Integrative biology of native cell extracts: a new era for structural characterization of life processes

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

Structural prediction of protein models using distance restraints derived from cross-linking mass spectrometry data

(2018) Zsuzsanna Orbán-Németh et al.   Nature Protocols

Validating Resolution Revolution

(2018) Piotr Neumann et al.   STRUCTURE

In situ architecture of the algal nuclear pore complex

(2018) Shyamal Mosalaganti et al.   Nature Communications

Classification of Single Particles from Human Cell Extract Reveals Distinct Structures

(2018) Eric J. Verbeke et al.   Cell Reports

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

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

From the resolution revolution to evolution: structural insights into the evolutionary relationships between vesicle coats and the nuclear pore

(2018) Martin Beck et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Structure of Type-I Mycobacterium tuberculosis fatty acid synthase at 3.3 Å resolution

(2018) Nadav Elad et al.   Nature Communications

Enzymatic complexes across scales

(2018) Panagiotis L. Kastritis et al.   Essays in Biochemistry

A Membrane Protein Complex Docking Benchmark

(2018) Panagiotis I. Koukos et al.   JOURNAL OF MOLECULAR BIOLOGY

emClarity: software for high-resolution cryo-electron tomography and subtomogram averaging

(2018) Benjamin A. Himes et al.   NATURE METHODS

A cross-linking/mass spectrometry workflow based on MS-cleavable cross-linkers and the MeroX software for studying protein structures and protein–protein interactions

(2018) Claudio Iacobucci et al.   Nature Protocols

Cross-linking mass spectrometry: methods and applications in structural, molecular and systems biology

(2018) Francis J. O’Reilly et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Revisiting the Structure of Hemoglobin and Myoglobin with Cryo-Electron Microscopy

(2017) Maryam Khoshouei et al.   JOURNAL OF MOLECULAR BIOLOGY

Efficient 3D-CTF correction for cryo-electron tomography using NovaCTF improves subtomogram averaging resolution to 3.4 Å

(2017) Beata Turoňová et al.   JOURNAL OF STRUCTURAL BIOLOGY

Three-dimensional CTF correction improves the resolution of electron tomograms

(2017) Michael Kunz et al.   JOURNAL OF STRUCTURAL BIOLOGY

Implementation of a cryo-electron tomography tilt-scheme optimized for high resolution subtomogram averaging

(2017) Wim J.H. Hagen et al.   JOURNAL OF STRUCTURAL BIOLOGY

The interactome of intact mitochondria by cross-linking mass spectrometry provides evidence for coexisting respiratory supercomplexes

(2017) Fan Liu et al.   MOLECULAR & CELLULAR PROTEOMICS

Capturing protein communities by structural proteomics in a thermophilic eukaryote

(2017) Panagiotis L Kastritis et al.   Molecular Systems Biology

Cryo-EM structures of tau filaments from Alzheimer’s disease

(2017) Anthony W. P. Fitzpatrick et al.   NATURE

M3: an integrative framework for structure determination of molecular machines

(2017) Ezgi Karaca et al.   NATURE METHODS

Advances in the field of single-particle cryo-electron microscopy over the last decade

(2017) Joachim Frank   Nature Protocols

Integrative structure modeling with the Integrative Modeling Platform

(2017) Benjamin Webb et al.   PROTEIN SCIENCE

In-cell NMR: a topical review

(2017) Enrico Luchinat et al.   IUCrJ

Cell-free Xenopus egg extracts for studying DNA damage response pathways

(2016) Steven Cupello et al.   INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY

Structure Determination of the Nuclear Pore Complex with Three-Dimensional Cryo electron Microscopy

(2016) Alexander von Appen et al.   JOURNAL OF MOLECULAR BIOLOGY

The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes

(2016) G.C.P. van Zundert et al.   JOURNAL OF MOLECULAR BIOLOGY

Structural basis for the antifolding activity of a molecular chaperone

(2016) Chengdong Huang et al.   NATURE

OpenMS: a flexible open-source software platform for mass spectrometry data analysis

(2016) Hannes L Röst et al.   NATURE METHODS

Sense and simplicity in HADDOCK scoring: Lessons from CASP-CAPRI round 1

(2016) A. Vangone et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

An atomic model of HIV-1 capsid-SP1 reveals structures regulating assembly and maturation

(2016) Florian K. M. Schur et al.   SCIENCE

Architecture of the symmetric core of the nuclear pore

(2016) D. H. Lin et al.   SCIENCE

Molecular architecture of the inner ring scaffold of the human nuclear pore complex

(2016) J. Kosinski et al.   SCIENCE

Visualizing the molecular sociology at the HeLa cell nuclear periphery

(2016) J. Mahamid et al.   SCIENCE

Cryo-Electron Tomography: Can it Reveal the Molecular Sociology of Cells in Atomic Detail?

(2016) Martin Beck et al.   TRENDS IN CELL BIOLOGY

Developing genetic tools to exploit Chaetomium thermophilum for biochemical analyses of eukaryotic macromolecular assemblies

(2016) Nikola Kellner et al.   Scientific Reports

Evolution of Orbitrap Mass Spectrometry Instrumentation

(2015) Shannon Eliuk et al.   Annual Review of Analytical Chemistry

Cell-Free Protein Synthesis: Pros and Cons of Prokaryotic and Eukaryotic Systems

(2015) Anne Zemella et al.   CHEMBIOCHEM

In situ structural analysis of the human nuclear pore complex

(2015) Alexander von Appen et al.   NATURE

Panorama of ancient metazoan macromolecular complexes

(2015) Cuihong Wan et al.   NATURE

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

(2015) Fan Liu et al.   NATURE METHODS

Cryo-EM structure of fatty acid synthase (FAS) fromRhodosporidium toruloidesprovides insights into the evolutionary development of fungal FAS

(2015) Manuel Fischer et al.   PROTEIN SCIENCE

Non-interacting surface solvation and dynamics in protein-protein interactions

(2015) Koen M. Visscher et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Architecture of the nuclear pore complex coat

(2015) T. Stuwe et al.   SCIENCE

Insights into Disease-Associated Mutations in the Human Proteome through Protein Structural Analysis

(2015) Mu Gao et al.   STRUCTURE

Integrative Modeling of Biomolecular Complexes: HADDOCKing with Cryo-Electron Microscopy Data

(2015) Gydo C.P. van Zundert et al.   STRUCTURE

Measuring the optimal exposure for single particle cryo-EM using a 2.6 Å reconstruction of rotavirus VP6

(2015) Timothy Grant et al.   eLife

Synthesis of 2.3 mg/ml of protein with an all Escherichia coli cell-free transcription–translation system

(2014) Filippo Caschera et al.   BIOCHIMIE

HADDOCK2P2I: A Biophysical Model for Predicting the Binding Affinity of Protein–Protein Interaction Inhibitors

(2014) Panagiotis L. Kastritis et al.   Journal of Chemical Information and Modeling

Proteins Feel More Than They See: Fine-Tuning of Binding Affinity by Properties of the Non-Interacting Surface

(2014) Panagiotis L. Kastritis et al.   JOURNAL OF MOLECULAR BIOLOGY

Volta potential phase plate for in-focus phase contrast transmission electron microscopy

(2014) R. Danev et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Resolution Revolution

(2014) W. Kuhlbrandt   SCIENCE

Comparison of optimal performance at 300keV of three direct electron detectors for use in low dose electron microscopy

(2014) G. McMullan et al.   ULTRAMICROSCOPY

A high-energy-density sugar biobattery based on a synthetic enzymatic pathway

(2014) Zhiguang Zhu et al.   Nature Communications

Atomic model of the F420-reducing [NiFe] hydrogenase by electron cryo-microscopy using a direct electron detector

(2014) Matteo Allegretti et al.   eLife

Sequence co-evolution gives 3D contacts and structures of protein complexes

(2014) Thomas A Hopf et al.   eLife

Solid-State NMR-Based Approaches for Supramolecular Structure Elucidation

(2013) Markus Weingarth et al.   ACCOUNTS OF CHEMICAL RESEARCH

On the usefulness of ion-mobility mass spectrometry and SAXS data in scoring docking decoys

(2013) Ezgi Karaca et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Integrated Structural Analysis of the Human Nuclear Pore Complex Scaffold

(2013) Khanh Huy Bui et al.   CELL

7.5-Å Cryo-EM Structure of the Mycobacterial Fatty Acid Synthase

(2013) Daniel Boehringer et al.   JOURNAL OF MOLECULAR BIOLOGY

Xmipp 3.0: An improved software suite for image processing in electron microscopy

(2013) J.M. de la Rosa-Trevín et al.   JOURNAL OF STRUCTURAL BIOLOGY

Site-specific NMR mapping and time-resolved monitoring of serine and threonine phosphorylation in reconstituted kinase reactions and mammalian cell extracts

(2013) Francois-Xavier Theillet et al.   Nature Protocols

Age-dependent dissociation of ATP synthase dimers and loss of inner-membrane cristae in mitochondria

(2013) B. Daum et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Three-dimensional electron crystallography of protein microcrystals

(2013) Dan Shi et al.   eLife

A Census of Human Soluble Protein Complexes

(2012) Pierre C. Havugimana et al.   CELL

A high-throughput approach for measuring temporal changes in the interactome

(2012) Anders R Kristensen et al.   NATURE METHODS

Outcome of the First Electron Microscopy Validation Task Force Meeting

(2012) Richard Henderson et al.   STRUCTURE

Insight into Structure and Assembly of the Nuclear Pore Complex by Utilizing the Genome of a Eukaryotic Thermophile

(2011) Stefan Amlacher et al.   CELL

A Bayesian View on Cryo-EM Structure Determination

(2011) Sjors H.W. Scheres   JOURNAL OF MOLECULAR BIOLOGY

Cell-free synthetic biology: Thinking outside the cell

(2011) C. Eric Hodgman et al.   METABOLIC ENGINEERING

Femtosecond X-ray protein nanocrystallography

(2011) Henry N. Chapman et al.   NATURE

Are Scoring Functions in Protein−Protein Docking Ready To Predict Interactomes? Clues from a Novel Binding Affinity Benchmark

(2010) Panagiotis L. Kastritis et al.   JOURNAL OF PROTEOME RESEARCH

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

Direct structural insight into the substrate-shuttling mechanism of yeast fatty acid synthase by electron cryomicroscopy

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

High-resolution multi-dimensional NMR spectroscopy of proteins in human cells

(2009) Kohsuke Inomata et al.   NATURE

In situ observation of protein phosphorylation by high-resolution NMR spectroscopy

(2008) Philipp Selenko et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Near-atomic resolution using electron cryomicroscopy and single-particle reconstruction

(2008) X. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA