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1. Full Text Selective esterase—ester pair for targeting small molecules with cellular specificity
by Lin Tian and Yunlei Yang and Laura M. Wysocki and Alma C. Arnold and Amy Hu and Balaji Ravichandran and Scott M. Sternson and Loren L. Looger and Luke D. Lavis
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 3/2012, Volume 109, Issue 13, pp. 4756 - 4761
Small molecules are important tools to measure and modulate intracellular signaling pathways. A longstanding limitation for using chemical compounds in complex... 
Molecules | Cell culture techniques | Neurons | Epithelial cells | Gap junctions | Cell lines | HeLa cells | Fluorescence | Esters | Kidney cells | Cellular imaging | Microscopy | Pharmacological agents | Enzyme substrates | Fluorophores | fluorophores | cellular imaging | NITROREDUCTASE | MULTIDISCIPLINARY SCIENCES | JUNCTIONAL INTERCELLULAR COMMUNICATION | enzyme substrates | pharmacological agents | DYE TRANSFER | CARBOXYLESTERASE | IN-VIVO | GENE-EXPRESSION | ABLATION | microscopy | ENDOPLASMIC-RETICULUM | PIG-LIVER ESTERASE | LIVING CELLS | Organ Specificity - drug effects | Gap Junctions - metabolism | Small Molecule Libraries - pharmacology | Hydrolysis - drug effects | Coculture Techniques | Humans | Fluorescent Dyes - metabolism | Esters - metabolism | Neurons - cytology | Biocatalysis - drug effects | Neurons - metabolism | Neurons - drug effects | Astrocytes - cytology | Astrocytes - drug effects | Cell Survival - drug effects | Cells - drug effects | Fluorescent Dyes - chemistry | Permeability - drug effects | Esterases - metabolism | Rats | Hippocampus - cytology | Animals | Cells - metabolism | Mice | HeLa Cells | Gap Junctions - drug effects | Microscopy, Fluorescence | Astrocytes - metabolism | Molecular dynamics | Biomolecules | Chemical properties | Research | Enzymes | Signal transduction | Tissue | Cells | Index Medicus | Biological Sciences | Physical Sciences
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2. Full Text A novel pathway for the production of hydrogen sulfide from D-cysteine in mammalian cells
by Shibuya, Norihiro and Koike, Shin and Tanaka, Makiko and Ishigami-Yuasa, Mari and Kimura, Yuka and Ogasawara, Yuki and Fukui, Kiyoshi and Nagahara, Noriyuki and Kimura, Hideo
Nature Communications, ISSN 2041-1723, 2013, Volume 4, Issue 1, pp. 1366 - 1366
In eukaryotes, hydrogen sulphide acts as a signalling molecule and cytoprotectant. Hydrogen sulphide is known to be produced from L-cysteine by cystathionine... 
D-SERINE | RAT-KIDNEY | SULFANE SULFUR | D-ASPARTATE | MULTIDISCIPLINARY SCIENCES | LIVER | AMINO-ACID OXIDASE | CYSTATHIONINE-GAMMA-LYASE | 3-MERCAPTOPYRUVATE SULFURTRANSFERASE | H2S | BRAIN | Hydrogen Sulfide - metabolism | Organ Specificity - drug effects | Neurons - pathology | Kidney - blood supply | Kidney - pathology | Brain - enzymology | Male | Cysteine - administration & dosage | Cysteine - pharmacology | Cytoprotection - drug effects | Cysteine - metabolism | D-Amino-Acid Oxidase - metabolism | Neurons - drug effects | Mammals - metabolism | Kidney - drug effects | Reperfusion Injury - pathology | Mice, Inbred C57BL | Cells, Cultured | Brain - drug effects | Animals | Biosynthetic Pathways - drug effects | Substrate Specificity - drug effects | Mice | Oxidative Stress - drug effects | Sulfurtransferases - metabolism | Index Medicus
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3. Full Text AcrB drug-binding pocket substitution confers clinically relevant resistance and altered substrate specificity
by Jessica M. A. Blair and Vassiliy N. Bavro and Vito Ricci and Niraj Modi and Pierpaolo Cacciotto and Ulrich Kleinekathӧfer and Paolo Ruggerone and Attilio V. Vargiu and Alison J. Baylay and Helen E. Smith and Yvonne Brandon and David Galloway and Laura J. V. Piddock
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 3/2015, Volume 112, Issue 11, pp. 3511 - 3516
The incidence of multidrug-resistant bacterial infections is increasing globally and the need to understand the underlying mechanisms is paramount to discover... 
Efflux | Antimicrobial resistance | Whole genome sequencing | AcrB | MOLECULAR-DYNAMICS | ENTERICA SEROVAR TYPHIMURIUM | MULTIDISCIPLINARY SCIENCES | ESCHERICHIA-COLI | MULTIDRUG TRANSPORTER ACRB | efflux | CIPROFLOXACIN RESISTANCE | whole genome sequencing | EFFLUX PUMP | antimicrobial resistance | PSEUDOMONAS-AERUGINOSA | SALMONELLA-TYPHIMURIUM | STAPHYLOCOCCUS-AUREUS | MULTIPLE ANTIBIOTIC-RESISTANCE | Minocycline - pharmacology | Escherichia coli - drug effects | Humans | Salmonella enterica - genetics | Doxorubicin - chemistry | Microbial Sensitivity Tests | Salmonella enterica - drug effects | Membrane Transport Proteins - genetics | Water - chemistry | Salmonella enterica - isolation & purification | Membrane Transport Proteins - metabolism | Multidrug Resistance-Associated Proteins - genetics | Doxorubicin - metabolism | Binding Sites | Genome, Bacterial | Bacterial Proteins - genetics | Ciprofloxacin - pharmacology | Models, Molecular | Escherichia coli Proteins - metabolism | Mutation - genetics | Genetic Fitness | Substrate Specificity - drug effects | Escherichia coli - genetics | Escherichia coli - isolation & purification | Escherichia coli Proteins - genetics | Polymorphism, Single Nucleotide - genetics | Bacterial Proteins - metabolism | Anti-Bacterial Agents - pharmacology | Drug Resistance, Multiple, Bacterial - drug effects | Multidrug Resistance-Associated Proteins - metabolism | Amino Acid Substitution | Drug resistance in microorganisms | Usage | Gene mutations | Genetic aspects | Ciprofloxacin | Identification and classification | Health aspects | Multidrug resistant organisms | Genomes | Gram-negative bacteria | Mutation | Antibiotics | Drug resistance | Index Medicus | Biological Sciences
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4. Full Text Targeted Deletion of AIF Decreases Mitochondrial Oxidative Phosphorylation and Protects from Obesity and Diabetes
by Pospisilik, J. Andrew and Knauf, Claude and Joza, Nicholas and Benit, Paule and Orthofer, Michael and Cani, Patrice D and Ebersberger, Ingo and Nakashima, Tomoki and Sarao, Renu and Neely, Gregory and Esterbauer, Harald and Kozlov, Andrey and Kahn, C. Ronald and Kroemer, Guido and Rustin, Pierre and Burcelin, Remy and Penninger, Josef M
Cell, ISSN 0092-8674, 2007, Volume 131, Issue 3, pp. 476 - 491
Type-2 diabetes results from the development of insulin resistance and a concomitant impairment of insulin secretion. Recent studies place altered... 
CELLBIO | HUMDISEASE | APOPTOSIS-INDUCING FACTOR | SKELETAL-MUSCLE | GLUCOSE-HOMEOSTASIS | INSULIN-RESISTANCE | PGC-1-ALPHA | BIOCHEMISTRY & MOLECULAR BIOLOGY | DOWN-REGULATION | DILATED CARDIOMYOPATHY | DYSFUNCTION | DNA GENE-EXPRESSION | DUAL ROLES | CELL BIOLOGY | Mosaicism - drug effects | Organ Specificity - drug effects | Diabetes Mellitus - genetics | Diet - adverse effects | Apoptosis Inducing Factor - deficiency | Obesity - genetics | Oxidative Phosphorylation - drug effects | Liver - drug effects | Gene Deletion | Cell Respiration - drug effects | Muscles - metabolism | Gene Targeting | Insulin - pharmacology | Liver - metabolism | Diabetes Mellitus - metabolism | Mitochondria - metabolism | Mitochondria - drug effects | Apoptosis Inducing Factor - genetics | Mice, Knockout | Obesity - metabolism | Diabetes Mellitus - prevention & control | Phenotype | Animals | Substrate Specificity - drug effects | Muscles - drug effects | Obesity - prevention & control | Glucose - metabolism | Liver - cytology | Mice | Muscles - cytology | Index Medicus | Obesity | Apoptosis Inducing Factor | Liver | Oxidative Phosphorylation | Muscles | Substrate Specificity | Glucose | Organ Specificity | Diabetes Mellitus | Insulin | Mitochondria | Cell Respiration | Diet | Mosaicism
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5. Full Text Structure-and function-based design of Plasmodium-selective proteasome inhibitors
by Li, Hao and O'Donoghue, Anthony J and Van Der Linden, Wouter A and Xie, Stanley C and Yoo, Euna and Foe, Ian T and Tilley, Leann and Craik, Charles S and Da Fonseca, Paula C. A and Bogyo, Matthew
Nature, ISSN 0028-0836, 02/2016, Volume 530, Issue 7589, pp. 233 - 236
The proteasome is a multi-component protease complex responsible for regulating key processes such as the cell cycle and antigen presentation(1). Compounds... 
VISUALIZATION | FALCIPARUM MALARIA | MECHANISM | SPECIFICITY | ARTEMISININ RESISTANCE | MULTIDISCIPLINARY SCIENCES | VALIDATION | ELECTRON-MICROSCOPY | IDENTIFICATION | PARASITE | HUMAN 20S PROTEASOME | Plasmodium falciparum - enzymology | Plasmodium - enzymology | Plasmodium chabaudi - enzymology | Species Specificity | Humans | Proteasome Inhibitors - chemistry | Plasmodium - drug effects | Plasmodium falciparum - drug effects | Protein Subunits - metabolism | Dose-Response Relationship, Drug | Artemisinins - pharmacology | Plasmodium chabaudi - physiology | Drug Design | Plasmodium - growth & development | Female | Drug Resistance | Antimalarials - adverse effects | Catalytic Domain | Proteasome Inhibitors - pharmacology | Models, Molecular | Proteasome Endopeptidase Complex - chemistry | Proteasome Inhibitors - toxicity | Proteasome Inhibitors - adverse effects | Antimalarials - pharmacology | Cryoelectron Microscopy | Drug Synergism | Animals | Substrate Specificity - drug effects | Proteasome Endopeptidase Complex - ultrastructure | Antimalarials - chemistry | Plasmodium chabaudi - drug effects | Mice | Mice, Inbred BALB C | Protein Subunits - antagonists & inhibitors | Protein Subunits - chemistry | Antimalarials - toxicity | Enzyme Activation | Plasmodium falciparum - growth & development | Proteasome Endopeptidase Complex - metabolism | Ubiquitin-proteasome system | Plasmodium | Health aspects | Proteins | Malaria | Protease inhibitors | Proteases | Erythrocytes | Ligands | Parasites | Drug dosages | Index Medicus
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6. Full Text Substrate specificity within a family of outer membrane carboxylate channels
by Eren, Elif and Vijayaraghavan, Jagamya and Liu, Jiaming and Cheneke, Belete R and Touw, Debra S and Lepore, Bryan W and Indic, Mridhu and Movileanu, Liviu and van den Berg, Bert and Brookhaven National Lab. (BNL), Upton, NY (United States)
PLoS Biology, ISSN 1544-9173, 01/2012, Volume 10, Issue 1, pp. e1001242 - e1001242
Many Gram-negative bacteria, including human pathogens such as Pseudomonas aeruginosa, do not have large-channel porins. This results in an outer membrane (OM)... 
HIGH-LEVEL EXPRESSION | PSEUDOMONAS-AERUGINOSA | CRYSTAL-STRUCTURE | BIOCHEMISTRY & MOLECULAR BIOLOGY | ESCHERICHIA-COLI | PORE | BIOLOGY | PORINS | BINDING-SITE | PROTEIN OPRD | LIPID BILAYER-MEMBRANES | DIFFUSION CHANNELS | Conserved Sequence - genetics | Multigene Family | Protein Structure, Secondary | Humans | Porins - metabolism | Bacterial Outer Membrane Proteins - chemistry | Models, Molecular | Anti-Bacterial Agents - metabolism | Crystallography, X-Ray | Protein Transport - drug effects | Pseudomonas aeruginosa - drug effects | Substrate Specificity - drug effects | Bacterial Outer Membrane Proteins - metabolism | Ion Channels - metabolism | Models, Biological | Pseudomonas aeruginosa - metabolism | Protein Binding - drug effects | Porins - chemistry | Anti-Bacterial Agents - pharmacology | Porosity - drug effects | Ion Channels - chemistry | Ion Channel Gating - drug effects | Microbiology | Colleges & universities | Permeability | Experiments | Bacteriology | Molecular weight | Proteins | Antibiotics | E coli | Bacteria | Gram-negative bacteria | Nosocomial infections | Binding sites | Index Medicus | BASIC BIOLOGICAL SCIENCES
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7. Full Text Effects of Gut Microbiota Manipulation by Antibiotics on Host Metabolism in Obese Humans: A Randomized Double-Blind Placebo-Controlled Trial
by Reijnders, Dorien and Goossens, Gijs H and Hermes, Gerben D.A and Neis, Evelien P.J.G and van der Beek, Christina M and Most, Jasper and Holst, Jens J and Lenaerts, Kaatje and Kootte, Ruud S and Nieuwdorp, Max and Groen, Albert K and Olde Damink, Steven W.M and Boekschoten, Mark V and Smidt, Hauke and Zoetendal, Erwin G and Dejong, Cornelis H.C and Blaak, Ellen E
Cell Metabolism, ISSN 1550-4131, 07/2016, Volume 24, Issue 1, pp. 63 - 74
The gut microbiota has been implicated in obesity and cardiometabolic diseases, although evidence in humans is scarce. We investigated how gut microbiota... 
BODY-WEIGHT | NORFLOXACIN | VANCOMYCIN | CHAIN FATTY-ACIDS | INSULIN-RESISTANCE | ENDOCRINOLOGY & METABOLISM | SENSITIVITY | CHROMATOGRAPHY-MASS SPECTROMETRY | SECRETION | GLUCOSE-TOLERANCE | MODULATION | CELL BIOLOGY | Organ Specificity - drug effects | Inflammation - pathology | Humans | Middle Aged | Male | Adipocytes - drug effects | Obesity - genetics | Obesity - microbiology | Vancomycin - pharmacology | Placebos | Adult | Butyric Acid - blood | Biomarkers - metabolism | Insulin - pharmacology | Double-Blind Method | Permeability | Adipocytes - pathology | Obesity - metabolism | Cell Shape - drug effects | Gene Expression Regulation - drug effects | Feces - chemistry | Gastrointestinal Microbiome - drug effects | Substrate Specificity - drug effects | Amoxicillin - pharmacology | Adipocytes - metabolism | Aged | Anti-Bacterial Agents - pharmacology | Energy Metabolism - drug effects | Obesity | Metabolites | Microbiota (Symbiotic organisms) | Physiological aspects | Clinical trials | Electric power production | Gene expression | Fatty acids | Antibacterial agents | Prediabetic state | Deoxycholic acid | Index Medicus | Nutrition, Metabolism and Genomics | Microbiologie | Microbiology | Chair Nutrition Metabolism and Genomics | HNE Voeding, Metabolisme en Genomics | VLAG | Voeding, Metabolisme en Genomica | Laboratorium voor Microbiologie | Microbiological Laboratory | HNE Nutrition, Metabolism and Genomics | WIMEK
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8. Full Text USP30 and parkin homeostatically regulate atypical ubiquitin chains on mitochondria
by Cunningham, Christian N and Baughman, Joshua M and Phu, Lilian and Tea, Joy S and Yu, Christine and Coons, Mary and Kirkpatrick, Donald S and Bingol, Baris and Corn, Jacob E
Nature Cell Biology, ISSN 1465-7392, 02/2015, Volume 17, Issue 2, pp. 160 - 169
Multiple lines of evidence indicate that mitochondrial dysfunction is central to Parkinson's disease. Here we investigate the mechanism by which parkin, an E3... 
PINK1 | PROTEASOMAL DEGRADATION | PHOSPHORYLATION | DEUBIQUITINASES | POLYUBIQUITIN CHAINS | MITOPHAGY | PROTEINS | SELECTIVE AUTOPHAGY | LIGASE | REVEALS | CELL BIOLOGY | Humans | Ubiquitin - metabolism | Membrane Potential, Mitochondrial - drug effects | Gene Knockdown Techniques | Peroxisomes - drug effects | Ubiquitination - drug effects | Mitochondrial Proteins - metabolism | Carbonyl Cyanide m-Chlorophenyl Hydrazone - pharmacology | Hydrogen-Ion Concentration - drug effects | Mass Spectrometry | HEK293 Cells | Lysine - metabolism | Homeostasis - drug effects | Ubiquitin-Specific Proteases - metabolism | Green Fluorescent Proteins - metabolism | Catalytic Domain | Ubiquitin-Protein Ligases - metabolism | Mitochondria - metabolism | Mitochondria - drug effects | Peroxisomes - metabolism | Substrate Specificity - drug effects | Mitochondrial Degradation - drug effects | Models, Biological | Mitochondrial Proteins - chemistry | Cell Extracts | Thiolester Hydrolases - metabolism | HeLa Cells | Thiolester Hydrolases - chemistry | Enzymes | Mitochondria | Cell research | Genetic aspects | Research | Ubiquitin-proteasome system | Properties | Index Medicus
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9. Full Text A Revised Architecture of Primary Cell Walls Based on Biomechanical Changes Induced by Substrate-Specific Endoglucanases
by Yong Bum Park and Daniel J. Cosgrove
Plant Physiology, ISSN 0032-0889, 4/2012, Volume 158, Issue 4, pp. 1933 - 1943
Xyloglucan is widely believed to function as a tether between cellulose microfibrils in the primary cell wall, limiting cell enlargement by restricting the... 
Enzymes | Hypocotyls | Polysaccharides | Cell growth | Architecture | Cell walls | BIOCHEMICAL PROCESSES AND MACROMOLECULAR STRUCTURES | Plants | Cucumbers | Acetates | Plant cells | ARABIDOPSIS-THALIANA | DIRECT VISUALIZATION | IN-VITRO | PEA XYLOGLUCAN | GROWTH | POPLAR CELLULASE | NEW-MODEL | CUCUMBER HYPOCOTYLS | XYLOGLUCAN-CELLULOSE INTERACTIONS | CROSS-LINKS | PLANT SCIENCES | Cucumis sativus - drug effects | Arabidopsis - physiology | Arabidopsis - drug effects | Gluconacetobacter xylinus - metabolism | Hydrolysis - drug effects | Hypocrea - enzymology | Arabidopsis - cytology | Hypocotyl - physiology | Stress, Mechanical | Chromatography, High Pressure Liquid | Cucumis sativus - physiology | Cell Wall - physiology | Cellulase - pharmacology | Compliance - drug effects | Cell Wall - drug effects | Substrate Specificity - drug effects | Cucumis sativus - cytology | Models, Biological | Biomechanical Phenomena - drug effects | Aspergillus nidulans - enzymology | Hypocotyl - drug effects | Gluconacetobacter xylinus - drug effects | Cellulose - metabolism | Biomechanics | Physiological aspects | Aspergillus | Research | Plant cell walls | Glucans | Index Medicus
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10. Full Text PELP1 is a reader of histone H3 methylation that facilitates oestrogen receptor-α target gene activation by regulating lysine demethylase 1 specificity
by Brann, Darrell W and Vadlamudi, Ratna K and Nair, Binoj C and Cortez, Valerie and Tekmal, Rajeshwar R and Nair, Sujit S and Schüle, Roland and Metzger, Eric and Chakravarty, Dimple
EMBO reports, ISSN 1469-221X, 06/2010, Volume 11, Issue 6, pp. 438 - 444
Histone methylation has a key role in oestrogen receptor (ERα)‐mediated transactivation of genes. Proline glutamic acid and leucine‐rich protein 1 (PELP1) is a... 
H3 methylation | ER | KDM1 | PELP1 | COREGULATOR | BIOCHEMISTRY & MOLECULAR BIOLOGY | LSD1 | CANCER | CELL BIOLOGY | Humans | Transcriptional Activation - drug effects | Promoter Regions, Genetic - genetics | Histone Demethylases - metabolism | Substrate Specificity - drug effects | Methylation - drug effects | Protein Binding - drug effects | Cell Line, Tumor | Estrogen Receptor alpha - metabolism | Trans-Activators - metabolism | Transcription Factors | Histones - metabolism | Co-Repressor Proteins | Estradiol - pharmacology | Index Medicus | Scientific Reports
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11. Full Text Systematic identification of allosteric protein-metabolite interactions that control enzyme activity in vivo
by Link, Hannes and Kochanowski, Karl and Sauer, Uwe
Nature Biotechnology, ISSN 1087-0156, 04/2013, Volume 31, Issue 4, pp. 357 - 361
Recent data suggest that the majority of proteins bind specific metabolites(1,2) and that such interactions are relevant to metabolic and gene regulation(3-5).... 
SITE | PHOSPHOFRUCTOKINASE | ACTIVATION | CARBOXYLASE | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | ESCHERICHIA-COLI | FLUXES | Allosteric Regulation - drug effects | Fructose-Bisphosphatase - metabolism | Reproducibility of Results | Escherichia coli - enzymology | Substrate Specificity - drug effects | Metabolome - drug effects | Escherichia coli - drug effects | Gluconeogenesis - drug effects | Bacterial Proteins - metabolism | Glycolysis - drug effects | Hexoses - pharmacology | Pyruvic Acid - pharmacology | Pyruvates | Metabolites | Allosteric proteins | Research | Properties | Protein-protein interactions | Protein binding | Proteins | Enzymes | Biotechnology | E coli | Index Medicus
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12. Full Text Selective spider toxins reveal a role for the Nav1.1 channel in mechanical pain
by Osteen, Jeremiah D and Herzig, Volker and Gilchrist, John and Emrick, Joshua J and Zhang, Chuchu and Wang, Xidao and Castro, Joel and Garcia-Caraballo, Sonia and Grundy, Luke and Rychkov, Grigori Y and Weyer, Andy D and Dekan, Zoltan and Undheim, Eivind A. B and Alewood, Paul and Stucky, Cheryl L and Brierley, Stuart M and Basbaum, Allan I and Bosmans, Frank and King, Glenn F and Julius, David
Nature, ISSN 0028-0836, 06/2016, Volume 534, Issue 7608, pp. 494 - 499
Voltage-gated sodium (Nav) channels initiate action potentials in most neurons, including primary afferent nerve fibres of the pain pathway. Local anaesthetics... 
Hyperalgesia - chemically induced | Temperature | Stress, Mechanical | Male | NAV1.1 Voltage-Gated Sodium Channel - metabolism | Spider Venoms - pharmacology | Pain - chemically induced | NAV1.1 Voltage-Gated Sodium Channel - chemistry | Pain - metabolism | Myelin Sheath - metabolism | Nociception - drug effects | Female | Sensory Receptor Cells - metabolism | Spiders - chemistry | Disease Models, Animal | Protein Structure, Tertiary | Nerve Fibers - metabolism | Irritable Bowel Syndrome - metabolism | Hyperalgesia - metabolism | Oocytes - metabolism | Nerve Fibers - drug effects | Animals | Ganglia, Sensory - cytology | Sensory Receptor Cells - drug effects | Substrate Specificity - drug effects | Nociceptors - metabolism | Nociceptors - drug effects | Physiological aspects | Nociceptors | Sodium channels | Spider venom | Pain | Index Medicus
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