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Diwakar Shukla's directory photo.

Diwakar Shukla

Associate Professor

Primary Affiliation

Theoretical and Computational Biophysics

Affiliations

Status Affiliate Faculty

Home Chemical and Biomolecular Engineering

Phone

Email diwakar@illinois.edu

Address

  • Biography

    Diwakar Shukla is an associate professor in the Department of Chemical and Biomolecular Engineering. His primary affiliation is Theoretical and Computational Biophysics.

    Education

    • B.Tech., chemical engineering, Indian Institute of Technology, Bombay, 2006

    • M.Tech., chemical engineering, Indian Institute of Technology Bombay, 2006

    • M.S., chemical engineering practice, Massachusetts Institute of Technology, 2009

    • Ph.D., chemical engineering, Massachusetts Institute of Technology, 2006-2011

  • Honors

    • 2022: Pivot Fellowship, Simons Foundation

    • 2019: Sloan Research Fellowship, Alfred P. Sloan Foundation

    • 2018: NSF Early Career Award, National Science Foundation

    • 2018: OpenEye Outstanding Junior Faculty in Computational Chemistry, American Chemical Society

    • 2018: CoMSEF Young Investigator Award, American Institute of Chemical Engineers

    • 2017: New Innovator Award in Food & Agriculture Research, Foundation for Food & Agriculture Research

    • 2015: Engineering Council Outstanding Advising Award, University of Illinois at Urbana-Champaign

    • 2016-2018: List of Excellent Teachers, University of Illinois at Urbana-Champaign

  • Research

    Research areas:

    • Computation

    • Experiment

    • Chemistry

    • Biology

    Research interests:

    • Molecular engineering

    • Molecular modeling and simulations

    • Biophysics

    The long-term research goal of Shukla group is to combine theory, computation, and experiments to develop quantitative models of biological phenomena relevant for health, energy and climate change. They integrate ideas from a wide range of disciplines tied together by a vision of “Dynamic” biology and its role in engineering products. Shukla group is developing machine learning methods to address the challenges of conformational sampling, accuracy and interpretability of large scale simulation data from molecular simulations. They are employing high-throughput experimental methods to decipher sequence-structure-dynamics-function relationship for protein engineering and drug design. They also employ computational and experimental techniques for interrogating protein dynamics to investigate regulation of plant proteins such as membrane transporters and hormone receptors to guide future crop innovation. Shukla group is interested in deciphering the mechanisms of regulation of protein function in human health with a particular focus on membrane transporter proteins and G-protein coupled receptors (GPCRs).

  • 2023

    • Anaira Román Santiago, Song Yin, Johannes Elbert, Jiho Lee, Diwakar Shukla, and Xiao Su*, Imparting selective fluorophilic interactions in redox copolymers for the electrochemically mediated capture of short-chain perfluoroalkyl substances. Journal of American Chemical Society, Volume 145, Issue 17, Pages 9508–9519, 2023.
    • Diego E. Kleiman and Diwakar Shukla*, Active Learning of the Conformational Ensemble of Proteins using Maximum Entropy VAMPNets. Journal of Chemical Theory and Computation, Volume 19, Issue 14, Pages 4377–4388, 2023.
    • Jiming Chen and Diwakar Shukla*, Effect of Histidine Covalent Modification on Strigolactone Receptor Activation and Selectivity. Biophysical Journal, Volume 122, Issue 7, Pages 1219-1228, 2023.
    • Matthew C. Chan and Diwakar Shukla*, Markov state modeling of membrane transport protein. Journal of Structural Biology, Volume 213, Issue 4, Article 107800, 2023.
    • Matthew C. Chan, Kui K. Chan, Erik Procko and Diwakar Shukla*, Machine learning guided design of high affinity ACE2 decoys for SARS-CoV-2 neutralization. Journal of Physical Chemistry B, Volume 127, Issue 9, Pages 1995–2001, 2023.
    • Matthew Chan and Diwakar Shukla*, The Effects of N-linked Glycosylation on SLC6 Transporters. Journal of Chemical Information and Modeling, Volume 63, Issue 9, Pages 2748–27582023.
    • Prateek Bansal, Soumajit Dutta and Diwakar Shukla*, Activation Mechanism of the Human Smoothened Receptor. Biophysical Journal, Volume 122, Issue 7, Pages 1400-1413, 2023.
    • Sarah E. Lindley, Yiyang Lu and Diwakar Shukla*, The Experimentalist’s Guide to Machine Learning for Small Molecule Design. ACS Applied Bio Materials, In press, 2023.
    • Shriyaa Mittal, Soumajit Dutta and Diwakar Shukla*, Reconciling Membrane Protein Simulations with Experimental DEER Spectroscopy Data. Physical Chemistry Chemical Physics, Volume 25, Issue 8, Pages 6253-6262, 2023.
    • Soumajit Dutta and Diwakar Shukla*, Distinct Activation Mechanisms Regulate Subtype Selectivity of Cannabinoid Receptors. Communications Biology, Volume 6, Article number: 4852022, 2023.
    • Xuenan Mi, Emily K. Desormeaux, Tung T. Le, Wilfred A. van der Donk and Diwakar Shukla*, Sequence controlled secondary structure is important for the site-selectivity of lanthipeptide cyclization. Chemical Science, Volume 14, Pages 6904-6914, 2023.

    2022

    • Archit Kumar Vasan, Nandan Haloi, Rebecca Joy Ulrich, Mary Elizabeth Metcalf, Po-Chao Wen, William W Metcalf, Paul J Hergenrother, Diwakar Shukla and Emad Tajkhorshid*, Role of internal loop dynamics in antibiotic permeability of outer membrane porins, Proceedings of the National Academy of Sciences USA, Volume 119, Issue 8, Article number e2117009119, 2022.
    • Austin T Weigle, Jiangyan Feng and Diwakar Shukla*, Thirty years of molecular dynamics simulations on post-translational modifications of proteins, Physical Chemistry Chemical Physics, Volume 24, Pages 26371-26397, 2022.
    • Briana L Sobecks, Jiming Chen and Diwakar Shukla*, Dual Role of Strigolactone Receptor Signaling Partner in Inhibiting Substrate Hydrolysis, Journal of Physical Chemistry B, Volume 126, Issue 11, Pages 2188-2195, 2022.
    • Chuankai Zhao and Diwakar Shukla*, Molecular basis of the activation and dissociation of dimeric PYL2 receptor in abscisic acid signaling, Physical Chemistry Chemical Physics, Volume 24, Issue 2, Pages 724-734, 2022.
    • Corina N D’Alessandro-Gabazza, Taro Yasuma, Tetsu Kobayashi, Masaaki Toda, Ahmed M Abdel-Hamid, Hajime Fujimoto, Osamu Hataji, Hiroki Nakahara, Atsuro Takeshita, Kota Nishihama, Tomohito Okano, Haruko Saiki, Yuko Okano, Atsushi Tomaru, Valeria Fridman D’Alessandro, Miyako Shiraishi, Akira Mizoguchi, Ryoichi Ono, Junpei Ohtsuka, Masayuki Fukumura, Tetsuya Nosaka, Xuenan Mi, Diwakar Shukla, Kensuke Kataoka, Yasuhiro Kondoh, Masaki Hirose, Toru Arai, Yoshikazu Inoue, Yutaka Yano, Roderick I Mackie, Isaac Cann, Esteban C Gabazza. Inhibition of lung microbiota-derived proapoptotic peptides ameliorates acute exacerbation of pulmonary fibrosis, Nature Communications, Volume 13, Issue 1, Article number 1558, 2022.
    • Diego E Kleiman and Diwakar Shukla*, Multiagent reinforcement learning-based adaptive sampling for conformational dynamics of proteins, Journal of Chemical Theory and Computation, Volume 18, Issue 9, Pages 5422-5434, 2022.
    • Jesse R. Horne and Diwakar Shukla*, Recent Advances in Machine Learning Variant Effect Prediction Tools for Protein Engineering, Industrial & Engineering Chemistry Research, Volume 61, Issue 19, Pages 6235–6245, 2022.
    • Jiming Chen and Diwakar Shukla*, Integration of machine learning with computational structural biology of plants, Biochemical Journal, Volume 479, Issue 8, Pages 921-928, 2022.
    • Jiming Chen, David C. Nelsonand Diwakar Shukla*, Activation Mechanism of Strigolactone Receptors and Its Impact on Ligand Selectivity between Host and Parasitic Plants, Journal of Chemical Information and Modeling, Volume 62, Issue 7, Pages 1712–1722, 2022.
    • Kyung Sun Park, Zhengyuan Xue, Bijal B. Patel, Hyosung An, Justin J. Kwok, Prapti Kafle, Qian Chen, Diwakar Shukla and Ying Diao*, Chiral emergence in multistep hierarchical assembly of achiral conjugated polymers, Nature Communications, Volume 13, Article number 2738, 2022.
    • Lars H Kruse, Austin T Weigle, Mohammad Irfan, Jesús Martínez-Gómez, Jason D Chobirko, Jason E Schaffer, Alexandra A Bennett, Chelsea D Specht, Joseph M Jez, Diwakar Shukla, Gaurav D Moghe*, Orthology-based analysis helps map evolutionary diversification and predict substrate class use of BAHD acyltransferases, The Plant Journal, Volume 111, Issue 5, Pages 1453-1468, 2022.
    • Lianghui Zhang, Soumajit Dutta, Shiqin Xiong, Matthew Chan, Kui K Chan, Timothy M Fan, Keith L Bailey, Matthew Lindeblad, Laura M Cooper, Lijun Rong, Anthony F Gugliuzza, Diwakar Shukla, Erik Procko, Jalees Rehman, Asrar B Malik, Mechanistic origin of partial agonism of tetrahydrocannabinol for cannabinoid receptors, Nature Chemical Biology, Volume 18, Issue 3, Pages 342-351, 2022.
    • Matthew C Chan, Balaji Selvam, Heather J Young, Erik Procko and Diwakar Shukla*, The substrate import mechanism of the human serotonin transporter, Biophysical Journal, Volume 121, Issue 5, Pages 715-730, 2022.
    • Matthew C. Chan, Erik Procko, and Diwakar Shukla*, Structural Rearrangement of the Serotonin Transporter Intracellular Gate Induced by Thr276 Phosphorylation, ACS Chemical Neuroscience, Volume 13, Issue 7, Pages 933-945, 2022.
    • Michael I. Jacobs, Prateek Bansal, Diwakar Shukla, and Charles M. Schroeder*, Understanding Supramolecular Assembly of Supercharged Proteins, ACS Central Science, Volume 8, Issue 9, Pages 1350–1361, 2022.
    • Soumajit Dutta, Balaji Selvam and Diwakar Shukla*, Distinct Binding Mechanisms for Allosteric Sodium Ion in Cannabinoid Receptors, ACS Chemical Neuroscience, Volume 13, Issue 3, Pages 379-389, 2022.
    • Soumajit Dutta, Balaji Selvam, Aditi Das, Diwakar Shukla*, Mechanistic origin of partial agonism of tetrahydrocannabinol for cannabinoid receptors, Journal of Biological Chemistry, Volume 298, Issue 4, Article number 101764, 2022.
    • Xuenan Mi and Diwakar Shukla*, Predicting the Activities of Drug Excipients on Biological Targets using One-Shot Learning, Journal of Physical Chemistry B, Volume 126, Issue 7, Pages 1492–1503, 2022.
    • Xueyi Xue, Jiang Wang, Diwakar Shukla, Lily S. Cheung, and Li-Qing Chen, When SWEETs Turn Tweens: Updates and Perspectives, Annual Review of Plant Biology, Vol. 73, Issue 1, Pages 379-403, 2022.

    2021

    • Austin Tyler Weigle, Matthew Carr, Diwakar Shukla*, Impact of increased membrane realism on conformational sampling of proteins. Journal of Chemical Theory and Computation, Volume 61, Issue 10, Pages 4827–4831, 2021.
    • Daniel T Bregante, Matthew C Chan, Jun Zhi Tan, E Zeynep Ayla, Christopher P Nicholas, Diwakar Shukla, David W Flaherty*, The shape of water in zeolites and its impact on epoxidation catalysis. Nature Catalysis, Volume 4, Issue 9, Pages 797-808, 2021.
    • Gabriel V Pereira, Ahmed M Abdel-Hamid, Soumajit Dutta, Corina N D’Alessandro-Gabazza, Daniel Wefers, Jacob A Farris, Shiv Bajaj, Zdzislaw Wawrzak, Haruyuki Atomi, Roderick I Mackie, Esteban C Gabazza, Diwakar Shukla, Nicole M Koropatkin, Isaac Cann*, Degradation of complex arabinoxylans by human colonic Bacteroidetes. Nature Communications, Volume 12, Article 459, 2021.
    • Jiangyan Feng, Balaji Selvam and Diwakar Shukla*, How do antiporters exchange substrates across the cell membrane? An atomic-level description of the complete exchange cycle in NarK. Structure, Volume 29, Issue 8, Pages 922-933. e3, 2021.
    • Jiming Chen, Alexandra White, David C Nelson and Diwakar Shukla*, Role of substrate recognition in modulating strigolactone receptor selectivity in witchweed. Journal of Biological Chemistry, Volume 297, Issue 4, Article 101092, 2021.
    • Nurzhan Kuanyshev, Anshu Deewan, Sujit Sadashiv Jagtap, Jingjing Liu, Balaji Selvam, Li-Qing Chen, Diwakar Shukla*, Christopher V Rao*, Yong-Su Ji*, Structure and Potential-Dependent Selectivity in Redox-Metallopolymers: Electrochemically Mediated Multicomponent Metal Separations. Biotechnology Journal, Volume 16, Issue 11, Article 2100238, 2021.
    • Raylin Chen, Jiangyan Feng, Jemin Jeon, Thomas Sheehan, Christian Rüttiger, Markus Gallei, Diwakar Shukla, Xiao Su*, Structure and Potential-Dependent Selectivity in Redox-Metallopolymers: Electrochemically Mediated Multicomponent Metal Separations. Advanced Functional Materials, Volume 31, Issue 15, Article 2009307, 2021.

    2019

    • S. Shukla, C. Zhao and D. Shukla. Dewetting Controls Plant Hormone Perception and Initiation of Drought Resistance Signaling. Structure, Vol. 27, 1-11, 2019.

    2018

    • B. Selvam, Z. Shamsi and D. Shukla. Universality of Sodium Ion Binding Mechanism in G-Protein-Coupled Receptors. Angew. Chem. Int. Ed., 57, 12, 3048-3053, 2018.
    • Balaji Selvam, Shriyaa Mittal and Diwakar Shukla. Free energy landscape of the complete transport cycle in a key bacterial transporter. ACS Central Science, Vol. 4, 9, 1146–1154, 2018.
    • C. Zhao and D. Shukla. SAXS-guided Enhanced Unbiased Sampling for Structure Determination of Proteins and Complexes. Scientific Reports, Vol. 8, Article number: 17748, 2018.
    • J. Feng and D. Shukla. Characterizing Conformational Dynamics of Proteins using Evolutionary Couplings., J. Phys. Chem. B, Vol. 122, 3, 1017–1025, 2018.
    • Z. Shamsi, K. J. Cheng and D. Shukla. REinforcement learning based Adaptive samPling: REAPing Rewards by Exploring Protein Conformational Landscapes. J. Phys. Chem. B, Vol. 122, 35, 8386-8395, 2018.