Current Opinion in Structural Biology, ISSN 0959-440X, 04/2015, Volume 31, Issue C, pp. 64 - 74
Connecting dynamics to structural data from diverse experimental sources, molecular dynamics simulations permit the exploration of biological phenomena in...
ANTIBIOTICS | VIRUS | BACTERIAL RIBOSOME | MECHANISM | STRUCTURAL BASIS | CRYOELECTRON MICROSCOPY | MEMBRANE | BIOCHEMISTRY & MOLECULAR BIOLOGY | ARP2/3 COMPLEX | COMPUTATIONAL MODEL | ESSENTIAL MEDICINES | CELL BIOLOGY | Macromolecular Substances - chemistry | Energy Metabolism | Viruses - chemistry | Humans | Viruses - metabolism | Ribosomes - chemistry | Ribosomes - metabolism | Macromolecular Substances - metabolism | Molecular Dynamics Simulation | Biochemistry & Molecular Biology | Cell Biology
ANTIBIOTICS | VIRUS | BACTERIAL RIBOSOME | MECHANISM | STRUCTURAL BASIS | CRYOELECTRON MICROSCOPY | MEMBRANE | BIOCHEMISTRY & MOLECULAR BIOLOGY | ARP2/3 COMPLEX | COMPUTATIONAL MODEL | ESSENTIAL MEDICINES | CELL BIOLOGY | Macromolecular Substances - chemistry | Energy Metabolism | Viruses - chemistry | Humans | Viruses - metabolism | Ribosomes - chemistry | Ribosomes - metabolism | Macromolecular Substances - metabolism | Molecular Dynamics Simulation | Biochemistry & Molecular Biology | Cell Biology
Journal Article
Proteins: Structure, Function, and Bioinformatics, ISSN 0887-3585, 08/2005, Volume 60, Issue 2, pp. 269 - 274
This article describes our attempts to dock the targets in CAPRI Rounds 3–5 using Hex 4.2, and it introduces a novel essential dynamics approach to generate...
polar Fourier correlation | essential dynamics | protein docking | eigenvector analysis | distance constraints | CAPRI | Hex | eigenstructures | Eigenvector analysis | Polar Fourier correlation | Distance constraints | Eigenstructures | Protein docking | Essential dynamics | DOMAIN | RECOGNITION | PHOSPHATASE | BIOCHEMISTRY & MOLECULAR BIOLOGY | SUBUNITS | COMPLEMENTARITY | BIOPHYSICS | STRUCTURAL BASIS | eigen-vector analysis | BINDING | Protein Structure, Tertiary | Computational Biology - methods | Reproducibility of Results | Molecular Conformation | Models, Molecular | Crystallography, X-Ray | Models, Statistical | Protein Folding | Macromolecular Substances | Protein Interaction Mapping - methods | Algorithms | Computer Simulation | Databases, Protein | Protein Binding | Protein Conformation | Software | Structural Homology, Protein | Internet | Mutation | Proteomics - methods | Dimerization
polar Fourier correlation | essential dynamics | protein docking | eigenvector analysis | distance constraints | CAPRI | Hex | eigenstructures | Eigenvector analysis | Polar Fourier correlation | Distance constraints | Eigenstructures | Protein docking | Essential dynamics | DOMAIN | RECOGNITION | PHOSPHATASE | BIOCHEMISTRY & MOLECULAR BIOLOGY | SUBUNITS | COMPLEMENTARITY | BIOPHYSICS | STRUCTURAL BASIS | eigen-vector analysis | BINDING | Protein Structure, Tertiary | Computational Biology - methods | Reproducibility of Results | Molecular Conformation | Models, Molecular | Crystallography, X-Ray | Models, Statistical | Protein Folding | Macromolecular Substances | Protein Interaction Mapping - methods | Algorithms | Computer Simulation | Databases, Protein | Protein Binding | Protein Conformation | Software | Structural Homology, Protein | Internet | Mutation | Proteomics - methods | Dimerization
Journal Article
Plant Cell, ISSN 1040-4651, 11/2015, Volume 27, Issue 11, pp. 3190 - 3212
Plant organelle function must constantly adjust to environmental conditions, which requires dynamic coordination. Ca signaling may play a central role in this...
Mitochondria | Calcium | RESEARCH ARTICLES | Imaging | Plant roots | Guard cells | Gene expression regulation | Plants | Sensors | Plant cells | Seedlings | ESSENTIAL COMPONENT | HIGH-THROUGHPUT | HELIANTHUS-TUBEROSUS | BIOCHEMISTRY & MOLECULAR BIOLOGY | ROOT-GROWTH | PERMEABILITY TRANSITION | PLANT SCIENCES | CELL BIOLOGY | SIGNAL-TRANSDUCTION | CALCIUM UNIPORTER | FLUORESCENT INDICATORS | NAD(P)H DEHYDROGENASES | PLANT-MITOCHONDRIA | Calcium-Binding Proteins - metabolism | Plant Roots - metabolism | EF Hand Motifs | Mitochondria - metabolism | Phylogeny | Mitochondria - ultrastructure | Subcellular Fractions - metabolism | Mutagenesis, Insertional - genetics | Plant Roots - ultrastructure | Arabidopsis - metabolism | Protein Transport | Arabidopsis - genetics | Arabidopsis Proteins - metabolism | Sequence Homology, Amino Acid | DNA, Bacterial - genetics | Cell Respiration | Protein Binding | Cytosol - metabolism | Calcium Signaling | Seedlings - metabolism
Mitochondria | Calcium | RESEARCH ARTICLES | Imaging | Plant roots | Guard cells | Gene expression regulation | Plants | Sensors | Plant cells | Seedlings | ESSENTIAL COMPONENT | HIGH-THROUGHPUT | HELIANTHUS-TUBEROSUS | BIOCHEMISTRY & MOLECULAR BIOLOGY | ROOT-GROWTH | PERMEABILITY TRANSITION | PLANT SCIENCES | CELL BIOLOGY | SIGNAL-TRANSDUCTION | CALCIUM UNIPORTER | FLUORESCENT INDICATORS | NAD(P)H DEHYDROGENASES | PLANT-MITOCHONDRIA | Calcium-Binding Proteins - metabolism | Plant Roots - metabolism | EF Hand Motifs | Mitochondria - metabolism | Phylogeny | Mitochondria - ultrastructure | Subcellular Fractions - metabolism | Mutagenesis, Insertional - genetics | Plant Roots - ultrastructure | Arabidopsis - metabolism | Protein Transport | Arabidopsis - genetics | Arabidopsis Proteins - metabolism | Sequence Homology, Amino Acid | DNA, Bacterial - genetics | Cell Respiration | Protein Binding | Cytosol - metabolism | Calcium Signaling | Seedlings - metabolism
Journal Article
Research Policy, ISSN 0048-7333, 11/2016, Volume 45, Issue 9, pp. 1762 - 1773
We analyze the rate and direction of technological progress of standards subject to declared standard-essential patents (SEP). We observe continuous and...
Cumulative innovation | Disruptive innovation | Incremental innovation | Complex technologies | Technology standards | Standard-essential patents | MANAGEMENT | INNOVATION | COMPATIBILITY | COURTS | ENTREPRENEURSHIP | PLANNING & DEVELOPMENT | Patents | Law schools | Business schools
Cumulative innovation | Disruptive innovation | Incremental innovation | Complex technologies | Technology standards | Standard-essential patents | MANAGEMENT | INNOVATION | COMPATIBILITY | COURTS | ENTREPRENEURSHIP | PLANNING & DEVELOPMENT | Patents | Law schools | Business schools
Journal Article
Journal of Computational Chemistry, ISSN 0192-8651, 11/2006, Volume 27, Issue 14, pp. 1765 - 1768
A computer program has been developed to aid the analysis of molecular dynamics trajectories. The program is tuned for macromolecular large‐scale problems and...
essential dynamics | molecular dynamics | principal component analysis | trajectory viewer | Molecular dynamics | Trajectory viewer | Essential dynamics | Principal component analysis | PROTEINS | CHEMISTRY, MULTIDISCIPLINARY | Motion | Macromolecular Substances - chemistry | Computer Simulation | Water - chemistry | Software | Principal Component Analysis | Rotation
essential dynamics | molecular dynamics | principal component analysis | trajectory viewer | Molecular dynamics | Trajectory viewer | Essential dynamics | Principal component analysis | PROTEINS | CHEMISTRY, MULTIDISCIPLINARY | Motion | Macromolecular Substances - chemistry | Computer Simulation | Water - chemistry | Software | Principal Component Analysis | Rotation
Journal Article
Biopolymers, ISSN 0006-3525, 12/2016, Volume 105, Issue 12, pp. 898 - 904
The conformational behavior of the wild‐type endonucleases I‐DmoI and two of its mutants has been studied in the presence and in the absence of DNA target...
essential motions | Conformational behavior | molecular dynamics | endonucleases | DNA‐binding | DNA-binding | COMPLEX | PROTEIN | SPECIFICITY | RECOGNITION | BIOCHEMISTRY & MOLECULAR BIOLOGY | CLEAVAGE | SCEL | BIOPHYSICS | INTRONS | BINDING | DNA - chemistry | Molecular Dynamics Simulation | Deoxyribonucleases, Type I Site-Specific - chemistry | Molecular dynamics | Genetic research | Chemical properties | DNA | Proteins | Residues | Simulation | Deoxyribonucleic acid | Subspaces | Biopolymers | Gene sequencing
essential motions | Conformational behavior | molecular dynamics | endonucleases | DNA‐binding | DNA-binding | COMPLEX | PROTEIN | SPECIFICITY | RECOGNITION | BIOCHEMISTRY & MOLECULAR BIOLOGY | CLEAVAGE | SCEL | BIOPHYSICS | INTRONS | BINDING | DNA - chemistry | Molecular Dynamics Simulation | Deoxyribonucleases, Type I Site-Specific - chemistry | Molecular dynamics | Genetic research | Chemical properties | DNA | Proteins | Residues | Simulation | Deoxyribonucleic acid | Subspaces | Biopolymers | Gene sequencing
Journal Article
Journal of Marine Systems, ISSN 0924-7963, 09/2016, Volume 161, pp. 26 - 41
Reliable statements about variability and change in marine ecosystems and their underlying causes are needed to report on their status and to guide management....
Ocean observing | Ecosystem management | Southern Ocean Observing System | Essential variables | Monitoring systems | Antarctica | Ecosystem change | Indicators | FOOD-WEB | CLIMATE-CHANGE | TRENDS | WEST ANTARCTIC PENINSULA | MARINE ECOSYSTEM | CCAMLR | MANAGING FISHERIES | GEOSCIENCES, MULTIDISCIPLINARY | EUPHAUSIA-SUPERBA | MARINE & FRESHWATER BIOLOGY | OCEANOGRAPHY | ROSS SEA | Environmental aspects | Population ecology | Ocean | Analysis | Computer simulation | Oceans | Ecosystems | Southern Ocean | Ecological monitoring | Mathematical models | Trends | Assessments | Earth Sciences | Sciences of the Universe | Oceanography
Ocean observing | Ecosystem management | Southern Ocean Observing System | Essential variables | Monitoring systems | Antarctica | Ecosystem change | Indicators | FOOD-WEB | CLIMATE-CHANGE | TRENDS | WEST ANTARCTIC PENINSULA | MARINE ECOSYSTEM | CCAMLR | MANAGING FISHERIES | GEOSCIENCES, MULTIDISCIPLINARY | EUPHAUSIA-SUPERBA | MARINE & FRESHWATER BIOLOGY | OCEANOGRAPHY | ROSS SEA | Environmental aspects | Population ecology | Ocean | Analysis | Computer simulation | Oceans | Ecosystems | Southern Ocean | Ecological monitoring | Mathematical models | Trends | Assessments | Earth Sciences | Sciences of the Universe | Oceanography
Journal Article
Journal of Biological Chemistry, ISSN 0021-9258, 02/2009, Volume 284, Issue 7, pp. 4041 - 4045
This review discusses recent insights in the roles of DNA polymerases (Pol) δ and ϵ in eukaryotic DNA replication. A growing body of evidence specifies Pol...
YEAST | DELTA | BIOCHEMISTRY & MOLECULAR BIOLOGY | CATALYTIC DOMAINS | COMPONENTS | OKAZAKI FRAGMENT MATURATION | ESSENTIAL IN-VIVO | FLAP ENDONUCLEASE-1 | SACCHAROMYCES-CEREVISIAE | LIGATABLE NICK | EPSILON | Eukaryotic Cells - enzymology | DNA Polymerase III - genetics | Humans | DNA - metabolism | DNA Polymerase II - metabolism | Flap Endonucleases - metabolism | DNA - genetics | DNA Helicases - metabolism | Animals | DNA Replication - physiology | Eukaryotic Cells - cytology | Mutation | DNA Polymerase III - metabolism | DNA Helicases - genetics | DNA Polymerase II - genetics | Flap Endonucleases - genetics | Minireviews
YEAST | DELTA | BIOCHEMISTRY & MOLECULAR BIOLOGY | CATALYTIC DOMAINS | COMPONENTS | OKAZAKI FRAGMENT MATURATION | ESSENTIAL IN-VIVO | FLAP ENDONUCLEASE-1 | SACCHAROMYCES-CEREVISIAE | LIGATABLE NICK | EPSILON | Eukaryotic Cells - enzymology | DNA Polymerase III - genetics | Humans | DNA - metabolism | DNA Polymerase II - metabolism | Flap Endonucleases - metabolism | DNA - genetics | DNA Helicases - metabolism | Animals | DNA Replication - physiology | Eukaryotic Cells - cytology | Mutation | DNA Polymerase III - metabolism | DNA Helicases - genetics | DNA Polymerase II - genetics | Flap Endonucleases - genetics | Minireviews
Journal Article
Biochemical Journal, ISSN 0264-6021, 01/2014, Volume 458, Issue 1, pp. 33 - 40
MICU1 (Ca2+ uptake protein 1, mitochondrial) is an important regulator of the MCU (Ca2+ uniporter protein, mitochondrial) that has been shown recently to act...
Mitochondrion | uniporter protein | Knockdown | Mitochondrial (MICU1) | uptake protein 1 | uniporter | Aequorin | Mitochondrial (MCU) | Ca2+ uniporter protein | PROTEIN | knockdown | ESSENTIAL COMPONENT | BIOCHEMISTRY & MOLECULAR BIOLOGY | mitochondrial (MCU) | Ca2+ uptake protein 1 | aequorin | mitochondrion | mitochondrial (MICU1) | Ca2+ uniporter | CALCIUM UNIPORTER | MICU1 | MCU | Calcium-Binding Proteins - metabolism | Mitochondrial Membrane Transport Proteins - metabolism | Calcium - metabolism | Cation Transport Proteins - metabolism | Humans | Membrane Potential, Mitochondrial | Cation Transport Proteins - genetics | Mitochondria - metabolism | HeLa Cells | Calcium-Binding Proteins - genetics | Mitochondrial Membrane Transport Proteins - genetics
Mitochondrion | uniporter protein | Knockdown | Mitochondrial (MICU1) | uptake protein 1 | uniporter | Aequorin | Mitochondrial (MCU) | Ca2+ uniporter protein | PROTEIN | knockdown | ESSENTIAL COMPONENT | BIOCHEMISTRY & MOLECULAR BIOLOGY | mitochondrial (MCU) | Ca2+ uptake protein 1 | aequorin | mitochondrion | mitochondrial (MICU1) | Ca2+ uniporter | CALCIUM UNIPORTER | MICU1 | MCU | Calcium-Binding Proteins - metabolism | Mitochondrial Membrane Transport Proteins - metabolism | Calcium - metabolism | Cation Transport Proteins - metabolism | Humans | Membrane Potential, Mitochondrial | Cation Transport Proteins - genetics | Mitochondria - metabolism | HeLa Cells | Calcium-Binding Proteins - genetics | Mitochondrial Membrane Transport Proteins - genetics
Journal Article
Molecular Plant, ISSN 1674-2052, 03/2012, Volume 5, Issue 2, pp. 318 - 333
Isoprenoids are functionally and structurally the most diverse group of plant metabolites reported to date. They can function as primary metabolites,...
