High-density chemical cross-linking for modeling protein interactions

XPlex: An Effective, Multiplex Cross-Linking Chemistry for Acidic Residues

(2018) Mariana Fioramonte et al.   ANALYTICAL CHEMISTRY

Integrating Cross-Linking Experiments with Ab Initio Protein–Protein Docking

(2018) Thom Vreven et al.   JOURNAL OF MOLECULAR BIOLOGY

Human Ska complex and Ndc80 complex interact to form a load-bearing assembly that strengthens kinetochore–microtubule attachments

(2018) Luke A. Helgeson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Chemical Crosslinking Mass Spectrometry Analysis of Protein Conformations and Supercomplexes in Heart Tissue

(2018) Juan D. Chavez et al.   Cell Systems

Integrative structure and functional anatomy of a nuclear pore complex

(2018) Seung Joong Kim et al.   NATURE

Chemical cross-linking with mass spectrometry: a tool for systems structural biology

(2018) Juan D Chavez et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Structure and energetics of pairwise interactions between proteasome subunits RPN2, RPN13, and ubiquitin clarify a substrate recruitment mechanism

(2017) Ryan T. VanderLinden et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Molecular Details Underlying Dynamic Structures and Regulation of the Human 26S Proteasome

(2017) Xiaorong Wang et al.   MOLECULAR & CELLULAR PROTEOMICS

M3: an integrative framework for structure determination of molecular machines

(2017) Ezgi Karaca et al.   NATURE METHODS

Mitochondrial protein interactome elucidated by chemical cross-linking mass spectrometry

(2017) Devin K. Schweppe et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural insights into the functional cycle of the ATPase module of the 26S proteasome

(2017) Marc Wehmer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Solving protein structures using short-distance cross-linking constraints as a guide for discrete molecular dynamics simulations

(2017) Nicholas I. Brodie et al.   Science Advances

Divide and conquer: cleavable cross-linkers to study protein conformation and protein–protein interactions

(2016) Andrea Sinz   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Modeling Protein Excited-state Structures from “Over-length” Chemical Cross-links

(2016) Yue-He Ding et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Automated structure modeling of large protein assemblies using crosslinks as distance restraints

(2016) Mathias Ferber et al.   NATURE METHODS

Structure of an endogenous yeast 26S proteasome reveals two major conformational states

(2016) Bai Luan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structure of the human 26S proteasome at a resolution of 3.9 Å

(2016) Andreas Schweitzer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Atomic structure of the 26S proteasome lid reveals the mechanism of deubiquitinase inhibition

(2016) Corey M Dambacher et al.   eLife

The BioPlex Network: A Systematic Exploration of the Human Interactome

(2015) Edward L. Huttlin et al.   CELL

Probing structures of large protein complexes using zero-length cross-linking

(2015) Roland F. Rivera-Santiago et al.   METHODS

Serum Albumin Domain Structures in Human Blood Serum by Mass Spectrometry and Computational Biology

(2015) Adam Belsom et al.   MOLECULAR & CELLULAR PROTEOMICS

xiNET: Cross-link Network Maps With Residue Resolution

(2015) Colin W. Combe et al.   MOLECULAR & CELLULAR PROTEOMICS

xTract: software for characterizing conformational changes of protein complexes by quantitative cross-linking mass spectrometry

(2015) Thomas Walzthoeni et al.   NATURE METHODS

A strategy for dissecting the architectures of native macromolecular assemblies

(2015) Yi Shi et al.   NATURE METHODS

Proteome-wide profiling of protein assemblies by cross-linking mass spectrometry

(2015) Fan Liu et al.   NATURE METHODS

2016 update of the PRIDE database and its related tools

(2015) Juan Antonio Vizcaíno et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

The molecular architecture of the Dam1 kinetochore complex is defined by cross-linking based structural modelling

(2015) Alex Zelter et al.   Nature Communications

Molecular architecture of the yeast Mediator complex

(2015) Philip J Robinson et al.   eLife

Molecular Architecture of the 40S⋅eIF1⋅eIF3 Translation Initiation Complex

(2014) Jan P. Erzberger et al.   CELL

Deep classification of a large cryo-EM dataset defines the conformational landscape of the 26S proteasome

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

Chemical cross-linking/mass spectrometry targeting acidic residues in proteins and protein complexes

(2014) Alexander Leitner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Distance restraints from crosslinking mass spectrometry: Mining a molecular dynamics simulation database to evaluate lysine-lysine distances

(2014) Eric D. Merkley et al.   PROTEIN SCIENCE

A bis-Benzylidine Piperidone Targeting Proteasome Ubiquitin Receptor RPN13/ADRM1 as a Therapy for Cancer

(2013) Ravi K. Anchoori et al.   CANCER CELL

Cross-Link Guided Molecular Modeling with ROSETTA

(2013) Abdullah Kahraman et al.   PLoS One

Integrative Structural Biology

(2013) A. B. Ward et al.   SCIENCE

Formation of an Intricate Helical Bundle Dictates the Assembly of the 26S Proteasome Lid

(2013) Eric Estrin et al.   STRUCTURE

Protein–Protein Interactions: Inhibition of Mammalian Carbonic Anhydrases I–XV by the Murine Inhibitor of Carbonic Anhydrase and Other Members of the Transferrin Family

(2012) Serdar Durdagi et al.   JOURNAL OF MEDICINAL CHEMISTRY

Expanding the Chemical Cross-Linking Toolbox by the Use of Multiple Proteases and Enrichment by Size Exclusion Chromatography

(2012) Alexander Leitner et al.   MOLECULAR & CELLULAR PROTEOMICS

False discovery rate estimation for cross-linked peptides identified by mass spectrometry

(2012) Thomas Walzthoeni et al.   NATURE METHODS

Identification of cross-linked peptides from complex samples

(2012) Bing Yang et al.   NATURE METHODS

Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach

(2012) K. Lasker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Near-atomic resolution structural model of the yeast 26S proteasome

(2012) F. Beck et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Structure of the 26S Proteasome Subunit Rpn2 Reveals Its PC Repeat Domain as a Closed Toroid of Two Concentric α-Helical Rings

(2012) Jun He et al.   STRUCTURE

Interfering with pH regulation in tumours as a therapeutic strategy

(2011) Dario Neri et al.   NATURE REVIEWS DRUG DISCOVERY

Rosetta FlexPepDock ab-initio: Simultaneous Folding, Docking and Refinement of Peptides onto Their Receptors

(2011) Barak Raveh et al.   PLoS One

The beginning of a beautiful friendship: Cross-linking/mass spectrometry and modelling of proteins and multi-protein complexes

(2010) Juri Rappsilber   JOURNAL OF STRUCTURAL BIOLOGY

The structure and evolution of the murine inhibitor of carbonic anhydrase: A member of the transferrin superfamily

(2010) Brian E. Eckenroth et al.   PROTEIN SCIENCE

Intra-Molecular Cross-Linking of Acidic Residues for Protein Structure Studies

(2009) Petr Novák et al.   EUROPEAN JOURNAL OF MASS SPECTROMETRY

Macromolecular Modeling with Rosetta

(2008) Rhiju Das et al.   Annual Review of Biochemistry

Evolution Reversed: The Ability To Bind Iron Restored to the N-Lobe of the Murine Inhibitor of Carbonic Anhydrase by Strategic Mutagenesis†

(2008) Anne B. Mason et al.   BIOCHEMISTRY

Carbonic anhydrases: novel therapeutic applications for inhibitors and activators

(2008) Claudiu T. Supuran   NATURE REVIEWS DRUG DISCOVERY