Protein target highlights in CASP15: Analysis of models by structure providers

Deciphering Bacteriophage T5 Host Recognition Mechanism and Infection Trigger

(2023) Séraphine Degroux et al.   JOURNAL OF VIROLOGY

Structural basis for bacterial energy extraction from atmospheric hydrogen

(2023) Rhys Grinter et al.   NATURE

Prediction of protein structures, functions and interactions using the IntFOLD7, MultiFOLD and ModFOLDdock servers

(2023) Liam J McGuffin et al.   NUCLEIC ACIDS RESEARCH

Native structure of mosquito salivary protein uncovers domains relevant to pathogen transmission

(2023) Shiheng Liu et al.   Nature Communications

Structural basis of bacteriophage T5 infection trigger and E. coli cell wall perforation

(2023) Romain Linares et al.   Science Advances

Can AlphaFold2 predict the impact of missense mutations on structure?

(2022) Gwen R. Buel et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The naked truth: An updated review on nudiviruses and their relationship to bracoviruses and baculoviruses

(2022) Jirka M. Petersen et al.   JOURNAL OF INVERTEBRATE PATHOLOGY

Microbial oxidation of atmospheric trace gases

(2022) Chris Greening et al.   NATURE REVIEWS MICROBIOLOGY

Direct interaction of a chaperone-bound type III secretion substrate with the export gate

(2022) Dominic Gilzer et al.   Nature Communications

Copper starvation induces antimicrobial isocyanide integrated into two distinct biosynthetic pathways in fungi

(2022) Tae Hyung Won et al.   Nature Communications

Expanding the eukaryotic genetic code with a biosynthesized 21st amino acid

(2022) Kuan‐Lin Wu et al.   PROTEIN SCIENCE

Conservation and Diversification of tRNA t6A-Modifying Enzymes across the Three Domains of Life

(2022) Chenchen Su et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

AlphaFill: enriching AlphaFold models with ligands and cofactors

(2022) Maarten L. Hekkelman et al.   NATURE METHODS

Aedes aegypti SGS1 is critical for Plasmodium gallinaceum infection of both the mosquito midgut and salivary glands

(2021) Bianca B. Kojin et al.   MALARIA JOURNAL

A molecular mechanism for LINC complex branching by structurally diverse SUN-KASH 6:6 assemblies

(2021) Manickam Gurusaran et al.   eLife

EDEM3 Domains Cooperate to Perform Its Overall Cell Functioning

(2021) Georgiana Manica et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Dual-purpose isocyanides produced by Aspergillus fumigatus contribute to cellular copper sufficiency and exhibit antimicrobial activity

(2021) Nicholas Raffa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Medicinal Chemistry of Isocyanides

(2021) Alberto Massarotti et al.   CHEMICAL REVIEWS

Molecular models of LINC complex assembly at the nuclear envelope

(2021) Zeinab Jahed et al.   JOURNAL OF CELL SCIENCE

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

Nonameric structures of the cytoplasmic domain of FlhA and SctV in the context of the full-length protein

(2021) Lucas Kuhlen et al.   PLoS One

Critical Assessment of Methods of Protein Structure Prediction ( CASP ) – Round XIV

(2021) Andriy Kryshtafovych et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

GH47 and Other Glycoside Hydrolases Catalyze Glycosidic Bond Cleavage with the Assistance of Substrate Super-Arming at the Transition State

(2021) Jonathan C. K. Quirke et al.   ACS Catalysis

A counter-enzyme complex regulates glutamate metabolism in Bacillus subtilis

(2021) Vijay Jayaraman et al.   Nature Chemical Biology

AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models

(2021) Mihaly Varadi et al.   NUCLEIC ACIDS RESEARCH

Target highlights in CASP14 : Analysis of models by structure providers

(2021) Leila T. Alexander et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

High resolution proteomics of Aedes aegypti salivary glands infected with either dengue, Zika or chikungunya viruses identify new virus specific and broad antiviral factors

(2021) Avisha Chowdhury et al.   Scientific Reports

De novo synthesized polyunsaturated fatty acids operate as both host immunomodulators and nutrients for Mycobacterium tuberculosis

