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Research Output 2005 2019

2019

Dewetting Controls Plant Hormone Perception and Initiation of Drought Resistance Signaling

Shukla, S., Zhao, C. & Shukla, D., Apr 2 2019, In : Structure. 27, 4, p. 692-702.e3

Research output: Contribution to journalArticle

Abscisic Acid
Plant Growth Regulators
Droughts
Post Translational Protein Processing

Distinct Substrate Transport Mechanism Identified in Homologous Sugar Transporters

Cheng, K. J., Selvam, B., Chen, L. & Shukla, D., Oct 10 2019, In : Journal of Physical Chemistry B. 123, 40, p. 8411-8418 8 p.

Research output: Contribution to journalArticle

transporter
sugars
Sugars
glucose
Glucose

Dodine as a Kosmo-Chaotropic Agent

Guin, D., Mittal, S., Bozymski, B., Shukla, D. & Gruebele, M. H. W., May 16 2019, In : Journal of Physical Chemistry Letters. 10, 10, p. 2600-2605 6 p.

Research output: Contribution to journalArticle

proteins
Proteins
helices
Spectroscopy
Janus

Ion Gel Dynamic Templates for Large Modulation of Morphology and Charge Transport Properties of Solution-Coated Conjugated Polymer Thin Films

Mohammadi, E., Zhao, C., Zhang, F., Qu, G., Jung, S. H., Zhao, Q., Evans, C., Lee, J. K., Shukla, D. & Diao, Y., Jan 1 2019, In : ACS Applied Materials and Interfaces.

Research output: Contribution to journalArticle

Conjugated polymers
Polymer films
Transport properties
Charge transfer
Gels

Molecular Basis of the Glucose Transport Mechanism in Plants

Selvam, B., Yu, Y. C., Chen, L. & Shukla, D., Jun 26 2019, In : ACS Central Science. 5, 6, p. 1085-1096 12 p.

Research output: Contribution to journalArticle

Open Access
Facings
Glucose
Sugars
Free energy
Molecular dynamics

Structural architecture of a dimeric class C GPCR based on co-trafficking of sweet taste receptor subunits

Park, J., Selvam, B., Sanematsu, K., Shigemura, N., Shukla, D. & Procko, E., Jan 1 2019, In : Journal of Biological Chemistry. 294, 13, p. 4759-4774 16 p.

Research output: Contribution to journalArticle

G-Protein-Coupled Receptors
Dimerization
Dimers
Cysteine
Cells
2018

Characterizing Conformational Dynamics of Proteins Using Evolutionary Couplings

Feng, J. & Shukla, D., Jan 25 2018, In : Journal of Physical Chemistry B. 122, 3, p. 1017-1025 9 p.

Research output: Contribution to journalArticle

proteins
Proteins
folding
Sampling
sampling

Free Energy Landscape of the Complete Transport Cycle in a Key Bacterial Transporter

Selvam, B., Mittal, S. & Shukla, D., Sep 26 2018, In : ACS Central Science. 4, 9, p. 1146-1154 9 p.

Research output: Contribution to journalArticle

Facings
Free energy
Molecular dynamics
Energy barriers
Protons

Maximizing Kinetic Information Gain of Markov State Models for Optimal Design of Spectroscopy Experiments

Mittal, S. & Shukla, D., Dec 6 2018, In : Journal of Physical Chemistry B. 122, 48, p. 10793-10805 13 p.

Research output: Contribution to journalArticle

Spectroscopy
proteins
Proteins
Kinetics
kinetics

Recruiting machine learning methods for molecular simulations of proteins

Mittal, S. & Shukla, D., Jul 24 2018, In : Molecular Simulation. 44, 11, p. 891-904 14 p.

Research output: Contribution to journalArticle

Molecular Simulation
machine learning
Molecular Dynamics
Molecular Dynamics Simulation
Learning systems

Reinforcement Learning Based Adaptive Sampling: REAPing Rewards by Exploring Protein Conformational Landscapes

Shamsi, Z., Cheng, K. J. & Shukla, D., Sep 6 2018, In : Journal of Physical Chemistry B. 122, 35, p. 8386-8395 10 p.

Research output: Contribution to journalArticle

Reinforcement learning
reinforcement
Reward
learning
sampling

SAXS-guided Enhanced Unbiased Sampling for Structure Determination of Proteins and Complexes

Zhao, C. & Shukla, D., Dec 1 2018, In : Scientific reports. 8, 1, 17748.

Research output: Contribution to journalArticle

X-Rays
Proteins
Protein Conformation
Thermodynamics

Universality of the Sodium Ion Binding Mechanism in Class A G-Protein-Coupled Receptors

Selvam, B., Shamsi, Z. & Shukla, D., Mar 12 2018, In : Angewandte Chemie - International Edition. 57, 12, p. 3048-3053 6 p.

Research output: Contribution to journalArticle

G-Protein-Coupled Receptors
Sodium
Ions
Proteins
Free energy

Using molecular simulation to explore the nanoscale dynamics of the plant kinome

Moffett, A. S. & Shukla, D., Mar 15 2018, In : Biochemical Journal. 475, 5, p. 905-921 17 p.

Research output: Contribution to journalArticle

Protein Kinases
Molecular Dynamics Simulation
Molecular dynamics
Plant Proteins
Phosphorylation
2017

Allosteric Control of a Plant Receptor Kinase through S-Glutathionylation

Moffett, A. S., Bender, K. W., Huber, S. C. & Shukla, D., Dec 5 2017, In : Biophysical journal. 113, 11, p. 2354-2363 10 p.

Research output: Contribution to journalArticle

Protein S
Protein Kinases
Oxidation-Reduction
Phosphotransferases
Brassinosteroids

Application of Hidden Markov models in biomolecular simulations

Shukla, S., Shamsi, Z., Moffett, A. S., Selvam, B. & Shukla, D., Jan 1 2017, Methods in Molecular Biology. Humana Press Inc., Vol. 1552. p. 29-41 13 p. (Methods in Molecular Biology; vol. 1552).

Research output: Chapter in Book/Report/Conference proceedingChapter

Methionine Enkephalin
Peptides
Datasets

Crops in silico: Generating virtual crops using an integrative and multi-scale modeling platform

Marshall-Colon, A., Long, S. P., Allen, D. K., Allen, G. D., Beard, D. A., Benes, B., Von Caemmerer, S., Christensen, A. J., Cox, D. J., Hart, J. C., Hirst, P. M., Kannan, K., Katz, D. S., Lynch, J. P., Millar, A. J., Panneerselvam, B., Price, N. D., Prusinkiewicz, P., Raila, D., Shekar, R. G. & 9 others, Shrivastava, S., Shukla, D., Srinivasan, V., Stitt, M., Turk, M. J., Voit, E. O., Wang, Y., Yin, X. & Zhu, X. G., May 15 2017, In : Frontiers in Plant Science. 8, 786.

Research output: Contribution to journalArticle

crops
engineering
ecosystems
plant biology
climate models

Dynamic-template-directed multiscale assembly for large-area coating of highly-aligned conjugated polymer thin films

Mohammadi, E., Zhao, C., Meng, Y., Qu, G., Zhang, F., Zhao, X., Mei, J., Zuo, J. M., Shukla, D. & Diao, Y., Jul 13 2017, In : Nature communications. 8, 16070.

Research output: Contribution to journalArticle

Conjugated polymers
Polymer films
coating
Polymers
templates

Enhanced unbiased sampling of protein dynamics using evolutionary coupling information

Shamsi, Z., Moffett, A. S. & Shukla, D., Dec 1 2017, In : Scientific reports. 7, 1, 12700.

Research output: Contribution to journalArticle

Proteins
Adrenergic Receptors
Protein Folding
Dimerization
Escherichia coli

Molecular dynamics simulations reveal the conformational dynamics of Arabidopsis thaliana BRI1 and BAK1 receptor-like kinases

Moffett, A. S., Bender, K. W., Huber, S. C. & Shukla, D., Jan 1 2017, In : Journal of Biological Chemistry. 292, 30, p. 12643-12652 10 p.

Research output: Contribution to journalArticle

Brassinosteroids
Molecular Dynamics Simulation
Arabidopsis
Molecular dynamics
Phosphotransferases

Predicting Optimal DEER Label Positions to Study Protein Conformational Heterogeneity

Mittal, S. & Shukla, D., Oct 26 2017, In : Journal of Physical Chemistry B. 121, 42, p. 9761-9770 10 p.

Research output: Contribution to journalArticle

Electron resonance
Labels
Electrons
proteins
Proteins
2016

Conformational heterogeneity of the calmodulin binding interface

Shukla, D., Peck, A. & Pande, V. S., Apr 4 2016, In : Nature communications. 7, 10910.

Research output: Contribution to journalArticle

calmodulin
Calmodulin
Molecular Dynamics Simulation
G-Protein-Coupled Receptors
Ion Channels

Markov state models and tICA reveal a nonnative folding nucleus in simulations of NuG2

Schwantes, C. R., Shukla, D. & Pande, V. S., Apr 26 2016, In : Biophysical journal. 110, 8, p. 1716-1719 4 p.

Research output: Contribution to journalArticle

Mutant Proteins
Peptides

Transition path theory analysis of c-Src kinase activation

Meng, Y., Shukla, D., Pande, V. S. & Roux, B., Aug 16 2016, In : Proceedings of the National Academy of Sciences of the United States of America. 113, 33, p. 9193-9198 6 p.

Research output: Contribution to journalArticle

src-Family Kinases
Protein-Tyrosine Kinases
Catalytic Domain
Proteins
CSK tyrosine-protein kinase
2015

A network of molecular switches controls the activation of the two-component response regulator NtrC

Vanatta, D. K., Shukla, D., Lawrenz, M. & Pande, V. S., Jun 15 2015, In : Nature communications. 6, 7283.

Research output: Contribution to journalArticle

PII Nitrogen Regulatory Proteins
regulators
Molecular Dynamics Simulation
Protein C
switches

Cloud computing approaches for prediction of ligand binding poses and pathways

Lawrenz, M., Shukla, D. & Pande, V. S., Jan 22 2015, In : Scientific reports. 5, 7918.

Research output: Contribution to journalArticle

Ligands
Tacrolimus Binding Protein 1A
Immunophilins
Protein Engineering
Molecular Dynamics Simulation

Conserve water: A method for the analysis of solvent in molecular dynamics

Harrigan, M. P., Shukla, D. & Pande, V. S., Mar 10 2015, In : Journal of Chemical Theory and Computation. 11, 3, p. 1094-1101 8 p.

Research output: Contribution to journalArticle

Molecular dynamics
molecular dynamics
Water
water
drying

Elucidating ligand-modulated conformational landscape of GPCRs using cloud-computing approaches

Shukla, D., Lawrenz, M. & Pande, V. S., Jan 1 2015, Methods in Enzymology. Academic Press Inc., p. 551-572 22 p. (Methods in Enzymology; vol. 557).

Research output: Chapter in Book/Report/Conference proceedingChapter

Cloud computing
G-Protein-Coupled Receptors
Chemical activation
Ligands
CCR10 Receptors

Erratum: Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways (Nature Chemistry (2014) 6:15-21)

Kohlhoff, K. J., Shukla, D., Lawrenz, M., Bowman, G. R., Konerding, D. E., Belov, D., Altman, R. B. & Pande, V. S., Aug 20 2015, In : Nature Chemistry. 7, 9, 1 p.

Research output: Contribution to journalComment/debate

Heat dissipation guides activation in signaling proteins

Weber, J. K., Shukla, D. & Pande, V. S., Aug 18 2015, In : Proceedings of the National Academy of Sciences of the United States of America. 112, 33, p. 10377-10382 6 p.

Research output: Contribution to journalArticle

Entropy
Hot Temperature
Proteins
Cyclic GMP-Dependent Protein Kinases
Phase Transition

Markov state models provide insights into dynamic modulation of protein function

Shukla, D., Hernández, C. X., Weber, J. K. & Pande, V. S., Feb 17 2015, In : Accounts of chemical research. 48, 2, p. 414-422 9 p.

Research output: Contribution to journalReview article

Modulation
Proteins
Amyloid
Intrinsically Disordered Proteins
Sampling
2014

Activation pathway of Src kinase reveals intermediate states as targets for drug design

Shukla, D., Meng, Y., Roux, B. & Pande, V. S., Mar 3 2014, In : Nature communications. 5, 3397.

Research output: Contribution to journalArticle

src-Family Kinases
Drug Design
drugs
Phosphotransferases
Chemical activation

Automatic selection of order parameters in the analysis of large scale molecular dynamics simulations

Sultan, M. M., Kiss, G., Shukla, D. & Pande, V. S., Dec 9 2014, In : Journal of Chemical Theory and Computation. 10, 12, p. 5217-5223 7 p.

Research output: Contribution to journalArticle

Molecular dynamics
Feature extraction
molecular dynamics
Cell signaling
Computer simulation

Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways

Kohlhoff, K. J., Shukla, D., Lawrenz, M., Bowman, G. R., Konerding, D. E., Belov, D., Altman, R. B. & Pande, V. S., Jan 1 2014, In : Nature Chemistry. 6, 1, p. 15-21 7 p.

Research output: Contribution to journalArticle

Cloud computing
CCR10 Receptors
Chemical activation
Ligands
Modulation

Complex pathways in folding of protein G explored by simulation and experiment

Lapidus, L. J., Acharya, S., Schwantes, C. R., Wu, L., Shukla, D., King, M., Decamp, S. J. & Pande, V. S., Aug 19 2014, In : Biophysical journal. 107, 4, p. 947-955 9 p.

Research output: Contribution to journalArticle

Protein Folding
Microfluidics
Molecular Dynamics Simulation
Circular Dichroism
Tryptophan
2013

OpenMM 4: A reusable, extensible, hardware independent library for high performance molecular simulation

Eastman, P., Friedrichs, M. S., Chodera, J. D., Radmer, R. J., Bruns, C. M., Ku, J. P., Beauchamp, K. A., Lane, T. J., Wang, L. P., Shukla, D., Tye, T., Houston, M., Stich, T., Klein, C., Shirts, M. R. & Pande, V. S., Jan 8 2013, In : Journal of Chemical Theory and Computation. 9, 1, p. 461-469 9 p.

Research output: Contribution to journalArticle

application programming interface
hardware
Hardware
Application programming interfaces (API)
simulation

To milliseconds and beyond: Challenges in the simulation of protein folding

Lane, T. J., Shukla, D., Beauchamp, K. A. & Pande, V. S., Feb 1 2013, In : Current Opinion in Structural Biology. 23, 1, p. 58-65 8 p.

Research output: Contribution to journalReview article

Protein Folding
Molecular Dynamics Simulation
Computational Biology
Proteins
Datasets

Understanding the role of arginine and citrate as eluents in affinity chromatography

Shukla, D. & Trout, B. L., Mar 8 2013, Developments in Biotechnology and Bioprocessing. American Chemical Society, p. 67-86 20 p. (ACS Symposium Series; vol. 1125).

Research output: Chapter in Book/Report/Conference proceedingChapter

Affinity chromatography
Arginine
Antibodies
Citric Acid
Staphylococcal Protein A
2011

Arginine and the hofmeister series: The role of ion-ion interactions in protein aggregation suppression

Schneider, C. P., Shukla, D. & Trout, B. L., Jun 9 2011, In : Journal of Physical Chemistry B. 115, 22, p. 7447-7458 12 p.

Research output: Contribution to journalArticle

Arginine
Agglomeration
retarding
Ions
salts

Complex interactions between molecular ions in solution and their effect on protein stability

Shukla, D., Schneider, C. P. & Trout, B. L., Nov 23 2011, In : Journal of the American Chemical Society. 133, 46, p. 18713-18718 6 p.

Research output: Contribution to journalArticle

Molecular interactions
Protein Stability
Ions
Proteins
protein

Effects of PAMAM dendrimer salt solutions on protein stability

Shukla, D., Schneider, C. P. & Trout, B. L., Jul 21 2011, In : Journal of Physical Chemistry Letters. 2, 14, p. 1782-1788 7 p.

Research output: Contribution to journalArticle

Dendrimers
dendrimers
Salts
salts
proteins

Effects of Solute-Solute Interactions on Protein Stability Studied Using Various Counterions and Dendrimers

Schneider, C. P., Shukla, D. & Trout, B. L., Dec 1 2011, In : PloS one. 6, 11, e27665.

Research output: Contribution to journalArticle

Dendrimers
Protein Stability
Guanidine
solutes
Hydrogen

Molecular level insight into intra-solvent interaction effects on protein stability and aggregation

Shukla, D., Schneider, C. P. & Trout, B. L., Oct 1 2011, In : Advanced Drug Delivery Reviews. 63, 13, p. 1074-1085 12 p.

Research output: Contribution to journalReview article

Protein Stability
Proteins
Therapeutics
Pharmaceutical Preparations

Preferential interaction coefficients of proteins in aqueous arginine solutions and their molecular origins

Shukla, D. & Trout, B. L., Feb 10 2011, In : Journal of Physical Chemistry B. 115, 5, p. 1243-1253 11 p.

Research output: Contribution to journalArticle

Arginine
aqueous solutions
proteins
Proteins
coefficients

Understanding the role of arginine as an eluent in affinity chromatography via molecular computations

Shukla, D., Zamolo, L., Cavallotti, C. & Trout, B. L., Mar 24 2011, In : Journal of Physical Chemistry B. 115, 11, p. 2645-2654 10 p.

Research output: Contribution to journalArticle

Molecular Computers
Affinity chromatography
Arginine
chromatography
antibodies

Understanding the synergistic effect of arginine and glutamic acid mixtures on protein solubility

Shukla, D. & Trout, B. L., Oct 20 2011, In : Journal of Physical Chemistry B. 115, 41, p. 11831-11839 9 p.

Research output: Contribution to journalArticle

Arginine
glutamic acid
Solubility
Glutamic Acid
solubility
2010

Interaction of arginine with proteins and the mechanism by which it inhibits aggregation

Shukla, D. & Trout, B. L., Oct 28 2010, In : Journal of Physical Chemistry B. 114, 42, p. 13426-13438 13 p.

Research output: Contribution to journalArticle

Arginine
Agglomeration
proteins
Proteins
interactions
2009

Modeling of formation of nanoparticles in reverse micellar systems: Ostwald ripening of silver halide particles

Shukla, D., Josbi, A. A. & Mehra, A., Mar 17 2009, In : Langmuir. 25, 6, p. 3786-3793 8 p.

Research output: Contribution to journalArticle

Silver halides
Ostwald ripening
silver halides
Nanoparticles
nanoparticles

Molecular computations of preferential interaction coefficients of proteins

Shukla, D., Shinde, C. & Trout, B. L., Sep 17 2009, In : Journal of Physical Chemistry B. 113, 37, p. 12546-12554 9 p.

Research output: Contribution to journalArticle

Molecular Computers
proteins
Proteins
coefficients
field theory (physics)
2008

Preferential interaction parameters of proteins in mixed solvents

Shukla, D. & Trout, B. L., 2008, AIChE100 - 2008 AIChE Annual Meeting, Conference Proceedings.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Proteins