Cell biology 2.0.
Wendell A. Lim, Rebecca Alvania, Wallace F. Marshall
Trends Cell Biol. 22(12):611-2 (2013)
Abstract. PDF.

Design principles of regulatory networks: searching for the molecular algorithms of the cell.
Wendell A. Lim, Connie M. Lee, Chao Tang
Mol. Cell 49(2):202-12 (2013)
Abstract. PDF.

Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression.
Lei S. Qi, Matthew H. Larson, Luke A. Gilbert, Jennifer A. Doudna, Jonathan S. Weissman, Adam P. Arkin, Wendell A. Lim
Cell 28;152(5):1173-83 (2013)
Abstract. PDF. Supplemental Data. Supplemental Sequences.

Designing synthetic regulatory networks capable of self-organizing cell polarization.
Angela H. Chau*, Jessica M. Walter*, Jaline Gerardin, Chao Tang, Wendell A. Lim
Cell 151(2):320-32 (2012)
Abstract. PDF. Supplemental Data. Supplemental Movie 1. Supplemental Movie 2. Simulation Code and Scripts.

Conformational Control of the Ste5 Scaffold Protein Insulates Against MAP Kinase Misactivation.
Jesse G. Zalatan*, Scott M. Coyle*, Saravanan Rajan, Sachdev S. Sidhu, Wendell A. Lim
Science 337 (6099): 1218-1222 (2012)
Abstract. PDF. Supplemental Data.

Bacterial virulence proteins as tools to rewire kinase pathways in yeast and immune cells.
Ping Wei*, Wilson W. Wong*, Jason S. Park, Ethan E. Corcoran, Sergio G. Peisajovich, James J. Onuffer, Arthur Weiss, Wendell A. Lim
Nature 488, 384–388 (2012)
Abstract. PDF. Supplemental Data.

Systematic functional prioritization of protein posttranslational modifications.
Pedro Beltrao, Véronique Albanèse, Lillian R. Kenner, Danielle L. Swaney, Alma Burlingame, Judit Villén, Wendell A. Lim, James S. Fraser, Judith Frydman, Nevan J. Krogan
Cell 150(2):413-25 (2012)
Abstract. PDF. Article + Supplemental Data. Supplemental Tables.

SYNZIP Protein Interaction Toolbox: in Vitro and in Vivo Specifications of Heterospecific Coiled-Coil Interaction Domains.
Kenneth Evan Thompson, Caleb J. Bashor, Wendell A. Lim, Amy E. Keating
ACS Synth Biol. 1(4): 118–129 (2012)
Abstract. PDF. Supplemental Data.

Control of protein signaling using a computationally designed GTPase/GEF orthogonal pair.
Gregory T. Kapp, Sen Liu, Amelie Stein, Derek T. Wong, Attila Reményi, Brian J. Yeh, James S. Fraser, Jack Taunton, Wendell A. Lim, Tanja Kortemme
Proceedings of the National Academy of Sciences 109(14): 5277-5282 (2012)
Abstract. PDF. Supplemental Data.

Light-based feedback for controlling intracellular signaling dynamics
Jared E. Toettcher, Delquin Gong, Wendell A. Lim, Orion D. Weiner
Nature Methods 8, 837-839 (2011)
Abstract. PDF. Supplemental Data.

Recruitment interactions can override catalytic interactions in determining the functional identity of a protein kinase
Angela P. Won, Joan E. Garbarino, Wendell A. Lim
Proceedings of the National Academy of Sciences 108, 9809-9814 (2011)
Abstract. PDF. Supplemental Data.

Light Control of Plasma Membrane Recruitment Using the Phy-PIF System
Jared E. Toettcher, Delquin Gong, Wendell A. Lim, Orion D. Weiner
Methods Enzymology 497, 409-23 (2011)
Abstract. PDF.

Scaffold proteins: hubs for controlling the flow of cellular information
Matthew C. Good, Jesse G. Zalatan, Wendell A. Lim
Science 332, 680-6 (2011)
Abstract. PDF. Supplemental Video.

The promise of optogenetics in cell biology: interrogating molecular circuits in space and time
Jared E. Toettcher, Christopher A. Voigt, Orion D. Weiner, Wendell A. Lim
Nature Methods 1, 35-38 (2011)
Abstract. PDF.

Build life to understand it
Michael Elowitz, Wendell A. Lim
Nature 468, 889-890 (2010)
Abstract. PDF.

Phosphotyrosine signaling: evolving a new cellular communication system
Wendell A. Lim, Tony Pawson
Cell 142, 661-667 (2010)
Abstract. PDF.

