Research at Columbia

Research Articles

Proximity-labeling proteomics reveals remodeled interactomes and altered localization of pathogenic SHP2 variants

Anne E. van Vlimmeren, Lauren C. Tang, Ziyuan Jiang, Abhishek Iyer, Rashmi Voleti, Konstantin Krismer, Jellert T. Gaublomme, Marko Jovanovic, and Neel H. Shah*

bioRxiv

2025

DOI: 10.1101/2025.02.26.640373

Allosteric inhibition rescues hydrocephalus caused by catalytically inactive Shp2

Neoklis Makrides, Emily Sun, Hilal Mir, Ziyuan Jiang, Yihua Wu, Carlos Serra, Wellington V Cardoso, Neel H. Shah, and Xin Zhang*

bioRxiv

2025

DOI: 10.1101/2025.01.28.635289

Accurate sequence-to-affinity models for SH2 domains from multi-round peptide binding assays coupled with free-energy regression

Dejan Gagoski†, H. Tomas Rube†, Chaitanya Rastogi, Lucas Melo, Xiaoting Li, Rashmi Voleti, Neel H. Shah*, and Harmen J. Bussemaker*

bioRxiv

2024

DOI: 10.1101/2024.12.23.630085

Deep mutational scanning of a multi-domain signaling protein reveals mechanisms of regulation and pathogenicity

Ziyuan Jiang, Anne E. van Vlimmeren, Deepti Karandur, Alyssa Semmelman, and Neel H. Shah*

bioRxiv

2024

DOI: 10.1101/2024.05.13.593907

SEC-MX: An approach to systematically study the interplay between protein assembly states and phosphorylation

Ella Doron-Mandel†,*, Benjamin J. Bokor†, Yanzhe Ma†, Lena A. Street, Lauren C. Tang, Ahmed A. Abdou, Neel H. Shah, George Rosenberger, and Marko Jovanovic*.

Nature Communications

2025, 16, 1176.

DOI: 10.1038/s41467-025-56303-0

Allosteric regulation of the tyrosine phosphatase PTP1B by a protein-protein interaction

Cassandra A. Chartier, Virgil A. Woods, Yunyao Xu, Anne E. van Vlimmeren, Marko Jovanovic, Ann E. McDermott, Daniel A. Keedy, and Neel H. Shah*

Protein Science

2025, 35(1), e70016

DOI: 10.1002/pro.70016

Crafting Unnatural Peptide Macrocycles via Rh(III)-Catalyzed Carboamidation

Christopher W. Lamartina, Cassandra A. Chartier, Jillian M. Hirano, Neel H. Shah*, and Tomislav Rovis*

Journal of the American Chemical Society

2024, 146, 20868–20877

DOI: 10.1021/jacs.4c05248

The pathogenic T42A mutation in SHP2 rewires the interaction specificity of its N-terminal regulatory domain

Anne E. van Vlimmeren†, Rashmi Voleti†, Cassandra A. Chartier, Ziyuan Jiang, Deepti Karandur, Preston A. Humphries, Wan-Lin Lo, and Neel H. Shah*

Proceedings of the National Academy of Sciences

2024, 121(30), e2407159121

DOI: 10.1073/pnas.2407159121

Photocatalytic Activation of Aryl(trifluoromethyl) Diazos to Carbenes for High-Resolution Protein Labeling with Red Light

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*

Journal of the American Chemical Society

2024, 146, 1337–1345

DOI: 10.1021/jacs.3c09545

High-throughput profiling of sequence recognition by tyrosine kinases and SH2 domains using bacterial peptide display

Allyson Li, Rashmi Voleti, Minhee Lee, Dejan Gagoski, and Neel H. Shah*

eLife

2023, 12, e82345

DOI: 10.7554/eLife.82345

Mapping the chemical space of active-site targeted covalent ligands for protein tyrosine phosphatases

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*

ChemBioChem

2023, 24, e202200706

DOI: 10.1002/cbic.202200706

Modular Synthesis of Unnatural Peptides via Rh(III)-Catalyzed Diastereoselective Three-Component Carboamidation Reaction

Christopher W. Lamartina, Cassandra A. Chartier, Sumin Lee, Neel H. Shah*, and Tomislav Rovis*

Journal of the American Chemical Society

2023, 145, 1129-1135

DOI: 10.1021/jacs.2c10793

Prediction of protein–ligand binding affinity from sequencing data with interpretable machine learning

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*

Nature Biotechnology

2022, 40, 1520-1527

DOI: 10.1038/s41587-022-01307-0

Research before Columbia

TCR signaling promotes formation of an STS1-Cbl-b complex with pH-sensitive phosphatase activity that suppresses T cell function in acidic environments

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.*

Immunity

2023, 56, 2682-2698

DOI: 10.1016/j.immuni.2023.11.010

Saturation mutagenesis of a predicted ancestral Syk-family kinase

Helen T. Hobbs, Neel H. Shah, Sophie R. Shoemaker, Jeanine F. Amacher, Susan Marqusee, and John Kuriyan*

Protein Science

2022, 31, e4411

DOI: 10.1002/pro.4411

A Saturation-Mutagenesis Analysis of the Interplay Between Stability and Activation in Ras

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*

eLife

2022, 11, e76595

DOI: 10.7554/eLife.76595

Differences in the dynamics of the tandem-SH2 modules of the Syk and ZAP-70 tyrosine kinases

Helen T. Hobbs, Neel H. Shah, Jean M. Badroos, Christine L. Gee, Susan Marqusee*, and John Kuriyan*

Protein Science

2021, 30, 2373-2384.

DOI: 10.1002/pro.4199

Slow phosphorylation of a tyrosine residue in LAT optimizes T cell ligand discrimination

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*

Nature Immunology

2019, 20, 1481-1493

DOI: 10.1038/s41590-019-0502-2

Variation in assembly stoichiometry in non-metazoan homologs of the hub domain of Ca2+/calmodulin-dependent protein kinase II

Ethan D. McSpadden, Zijie Xia, Chris C. Chi, Anna C. Susa, Neel H. Shah, Christine L. Gee, Evan R. Williams, John Kuriyan*

Protein Science

2019, 28, 1071-1082

DOI: 10.1002/pro.3614

Deep mutational analysis reveals functional trade-offs in the sequences of EGFR autophosphorylation sites

Aaron J. Cantor, Neel H. Shah, and John Kuriyan*

Proceedings of the National Academy of Sciences

2018, 115, E7303-E7312

DOI: 10.1073/pnas.1803598115

Lck promotes Zap70-dependent LAT phosphorylation by bridging Zap70 to LAT

Wan-Lin Lo, Neel H. Shah, Nagib Ahsan, Veronika Horkova, Ondrej Stepanek, Arthur R. Salomon, John Kuriyan, and Arthur Weiss*

Nature Immunology

2018, 19, 733-741

DOI: 10.1038/s41590-018-0131-1

Fine-tuning of substrate preferences of the Src-family kinase Lck revealed through a high-throughput specificity screen

Neel H. Shah, Mark Löbel, Arthur Weiss, and John Kuriyan*

eLife

2018, 7:e35190

DOI: 10.7554/eLife.35190

A Promiscuous Split Intein with Expanded Protein Engineering Applications

Adam J. Stevens, Giridhar Sekar, Neel H. Shah, Anahita Z. Mostafavi, David Cowburn, and Tom W. Muir*

Proceedings of the National Academy of Sciences

2017, 114, 8538-8543

DOI: 10.1073/pnas.1701083114

Deconstruction of the Ras switching cycle through saturation mutagenesis

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*

eLife

2017, 6, e278103

DOI: 10.7554/eLife.27810

An Electrostatic Selection Mechanism Controls Sequential Kinase Signaling Downstream of the T Cell Receptor

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*

eLife

2016, 5, e20105

DOI: 10.7554/eLife.20105

Design of a Split Intein with Exceptional Protein Splicing Activity

Adam J. Stevens, Zachary Z. Brown, Neel H. Shah, Giridhar Sekar, David Cowburn, and Tom W. Muir*

Journal of the American Chemical Society

2016, 5, e20105

DOI: 10.1021/jacs.5b13528

Modification by covalent reaction or oxidation of cysteine residues in the tandem-SH2 domains of ZAP-70 and Syk can block phosphopeptide binding

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*

Biochemical Journal

2015, 465, 149-161

DOI: 10.1042/BJ20140793

Naturally Split Inteins Assemble through a ‘Capture and Collapse’ Mechanism

Neel H. Shah†, Ertan Eryilmaz†, David Cowburn, and Tom W. Muir*

Journal of the American Chemical Society

2013, 135, 18673-18681

DOI: 10.1021/ja4104364

Extein Residues Play an Intimate Role in the Rate-Limiting Step of Protein Trans-Splicing

Neel H. Shah, Ertan Eryilmaz, David Cowburn, and Tom W. Muir*

Journal of the American Chemical Society

2013, 135, 5839-5847

DOI: 10.1021/ja401015p

Streamlined Expressed Protein Ligation Using Split Inteins

Miquel Vila-Perelló†, Zhihua Liu†, Neel H. Shah, John A. Willis, Juliana Idoyaga, and Tom W. Muir*

Journal of the American Chemical Society

2013, 135, 286-292

DOI: 10.1021/ja309126m

Ultrafast Protein Splicing is Common among Cyanobacterial Split Inteins

Neel H. Shah, Geoffrey P. Dann, Miquel Vila-Perelló, Zhihua Liu, and Tom W. Muir*

Journal of the American Chemical Society

2012, 134, 11338-11341

DOI: 10.1021/ja303226x

Kinetic Control of One-Pot Trans-Splicing Reactions by Using a Wild-Type and Designed Split Intein

Neel H. Shah, Miquel Vila-Perelló* and Tom W. Muir*

Angewandte Chemie International Edition

2011, 50, 6511-6515

DOI: 10.1002/anie.201102909

Peptoid Atropisomers

Bishwajit Paul, Glenn L. Butterfoss, Mikki G. Boswell, P. Douglas Renfrew, Fanny G. Yeung, Neel H. Shah, Christian Wolf, Richard Bonneau, and Kent Kirshenbaum*

Journal of the American Chemical Society

2011, 133, 10910-10919

DOI: 10.1021/ja2028684