(2021) Thomas Laval et al.   eLife

A mycobacterial ABC transporter mediates the uptake of hydrophilic compounds

(2020) S. Rempel et al.   NATURE

The ABC exporter IrtAB imports and reduces mycobacterial siderophores

(2020) Fabian M. Arnold et al.   NATURE

Trends in U.S. Burden of Clostridioides difficile Infection and Outcomes

(2020) Alice Y. Guh et al.   NEW ENGLAND JOURNAL OF MEDICINE

Conserved and Diverse Traits of Adhesion Devices from Siphoviridae Recognizing Proteinaceous or Saccharidic Receptors

(2020) Adeline Goulet et al.   Viruses-Basel

Architecture and functional dynamics of the pentafunctional AROM complex

(2020) Harshul Arora Verasztó et al.   Nature Chemical Biology

The genetic requirements of fatty acid import by Mycobacterium tuberculosis within macrophages

(2019) Evgeniya V Nazarova et al.   eLife

The global prevalence of latent tuberculosis: a systematic review and meta-analysis

(2019) Adam Cohen et al.   EUROPEAN RESPIRATORY JOURNAL

High-Throughput Analysis of Gene Function in the Bacterial Predator Bdellovibrio bacteriovorus

(2019) Miles C. Duncan et al.   mBio

Target highlights in CASP13: Experimental target structures through the eyes of their authors

(2019) Rosalba Lepore et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Two uptake hydrogenases differentially interact with the aerobic respiratory chain during mycobacterial growth and persistence

(2019) Paul R. F. Cordero et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

ER-associated degradation in health and disease – from substrate to organism

(2019) Asmita Bhattacharya et al.   JOURNAL OF CELL SCIENCE

Bottom-up structural proteomics: cryoEM of protein complexes enriched from the cellular milieu

(2019) Chi-Min Ho et al.   NATURE METHODS

Mix-and-inject XFEL crystallography reveals gated conformational dynamics during enzyme catalysis

(2019) Medhanjali Dasgupta et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Clinical Practice Guidelines for Clostridium difficile Infection in Adults and Children: 2017 Update by the Infectious Diseases Society of America (IDSA) and Society for Healthcare Epidemiology of America (SHEA)

(2018) L Clifford McDonald et al.   CLINICAL INFECTIOUS DISEASES

Jaw1/LRMP has a role in maintaining nuclear shape via interaction with SUN proteins

(2018) Takuma Kozono et al.   JOURNAL OF BIOCHEMISTRY

ER-resident protein 46 (ERp46) triggers the mannose-trimming activity of ER degradation–enhancing α-mannosidase–like protein 3 (EDEM3)

(2018) Shangyu Yu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

MetaGO: Predicting Gene Ontology of Non-homologous Proteins Through Low-Resolution Protein Structure Prediction and Protein–Protein Network Mapping

(2018) Chengxin Zhang et al.   JOURNAL OF MOLECULAR BIOLOGY

Structure and mechanism of a bacterial t6A biosynthesis system

(2018) Amit Luthra et al.   NUCLEIC ACIDS RESEARCH

The structure of the TsaB/TsaD/TsaE complex reveals an unexpected mechanism for the bacterial t6A tRNA-modification

(2018) Sophia Missoury et al.   NUCLEIC ACIDS RESEARCH

Mosquito saliva alone has profound effects on the human immune system

(2018) Megan B. Vogt et al.   PLoS Neglected Tropical Diseases

Enzyme fusions in biocatalysis - Coupling reactions by pairing enzymes

(2018) Friso Aalbers et al.   CHEMBIOCHEM

Saliva of hematophagous insects: a multifaceted toolkit

(2018) Bruno Arcà et al.   Current Opinion in Insect Science

Enzymatic complexes across scales

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

COFACTOR: improved protein function prediction by combining structure, sequence and protein–protein interaction information

(2017) Chengxin Zhang et al.   NUCLEIC ACIDS RESEARCH

Target highlights from the first post-PSI CASP experiment (CASP12, May-August 2016)

(2017) Andriy Kryshtafovych et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

