Mapping low-affinity/high-specificity peptide–protein interactions using ligand-footprinting mass spectrometry

Cross-Linking/Mass Spectrometry for Studying Protein Structures and Protein-Protein Interactions: Where Are We Now and Where Should We Go from Here?

(2018) Andrea Sinz   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Rapid Mapping of Protein Interactions Using Tag-Transfer Photocrosslinkers

(2018) Jim E. Horne et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Genetically encoded releasable photo-cross-linking strategies for studying protein–protein interactions in living cells

(2017) Yi Yang et al.   Nature Protocols

Structural Basis for the Subversion of MAP Kinase Signaling by an Intrinsically Disordered Parasite Secreted Agonist

(2017) Erika Pellegrini et al.   STRUCTURE

An Integrated Mass Spectrometry Based Approach to Probe the Structure of the Full-Length Wild-Type Tetrameric p53 Tumor Suppressor

(2016) Christian Arlt et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Revealing Higher Order Protein Structure Using Mass Spectrometry

(2016) Brian T. Chait et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Modeling of protein–peptide interactions using the CABS-dock web server for binding site search and flexible docking

(2016) Maciej Blaszczyk et al.   METHODS

Blind Evaluation of Hybrid Protein Structure Analysis Methods based on Cross-Linking

(2016) Adam Belsom et al.   TRENDS IN BIOCHEMICAL SCIENCES

Genetically encoded protein photocrosslinker with a transferable mass spectrometry-identifiable label

(2016) Yi Yang et al.   Nature Communications

A conserved motif in JNK/p38-specific MAPK phosphatases as a determinant for JNK1 recognition and inactivation

(2016) Xin Liu et al.   Nature Communications

Catalytically Important Residues of E6AP Ubiquitin Ligase Identified Using Acid-Cleavable Photo-Cross-Linkers

(2015) David T. Krist et al.   BIOCHEMISTRY

Short linear motifs – ex nihilo evolution of protein regulation

(2015) Norman E. Davey et al.   Cell Communication and Signaling

Two Hydrophobic Residues Can Determine the Specificity of Mitogen-activated Protein Kinase Docking Interactions

(2015) A. Jane Bardwell et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A Deeper Look into Comet—Implementation and Features

(2015) Jimmy K. Eng et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Systematic discovery of linear binding motifs targeting an ancient protein interaction surface on MAP kinases

(2015) A. Zeke et al.   Molecular Systems Biology

CABS-dock web server for the flexible docking of peptides to proteins without prior knowledge of the binding site

(2015) Mateusz Kurcinski et al.   NUCLEIC ACIDS RESEARCH

Structure of full-length p53 tumor suppressor probed by chemical cross-linking and mass spectrometry

(2015) Christian Arlt et al.   PROTEOMICS

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

(2014) Kim Van Roey et al.   CHEMICAL REVIEWS

Genetically Encoded Cleavable Protein Photo-Cross-Linker

(2014) Shixian Lin et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Proteome-wide analysis of human disease mutations in short linear motifs: neglected players in cancer?

(2014) Bora Uyar et al.   Molecular BioSystems

A Million Peptide Motifs for the Molecular Biologist

(2014) Peter Tompa et al.   MOLECULAR CELL

Molecular basis of MAP kinase regulation

(2013) Wolfgang Peti et al.   PROTEIN SCIENCE

Understanding Pre-Structured Motifs (PreSMos) in Intrinsically Unfolded Proteins

(2012) Si-Hyung Lee et al.   CURRENT PROTEIN & PEPTIDE SCIENCE

Discovery of Checkpoint Kinase Inhibitor (S)-5-(3-Fluorophenyl)-N-(piperidin-3-yl)-3-ureidothiophene-2-carboxamide (AZD7762) by Structure-Based Design and Optimization of Thiophenecarboxamide Ureas

(2012) Vibha Oza et al.   JOURNAL OF MEDICINAL CHEMISTRY

Peptide Array X-Linking (PAX): A New Peptide-Protein Identification Approach

(2012) Hirokazu Okada et al.   PLoS One

Comet: An open-source MS/MS sequence database search tool

(2012) Jimmy K. Eng et al.   PROTEOMICS

Specificity of Linear Motifs That Bind to a Common Mitogen-Activated Protein Kinase Docking Groove

(2012) A. Garai et al.   Science Signaling

Diazirine based photoaffinity labeling

(2011) Luba Dubinsky et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Attributes of short linear motifs

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

Multiplexed RNA structure characterization with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq)

(2011) J. B. Lucks et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolving specificity from variability for protein interaction domains

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

Hydrogen exchange mass spectrometry: what is it and what can it tell us?

(2010) Sean R. Marcsisin et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Advances in RNA structure analysis by chemical probing

(2010) Kevin M Weeks   CURRENT OPINION IN STRUCTURAL BIOLOGY

Sub-angstrom modeling of complexes between flexible peptides and globular proteins

(2010) Barak Raveh et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Loops Govern SH2 Domain Specificity by Controlling Access to Binding Pockets

(2010) T. Kaneko et al.   Science Signaling

The Structural Basis of Peptide-Protein Binding Strategies

(2010) Nir London et al.   STRUCTURE

Selectivity of Docking Sites in MAPK Kinases

(2009) A. Jane Bardwell et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Influence of Solvent on Carbene Intersystem Crossing Rates

(2008) Jin Wang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY