Lim Lab | Downloads

Software

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)

Matlab toolbox for microscope control (via Micro-Manager) and the feedback controller

software.zip

Movies

Scaffold proteins: hubs for controlling the flow of cellular information

Matthew C. Good, Jesse G. Zalatan, Wendell A. Lim

Science 332, 680-6 (2011)

Mechanisms of scaffold protein Ste5
(animation by Janet Iwasa )
File

Quicktime video

matingPathway.mov

Windows Media video

matingPathway.wmv

MPEG-4 video

matingPathway.mp4

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)

Supplementary Movies File

Movie S1 - YFP memane recruitment

al_2009_s1.mov

Movie S2 - YFP memane dissociation

al_2009_s2.mov

Movie S3 - oscillating YFP translocation

al_2009_s3.mov

Movie S4 - YFP point recruitment

al_2009_s4.mov

Movie S5 - patterned recruitment of YFP

al_2009_s5.mov

Movie S6 - titrated recruitment of YFP

al_2009_s6.mov

Movie S7 - cell extrusion by Tiam (Rac GEF) recruitment

al_2009_s7.mov

Movie S8 - dynamic lamellipodia by Tiam (Rac GEF) recruitment

al_2009_s8.mov

Movie S9 - periodic contractions by Tim (Rho GEF) recruitment

al_2009_s9.mov

Movie S10 - PIF-YFP-only recruitment control

al_2009_s10.mov

Movie S11 - dynamics of memane-bound Cdc42-GTP in TIRF

al_2009_s11.mov

Structures

The Ste5 Scaffold Directs Mating Signaling by Catalytically Unlocking the Fus3 MAP Kinase for Activation

Matthew Good, Grace Tang, Julie Singleton, Attila Reményi, and Wendell A. Lim

Cell 136, 1085-97 (2009)

Structure File

'Minimal scaffold' (ms) domain of Ste5

3FZE.pdb

The Ste5 Scaffold Allosterically Modulates Signaling Output of the YeastMating Pathway

Roby P. Bhattacharyya*, Attila Reményi*,Matthew C. Good, Caleb J. Bashor, Arnold M. Falick, and Wendell A. Lim

Science 311, 822-826 (2006)

Structure File

Fus3 in complex with a Ste5 peptide

2F49.pdb

Fus3 without a peptide from Ste5

2FA2.pdb

Fus3 phosphorylated on Tyr182

2F9G.pdb

The role of docking interactions in mediating signaling input, output, anddiscrimination in the yeast MAPK network

AttilaReményi, Matthew C. Good, Roby P. Bhattacharyya, andWendell A. Lim

Molecular Cell 20, 951-962 (2005)

Structure File

Mitogen activated protein kinase Fus3 (non-phosphorylated)

2B9F.pdb

Fus3 with a docking motif from Ste7

2B9H.pdb

Fus3 with a docking motif from Msg5

2B9I.pdb

Fus3 with a docking motif from Far1

2B9J.pdb

Structure of the N-WASP EVH1 Domain-WIP Complex: Insight into the Molecular Basisof Wiskott-Aldrich Syndrome

ian F. Volkman, Kenneth E. Prehoda, Jessica A.Scott, Francis C. Peterson, and Wendell A. Lim

Cell 111, 565–576 (2002)

Structure File

N-WASP EVH1 Domain - WIP complex

1MKE.pdb

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. edt, Wendell A. Lim, and Kenneth E. Prehoda

Molecular Cell 8, 1291-1301 (2001)

Structure File

SH3-guanylate kinase module from PSD-95

1KJW.pdb

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)

Structure File

Enabled/VASP Homology 1 (EVH1) domain from mouse Enabled in complex with ActA peptide

1EVH.pdb

Unexpected Modes of PDZ Domain Scaffolding Revealed by Structure of nNOS-SyntrophinComplex

ian J. Hillier, Karen S. Christopherson, Kenneth E. Prehoda, David S. edt, and Wendell A. Lim

Science 284, 812-815 (1999)

Structure File

Neuronal nitric oxide synthase (nNOS) PDZ domain

1QAU.pdb

nNOS PDZ-syntrophin PDZ complex

1QAV.pdb

Exploiting the Basis of Proline Recognition by SH3 andWW 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)

Structure File

Sem5 C-term. SH3 in complex with Sos peptide

1SEM.pdb

Sem5 C-term. SH3 in complex with isopropyl peptoid/peptide

2SEM.pdb

Sem5 C-term. SH3 in complex with cyclopropyl methyl peptoid/peptide

3SEM.pdb

Crk SH3 in complex with peptoid/peptide

1B07.pdb