Protein structure, amino acid composition and sequence determine proteome vulnerability to oxidation‐induced damage

Ionizing Radiation-induced Proteomic Oxidation in Escherichia coli

(2020) Steven T. Bruckbauer et al.   MOLECULAR & CELLULAR PROTEOMICS

Protein damage, ageing and age-related diseases

(2019) Anita Krisko et al.   Open Biology

UniProt: the universal protein knowledgebase

(2018) The UniProt Consortium   NUCLEIC ACIDS RESEARCH

OUP accepted manuscript

(2018)   NUCLEIC ACIDS RESEARCH

Environmental Data and Survival Data of Deinococcus aetherius from the Exposure Facility of the Japan Experimental Module of the International Space Station Obtained by the Tanpopo Mission

(2018) Akihiko Yamagishi et al.   ASTROBIOLOGY

Microalgae for the production of lipid and carotenoids: a review with focus on stress regulation and adaptation

(2018) Xiao-Man Sun et al.   Biotechnology for Biofuels

High-coverage proteomics reveals methionine auxotrophy in Deinococcus radiodurans

(2017) Yanxia Zhou et al.   PROTEOMICS

Estimating the total number of phosphoproteins and phosphorylation sites in eukaryotic proteomes

(2017) Panayotis Vlastaridis et al.   GigaScience

Happily (n)ever after: Aging in the context of oxidative stress, proteostasis loss and cellular senescence

(2017) Annika Höhn et al.   Redox Biology

Fluorescent proteins such as eGFP lead to catalytic oxidative stress in cells

(2017) Douglas Ganini et al.   Redox Biology

In situ real-time evaluation of radiation-responsive promoters in the extremely radioresistant microbe Deinococcus radiodurans

(2016) Narasimha Anaganti et al.   JOURNAL OF BIOSCIENCES

ResQ: An Approach to Unified Estimation of B -Factor and Residue-Specific Error in Protein Structure Prediction

(2016) Jianyi Yang et al.   JOURNAL OF MOLECULAR BIOLOGY

Screen for genes involved in radiation survival of Escherichia coli and construction of a reference database

(2016) Neil J. Sargentini et al.   MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS

Expansion of the Gene Ontology knowledgebase and resources

(2016)   NUCLEIC ACIDS RESEARCH

The EcoCyc database: reflecting new knowledge aboutEscherichia coliK-12

(2016) Ingrid M. Keseler et al.   NUCLEIC ACIDS RESEARCH

Understanding and predicting protein misfolding and aggregation: Insights from proteomics

(2016) Irantzu Pallarès et al.   PROTEOMICS

Identification of Escherichia coli ygaQ and rpmG as novel mitomycin C resistance factors implicated in DNA repair

(2015) E. L. Bolt et al.   BIOSCIENCE REPORTS

Global Shifts in Genome and Proteome Composition Are Very Tightly Coupled

(2015) Maria Brbić et al.   Genome Biology and Evolution

Avoiding abundance bias in the functional annotation of posttranslationally modified proteins

(2015) Christian Schölz et al.   NATURE METHODS

The I-TASSER Suite: protein structure and function prediction

(2015) Jianyi Yang et al.   NATURE METHODS

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

(2015) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

Bactericidal Antibiotics Induce Toxic Metabolic Perturbations that Lead to Cellular Damage

(2015) Peter Belenky et al.   Cell Reports

Local Geometry and Evolutionary Conservation of Protein Surfaces Reveal the Multiple Recognition Patches in Protein-Protein Interactions

(2015) Elodie Laine et al.   PLoS Computational Biology

Identification of New Genes Contributing to the Extreme Radioresistance of Deinococcus radiodurans Using a Tn5-Based Transposon Mutant Library

(2015) Rémi Dulermo et al.   PLoS One

Structure Based Thermostability Prediction Models for Protein Single Point Mutations with Machine Learning Tools

(2015) Lei Jia et al.   PLoS One

PhosphoSVM: prediction of phosphorylation sites by integrating various protein sequence attributes with a support vector machine

(2014) Yongchao Dou et al.   AMINO ACIDS

Prediction of fatty acid-binding residues on protein surfaces with three-dimensional probability distributions of interacting atoms

(2014) Rajasekaran Mahalingam et al.   BIOPHYSICAL CHEMISTRY

Genome-Wide Transcriptome and Antioxidant Analyses on Gamma-Irradiated Phases of Deinococcus radiodurans R1

(2014) Hemi Luan et al.   PLoS One

CarSPred: A Computational Tool for Predicting Carbonylation Sites of Human Proteins

(2014) Hongqiang Lv et al.   PLoS One

Detecting local residue environment similarity for recognizing near-native structure models

(2014) Hyungrae Kim et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Signatures of Conformational Stability and Oxidation Resistance in Proteomes of Pathogenic Bacteria

(2014) Anita Vidovic et al.   Cell Reports

Inferring gene function from evolutionary change in signatures of translation efficiency

(2014) Anita Krisko et al.   GENOME BIOLOGY

FFAS-3D: improving fold recognition by including optimized structural features and template re-ranking

(2013) Dong Xu et al.   BIOINFORMATICS

Metabolic costs of amino acid and protein production inEscherichia coli

(2013) Christoph Kaleta et al.   Biotechnology Journal

Antibacterial mechanisms identified through structural systems pharmacology

(2013) Roger L Chang et al.   BMC Systems Biology

Genome-Wide Screening with Hydroxyurea Reveals a Link between Nonessential Ribosomal Proteins and Reactive Oxygen Species Production

(2013) T. Nakayashiki et al.   JOURNAL OF BACTERIOLOGY

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)

(2013) Ross Overbeek et al.   NUCLEIC ACIDS RESEARCH

Shotgun Redox Proteomics: Identification and Quantitation of Carbonylated Proteins in the UVB-Resistant Marine Bacterium, Photobacterium angustum S14

(2013) Sabine Matallana-Surget et al.   PLoS One

Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era

(2013) H. Kamisetty et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Toward optimal fragment generations forab initioprotein structure assembly

(2013) Dong Xu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Structural Systems Biology Evaluation of Metabolic Thermotolerance in Escherichia coli

(2013) R. L. Chang et al.   SCIENCE

A comparative study of ribosomal proteins: linkage between amino acid distribution and ribosomal assembly

(2013) Brittany Lott et al.   BMC Biophysics

Ab Initio structure prediction for Escherichia coli: towards genome-wide protein structure modeling and fold assignment

(2013) Dong Xu et al.   Scientific Reports

Increased Survival of Antibiotic-Resistant Escherichia coli inside Macrophages

(2012) Migla Miskinyte et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Prediction of active sites of enzymes by maximum relevance minimum redundancy (mRMR) feature selection

(2012) Yu-Fei Gao et al.   Molecular BioSystems

Protein structure prediction from sequence variation

(2012) Debora S Marks et al.   NATURE BIOTECHNOLOGY

Enhancing E. coli Tolerance towards Oxidative Stress via Engineering Its Global Regulator cAMP Receptor Protein (CRP)

(2012) Souvik Basak et al.   PLoS One

Death by protein damage in irradiated cells

(2011) Michael J. Daly   DNA REPAIR

Oxidative Stress Resistance in Deinococcus radiodurans

(2011) D. Slade et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Gamma Radiation-induced Proteome ofDeinococcus radioduransPrimarily Targets DNA Repair and Oxidative Stress Alleviation

(2011) Bhakti Basu et al.   MOLECULAR & CELLULAR PROTEOMICS

Pattern of occurrence and occupancy of carbonylation sites in proteins

(2011) R. Shyama Prasad Rao et al.   PROTEOMICS

Heterologous production of polyunsaturated fatty acids in Saccharomyces cerevisiae causes a global transcriptional response resulting in reduced proteasomal activity and increased oxidative stress

(2010) Rawisara Ruenwai et al.   Biotechnology Journal

Lon Protease Quality Control of Presecretory Proteins inEscherichia coliand Its Dependence on the SecB and DnaJ (Hsp40) Chaperones

(2010) Samer Sakr et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Unstructured Hydrophilic Sequences in Prokaryotic Proteomes Correlate with Dehydration Tolerance and Host Association

(2010) Anita Kriško et al.   JOURNAL OF MOLECULAR BIOLOGY

High-throughput generation, optimization and analysis of genome-scale metabolic models

(2010) Christopher S Henry et al.   NATURE BIOTECHNOLOGY

Small-Molecule Antioxidant Proteome-Shields in Deinococcus radiodurans

(2010) Michael J. Daly et al.   PLoS One

Protein damage and death by radiation in Escherichia coli and Deinococcus radiodurans

(2010) A. Krisko et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

FINDSITE-metal: Integrating evolutionary information and machine learning for structure-based metal-binding site prediction at the proteome level

(2010) Michal Brylinski et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Effects of carotenoids fromDeinococcus radioduranson protein oxidation

(2009) B. Tian et al.   LETTERS IN APPLIED MICROBIOLOGY

A new perspective on radiation resistance based on Deinococcus radiodurans

(2009) Michael J. Daly   NATURE REVIEWS MICROBIOLOGY

Rules Governing Selective Protein Carbonylation

(2009) Etienne Maisonneuve et al.   PLoS One

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS

Carbonylated Proteins Are Detectable Only in a Degradation-Resistant Aggregate State in Escherichia coli

(2008) E. Maisonneuve et al.   JOURNAL OF BACTERIOLOGY

Ab initio folding of terminal segments with secondary structures reveals the fine difference between two closely related all-atom statistical energy functions

(2008) Yuedong Yang et al.   PROTEIN SCIENCE

Specific interactions for ab initio folding of protein terminal regions with secondary structures

(2008) Yuedong Yang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS