Chronological list of publications
(* = corresponding author, † = equal contribution)
Dejan Gagoski†, H. Tomas Rube†, Chaitanya Rastogi, Lucas Melo, Xiaoting Li, Rashmi Voleti, Neel H. Shah*, and Harmen J. Bussemaker*. “Accurate sequence-to-affinity models for SH2 domains from multi-round peptide binding assays coupled with free-energy regression.” bioRxiv 2024, DOI: 10.1101/2024.12.23.630085 [preprint]
Cassandra A. Chartier, Virgil A. Woods, Yunyao Xu, Anne E. van Vlimmeren, Marko Jovanovic, Ann E. McDermott, Daniel A. Keedy, Neel H. Shah*. “Allosteric regulation of the tyrosine phosphatase PTP1B by a protein-protein interaction.” bioRxiv 2024, DOI: 10.1101/2024.07.16.603632 [preprint]
Ziyuan Jiang, Anne E. van Vlimmeren, Deepti Karandur, Alyssa Semmelman, and Neel H. Shah*. “Deep mutational scanning of a multi-domain signaling protein reveals mechanisms of regulation and pathogenicity.” bioRxiv 2024, DOI: 10.1101/2024.05.13.593907 [preprint]
Ella Doron-Mandel†,*, Benjamin J. Bokor†, Yanzhe Ma†, Lena A. Street, Lauren C. Tang, Ahmed A. Abdou, Neel H. Shah, George A. Rosenberger, and Marko Jovanovic*. “A Multiplexed SEC-MS Approach to Systematically Study the Interplay Between Protein Assembly-States and Phosphorylation Events.” bioRxiv 2024, DOI: 10.1101/2023.01.12.523793 [preprint]
Christopher W. Lamartina, Cassandra A. Chartier, Jillian M. Hirano, Neel H. Shah*, Tomislav Rovis*. “Crafting Unnatural Peptide Macrocycles via Rh(III)-Catalyzed Carboamidation." Journal of the American Chemical Society 2024, 146, 20868–20877.
Anne E. van Vlimmeren†, Rashmi Voleti†, Cassandra A. Chartier, Ziyuan Jiang, Deepti Karandur, Preston A. Humphries, Wan-Lin Lo, and Neel H. Shah*. “The pathogenic T42A mutation in SHP2 rewires the interaction specificity of its N-terminal regulatory domain.” Proceedings of the National Academy of Sciences 2024, 121(30), e2407159121. [preprint]
David C. Cabanero†, Stavros K. Kariofillis†, Andrew C. Johns, Jinwoo Kim, Jizhi Ni, Sangho Park, Dann L. Parker, Jr., Carlo Ramil, Xavier Roy, Neel H. Shah*, and Tomislav Rovis*. “Photocatalytic Activation of Aryl(trifluoromethyl) Diazos to Carbenes for High-Resolution Protein Labeling with Red Light.” Journal of the American Chemical Society 2024, 146, 1337–1345. [preprint]
Yuan-Li Tsai, Marcel Arias-Badia, Theresa A. Kadlecek, Yee May Lwin, Aahir Srinath, Neel H. Shah, Zhi-En Wang, Diane Barber, John Kuriyan, Lawrence Fong, and Arthur Weiss. “TCR signaling promotes formation of an STS1-Cbl-b complex with pH-sensitive phosphatase activity that suppresses T cell function in acidic environments.” Immunity, 2023, 56, 2682-2698.
Allyson Li, Rashmi Voleti, Minhee Lee, Dejan Gagoski, and Neel H. Shah*. “High-throughput profiling of sequence recognition by tyrosine kinases and SH2 domains using bacterial peptide display." eLife 2023, 12, e82345. [preprint]
Suk ho Hong†, Sarah Y. Xi†, Andrew C. Johns, Lauren C. Tang, Allyson Li, Madeleine N. Hum, Cassandra A. Chartier, Marko Jovanovic, and Neel H. Shah*. “Mapping the chemical space of active-site targeted covalent ligands for protein tyrosine phosphatases." ChemBioChem 2023, 24, e202200706. [preprint]
Christopher W. Lamartina, Cassandra A. Chartier, Sumin Lee, Neel H. Shah*, and Tomislav Rovis*. “Modular Synthesis of Unnatural Peptides via Rh(III)-Catalyzed Diastereoselective Three-Component Carboamidation Reaction.” Journal of the American Chemical Society 2023, 145, 1129-1135.
H. Tomas Rube, Chaitanya Rastogi, Siqian Feng†, Judith F. Kribelbauer†, Allyson Li†, Basheer Becerra, Lucas A. N. Melo, Bach Viet Do, Xiaoting Li, Hammaad H. Adam, Neel H. Shah, Richard S. Mann, and Harmen J. Bussemaker*. “Prediction of protein-ligand binding affinity from sequencing data with interpretable machine learning.” Nature Biotechnology 2022, 40, 1520-1527. [preprint]
Helen T. Hobbs, Neel H. Shah, Sophie R. Shoemaker, Jeanine F. Amacher, Susan Marqusee, and John Kuriyan*. “Saturation mutagenesis of a predicted ancestral Syk-family kinase.” Protein Science 2022, 31, e4411. [preprint]
Frank Hidalgo†, Laura M. Nocka†, Neel H. Shah, Kent Gorday, Naomi R. Latorraca, Pradeep Bandaru, Sage Templeton, David Lee, Deepti Karandur, Jeffrey G. Pelton, Susan Marqusee, David Wemmer, and John Kuriyan*. “A Saturation-Mutagenesis Analysis of the Interplay Between Stability and Activation in Ras.” eLife 2022, 11, e76595. [preprint]
Helen T. Hobbs, Neel H. Shah, Jean M. Badroos, Christine L. Gee, Susan Marqusee*, and John Kuriyan*. “Differences in the dynamics of the tandem-SH2 modules of the Syk and ZAP-70 tyrosine kinases.” Protein Science 2021, 30, 2373-2384. [preprint]
Neel H. Shah* and Adam J. Stevens. “Identification, Characterization, and Optimization of Split Inteins.” Methods in Molecular Biology 2020, 2133, 31-54.
Suk ho Hong and Neel H. Shah*. “Cell Signaling: Learning from ancestors.” eLife (Insight Article) 2019, 8, e49976.
Neel H. Shah* and John Kuriyan*. “Understanding molecular mechanisms in cell signaling through natural and artificial sequence variation.” Nature Structural and Molecular Biology 2019, 26, 25-34.
Wan-Lin Lo, Neel H. Shah, Sara A. Rubin, Weiguo Zhang, Veronika Horkova, Ian R. Fallahee, Ondrej Stepanek, Leonard Zon, John Kuriyan, and Arthur Weiss*. “Slow phosphorylation of a tyrosine residue in LAT optimizes T cell ligand discrimination.” Nature Immunology 2019, 20, 1481-1493.
Ethan D. McSpadden, Zijie Xia, Chris C. Chi, Anna C. Susa, Neel H. Shah, Christine L. Gee, Evan R. Williams, John Kuriyan*. “Variation in assembly stoichiometry in non-metazoan homologs of the hub domain of Ca2+/calmodulin-dependent protein kinase II.” Protein Science 2019, 28, 1071-1082.
Aaron J. Cantor, Neel H. Shah, and John Kuriyan*. “Deep mutational analysis reveals functional trade-offs in the sequences of EGFR autophosphorylation sites.” Proceedings of the National Academy of Sciences 2018, 115, E7303-E7312. [preprint]
Neel H. Shah, Jeanine F. Amacher, Laura M. Nocka, and John Kuriyan*. “The Src module: an ancient scaffold in the evolution of cytoplasmic tyrosine kinases.” Critical Reviews in Biochemistry & Molecular Biology 2018, 53, 535-563.
Wan-Lin Lo, Neel H. Shah, Nagib Ahsan, Veronika Horkova, Ondrej Stepanek, Arthur R. Salomon, John Kuriyan, and Arthur Weiss*. “Lck promotes Zap70-dependent LAT phosphorylation by bridging Zap70 to LAT.” Nature Immunology 2018, 19, 733-741.
Byron B. Au-Yeung, Neel H. Shah, Lin Shen, and Arthur Weiss*. “ZAP-70 in signaling, biology, and disease.” Annual Reviews of Immunology 2018, 36, 127-156.
Neel H. Shah, Mark Löbel, Arthur Weiss, and John Kuriyan*. “Fine-tuning of substrate preferences of the Src-family kinase Lck revealed through a high-throughput specificity screen.” eLife 2018, 7, e35190. [preprint]
Adam J. Stevens, Giridhar Sekar, Neel H. Shah, Anahita Z. Mostafavi, David Cowburn, and Tom W. Muir*. “A Promiscuous Split Intein with Expanded Protein Engineering Applications.” Proceedings of the National Academy of Sciences 2017, 114, 8538-8543.
Pradeep Bandaru, Neel H. Shah, Moitrayee Bhattacharyya, John P. Barton, Yasushi Kondo, Joshua C. Cofsky, Christine L. Gee, Arup K. Chakraborty, Tanja Kortemme, Rama Ranganathan*, and John Kuriyan*. “Deconstruction of the Ras switching cycle through saturation mutagenesis.” eLife 2017, 6, e27810.
Neel H. Shah, Qi Wang, Qingrong Yan, Deepti Karandur, Theresa A. Kadlecek, Ian R. Fallahee, William P. Russ, Rama Ranganathan, Arthur Weiss, and John Kuriyan*. “An Electrostatic Selection Mechanism Controls Sequential Kinase Signaling Downstream of the T Cell Receptor.” eLife 2016, 5, e20105.
Adam J. Stevens, Zachary Z. Brown, Neel H. Shah, Giridhar Sekar, David Cowburn, and Tom W. Muir*. “Design of a Split Intein with Exceptional Protein Splicing Activity.” Journal of the American Chemical Society 2016, 138, 2162-2165.
Patrick R. Visperas, Jonathan A. Winger, Timothy M. Horton, Neel H. Shah, Diane J. Aum, Alyssa Tao, Tiago Barros, Qingrong Yan, Christopher G. Wilson, Michelle R. Arkin, Arthur Weiss, John Kuriyan*. “Modification by covalent reaction or oxidation of cysteine residues in the tandem-SH2 domains of ZAP-70 and Syk can block phosphopeptide binding.” Biochemical Journal 2015, 465, 149-161.
Ertan Eryilmaz, Neel H. Shah, Tom W. Muir, and David Cowburn*. “Structural and Dynamical Features of Inteins and Implications on Protein Splicing.” Journal of Biological Chemistry 2014, 289, 14506-14511.
Neel H. Shah and Tom W. Muir*. “Inteins: Nature’s Gift to Protein Chemists.” Chemical Science 2014, 5, 446-461.
Neel H. Shah†, Ertan Eryilmaz†, David Cowburn, and Tom W. Muir*. “Naturally Split Inteins Assemble through a ‘Capture and Collapse’ Mechanism.” Journal of the American Chemical Society 2013, 135, 18673-18681.
Neel H. Shah, Ertan Eryilmaz, David Cowburn, and Tom W. Muir*. “Extein Residues Play an Intimate Role in the Rate-Limiting Step of Protein Trans-Splicing.” Journal of the American Chemical Society 2013, 135, 5839-5847.
Miquel Vila-Perelló†, Zhihua Liu†, Neel H. Shah, John A. Willis, Juliana Idoyaga, and Tom W. Muir*. “Streamlined Expressed Protein Ligation Using Split Inteins.” Journal of the American Chemical Society 2013, 135, 286-292.
Neel H. Shah, Geoffrey P. Dann, Miquel Vila-Perelló, Zhihua Liu, and Tom W. Muir*. “Ultrafast Protein Splicing is Common among Cyanobacterial Split Inteins.” Journal of the American Chemical Society 2012, 134, 11338-11341.
Neel H. Shah and Tom W. Muir*. “Split Inteins: Nature’s Protein Ligases.” Israel Journal of Chemistry 2011, 51, 854-861.
Neel H. Shah, Miquel Vila-Perelló* and Tom W. Muir*. “Kinetic Control of One-Pot Trans-Splicing Reactions by Using a Wild-Type and Designed Split Intein.” Angewandte Chemie International Edition 2011, 50, 6511-6515.
Bishwajit Paul, Glenn L. Butterfoss, Mikki G. Boswell, P. Douglas Renfrew, Fanny G. Yeung, Neel H. Shah, Christian Wolf, Richard Bonneau, and Kent Kirshenbaum*. “Peptoid Atropisomers.” Journal of the American Chemical Society 2011, 133, 10910-10919.
Neel H. Shah, Glenn L. Butterfoss, Khanh Nguyen, Barney Yoo, Richard Bonneau, Dallas L. Rabenstein, and Kent Kirshenbaum*. “Oligo-(N-aryl glycines): A New Twist on Structured Peptoids.” Journal of the American Chemical Society 2008, 130, 16622-16632.
Neel H. Shah and Kent Kirshenbaum*. “Photoresponsive Peptoid Oligomers Bearing Azobenzene Side Chains.” Organic and Biomolecular Chemistry 2008, 6, 2516-2521.
Neel H. Shah and Kent Kirshenbaum*. “Direct Generation of Polymer Films on Copper Surfaces through Azide-Alkyne Cycloaddition Reactions between Peptidomimetic Oligomers.” Macromolecular Rapid Communications 2008, 29, 1134-1139.