LINC complexes and nuclear positioning

(2017) Yin Loon Lee et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Secretory proteins are delivered to the septin-organized penetration interface during root infection by Verticillium dahliae

(2017) Ting-Ting Zhou et al.   PLoS Pathogens

Rv3723/LucA coordinates fatty acid and cholesterol uptake in Mycobacterium tuberculosis

(2017) Evgeniya V Nazarova et al.   eLife

Structure and function of [NiFe] hydrogenases

(2016) Hideaki Ogata et al.   JOURNAL OF BIOCHEMISTRY

At the Interface of Chemical and Biological Synthesis: An Expanded Genetic Code

(2016) Han Xiao et al.   Cold Spring Harbor Perspectives in Biology

Clostridium difficile infection

(2016) Wiep Klaas Smits et al.   Nature Reviews Disease Primers

LINC'ing form and function at the nuclear envelope

(2015) Peter Meinke et al.   FEBS LETTERS

The ATP-mediated formation of the YgjD–YeaZ–YjeE complex is required for the biosynthesis of tRNA t6A in Escherichia coli

(2015) Wenhua Zhang et al.   NUCLEIC ACIDS RESEARCH

Biosynthesis of the Anti-infective Marformycins Featuring Pre-NRPS Assembly Line N-Formylation and O-Methylation and Post-Assembly Line C-Hydroxylation Chemistries

(2015) Jing Liu et al.   ORGANIC LETTERS

Some of the most interesting CASP11 targets through the eyes of their authors

(2015) Andriy Kryshtafovych et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Hydrogenases

(2014) Wolfgang Lubitz et al.   CHEMICAL REVIEWS

The Genome of the Nucleopolyhedrosis-Causing Virus from Tipula oleracea Sheds New Light on the Nudiviridae Family

(2014) Annie Bézier et al.   JOURNAL OF VIROLOGY

A soil actinobacterium scavenges atmospheric H2 using two membrane-associated, oxygen-dependent [NiFe] hydrogenases

(2014) C. Greening et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Vps/VacJ ABC Transporter Is Required for Intercellular Spread of Shigella flexneri

(2013) Chandra D. Carpenter et al.   INFECTION AND IMMUNITY

IntracellularMycobacterium tuberculosisExploits Host-derived Fatty Acids to Limit Metabolic Stress

(2013) Wonsik Lee et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Assessing the Conformational Changes of pb5, the Receptor-binding Protein of Phage T5, upon Binding to ItsEscherichia coliReceptor FhuA

(2013) Cécile Breyton et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A mammalian KASH domain protein coupling meiotic chromosomes to the cytoskeleton

(2013) Henning F. Horn et al.   JOURNAL OF CELL BIOLOGY

Free mycolic acid accumulation in the cell wall of the mce1 operon mutant strain of Mycobacterium tuberculosis

(2013) Sally A. Cantrell et al.   JOURNAL OF MICROBIOLOGY

Crystallographic Analysis of the Reaction Cycle of 2′,3′-Cyclic Nucleotide 3′-Phosphodiesterase, a Unique Member of the 2H Phosphoesterase Family

(2013) Matti Myllykoski et al.   JOURNAL OF MOLECULAR BIOLOGY

Insights into Bacteriophage T5 Structure from Analysis of Its Morphogenesis Genes and Protein Components

(2013) Y. Zivanovic et al.   JOURNAL OF VIROLOGY

Crystal structure of the dimer of two essentialSalmonella typhimuriumproteins, YgjD & YeaZ and calorimetric evidence for the formation of a ternary YgjD-YeaZ-YjeE complex

(2013) C. E. Nichols et al.   PROTEIN SCIENCE

Challenging the state of the art in protein structure prediction: Highlights of experimental target structures for the 10th Critical Assessment of Techniques for Protein Structure Prediction Experiment CASP10

(2013) Andriy Kryshtafovych et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Mechanism of N6-Threonylcarbamoyladenonsine (t6A) Biosynthesis: Isolation and Characterization of the Intermediate Threonylcarbamoyl-AMP

(2012) Charles T. Lauhon   BIOCHEMISTRY

New insights into pb5, the receptor binding protein of bacteriophage T5, and its interaction with its Escherichia coli receptor FhuA

(2012) Ali Flayhan et al.   BIOCHIMIE

LINC Complexes Form by Binding of Three KASH Peptides to Domain Interfaces of Trimeric SUN Proteins

(2012) Brian A. Sosa et al.   CELL

Structural insights into SUN-KASH complexes across the nuclear envelope

(2012) Wenjia Wang et al.   CELL RESEARCH

Insect virus polyhedra, infectious protein crystals that contain virus particles

(2012) Elaine Chiu et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Biosynthesis of Threonylcarbamoyl Adenosine (t6A), a Universal tRNA Nucleoside

(2012) Christopher Deutsch et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The mammalian cell entry (Mce) protein of pathogenic Leptospira species is responsible for RGD motif-dependent infection of cells and animals

(2012) Lei Zhang et al.   MOLECULAR MICROBIOLOGY

Small molecule perimeter defense in entomopathogenic bacteria

(2012) J. M. Crawford et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The LINC complex and human disease

(2011) Peter Meinke et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

A role for the universal Kae1/Qri7/YgjD (COG0533) family in tRNA modification

(2011) Basma El Yacoubi et al.   EMBO JOURNAL

Members of the Salivary Gland Surface Protein (SGS) Family Are Major Immunogenic Components of Mosquito Saliva

(2011) Jonas G. King et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Target highlights in CASP9: Experimental target structures for the critical assessment of techniques for protein structure prediction

(2011) Andriy Kryshtafovych et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Molecular Basis of Increased Serum Resistance among Pulmonary Isolates of Non-typeable Haemophilus influenzae

(2011) Shigeki Nakamura et al.   PLoS Pathogens

Interactions Between Nuclei and the Cytoskeleton Are Mediated by SUN-KASH Nuclear-Envelope Bridges

(2010) Daniel A. Starr et al.   Annual Review of Cell and Developmental Biology

Evolution of New Enzymatic Function by Structural Modulation of Cysteine Reactivity inPseudomonas fluorescensIsocyanide Hydratase

(2010) Mahadevan Lakshminarasimhan et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The First Bite— Profiling the Predatosome in the Bacterial Pathogen Bdellovibrio

(2010) Carey Lambert et al.   PLoS One

Predatory Lifestyle ofBdellovibrio bacteriovorus

(2009) Renee Elizabeth Sockett   Annual Review of Microbiology

How baculovirus polyhedra fit square pegs into round holes to robustly package viruses

(2009) Xiaoyun Ji et al.   EMBO JOURNAL

FhuA (TonA), the Career of a Protein

(2009) V. Braun   JOURNAL OF BACTERIOLOGY

Conserved Network of Proteins Essential for Bacterial Viability

(2009) J. I. Handford et al.   JOURNAL OF BACTERIOLOGY

Roles of Protein-disulfide Isomerase-mediated Disulfide Bond Formation of Yeast Mnl1p in Endoplasmic Reticulum-associated Degradation

(2009) Machiko Sakoh-Nakatogawa et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The universal YrdC/Sua5 family is required for the formation of threonylcarbamoyladenosine in tRNA

(2009) B. El Yacoubi et al.   NUCLEIC ACIDS RESEARCH

The atomic structure of baculovirus polyhedra reveals the independent emergence of infectious crystals in DNA and RNA viruses

(2009) Fasséli Coulibaly et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Engineering the spatial organization of metabolic enzymes: mimicking nature's synergy

(2008) Robert J Conrado et al.   CURRENT OPINION IN BIOTECHNOLOGY

Mycobacterium tuberculosis strains disrupted in mce3 and mce4 operons are attenuated in mice

(2008) R. H. Senaratne et al.   JOURNAL OF MEDICAL MICROBIOLOGY

Defining the Glycan Destruction Signal for Endoplasmic Reticulum-Associated Degradation

(2008) Erin M. Quan et al.   MOLECULAR CELL

webPIPSA: a web server for the comparison of protein interaction properties

(2008) S. Richter et al.   NUCLEIC ACIDS RESEARCH

Mycobacterial persistence requires the utilization of host cholesterol

(2008) A. K. Pandey et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA