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.
Prateek Bansal, Soumajit Dutta and Diwakar Shukla*, Activation Mechanism of the Human Smoothened Receptor. Biophysical Journal, Volume 122, Issue 7, Pages 1400-1413, 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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Matthew C. Chan and Diwakar Shukla*
Jihye Park, Balaji Selvam, Keisuke Sanematsu, Noriatsu Shigemura, Diwakar Shukla, Erik Procko*, Structural architecture of a dimeric class C GPCR based on co-trafficking of sweet taste receptor subunits, Journal of Biological Chemistry, Volume 294, Issue 13, Pages 4759-4774, 2019.
Jiangyan Feng, Jiming Chen, Balaji Selvam and Diwakar Shukla*, Computational microscopy: Revealing molecular mechanisms in plants using molecular dynamics simulations, The Plant Cell, Volume 31, Issue 12, doi:10.1105/tpc.119.tt1219, 2019.
Saurabh Shukla, Chuankai Zhao and Diwakar Shukla*, Dewetting controls plant hormone perception and initiation of drought resistance signaling, Structure, Volume 27, Issue 4, Pages692-702.e3, 2019.
Balaji Selvam, Zahra Shamsi and Diwakar Shukla*, Universality of the sodium ion binding mechanism in class AG‐protein‐coupled receptors, Angewandte Chemie, Volume 12, Pages 3102-3107, 2018.
Alexander S Moffett and Diwakar Shukla*, Using molecular simulation to explore the nanoscale dynamics of the plant kinome. Biochemical Journal, Volume 475, Issue 5, Pages 905-921, 2018.
Invited Review Article
Shriyaa Mittal and Diwakar Shukla*, Predicting optimal deer label positions to study protein conformational heterogeneity, The Journal of Physical Chemistry B, Volume 121, Issue 42, Pages 9761-9770, 2017.
Alexander S Moffett, Kyle W Bender, Steven C Huber, Diwakar Shukla*, Allosteric control of a plant receptor kinase through S-glutathionylation. Biophysical Journal, Volume 113, Issue 11, Pages 2354-2363, 2017.
Alexander S Moffett, Kyle W Bender, Steven C Huber, Diwakar Shukla*, Molecular dynamics simulations reveal the conformational dynamics of Arabidopsis thaliana BRI1 and BAK1 receptor-like kinases. Journal of Biological Chemistry, Volume 292, Issue 30, Pages 12643-12652, 2017.
Diwakar Shukla#, Curtiss P. Schneider# and Bernhardt L. Trout*. Complex interactions between molecular ions in solution and their effect on protein stability. Journal of the American Chemical Society, Volume 133, Issue 46, Pages 18713-18718, 2011.
Diwakar Shukla and Bernhardt L. Trout*. Interaction of arginine with proteins and the mechanism by which it inhibits aggregation, Journal of Physical Chemistry B, Volume 114, Issue 42, Pages 13426-13438, 2010.
Diwakar Shukla, Chetan Shinde and Bernhardt L. Trout*. Molecular computations of preferential interaction coefficients of proteins, Journal of Physical Chemistry B, Volume 113, Issue 37, Pages 12546-12554, 2009.
Diwakar Shukla, Abhijeet A. Joshi and Anurag Mehra*. Modeling of formation of nanoparticles in reverse micellar systems: Ostwald ripening of silver halide particles, Langmuir, Volume 25, Issue 6, Pages 3786-3793, 2009.
Briana L Sobecks, Jiming Chen and Diwakar Shukla*, Mechanistic Basis for Enhanced Strigolactone Sensitivity in KAI2 Triple Mutant. bioRxiv, 2023. doi: 10.1101/2023.01.18.524622.
Austin T. Weigle and Diwakar Shukla*, AtSWEET13 transporter discriminates sugars by selective facial and positional substrate recognition. bioRxiv, 2022, doi: 10.1101/2022.10.12.511964.
Publication Link
Balaji Selvam#, Jiangyan Feng# and Diwakar Shukla*, Atomistic Insights Into The Mechanism of Dual Affinity Switching In Plant Nitrate Transporter NRT1.1. bioRxiv, 2022. doi: 10.1101/2022.10.17.512638.
Publication Link