The spatial structure of cell signaling systems

The Underappreciated Role of Allostery in the Cellular Network

(2013) Ruth Nussinov et al.   Annual Review of Biophysics

Nuclear organization of RNA polymerase II transcription

(2013) Scott Davidson et al.   Biochemistry and Cell Biology

A broad view of scaffolding suggests that scaffolding proteins can actively control regulation and signaling of multienzyme complexes through allostery

(2013) Ruth Nussinov et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Allostery in Disease and in Drug Discovery

(2013) Ruth Nussinov et al.   CELL

Distinct Chromatin Configurations Regulate the Initiation and the Maintenance of hGH Gene Expression

(2013) Yugong Ho et al.   MOLECULAR AND CELLULAR BIOLOGY

Systematic identification of allosteric protein-metabolite interactions that control enzyme activity in vivo

(2013) Hannes Link et al.   NATURE BIOTECHNOLOGY

Optogenetic protein clustering and signaling activation in mammalian cells

(2013) Lukasz J Bugaj et al.   NATURE METHODS

Lipid binding by the Unique and SH3 domains of c-Src suggests a new regulatory mechanism

(2013) Yolanda Pérez et al.   Scientific Reports

Discovery of Allosteric Inhibitors of Kinesin Spindle Protein (KSP) for the Treatment of Taxane-Refractory Cancer: MK-0731 and Analogs

(2012) Christopher D. Cox et al.   Anti-Cancer Agents in Medicinal Chemistry

The lipid raft hypothesis revisited - New insights on raft composition and function from super-resolution fluorescence microscopy

(2012) Dylan M. Owen et al.   BIOESSAYS

An ensemble view of thrombin allostery

(2012) Bernhard C. Lechtenberg et al.   BIOLOGICAL CHEMISTRY

Protein dynamics and conformational selection in bidirectional signal transduction

(2012) Ruth Nussinov et al.   BMC BIOLOGY

Cooperativity and complementarity: Synergies in non-classical and classical glucocorticoid signaling

(2012) Ranmal A. Samarasinghe et al.   CELL CYCLE

The role of allostery in the ubiquitin–proteasome system

(2012) Jin Liu et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

Raf Inhibitors Target Ras Spatiotemporal Dynamics

(2012) Kwang-jin Cho et al.   CURRENT BIOLOGY

Assembly and disassembly of cell matrix adhesions

(2012) Bernhard Wehrle-Haller   CURRENT OPINION IN CELL BIOLOGY

Super-resolution characterization of TCR-dependent signaling clusters

(2012) Eilon Sherman et al.   IMMUNOLOGICAL REVIEWS

IκB kinase regulation of the TPL-2/ERK MAPK pathway

(2012) Thorsten Gantke et al.   IMMUNOLOGICAL REVIEWS

Allosteric Modulation of Ca2+flux in Ligand-gated Cation Channel (P2X4) by Actions on Lateral Portals

(2012) Damien S. K. Samways et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Antibody-induced Enhancement of Factor VIIa Activity through Distinct Allosteric Pathways

(2012) Lisbeth M. Andersen et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Myosin and Tropomyosin Stabilize the Conformation of Formin-nucleated Actin Filaments

(2012) Zoltán Ujfalusi et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Cholesterol and Sphingomyelin Drive Ligand-independent T-cell Antigen Receptor Nanoclustering

(2012) Eszter Molnár et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Cell surface dynamics - how Rho GTPases orchestrate the interplay between the plasma membrane and the cortical cytoskeleton

(2012) I. de Curtis et al.   JOURNAL OF CELL SCIENCE

Mapping L1 Ligase Ribozyme Conformational Switch

(2012) George M. Giambaşu et al.   JOURNAL OF MOLECULAR BIOLOGY

Multistate Allostery in Response Regulators: Phosphorylation and Mutagenesis Activate RegA via Alternate Modes

(2012) Balakrishnan Shenbaga Moorthy et al.   JOURNAL OF MOLECULAR BIOLOGY

Investigating Allostery in Molecular Recognition: Insights from a Computational Study of Multiple Antibody–Antigen Complexes

(2012) Dario Corrada et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Formation and Domain Partitioning of H-ras Peptide Nanoclusters: Effects of Peptide Concentration and Lipid Composition

(2012) Zhenlong Li et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

RhoD regulates cytoskeletal dynamics via the actin nucleation–promoting factor WASp homologue associated with actin Golgi membranes and microtubules

(2012) Annica K. B. Gad et al.   MOLECULAR BIOLOGY OF THE CELL

The spatial architecture of protein function and adaptation

(2012) Richard N. McLaughlin Jr et al.   NATURE

Conformational states of the kinase Lck regulate clustering in early T cell signaling

(2012) Jérémie Rossy et al.   NATURE IMMUNOLOGY

Transcription factor Foxp3 and its protein partners form a complex regulatory network

(2012) Dipayan Rudra et al.   NATURE IMMUNOLOGY

Interactome3D: adding structural details to protein networks

(2012) Roberto Mosca et al.   NATURE METHODS

The condensed chromatin fiber: an allosteric chemo-mechanical machine for signal transduction and genome processing

(2012) Annick Lesne et al.   PHYSICAL BIOLOGY

Intracellular Spatial Localization Regulated by the Microtubule Network

(2012) Jing Chen et al.   PLoS One

Allosteric pathways in imidazole glycerol phosphate synthase

(2012) I. Rivalta et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Force measurements on cargoes in living cells reveal collective dynamics of microtubule motors

(2012) A. G. Hendricks et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Allosteric networks in thrombin distinguish procoagulant vs. anticoagulant activities

(2012) P. M. Gasper et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Organization, dynamics, and segregation of Ras nanoclusters in membrane domains

(2012) L. Janosi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural basis for intersubunit signaling in a protein disaggregating machine

(2012) A. B. Biter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Allosteric inhibition of individual enzyme molecules trapped in lipid vesicles

(2012) H. M. Piwonski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conformational Control of the Ste5 Scaffold Protein Insulates Against MAP Kinase Misactivation

(2012) J. G. Zalatan et al.   SCIENCE

Structural Basis for Allosteric Regulation of GPCRs by Sodium Ions

(2012) W. Liu et al.   SCIENCE

Allosteric post-translational modification codes

(2012) Ruth Nussinov et al.   TRENDS IN BIOCHEMICAL SCIENCES

Mechanical feedback between membrane tension and dynamics

(2012) Nils C. Gauthier et al.   TRENDS IN CELL BIOLOGY

PI3K and mTOR Signaling Pathways in Cancer: New Data on Targeted Therapies

(2012) Lise Willems et al.   Current Oncology Reports

Convergent Transmission of RNAi Guide-Target Mismatch Information across Argonaute Internal Allosteric Network

(2012) Thomas T. Joseph et al.   PLoS Computational Biology

Allosteric Communication across the Native and Mutated KIT Receptor Tyrosine Kinase

(2012) Elodie Laine et al.   PLoS Computational Biology

Conformational Control of the Binding of the Transactivation Domain of the MLL Protein and c-Myb to the KIX Domain of CREB

(2012) Elif Nihal Korkmaz et al.   PLoS Computational Biology

Lipid Rafts and Alzheimer’s Disease: Protein-Lipid Interactions and Perturbation of Signaling

(2012) David A. Hicks et al.   Frontiers in Physiology

Gene-specific transcription activation via long-range allosteric shape-shifting

(2011) Chung-Jung Tsai et al.   BIOCHEMICAL JOURNAL

Allosteric interactions and proton conducting pathways in proton pumping aa3 oxidases: Heme a as a key coupling element

(2011) Nazzareno Capitanio et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

Allosteric modulators can restore function in an amino acid neurotransmitter receptor by slightly altering intra-molecular communication pathways

(2011) Ruth Nussinov   BRITISH JOURNAL OF PHARMACOLOGY

Function of hyperekplexia-causing α1R271Q/L glycine receptors is restored by shifting the affected residue out of the allosteric signalling pathway

(2011) Qiang Shan et al.   BRITISH JOURNAL OF PHARMACOLOGY

The Powerstroke and Camshaft of the RIG-I Antiviral RNA Detection Machine

(2011) Luke A.J. O'Neill et al.   CELL

Hot Spots for Allosteric Regulation on Protein Surfaces

(2011) Kimberly A. Reynolds et al.   CELL

Transport of Germ Plasm on Astral Microtubules Directs Germ Cell Development in Drosophila

(2011) Dorothy A. Lerit et al.   CURRENT BIOLOGY

WNK1 Promotes PIP2 Synthesis to Coordinate Growth Factor and GPCR-Gq Signaling

(2011) Sung-Wan An et al.   CURRENT BIOLOGY

Regulation of protein kinases by lipids

(2011) Thomas A Leonard et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Regulation of the catalytic activity of the EGF receptor

(2011) Nicholas F Endres et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Detection of allosteric signal transmission by information-theoretic analysis of protein dynamics

(2011) Alessandro Pandini et al.   FASEB JOURNAL

Flexible Cullins in Cullin-RING E3 Ligases Allosterically Regulate Ubiquitination

(2011) Jin Liu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Signal Integration and Coincidence Detection in the Mitogen-activated Protein Kinase/Extracellular Signal-regulated Kinase (ERK) Cascade

(2011) Nishamol Geetha et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Actin Filament Dynamics in the Actomyosin VI Complex Is Regulated Allosterically by Calcium–Calmodulin Light Chain

(2011) Ewa Prochniewicz et al.   JOURNAL OF MOLECULAR BIOLOGY

Mechanisms of Allosteric Gene Regulation by NMR Quantification of Microsecond–Millisecond Protein Dynamics

(2011) Ian R. Kleckner et al.   JOURNAL OF MOLECULAR BIOLOGY

Atomistic Kinetic Model for Population Shift and Allostery in Biomolecules

(2011) Dong Long et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Raft Protein Clustering Alters N-Ras Membrane Interactions and Activation Pattern

(2011) S. Eisenberg et al.   MOLECULAR AND CELLULAR BIOLOGY

How do dynamic cellular signals travel long distances?

(2011) Ruth Nussinov   Molecular BioSystems

Queueing up for enzymatic processing: correlated signaling through coupled degradation

(2011) N. A. Cookson et al.   Molecular Systems Biology

Mapping allostery through the covariance analysis of NMR chemical shifts

(2011) R. Selvaratnam et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dynamic Allostery: Linkers Are Not Merely Flexible

(2011) Buyong Ma et al.   STRUCTURE

Dynamic protein–DNA recognition: beyond what can be seen

(2011) Monika Fuxreiter et al.   TRENDS IN BIOCHEMICAL SCIENCES

Identification of Biochemical Network Modules Based on Shortest Retroactive Distances

(2011) Gautham Vivek Sridharan et al.   PLoS Computational Biology

Computational Modeling of Allosteric Communication Reveals Organizing Principles of Mutation-Induced Signaling in ABL and EGFR Kinases

(2011) Anshuman Dixit et al.   PLoS Computational Biology

Change in Allosteric Network Affects Binding Affinities of PDZ Domains: Analysis through Perturbation Response Scanning

(2011) Z. Nevin Gerek et al.   PLoS Computational Biology

Changes in Dynamics upon Oligomerization Regulate Substrate Binding and Allostery in Amino Acid Kinase Family Members

(2011) Enrique Marcos et al.   PLoS Computational Biology

Why Does Binding of Proteins to DNA or Proteins to Proteins Not Necessarily Spell Function?

(2010) Buyong Ma et al.   ACS Chemical Biology

Long-Range Interaction Networks in the Function and Fidelity of Poliovirus RNA-Dependent RNA Polymerase Studied by Nuclear Magnetic Resonance

(2010) Xiaorong Yang et al.   BIOCHEMISTRY

Crystallographic and Nuclear Magnetic Resonance Evaluation of the Impact of Peptide Binding to the Second PDZ Domain of Protein Tyrosine Phosphatase 1E

(2010) Jun Zhang et al.   BIOCHEMISTRY

Rbx1 Flexible Linker Facilitates Cullin-RING Ligase Function Before Neddylation and After Deneddylation

(2010) Jin Liu et al.   BIOPHYSICAL JOURNAL

The Palmitoylation Machinery Is a Spatially Organizing System for Peripheral Membrane Proteins

(2010) Oliver Rocks et al.   CELL

Cell Signaling by Receptor Tyrosine Kinases

(2010) Mark A. Lemmon et al.   CELL

Ras nanoclusters: Combining digital and analog signaling

(2010) Angus Harding et al.   CELL CYCLE

Allostery and population shift in drug discovery

(2010) Gozde Kar et al.   CURRENT OPINION IN PHARMACOLOGY

Protein dynamics and allostery: an NMR view

(2010) Shiou-Ru Tzeng et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Spatial organization of transmembrane receptor signalling

(2010) Ioanna Bethani et al.   EMBO JOURNAL

Microtubule-associated Protein-like Binding of the Kinesin-1 Tail to Microtubules

(2010) Mark A. Seeger et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Signalling complexes and clusters: functional advantages and methodological hurdles

(2010) M. Cebecauer et al.   JOURNAL OF CELL SCIENCE

Molecular Dynamics Reveal the Essential Role of Linker Motions in the Function of Cullin–RING E3 Ligases

(2010) Jin Liu et al.   JOURNAL OF MOLECULAR BIOLOGY

Spatial organization and signal transduction at intercellular junctions

(2010) Boryana N. Manz et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

A membranous spindle matrix orchestrates cell division

(2010) Yixian Zheng   NATURE REVIEWS MOLECULAR CELL BIOLOGY

An extracellular steric seeding mechanism for Eph-ephrin signaling platform assembly

(2010) Elena Seiradake et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Allostery at G Protein-Coupled Receptor Homo- and Heteromers: Uncharted Pharmacological Landscapes

(2010) N. J. Smith et al.   PHARMACOLOGICAL REVIEWS

Seven Transmembrane Receptors as Shapeshifting Proteins: The Impact of Allosteric Modulation and Functional Selectivity on New Drug Discovery

(2010) T. Kenakin et al.   PHARMACOLOGICAL REVIEWS

Architecture of Eph receptor clusters

(2010) J. P. Himanen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Protein functional landscapes, dynamics, allostery: a tortuous path towards a universal theoretical framework

(2010) Pavel I. Zhuravlev et al.   QUARTERLY REVIEWS OF BIOPHYSICS

Restriction of Receptor Movement Alters Cellular Response: Physical Force Sensing by EphA2

(2010) K. Salaita et al.   SCIENCE

Induced fit, conformational selection and independent dynamic segments: an extended view of binding events

(2010) Peter Csermely et al.   TRENDS IN BIOCHEMICAL SCIENCES

Mechanisms of transcription factor selectivity

(2010) Yongping Pan et al.   TRENDS IN GENETICS

From signaling pathways to microtubule dynamics: the key players

(2009) Sandrine Etienne-Manneville   CURRENT OPINION IN CELL BIOLOGY

Frameworks for Understanding Long-Range Intra-Protein Communication

(2009) Matthew Whitley et al.   CURRENT PROTEIN & PEPTIDE SCIENCE

Specific phosphorylation and activation of ERK1c by MEK1b: a unique route in the ERK cascade

(2009) Y. D. Shaul et al.   GENES & DEVELOPMENT

The coreceptor CD2 uses plasma membrane microdomains to transduce signals in T cells

(2009) Yoshihisa Kaizuka et al.   JOURNAL OF CELL BIOLOGY

Protein allostery, signal transmission and dynamics: a classification scheme of allosteric mechanisms

(2009) Chung-Jung Tsai et al.   Molecular BioSystems

Ras acylation, compartmentalization and signaling nanoclusters (Review)

(2009) Yoav I. Henis et al.   MOLECULAR MEMBRANE BIOLOGY

Transcription factories: gene expression in unions?

(2009) Heidi Sutherland et al.   NATURE REVIEWS GENETICS

How do transcription factors select specific binding sites in the genome?

(2009) Yongping Pan et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Amplification of signaling via cellular allosteric relay and protein disorder

(2009) B. Ma et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DNA Binding Site Sequence Directs Glucocorticoid Receptor Structure and Activity

(2009) S. H. Meijsing et al.   SCIENCE

Allosteric Effects Govern Nuclear Receptor Action: DNA Appears as a Player

(2009) H. Gronemeyer et al.   Science Signaling

The Origin of Allosteric Functional Modulation: Multiple Pre-existing Pathways

(2009) Antonio del Sol et al.   STRUCTURE

Protein–protein interaction networks: how can a hub protein bind so many different partners?

(2009) Chung-Jung Tsai et al.   TRENDS IN BIOCHEMICAL SCIENCES

‘7TM Receptor Allostery: Putting Numbers to Shapeshifting Proteins

(2009) Terry P. Kenakin   TRENDS IN PHARMACOLOGICAL SCIENCES

The Mechanism of Ubiquitination in the Cullin-RING E3 Ligase Machinery: Conformational Control of Substrate Orientation

(2009) Jin Liu et al.   PLoS Computational Biology

Analyzing Protein Interaction Networks Using Structural Information

(2008) Christina Kiel et al.   Annual Review of Biochemistry

Macromolecular Crowding and Confinement: Biochemical, Biophysical, and Potential Physiological Consequences

(2008) Huan-Xiang Zhou et al.   Annual Review of Biophysics

Mediation, Modulation, and Consequences of Membrane-Cytoskeleton Interactions

(2008) Gary J. Doherty et al.   Annual Review of Biophysics

Controlling Proteins Through Molecular Springs

(2008) Giovanni Zocchi   Annual Review of Biophysics

Energy Flow in Proteins

(2008) David M. Leitner   Annual Review of Physical Chemistry

Design of an Optical Switch for Studying Conformational Dynamics in Individual Molecules of GroEL

(2008) Gabriel A. Frank et al.   BIOCONJUGATE CHEMISTRY

Tubulin acetylation favors Hsp90 recruitment to microtubules and stimulates the signaling function of the Hsp90 clients Akt/PKB and p53

(2008) Julien Giustiniani et al.   CELLULAR SIGNALLING

T Cell Costimulation via the Integrin VLA-4 Inhibits the Actin-Dependent Centralization of Signaling Microclusters Containing the Adaptor SLP-76

(2008) Ken Nguyen et al.   IMMUNITY

Spatiotemporal Regulation of T Cell Costimulation by TCR-CD28 Microclusters and Protein Kinase C θ Translocation

(2008) Tadashi Yokosuka et al.   IMMUNITY

Allostery: Absence of a Change in Shape Does Not Imply that Allostery Is Not at Play

(2008) Chung-Jung Tsai et al.   JOURNAL OF MOLECULAR BIOLOGY

Coupling between global dynamics and signal transduction pathways: a mechanism of allostery for chaperonin GroEL

(2008) Chakra Chennubhotla et al.   Molecular BioSystems

Allosteric regulation and catalysis emerge via a common route

(2008) Nina M Goodey et al.   Nature Chemical Biology

KEGG Atlas mapping for global analysis of metabolic pathways

(2008) S. Okuda et al.   NUCLEIC ACIDS RESEARCH

Allostery and cooperativity revisited

(2008) Qiang Cui et al.   PROTEIN SCIENCE

Using Engineered Scaffold Interactions to Reshape MAP Kinase Pathway Signaling Dynamics

(2008) C. J. Bashor et al.   SCIENCE

Cellular functions of GEF-H1, a microtubule-regulated Rho-GEF: is altered GEF-H1 activity a crucial determinant of disease pathogenesis?

(2008) Jörg Birkenfeld et al.   TRENDS IN CELL BIOLOGY

Multiple diverse ligands binding at a single protein site: A matter of pre-existing populations

(2002) Buyong Ma et al.   PROTEIN SCIENCE