Outer membrane utilisomes mediate glycan uptake in gut Bacteroidetes

HDX-MS performed on BtuB in E. coli outer membranes delineates the luminal domain’s allostery and unfolding upon B12 and TonB binding

(2022) Adam M. Zmyslowski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Insights into SusCD-mediated glycan import by a prominent gut symbiont

(2021) Declan A. Gray et al.   Nature Communications

Distinct protein architectures mediate species-specific beta-glucan binding and metabolism in the human gut microbiota

(2021) Kazune Tamura et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

Polysaccharide degradation by the Bacteroidetes: mechanisms and nomenclature

(2021) Lauren S. McKee et al.   Environmental Microbiology Reports

Structural intermediates observed only in intact Escherichia coli indicate a mechanism for TonB-dependent transport

(2021) Thushani D Nilaweera et al.   eLife

Phase separation in the outer membrane of Escherichia coli

(2021) Georgina Benn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Current approaches for automated model building into cryo-EM maps using Buccaneer with CCP-EM

(2020) Soon Wen Hoh et al.   Acta Crystallographica Section D-Structural Biology

Structural and functional insights into oligopeptide acquisition by the RagAB transporter from Porphyromonas gingivalis

(2020) Mariusz Madej et al.   Nature Microbiology

Gut microbiota in human metabolic health and disease

(2020) Yong Fan et al.   NATURE REVIEWS MICROBIOLOGY

Glycan utilization systems in the human gut microbiota: a gold mine for structural discoveries

(2020) Kazune Tamura et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Surface glycan-binding proteins are essential for cereal beta-glucan utilization by the human gut symbiont Bacteroides ovatus

(2019) Kazune Tamura et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

First crystal structure of an endo-levanase – the BT1760 from a human gut commensal Bacteroides thetaiotaomicron

(2019) Karin Ernits et al.   Scientific Reports

Complex N-glycan breakdown by gut Bacteroides involves an extensive enzymatic apparatus encoded by multiple co-regulated genetic loci

(2019) Justina Briliūtė et al.   Nature Microbiology

Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix

(2019) Dorothee Liebschner et al.   Acta Crystallographica Section D-Structural Biology

The Starch Utilization System Assembles around Stationary Starch-Binding Proteins

(2018) Hannah H. Tuson et al.   BIOPHYSICAL JOURNAL

TonB-dependent transport by the gut microbiota: novel aspects of an old problem

(2018) David N Bolam et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

DIALS: implementation and evaluation of a new integration package

(2018) Graeme Winter et al.   Acta Crystallographica Section D-Structural Biology

Distributed computing for macromolecular crystallography

(2018) Evgeny Krissinel et al.   Acta Crystallographica Section D-Structural Biology

A new MR-SAD algorithm for the automatic building of protein models from low-resolution X-ray data and a poor starting model

(2018) Pavol Skubák et al.   IUCrJ

S-Trap, an Ultrafast Sample-Preparation Approach for Shotgun Proteomics

(2018) Milkessa HaileMariam et al.   JOURNAL OF PROTEOME RESEARCH

A Local Agreement Filtering Algorithm for Transmission EM Reconstructions

(2018) Kailash Ramlaul et al.   JOURNAL OF STRUCTURAL BIOLOGY

New tools for automated high-resolution cryo-EM structure determination in RELION-3

(2018) Jasenko Zivanov et al.   eLife

Polysaccharide Utilization Loci: Fueling Microbial Communities

(2017) Julie M. Grondin et al.   JOURNAL OF BACTERIOLOGY

Structural basis for nutrient acquisition by dominant members of the human gut microbiota

(2017) Amy J. Glenwright et al.   NATURE

Complex pectin metabolism by gut bacteria reveals novel catalytic functions

(2017) Didier Ndeh et al.   NATURE

MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy

(2017) Shawn Q Zheng et al.   NATURE METHODS

PULDB: the expanded database of Polysaccharide Utilization Loci

(2017) Nicolas Terrapon et al.   NUCLEIC ACIDS RESEARCH

UCSF ChimeraX: Meeting modern challenges in visualization and analysis

(2017) Thomas D. Goddard et al.   PROTEIN SCIENCE

Recent developments in the CCP-EM software suite

(2017) Tom Burnley et al.   Acta Crystallographica Section D-Structural Biology

A Highly Active Endo-Levanase BT1760 of a Dominant Mammalian Gut Commensal Bacteroides thetaiotaomicron Cleaves Not Only Various Bacterial Levans, but Also Levan of Timothy Grass

(2017) Karin Mardo et al.   PLoS One

Review of Levan polysaccharide: From a century of past experiences to future prospects

(2016) Ebru Toksoy Öner et al.   BIOTECHNOLOGY ADVANCES

From Dietary Fiber to Host Physiology: Short-Chain Fatty Acids as Key Bacterial Metabolites

(2016) Ara Koh et al.   CELL

Gctf: Real-time CTF determination and correction

(2016) Kai Zhang   JOURNAL OF STRUCTURAL BIOLOGY

CTFFIND4: Fast and accurate defocus estimation from electron micrographs

(2015) Alexis Rohou et al.   JOURNAL OF STRUCTURAL BIOLOGY

Supramolecular assemblies underpin turnover of outer membrane proteins in bacteria

(2015) Patrice Rassam et al.   NATURE

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

A Perspective on the Complexity of Dietary Fiber Structures and Their Potential Effect on the Gut Microbiota

(2014) Bruce R. Hamaker et al.   JOURNAL OF MOLECULAR BIOLOGY

Suspension trapping (STrap) sample preparation method for bottom-up proteomics analysis

(2014) Alexandre Zougman et al.   PROTEOMICS

Superresolution Imaging Captures Carbohydrate Utilization Dynamics in Human Gut Symbionts

(2014) Krishanthi S. Karunatilaka et al.   mBio

How good are my data and what is the resolution?

(2013) Philip R. Evans et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

How glycan metabolism shapes the human gut microbiota

(2012) Nicole M. Koropatkin et al.   NATURE REVIEWS MICROBIOLOGY

Overview of theCCP4 suite and current developments

(2011) Martyn D. Winn et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Occurrence and functional significance of secondary carbohydrate binding sites in glycoside hydrolases

(2011) Sven Cuyvers et al.   CRITICAL REVIEWS IN BIOTECHNOLOGY

Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment

(2011) Jürgen Cox et al.   JOURNAL OF PROTEOME RESEARCH

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

Recognition and Degradation of Plant Cell Wall Polysaccharides by Two Human Gut Symbionts

(2011) Eric C. Martens et al.   PLOS BIOLOGY

XDS

(2010) Wolfgang Kabsch   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Features and development ofCoot

(2010) P. Emsley et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Specificity of Polysaccharide Use in Intestinal Bacteroides Species Determines Diet-Induced Microbiota Alterations

(2010) Erica D. Sonnenburg et al.   CELL

xia2: an expert system for macromolecular crystallography data reduction

(2009) G. Winter   JOURNAL OF APPLIED CRYSTALLOGRAPHY

Complex Glycan Catabolism by the Human Gut Microbiota: The Bacteroidetes Sus-like Paradigm

(2009) Eric C. Martens et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY

Starch Catabolism by a Prominent Human Gut Symbiont Is Directed by the Recognition of Amylose Helices

(2008) Nicole M. Koropatkin et al.   STRUCTURE