flux | pathway | isoprenoids | metabolites | network | COENZYME-A REDUCTASE | BIOCHEMISTRY & MOLECULAR BIOLOGY | FARNESYL-DIPHOSPHATE SYNTHASE | ESSENTIAL OIL COMPOSITION | PLANT SCIENCES | BIOSYNTHETIC GENE-CLUSTER | PHYTOCHROME-INTERACTING FACTORS | METHYLERYTHRITOL PHOSPHATE PATHWAYS | ARABIDOPSIS-THALIANA CONTAINS | PSEUDO-RESPONSE REGULATORS | TOMATO FRUIT-DEVELOPMENT | ENCODING SQUALENE SYNTHASE | Biotechnology | Terpenes - chemistry | Metabolic Networks and Pathways - genetics | Terpenes - metabolism | Genes, Plant - genetics | Models, Biological | Research | Physiological aspects | Structure | Terpenoids
flux | pathway | isoprenoids | metabolites | network | COENZYME-A REDUCTASE | BIOCHEMISTRY & MOLECULAR BIOLOGY | FARNESYL-DIPHOSPHATE SYNTHASE | ESSENTIAL OIL COMPOSITION | PLANT SCIENCES | BIOSYNTHETIC GENE-CLUSTER | PHYTOCHROME-INTERACTING FACTORS | METHYLERYTHRITOL PHOSPHATE PATHWAYS | ARABIDOPSIS-THALIANA CONTAINS | PSEUDO-RESPONSE REGULATORS | TOMATO FRUIT-DEVELOPMENT | ENCODING SQUALENE SYNTHASE | Biotechnology | Terpenes - chemistry | Metabolic Networks and Pathways - genetics | Terpenes - metabolism | Genes, Plant - genetics | Models, Biological | Research | Physiological aspects | Structure | Terpenoids
Journal Article
Phytochemistry, ISSN 0031-9422, 06/2018, Volume 150, Issue C, pp. 23 - 30
Briquet, commonly known as Japanese catnip, is used for the treatment of colds, headaches, fevers, and skin rashes in traditional Asian medicine (China, Japan...
Gas chromatography | Glandular trichome | Peltate | Capitate | Digitiform | Essential oil | Monoterpene biosynthesis | Volatile | ESSENTIAL OILS | MICROMORPHOLOGY | MONOTERPENE CYCLASE | BIOCHEMISTRY & MOLECULAR BIOLOGY | 4S-LIMONENE SYNTHASE | QUALITY-CONTROL | PLANT SCIENCES | HISTOCHEMISTRY | NEPETA-RACEMOSA | FUNCTIONAL EXPRESSION | SPEARMINT MENTHA-SPICATA | PEPPERMINT | Medicinal plants | Enzymes | Medicine, Botanic | Physiological aspects | Skin diseases | Medicine, Herbal | Chromatography | Biochemistry & Molecular Biology | Plant Sciences
Gas chromatography | Glandular trichome | Peltate | Capitate | Digitiform | Essential oil | Monoterpene biosynthesis | Volatile | ESSENTIAL OILS | MICROMORPHOLOGY | MONOTERPENE CYCLASE | BIOCHEMISTRY & MOLECULAR BIOLOGY | 4S-LIMONENE SYNTHASE | QUALITY-CONTROL | PLANT SCIENCES | HISTOCHEMISTRY | NEPETA-RACEMOSA | FUNCTIONAL EXPRESSION | SPEARMINT MENTHA-SPICATA | PEPPERMINT | Medicinal plants | Enzymes | Medicine, Botanic | Physiological aspects | Skin diseases | Medicine, Herbal | Chromatography | Biochemistry & Molecular Biology | Plant Sciences
Journal Article
Journal of Neurochemistry, ISSN 0022-3042, 08/2018, Volume 146, Issue 4, pp. 403 - 415
Recent studies have highlighted the role of mitochondria in dendritic protrusion growth and plasticity. However, the detailed mechanisms that mitochondria...
mitochondrial permeability transition | cyclophilin D | mitochondria | dendritic spine morphogenesis | depolarization | PERMEABILITY TRANSITION PORE | ACTIVATION | ESSENTIAL COMPONENT | BIOCHEMISTRY & MOLECULAR BIOLOGY | HIPPOCAMPAL | RECEPTOR | RELEASE | NEUROSCIENCES | TRANSIENTS | F1FO ATP SYNTHASE | SPINES | PLASTICITY | Mitochondrial Dynamics - genetics | Calcium - metabolism | Male | Cyclophilins - metabolism | Dendrites - ultrastructure | Mitochondrial Proteins - genetics | Mitochondrial Membrane Transport Proteins - genetics | Pseudopodia - drug effects | Mitochondrial Membrane Transport Proteins - physiology | Neurons - ultrastructure | Mitochondrial Proteins - metabolism | Potassium Chloride - pharmacology | Female | Neurons - metabolism | Calcium-Calmodulin-Dependent Protein Kinase Type 2 - metabolism | Animals, Newborn | Brain - cytology | Mice, Inbred C57BL | Cells, Cultured | Mice, Transgenic | Cyclophilins - genetics | Mitochondria - metabolism | Calcium-Calmodulin-Dependent Protein Kinase Type 2 - genetics | Animals | Mitochondrial Dynamics - drug effects | Mice | Pseudopodia - physiology | Physiological aspects | Permeability | Neurons | Genes | Neurophysiology | Oxidative stress | Calcium | Mitochondrial permeability transition pore | Membrane permeability | Homeostasis | Pseudopodia | Mitochondrial DNA | Potassium chloride | Calcium (mitochondrial) | Depolarization | Morphogenesis | Calcium signalling | Mitochondria | Plasticity | Physiology | Plastic properties | Dendritic structure | Calcium homeostasis | Plasticity (dendritic)
mitochondrial permeability transition | cyclophilin D | mitochondria | dendritic spine morphogenesis | depolarization | PERMEABILITY TRANSITION PORE | ACTIVATION | ESSENTIAL COMPONENT | BIOCHEMISTRY & MOLECULAR BIOLOGY | HIPPOCAMPAL | RECEPTOR | RELEASE | NEUROSCIENCES | TRANSIENTS | F1FO ATP SYNTHASE | SPINES | PLASTICITY | Mitochondrial Dynamics - genetics | Calcium - metabolism | Male | Cyclophilins - metabolism | Dendrites - ultrastructure | Mitochondrial Proteins - genetics | Mitochondrial Membrane Transport Proteins - genetics | Pseudopodia - drug effects | Mitochondrial Membrane Transport Proteins - physiology | Neurons - ultrastructure | Mitochondrial Proteins - metabolism | Potassium Chloride - pharmacology | Female | Neurons - metabolism | Calcium-Calmodulin-Dependent Protein Kinase Type 2 - metabolism | Animals, Newborn | Brain - cytology | Mice, Inbred C57BL | Cells, Cultured | Mice, Transgenic | Cyclophilins - genetics | Mitochondria - metabolism | Calcium-Calmodulin-Dependent Protein Kinase Type 2 - genetics | Animals | Mitochondrial Dynamics - drug effects | Mice | Pseudopodia - physiology | Physiological aspects | Permeability | Neurons | Genes | Neurophysiology | Oxidative stress | Calcium | Mitochondrial permeability transition pore | Membrane permeability | Homeostasis | Pseudopodia | Mitochondrial DNA | Potassium chloride | Calcium (mitochondrial) | Depolarization | Morphogenesis | Calcium signalling | Mitochondria | Plasticity | Physiology | Plastic properties | Dendritic structure | Calcium homeostasis | Plasticity (dendritic)
Journal Article