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Molecular dynamics simulations reveal the perception of brassinosteroids by the plant receptor BRI1

IllinoisPlant Biology
Faisal Aldukhi#, Aniket Deb#, Chuankai Zhao, Alexander S. Moffett and Diwakar Shukla. (# denotes co-first author)
In review, 2019.

How do brassinosteroids activate their receptors?

IllinoisPlant Biology
Alexander S. Moffett and Diwakar Shukla
In review, 2019.

Computational microscopy: revealing molecular mechanisms in plants using molecular dynamics simulations.

IllinoisPlant Biology
Jiangyan Feng#, Jiming Chen#, Balaji Selvam# and Diwakar Shukla. (# denotes co-first authors)
The Plant Cell, In press, 2019.

Distinct Substrate Transport Mechanism Identified in Homologous Sugar Transporters.

IllinoisPlant Biology
Kevin J. Cheng,# Balaji Selvam#, Li-Qing Chen, and Diwakar Shukla. (# denotes co-first authors)
In review, 2019.

The substrate import mechanism of the human serotonin transporter

Illinois
Matthew Chan#, Balaji Selvam#, Heather J. Young, Erik Procko and Diwakar Shukla*
In review, 2019.

TLmutation: predicting the effects of mutations using transfer learning.

IllinoisMethods
Zahra Shamsi, Matthew Chan and Diwakar Shukla
In review, 2019.

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

Illinois
Erfan Mohammadi, Chuankai Zhao, Fengjiao Zhang, Ge Qu, Seok-Heon Jung, Qiujie Zhao, Christopher M. Evans, Jin-Kyun Lee, Diwakar Shukla and Ying Diao.
ACS Applied Material and Interfaces, Volume 11(25), Pages 22561-22574, 2019.

Molecular Basis of Glucose Transport Mechanism in Plants.

IllinoisPlant Biology
Balaji Pannerselvam, Ya-Chi Yu, Li-Qing Chen and Diwakar Shukla*
ACS Central Science, Volume 5(6), Pages 1085-1096, 2019.

Divalent Cations Promote TALE DNA-binding Specificity.

Illinois
Luke Cuculis+, Chuankai Zhao+, Zhanar Abil, Huimin Zhao, Diwakar Shukla* and C. M. Schroeder*. (+ denotes co-first author)
In review, 2019.

Dodine as a Kosmo-chaotropic Agent.

Illinois
Drishti Guin, Shriyaa Mittal, Brian Bozymski, Diwakar Shukla* and Martin H. W. Gruebele*
Journal of Physical Chemistry Letters, Volume 10(10), Pages 2600-2605, 2019.

Dewetting Controls Plant Hormone Perception and Initiation of Drought Resistance Signaling.

IllinoisPlant Biology
Saurabh Shukla+, Chuankai Zhao+ and Diwakar Shukla. (+ denotes co-first author)
Structure, Volume 27, Pages 1–11, 2019.

Selection of the Dimeric Sweet Taste Receptor for Surface Expression and Inter-subunit Interactions.

Illinois
Jihye Park, Balaji Selvam, , Keisuke Sanematsu, Noriatsu Shigemura, Diwakar Shukla, and Erik Procko.
Journal of Biological Chemistry, Vol. 294, Pages 4759-4774, 2019.

Free energy landscape of the complete transport cycle in a key bacterial transporter

IllinoisPlant Biology
Balaji Pannerselvam+, Shriyaa Mittal+ and Diwakar Shukla (+ denotes co-first author)
ACS Central Science, Volume 4, Issue 9, Pages 1146–1154, 2018.

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

IllinoisMethods
Chuankai Zhao and Diwakar Shukla
Scientific Reports, Volume 8, Article number: 17748, 2018.

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

IllinoisMethods
Shriyaa Mittal and Diwakar Shukla
Journal of Physical Chemistry B, Volume 122, Issue 48, Pages 10793–10805, 2018

REinforcement learning based Adaptive samPling: REAPing Rewards by Exploring Protein Conformational Landscapes

IllinoisMethods
Zahra Shamsi, Kevin J. Cheng and Diwakar Shukla
Journal of Physical Chemistry B, Volume 122, Issue 35, Pages 8386–8395, 2018.

Automatic Feature Selection in Markov State Models Using Genetic Algorithm.

IllinoisMethods
Qihua Chen#+, Jiangyan Feng+, Shriyaa Mittal and Diwakar Shukla. (#denotes undergraduate first-author, + denotes co-first author)
Journal of Computational Science Education, Volume 9, Issue 2, Pages 14-22, 2018.

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

Illinois
Balaji Pannerselvam, Zahra Shamsi and Diwakar Shukla
Angewandte Chemie, Vol. 47, Issue 12, Pages 3048-3053, 2018.

Characterizing Conformational Dynamics of Proteins Using Evolutionary Couplings.

IllinoisMethods
Jiangyan Feng and Diwakar Shukla
The Journal of Physical Chemistry B, Volume 122, Issue 3, Pages 1017–1025, 2018.

Using Molecular Simulation to Explore the Nanoscale Dynamics of the Plant Kinome.

IllinoisPlant Biology
Alexander S. Moffett and Diwakar Shukla
Biochemical Journal, Vol. 475, Issue 5, Pages 905-921, 2018.

Recruiting Machine Learning Methods for Molecular Simulations of Proteins

IllinoisMethods
Shriyaa Mittal and Diwakar Shukla
Molecular Simulation, Vol. 44, Issue 11, Pages 891-904, 2018.

Predicting Optimal DEER Label Positions to Study Protein Conformational Heterogeneity.

IllinoisMethods
Shriyaa Mittal and Diwakar Shukla
Journal of Physical Chemistry B, Volume 121, Issue 42, Pages 9761–9770, 2017.

Allosteric control of a plant receptor kinase through S-glutathionylation.

IllinoisPlant Biology
Alexander S. Moffett, Kyle W. Bender, Steven C. Huber, and Diwakar Shukla
Biophysical Journal, Volume 113, Issue 11, Pages 2354-2363, 2017.

Enhanced unbiased sampling of protein dynamics using evolutionary coupling information.

IllinoisMethods
Zahra Shamsi*, Alexander S. Moffett* and Diwakar Shukla. * indicates co-first author.
Scientific Reports, 7, Article number: 12700, 2017. doi:10.1038/s41598-017-12874-7

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

IllinoisPlant Biology
Alexander S. Moffett, Kyle W. Bender, Steven C. Huber and Diwakar Shukla
Journal of Biological Chemistry, 292, 30, 12643–12652, 2017.

Crops in silico: A prospectus from the Plants in silico symposium and workshop

IllinoisPlant Biology
Amy Marshall-Colon, Stephen P. Long, Douglas K. Allen, Gabrielle Allen, Daniel A. Beard, Bedrich Benes, Susanne von Caemmerer, AJ Christensen, Donna J. Cox, John C. Hart, Peter M. Hirst, Kavya Kannan, Daniel S. Katz, Jonathan P. Lynch, Andrew J. Millar, Balaji Panneerselvam, Nathan D. Price, David Raila, Rachel G. Shekar, Stuti Shrivastava, Diwakar Shukla, Venkatraman Srinivasan, Mark Stitt, Eberhard O. Voit, Yu Wang, Xinyou Yin, Xin-Guang Zhu
Frontiers in Plant Science, Vol. 8, Article 786, 2017. doi: 10.3389/fpls.2017.00786

Dynamic-Template-Directed Multiscale Assembly for Large-Area Coating of Highly-Aligned Conjugated Polymer Thin Films

Illinois
Erfan Mohammadi, Chuankai Zhao, Y. Meng, Fengjiao Zhang, Ge Qu, X. Zhao, Jianguo Mei, J. M. Zuo, Diwakar Shukla, Ying Diao.
Nature Communications, Vol. 8, Article number: 16070, 2017. doi:10.1038/ncomms16070

Application of Hidden Markov Models in Biomolecular Simulations

Book ChapterIllinois
Saurabh Shukla, Zahra Shamsi, Alexander S. Moffett, Balaji Selvam and Diwakar Shukla*
Methods in Molecular Biology, Hidden Markov Models, pp 29-41, 2017.

Conformational Heterogeneity of the Calmodulin Binding Interface.

IllinoisStanford
Diwakar Shukla*, Ariana Peck* and Vijay S. Pande
Nature Communications, 7, Article number: 10910, 2016. doi:10.1038/ncomms10910

Elucidating Ligand-Modulated Conformational Landscape of GPCRs Using Cloud-computing Approaches.

Book ChapterIllinoisMethodsStanford
Diwakar Shukla*, Morgan Lawrenz and Vijay S. Pande
Methods in Enzymology, 557, 551-572, 2015.