Engineering proteins for allosteric control by light or ligands

The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design

(2017) Rebecca F. Alford et al.   Journal of Chemical Theory and Computation

Engineering Pak1 Allosteric Switches

(2017) Onur Dagliyan et al.   ACS Synthetic Biology

Affecting long-term fear memory formation through optical control of Rac1 GTPase and PAK activity in lateral amygdala

(2017) Aniruddha Das et al.   Scientific Reports

Profiling of engineering hotspots identifies an allosteric CRISPR-Cas9 switch

(2016) Benjamin L Oakes et al.   NATURE BIOTECHNOLOGY

LOVTRAP: an optogenetic system for photoinduced protein dissociation

(2016) Hui Wang et al.   NATURE METHODS

Engineering extrinsic disorder to control protein activity in living cells

(2016) Onur Dagliyan et al.   SCIENCE

Open source software for quantification of cell migration, protrusions, and fluorescence intensities

(2015) David J. Barry et al.   JOURNAL OF CELL BIOLOGY

Labelling and optical erasure of synaptic memory traces in the motor cortex

(2015) Akiko Hayashi-Takagi et al.   NATURE

The I-TASSER Suite: protein structure and function prediction

(2015) Jianyi Yang et al.   NATURE METHODS

CellGeo: A computational platform for the analysis of shape changes in cells with complex geometries

(2014) Denis Tsygankov et al.   JOURNAL OF CELL BIOLOGY

Dissecting motility signaling through activation of specific Src-effector complexes

(2014) Andrei V Karginov et al.   Nature Chemical Biology

Reversible protein inactivation by optogenetic trapping in cells

(2014) Sangkyu Lee et al.   NATURE METHODS

Factors That Control the Chemistry of the LOV Domain Photocycle

(2014) Josiah P. Zayner et al.   PLoS One

Engineered kinase activation reveals unique morphodynamic phenotypes and associated trafficking for Src family isoforms

(2014) P.-H. Chu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Engineering an improved light-induced dimer (iLID) for controlling the localization and activity of signaling proteins

(2014) Gurkan Guntas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An optimized optogenetic clustering tool for probing protein interaction and function

(2014) Amir Taslimi et al.   Nature Communications

A LOV2 Domain-Based Optogenetic Tool to Control Protein Degradation and Cellular Function

(2013) Christian Renicke et al.   CHEMISTRY & BIOLOGY

An optogenetic tool for the activation of endogenous diaphanous-related formins induces thickening of stress fibers without an increase in contractility

(2013) Megha Vaman Rao et al.   Cytoskeleton

MISTIC: mutual information server to infer coevolution

(2013) Franco L. Simonetti et al.   NUCLEIC ACIDS RESEARCH

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Rational design of a ligand-controlled protein conformational switch

(2013) O. Dagliyan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nuclear Actin Network Assembly by Formins Regulates the SRF Coactivator MAL

(2013) C. Baarlink et al.   SCIENCE

A comparative assessment and analysis of 20 representative sequence alignment methods for protein structure prediction

(2013) Renxiang Yan et al.   Scientific Reports

Identification of Natural and Artificial DNA Substrates for Light-Activated LOV–HTH Transcription Factor EL222

(2012) Giomar Rivera-Cancel et al.   BIOCHEMISTRY

Controlling the DNA Cleavage Activity of Light-Inducible Chimeric Endonucleases by Bidirectional Photoactivation

(2012) Benno Schierling et al.   BIOCONJUGATE CHEMISTRY

Rapid and orthogonal logic gating with a gibberellin-induced dimerization system

(2012) Takafumi Miyamoto et al.   Nature Chemical Biology

Spatiotemporal control of gene expression by a light-switchable transgene system

(2012) Xue Wang et al.   NATURE METHODS

Optical Control of Protein Activity by Fluorescent Protein Domains

(2012) X. X. Zhou et al.   SCIENCE

A Synthetic Photoactivated Protein to Generate Local or Global Ca2+ Signals

(2011) Elizabeth Pham et al.   CHEMISTRY & BIOLOGY

Small-molecule displacement of a cryptic degron causes conditional protein degradation

(2011) Kimberly M Bonger et al.   Nature Chemical Biology

Engineering a Photoactivated Caspase-7 for Rapid Induction of Apoptosis

(2011) Evan Mills et al.   ACS Synthetic Biology

Light Regulation of Protein Dimerization and Kinase Activity in Living Cells Using Photocaged Rapamycin and Engineered FKBP

(2010) Andrei V. Karginov et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Engineered allosteric activation of kinases in living cells

(2010) Andrei V Karginov et al.   NATURE BIOTECHNOLOGY

Light-mediated activation reveals a key role for Rac in collective guidance of cell movement in vivo

(2010) Xiaobo Wang et al.   NATURE CELL BIOLOGY

Rapid blue-light–mediated induction of protein interactions in living cells

(2010) Matthew J Kennedy et al.   NATURE METHODS

I-TASSER: a unified platform for automated protein structure and function prediction

(2010) Ambrish Roy et al.   Nature Protocols

Automated minimization of steric clashes in protein structures

(2010) Srinivas Ramachandran et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Mechanism of signal transduction of the LOV2-Jα photosensor from Avena sativa

(2010) Emanuel Peter et al.   Nature Communications

Designing switchable enzymes

(2009) Marc Ostermeier   CURRENT OPINION IN STRUCTURAL BIOLOGY

Spatiotemporal control of cell signalling using a light-switchable protein interaction

(2009) Anselm Levskaya et al.   NATURE

Coordination of Rho GTPase activities during cell protrusion

(2009) Matthias Machacek et al.   NATURE

A genetically encoded photoactivatable Rac controls the motility of living cells

(2009) Yi I. Wu et al.   NATURE

Induction of protein-protein interactions in live cells using light

(2009) Masayuki Yazawa et al.   NATURE BIOTECHNOLOGY

Linking the functions of unrelated proteins using a novel directed evolution domain insertion method

(2008) Wayne R. Edwards et al.   NUCLEIC ACIDS RESEARCH