The minimal autoinhibited unit of the guanine nucleotide exchange factor intersectin
K. Farid Ahmad, Wendell A. Lim
PLos ONE 5, e11291 (2010)
Abstract. PDF.

Designing customized cell signalling circuits
Wendell A. Lim
Nature Reviews Molecular Cell Biology 11, 393-403 (2010)
Abstract. PDF.

Rapid diversification of cell signaling phenotypes by modular domain recombination
Sergio G. Peisajovich, Joan E. Garbarino, Ping Wei, Wendell A. Lim
Science 328, 368-372 (2010)
Abstract. PDF. Supplemental Data.
Commentary in Nature Reviews Genetics by Katharine H. Wrighton (PDF)
Commentary in Nature Reviews Molecular Cell Biology by Katharine H. Wrighton (PDF)

Rewiring cells: synthetic biology as a tool to interrogate the organizational principles of living systems
Caleb J. Bashor, Andrew A. Horwitz, Sergio G. Peisajovich, and Wendell A. Lim
Annual Review of Biophysics 39, 515-537 (2010)
Abstract. PDF. (Copyright Annual Reviews)

Reengineering the signaling properties of a Src family kinase
Shalini S. Yadav, Brian J. Yeh, Barbara P. Craddock, Wendell A. Lim, and W. Todd Miller
Biochemistry 48, 10956-10962 (2009)
Abstract. PDF. Supplemental Data.

Spatiotemporal control of cell signalling using a light-switchable protein interaction
Anselm Levskaya, Orion D. Weiner, Wendell A. Lim, and Christopher A. Voigt
Nature 461, 997-1001 (2009)
Abstract. PDF. Supplemental Data.

Defining network topologies that can achieve biochemical adaptation
Wenzhe Ma, Ala Trusina, Hana El-Samad, Wendell A. Lim, and Chao Tang
Cell 138, 760-73 (2009)
Abstract. PDF. Supplemental Data. PaperFlick video summary.
Commentary in Cell by Alexander B. Artyukhin, Lani F. Wu, and Steven J. Altschuler (PDF)

Evolution of phosphoregulation: comparison of phosphorylation patterns across yeast species
Pedro Beltrao, Jonathan C. Trinidad, Dorothea Fiedler, Assen Roguev, Wendell A. Lim, Kevan M. Shokat, Alma L. Burlingame, and Nevan J. Krogan
PLoS Biology 7, e1000134 (2009).
Abstract. PDF. Supplemental Data.

The Ste5 Scaffold Directs Mating Signaling by Catalytically Unlocking the Fus3 MAP Kinase for Activation
Matthew C. Good, Grace Tang, Julie Singleton, Attila Reményi, and Wendell A. Lim
Cell 136, 1085-97 (2009)
Abstract. PDF. Supplemental Data.
Commentary in Cell by Markus A. Seeliger and John Kuriyan (PDF)

The pathogen protein EspF(U) hijacks actin polymerization using mimicry and multivalency
Nathan A. Sallee, Gonzalo M. Rivera, John E. Dueber, Dan Vasilescu, R. Dyche Mullins, Bruce J. Mayer, and Wendell A. Lim
Nature 454, 1005-8 (2008)
Abstract. PDF. Supplemental Data.

Evolution of the phospho-tyrosine signaling machinery in premetazoan lineages
David Pincus, Ivica Letunic, Peer Bork, and Wendell A. Lim
Proceedings of the National Academy of Sciences 105, 9680-4 (2008)
Abstract. PDF. Supplemental Data.
Commentary in Proceedings of the National Academy of Sciences by Bruce Mayer (PDF)

Using engineered scaffold interactions to reshape MAP kinase pathway signaling dynamics
Caleb J. Bashor, Noah C. Helman, Shude Yan, and Wendell A. Lim
Science 319, 1539-43 (2008)
Abstract. PDF. Supplemental Data.
Commentary in Science by Peter M. Pryciak (PDF)
Commentary in Nature Biotechnology by Patrick Guye and Ron Weiss (PDF)

Synthetic biology: lessons from the history of synthetic organic chemistry
Brian J. Yeh and Wendell A. Lim
Nature Chemical Biology 3, 521-5 (2007)
Abstract. PDF.

Rewiring cellular morphology pathways with synthetic guanine nucleotide exchange factors
Brian J. Yeh, Robert J. Rutigliano, Anrica Deb, Dafna Bar-Sagi, and Wendell A. Lim
Nature 447, 596-600 (2007)
Abstract. PDF. Supplemental Data. Supplemental Video.
Commentary in Molecular Systems Biology by Philippe Bastiaens (PDF)
Commentary in Developmental Cell by Christopher S. Chen (PDF)

Engineering synthetic signaling proteins with ultrasensitive input/output control
John E. Dueber, Ethan A. Mirsky, and Wendell A. Lim
Nature Biotechnology 25, 660-662 (2007)
Abstract. PDF. Supplemental Data.

Engineering modular protein interaction switches by sequence overlap
Nathan A. Sallee, Brian J. Yeh, and Wendell A. Lim
Journal of the American Chemical Society 129, 4606-4611 (2007)
Abstract. PDF. Supplemental Data.

Docking interactions in protein kinase and phosphatase networks
Attila Reményi, Matthew C. Good, and Wendell A. Lim
Current Opinion in Structural Biology 16, 676-685 (2006)
Abstract. PDF.

Domains, Motifs, and Scaffolds: The Role of Modular Interactions in the Evolution and Wiring of Cell Signaling Circuits
Roby P. Bhattacharyya, Attila Reményi, Brian J. Yeh, and Wendell A. Lim
Annual Review of Biochemistry 75, 655-680 (2006)
Abstract. PDF. (Copyright Annual Reviews)

The Ste5 Scaffold Allosterically Modulates Signaling Output of the Yeast Mating Pathway
Roby P. Bhattacharyya*, Attila Reményi*, Matthew C. Good, Caleb J. Bashor, Arnold M. Falick, and Wendell A. Lim
Science 311, 822-826 (2006)
Abstract. PDF.
Commentary in Science by Ashton Breitkreutz and Mike Tyers (PDF)

The role of docking interactions in mediating signaling input, output, and discrimination in the yeast MAPK network
Attila Reményi, Matthew C. Good, Roby P. Bhattacharyya, and Wendell A. Lim
Molecular Cell 20, 951-962 (2005)
Abstract. PDF. Supplemental Data.

A general model for preferential hetero-oligomerization of Lin-2/7 domains: Mechanism underlying directed assembly of supramolecular signaling complexes
Keiko Y. Petrosky, Horng D. Ou, Frank Löhr, Volker Dötsch, and Wendell A. Lim
Journal of Biological Chemistry 280, 38528-38536 (2005)
Abstract. PDF.

A Polybasic Motif Allows N-WASP to Act as a Sensor of PIP2 Density
Venizelos Papayannopoulos, Carl Co, Kenneth E. Prehoda, Scott Snapper, Jack Taunton, and Wendell A. Lim
Molecular Cell 17, 181-191 (2005)
Abstract. PDF. Supplemental Data.
Commentary in Developmental Cell by Diana Murray and Barry Honig (PDF)

Rewiring cell signaling: the logic and plasticity of eukaryotic protein circuitry
John E. Dueber, Brian J. Yeh, Roby P. Bhattacharyya, and Wendell A. Lim
Current Opinion in Structural Biology 14, 690-699 (2004)
Abstract. PDF.

Sho1 and Pbs2 Act as Coscaffolds Linking Components in the Yeast High Osmolarity MAP Kinase Pathway
Ali Zarrinpar, Roby P. Bhattacharyya, M. Paige Nittler, and Wendell A. Lim
Molecular Cell 14, 825–832 (2004)
Abstract. PDF. Supplemental Data.
Commentary in Current Biology by Bruce T. Seet and Tony Pawson (PDF)

Optimization of specificity in a cellular protein interaction network by negative selection
Ali Zarrinpar, Sang-Hyun Park, and Wendell A. Lim
Nature 426, 676-680 (2003)
Abstract. PDF. Supplemental Data.
Commentary in Nature by Drew Endy and Michael B. Yaffe (PDF)

Reprogramming Control of an Allosteric Signaling Switch Through Modular Recombination
John E. Dueber, Brian J. Yeh, Kayam Chak, and Wendell A. Lim
Science 301, 1904-1908 (2003)
Abstract. PDF. Supplemental Data.

The Structure and Function of Proline Recognition Domains
Ali Zarrinpar, Roby P. Bhattacharyya, and Wendell A. Lim
Science STKE 2003, re8 (2003)
Abstract. PDF. Structure Animations.

Role of Electrostatic Interactions in PDZ Domain Ligand Recognition
Baruch Z. Harris, Francis W. Lau, Naoaki Fujii, R. Kiplin Guy, and Wendell A. Lim
Biochemistry 42, 2797-2805 (2003)
Abstract. PDF.

Rewiring MAP Kinase Pathways Using Alternative Scaffold Assembly Mechanisms
Sang-Hyun Park, Ali Zarrinpar, and Wendell A. Lim
Science 299, 1061-1064 (2003)v
Abstract. PDF. Supplemental Data.
Commentary in Science by Mark Ptashne and Alexander Gann (PDF)
Commentary in Molecular Cell by James E. Ferrell, Jr. and Karlene A. Cimprich (PDF)

Structure of the N-WASP EVH1 Domain-WIP Complex: Insight into the Molecular Basis of Wiskott-Aldrich Syndrome
Brian F. Volkman, Kenneth E. Prehoda, Jessica A. Scott, Francis C. Peterson, and Wendell A. Lim
Cell 111, 565–576 (2002)
Abstract. PDF. Supplemental Data.

Coordinated folding and association of the LIN-2, -7 (L27) domain: An obligate heterodimerization involved in assembly of signaling and cell polarity complexes
Baruch Z. Harris, Shivkumar Venkatasubrahmanyam, and Wendell A. Lim
Journal of Biological Chemistry 277, 34902-34908 (2002)
Abstract. PDF.

How signaling proteins integrate multiple inputs: a comparison of N-WASP and Cdk2
Kenneth E. Prehoda and Wendell A. Lim
Current Opinion in Cell Biology14, 149-154 (2002)
Abstract. PDF.

The modular logic of signaling proteins: building allosteric switches from simple binding domains
Wendell A. Lim
Current Opinion in Structural Biology 12, 61-68 (2002)
Abstract. PDF.

Structure of the SH3-Guanylate Kinase Module from PSD-95 Suggests a Mechanism for Regulated Assembly of MAGUK Scaffolding Proteins
Aaron W. McGee, Srikanth R. Dakoji, Olav Olsen, David S. Bredt, Wendell A. Lim, and Kenneth E. Prehoda
Molecular Cell 8, 1291-1301 (2001)
Abstract. PDF.
Commentary in Structure by Michael B. Yaffe (PDF)

Mechanism and role of PDZ domains in signaling complex assembly
Baruch Z. Harris and Wendell A. Lim
Journal of Cell Science 114, 3219-3231 (2001)
Abstract. PDF.

The double life of PX domains
Kenneth E. Prehoda and Wendell A. Lim
Nature Structural Biology 8, 570-572 (2001)
Abstract. PDF.

Energetic Determinants of Internal Motif Recognition by PDZ Domains
Baruch Z. Harris, Brian J. Hillier, and Wendell A. Lim
Biochemistry 40, 5921-5930 (2001)
Abstract. PDF.

Integration of Multiple Signals Through Cooperative Regulation of the N-WASP-Arp2/3 Complex
Kenneth E. Prehoda, Jessica A. Scott, R. Dyche Mullins, and Wendell A. Lim
Science 290, 801-806 (2000)
Abstract. PDF. Supplemental Data.
Commentary in Science by James Fawcett and Tony Pawson (HTML)

Converging on proline: the mechanism of WW domain peptide recognition
Ali Zarrinpar and Wendell A. Lim
Nature Structural Biology 7, 611-613 (2000)
Abstract. PDF.

Improving SH3 domain ligand selectivity using a non-natural scaffold
Jack T. Nguyen, Margaret Porter, Mehran Amoui, W. Todd Miller, Ronald N. Zuckermann and Wendell A. Lim
Chemistry & Biology 7, 463-473 (2000)
Abstract. PDF.

PSD-95 Assembles a Ternary Complex with the N-Methyl-D-aspartic Acid Receptor and a Bivalent Neuronal NO Synthase PDZ Domain
Karen S. Christopherson, Brian J. Hillier, Wendell A. Lim, and David S. Bredt
Journal of Biological Chemistry 274, 27467-27473 (1999)
Abstract. PDF.

Structure of the Enabled/VASP Homology 1 Domain–Peptide Complex: A Key Component in the Spatial Control of Actin Assembly
Kenneth E. Prehoda, Do. J. Lee, and Wendell A. Lim
Cell 97, 471-480 (1999)
Abstract. PDF.

Unexpected Modes of PDZ Domain Scaffolding Revealed by Structure of nNOS-Syntrophin Complex
Brian J. Hillier, Karen S. Christopherson, Kenneth E. Prehoda, David S. Bredt, and Wendell A. Lim
Science 284, 812-815 (1999)
Abstract. PDF.
Commentary in Nature Structural Biology by Hartmut Oschkinat (PDF)

Exploiting the Basis of Proline Recognition by SH3 and WW Domains: Design of N-Substituted Inhibitors
Jack T. Nguyen, Christoph W. Turck, Fred E. Cohen, Ronald N. Zuckermann, and Wendell A. Lim
Science 282, 2088-2092 (1998)
Abstract. PDF.
Commentary in Chemistry and Biology by Behzad Aghazadeh and Michael K. Rosen (PDF)