Short linear motifs – ex nihilo evolution of protein regulation

The ABBA Motif Binds APC/C Activators and Is Shared by APC/C Substrates and Regulators

(2015) Barbara Di Fiore et al.   DEVELOPMENTAL CELL

Intrinsically disordered proteins in cellular signalling and regulation

(2015) Peter E. Wright et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The Structure of an NDR/LATS Kinase–Mob Complex Reveals a Novel Kinase–Coactivator System and Substrate Docking Mechanism

(2015) Gergő Gógl et al.   PLOS BIOLOGY

Short Linear Motifs: Ubiquitous and Functionally Diverse Protein Interaction Modules Directing Cell Regulation

(2014) Kim Van Roey et al.   CHEMICAL REVIEWS

The grammar of transcriptional regulation

(2014) Shira Weingarten-Gabbay et al.   HUMAN GENETICS

The Calcineurin Signaling Network Evolves via Conserved Kinase-Phosphatase Modules that Transcend Substrate Identity

(2014) Aaron Goldman et al.   MOLECULAR CELL

A Million Peptide Motifs for the Molecular Biologist

(2014) Peter Tompa et al.   MOLECULAR CELL

Disorder and residual helicity alter p53-Mdm2 binding affinity and signaling in cells

(2014) Wade Borcherds et al.   Nature Chemical Biology

Context-dependent control of alternative splicing by RNA-binding proteins

(2014) Xiang-Dong Fu et al.   NATURE REVIEWS GENETICS

Large-scale interaction profiling of PDZ domains through proteomic peptide-phage display using human and viral phage peptidomes

(2014) Y. Ivarsson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Detecting Functional Divergence after Gene Duplication through Evolutionary Changes in Posttranslational Regulatory Sequences

(2014) Alex N. Nguyen Ba et al.   PLoS Computational Biology

Interaction Analysis through Proteomic Phage Display

(2014) Gustav N. Sundell et al.   Biomed Research International

Multi-species, multi-transcription factor binding highlights conserved control of tissue-specific biological pathways

(2014) Benoit Ballester et al.   eLife

Ancestral resurrection reveals evolutionary mechanisms of kinase plasticity

(2014) Conor J Howard et al.   eLife

Turnover of protein phosphorylation evolving under stabilizing selection

(2014) Christian R. Landry et al.   Frontiers in Genetics

Insights into Degron Recognition by APC/C Coactivators from the Structure of an Acm1-Cdh1 Complex

(2013) Jun He et al.   MOLECULAR CELL

SH3 interactome conserves general function over specific form

(2013) X. Xin et al.   Molecular Systems Biology

A compendium of RNA-binding motifs for decoding gene regulation

(2013) Debashish Ray et al.   NATURE

Sequential primed kinases create a damage-responsive phosphodegron on Eco1

(2013) Nicholas A Lyons et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The eukaryotic linear motif resource ELM: 10 years and counting

(2013) Holger Dinkel et al.   NUCLEIC ACIDS RESEARCH

The switches.ELM Resource: A Compendium of Conditional Regulatory Interaction Interfaces

(2013) K. Van Roey et al.   Science Signaling

The Molecular Mechanism of Substrate Engagement and Immunosuppressant Inhibition of Calcineurin

(2013) Simina Grigoriu et al.   PLOS BIOLOGY

Disorder-function relationships for the cell cycle regulatory proteins p21 and p27

(2012) Diana M. Mitrea et al.   BIOLOGICAL CHEMISTRY

ncDNA and drift drive binding site accumulation

(2012) Troy Ruths et al.   BMC EVOLUTIONARY BIOLOGY

Conservation of caspase substrates across metazoans suggests hierarchical importance of signaling pathways over specific targets and cleavage site motifs in apoptosis

(2012) E D Crawford et al.   CELL DEATH AND DIFFERENTIATION

Motif switches: decision-making in cell regulation

(2012) Kim Van Roey et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Don't Make Me Mad, Bub!

(2012) Andrew W. Murray   DEVELOPMENTAL CELL

The Vertebrate Mitotic Checkpoint Protein BUBR1 Is an Unusual Pseudokinase

(2012) Saskia J.E. Suijkerbuijk et al.   DEVELOPMENTAL CELL

Structural basis for protein phosphatase 1 regulation and specificity

(2012) Wolfgang Peti et al.   FEBS Journal

Plasticity of PDZ domains in ligand recognition and signaling

(2012) Ylva Ivarsson   FEBS LETTERS

The language of SH2 domain interactions defines phosphotyrosine-mediated signal transduction

(2012) Bernard A. Liu et al.   FEBS LETTERS

Mapping N-Glycosylation Sites across Seven Evolutionarily Distant Species Reveals a Divergent Substrate Proteome Despite a Common Core Machinery

(2012) Dorota F. Zielinska et al.   MOLECULAR CELL

Proto-genes and de novo gene birth

(2012) Anne-Ruxandra Carvunis et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Balanced interactions of calcineurin with AKAP79 regulate Ca2+–calcineurin–NFAT signaling

(2012) Huiming Li et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Evolution of SH2 domains and phosphotyrosine signalling networks

(2012) B. A. Liu et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Tight coevolution of proliferating cell nuclear antigen (PCNA)-partner interaction networks in fungi leads to interspecies network incompatibility

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

Superbinder SH2 Domains Act as Antagonists of Cell Signaling

(2012) T. Kaneko et al.   Science Signaling

Intrinsically disordered proteins: a 10-year recap

(2012) Peter Tompa   TRENDS IN BIOCHEMICAL SCIENCES

Network Evolution: Rewiring and Signatures of Conservation in Signaling

(2012) Mark G. F. Sun et al.   PLoS Computational Biology

Rewiring of PDZ Domain-Ligand Interaction Network Contributed to Eukaryotic Evolution

(2012) Jinho Kim et al.   PLoS Genetics

Unstructural biology coming of age

(2011) Peter Tompa   CURRENT OPINION IN STRUCTURAL BIOLOGY

Attributes of short linear motifs

(2011) Norman E. Davey et al.   Molecular BioSystems

Molecular basis of purine-rich RNA recognition by the human SR-like protein Tra2-β1

(2011) Antoine Cléry et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Extensive DNA-binding specificity divergence of a conserved transcription regulator

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

From conformational chaos to robust regulation: the structure and function of the multi-enzyme RNA degradosome

(2011) Maria W. Górna et al.   QUARTERLY REVIEWS OF BIOPHYSICS

Spatial Exclusivity Combined with Positive and Negative Selection of Phosphorylation Motifs Is the Basis for Context-Dependent Mitotic Signaling

(2011) J. Alexander et al.   Science Signaling

Evolving specificity from variability for protein interaction domains

(2011) Tomonori Kaneko et al.   TRENDS IN BIOCHEMICAL SCIENCES

Does Positive Selection Drive Transcription Factor Binding Site Turnover? A Test with Drosophila Cis-Regulatory Modules

(2011) Bin Z. He et al.   PLoS Genetics

The relationship between proteome size, structural disorder and organism complexity

(2011) Eva Schad et al.   GENOME BIOLOGY

An overlapping kinase and phosphatase docking site regulates activity of the retinoblastoma protein

(2010) Alexander Hirschi et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE

(2010) et al.   SCIENCE

Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project

(2010) M. B. Gerstein et al.   SCIENCE

WD40 proteins propel cellular networks

(2010) Christian U. Stirnimann et al.   TRENDS IN BIOCHEMICAL SCIENCES

How viruses hijack cell regulation

(2010) Norman E. Davey et al.   TRENDS IN BIOCHEMICAL SCIENCES

Moving from transcriptional to phospho-evolution: generalizing regulatory evolution?

(2010) Alan M. Moses et al.   TRENDS IN GENETICS

Close encounters of the third kind: disordered domains and the interactions of proteins

(2009) Peter Tompa et al.   BIOESSAYS

Factors Affecting the Diversity of DNA Replication Licensing Control in Eukaryotes

(2009) Lucy S. Drury et al.   CURRENT BIOLOGY

Evolutionary Expansion and Specialization of the PDZ Domains

(2009) O. Sakarya et al.   MOLECULAR BIOLOGY AND EVOLUTION

Mutation of SHOC2 promotes aberrant protein N-myristoylation and causes Noonan-like syndrome with loose anagen hair

(2009) Viviana Cordeddu et al.   NATURE GENETICS

Global Analysis of Cdk1 Substrate Phosphorylation Sites Provides Insights into Evolution

(2009) L. J. Holt et al.   SCIENCE

Cell Signaling in Space and Time: Where Proteins Come Together and When They're Apart

(2009) J. D. Scott et al.   SCIENCE

CDK Inhibitors: Cell Cycle Regulators and Beyond

(2008) Arnaud Besson et al.   DEVELOPMENTAL CELL

Evolution of an insect-specific GROUCHO-interaction motif in the ENGRAILED selector protein

(2008) Chris Todd Hittinger et al.   EVOLUTION & DEVELOPMENT

Turning a hobby into a job: How duplicated genes find new functions

(2008) Gavin C. Conant et al.   NATURE REVIEWS GENETICS

Contextual Specificity in Peptide-Mediated Protein Interactions

(2008) Amelie Stein et al.   PLoS One

Evolution of the phospho-tyrosine signaling machinery in premetazoan lineages

(2008) D. Pincus et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetically destined potentials for N-linked glycosylation of influenza virus hemagglutinin

(2008) Manabu Igarashi et al.   VIROLOGY

A Specificity Map for the PDZ Domain Family

(2008) Raffi Tonikian et al.   PLOS BIOLOGY