole Electric Field Using Vibrational Stark Effect Spectroscopy Coupled with Molecular Dynamics Simulations.
TL;DR: It is demonstrated how a one-atom difference in a sterol changes the physicochemical and electric field properties of the bilayer, as well as the impact of the sterol on hydrogen bonding with surface water.
Journal ArticleDOI
Asynchronous Reciprocal Coupling of Martini 2.2 Coarse-Grained and CHARMM36 All-Atom Simulations in an Automated Multiscale Framework.
Cesar A. Lopez,Xiaohua Zhang,Fikret Aydin,Rebika Shrestha,Que N. Van,Christopher B. Stanley,Timothy S. Carpenter,Kien Nguyen,Lara A. Patel,De-ping Chen,Violetta Burns,Nicolas W. Hengartner,Tyler J E Reddy,Harsh Bhatia,Francesco Di Natale,Timothy H. Tran,Albert H. Chan,Dhirendra K. Simanshu,Dwight V. Nissley,Frederick H. Streitz,Andrew G. Stephen,Thomas J. Turbyville,Felice C. Lightstone,Sandrasegaram Gnanakaran,Helgi I. Ingólfsson,Chris Neale +25 more
TL;DR: An extension to Multiscale Machine-learned Modeling Infrastructure (MuMMI) is detailed, including an improved CG-to-AA conversion tool called sinceCG, which is reliable (∼98% weakly correlated repeat success rate), automatable, and yields AA models that generally preserve protein secondary structure and maintain correct stereochemistry.