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1. Full Text Genomic Changes in Resynthesized Brassica napus and Their Effect on Gene Expression and Phenotype
by Robert T. Gaeta and J. Chris Pires and Federico Iniguez-Luy and Enrique Leon and Thomas C. Osborn
The Plant Cell, ISSN 1040-4651, 11/2007, Volume 19, Issue 11, pp. 3403 - 3417
Many previous studies have provided evidence for genome changes in polyploids, but there are little data on the overall population dynamics of genome change... 
Allopolyploidy | Polyploidy | Complementary DNA | Genetic variation | DNA | Linkage groups | Genomics | Genomes | Data lines | Methylation | ARABIDOPSIS POLYPLOIDS | BIOCHEMISTRY & MOLECULAR BIOLOGY | ALLOPOLYPLOIDS | REARRANGEMENTS | CONCERTED EVOLUTION | PLANT SCIENCES | CELL BIOLOGY | QUANTITATIVE TRAIT LOCI | HOMEOLOGOUS RECOMBINATION | FLOWERING PLANTS | OILSEED RAPE | NICOTIANA | CYTOSINE METHYLATION | Chromosome Segregation | Brassica napus - genetics | Genome, Plant - genetics | RNA, Messenger - genetics | Genetic Markers | Phylogeny | Chromosomes, Plant - metabolism | DNA, Plant - metabolism | RNA, Messenger - metabolism | DNA Transposable Elements | Polymorphism, Single-Stranded Conformational | DNA Methylation | Phenotype | Gene Expression Regulation, Plant | Recombination, Genetic - genetics | DNA, Complementary - metabolism | Amplified Fragment Length Polymorphism Analysis | Genetic Linkage | Evaluation | Brassica | Gene mutations | Genetic aspects | Gene expression | Observations
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2. Full Text Interpretation of Protein Adsorption:  Surface-Induced Conformational Changes
by Roach, Paul and Farrar, David and Perry, Carole C
Journal of the American Chemical Society, ISSN 0002-7863, 06/2005, Volume 127, Issue 22, pp. 8168 - 8173
Protein adhesion plays a major role in determining the biocompatibility of materials. The first stage of implant integration is the adhesion of protein... 
ADHESION | HUMAN-SERUM-ALBUMIN | SPECTROSCOPY | BIOMATERIAL SURFACES | QUARTZ-CRYSTAL MICROBALANCE | SCANNING FORCE MICROSCOPY | INDUCED STRUCTURAL-CHANGES | BINDING | CHEMISTRY, MULTIDISCIPLINARY | FIBRINOGEN | POLYURETHANES | Gold - chemistry | Alcohols - chemistry | Coated Materials, Biocompatible - chemistry | Fibrinogen - chemistry | Spectroscopy, Fourier Transform Infrared | Wettability | Animals | Adsorption | Cattle | Surface Properties | Hydrophobic and Hydrophilic Interactions | Protein Conformation | Serum Albumin, Bovine - chemistry | Sulfhydryl Compounds - chemistry | Alkanes - chemistry | Infrared spectroscopy | Protein research | Research | Analysis | Surface chemistry | Conformational analysis
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3. Full Text Interaction between the AAA ATPase p97 and its cofactor ataxin3 in health and disease: Nucleotide-induced conformational changes regulate cofactor binding
by Rao, Maya V and Williams, Dewight R and Cocklin, Simon and Loll, Patrick J
Journal of Biological Chemistry, ISSN 0021-9258, 2017, Volume 292, Issue 45, pp. 18392 - 18407
p97 is an essential ATPase associated with various cellular activities (AAA(+)) that functions as a segregase in diverse cellular processes, including the... 
VCP | VALOSIN-CONTAINING PROTEIN | POLYGLUTAMINE DISEASE | BIOCHEMISTRY & MOLECULAR BIOLOGY | cofactor binding | multisystem proteinopathy 1 (MSP1) | VCP/P97 | surface plasmon resonance (SPR) | ATPases associated with diverse cellular activities (AAA) | ENDOPLASMIC-RETICULUM STRESS | conformational change | proteostasis | PAGET-DISEASE | electron microscopy (EM) | p97 | UBIQUITIN CHAINS | STRUCTURAL BASIS | MACHADO-JOSEPH-DISEASE | MOUSE MODEL | ataxin3 | nucleotide regulation | CRYO-EM STRUCTURE | Proteostasis Deficiencies - metabolism | Coenzymes - genetics | Humans | Protein Multimerization | Crystallography, X-Ray | Adenosine Diphosphate - chemistry | Recombinant Fusion Proteins - metabolism | Coenzymes - metabolism | Adenosine Triphosphate - metabolism | Databases, Protein | Distal Myopathies - metabolism | Proteostasis Deficiencies - enzymology | Ataxin-3 - chemistry | Protein Interaction Domains and Motifs | Valosin Containing Protein - chemistry | Ataxin-3 - metabolism | Coenzymes - chemistry | Binding Sites | Peptide Fragments - genetics | Repressor Proteins - metabolism | Binding, Competitive | Microscopy, Electron, Transmission | Peptide Fragments - metabolism | Repressor Proteins - chemistry | Valosin Containing Protein - genetics | Valosin Containing Protein - metabolism | Models, Molecular | Repressor Proteins - genetics | Recombinant Fusion Proteins - chemistry | Protein Interaction Mapping | Distal Myopathies - enzymology | Proteostasis Deficiencies - genetics | Distal Myopathies - genetics | Peptide Fragments - chemistry | Protein Conformation | Adenosine Diphosphate - metabolism | Mutation | Adenosine Triphosphate - chemistry | Amino Acid Substitution | Ataxin-3 - genetics | Molecular Bases of Disease
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4. Full Text Structural and dynamic changes adopted by EmrE, multidrug transporter protein—Studies by molecular dynamics simulation
by Padariya, Monikaben and Kalathiya, Umesh and Baginski, Maciej
BBA - Biomembranes, ISSN 0005-2736, 10/2015, Volume 1848, Issue 10, pp. 2065 - 2074
EmrE protein transports positively charged aromatic drugs (xenobiotics) in exchange for two protons and thus provides bacteria resistance to variety of drugs.... 
Molecular dynamics | Small multidrug resistance (SMR) transporter | EmrE | Multidrug transporter | Heterogeneous lipid bilayer | DOMAIN | RECOGNITION | MEMBRANE | BIOCHEMISTRY & MOLECULAR BIOLOGY | BILAYERS | CONFORMATIONAL-CHANGES | BIOPHYSICS | LANGEVIN | RESISTANCE | PROVIDES | BINDING | PLASTICITY | Hydrogen | Analysis | Chemical properties
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5. Full Text Identifying localized changes in large systems
: Change-point detection for biomolecular simulations
by Zhou Fan and Ron O. Dror and Thomas J. Mildorf and Stefano Piana and David E. Shaw
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 6/2015, Volume 112, Issue 24, pp. 1 - 6
Research on change-point detection, the classical problem of detecting abrupt changes in sequential data, has focused predominantly on datasets with a single... 
Penalized maximum likelihood | Molecular dynamics | SIMPLE | Conformational change | Multivariate | multivariate | penalized maximum likelihood | conformational change | molecular dynamics | SEQUENCES | MODELS | MULTIDISCIPLINARY SCIENCES | MOLECULAR-DYNAMICS TRAJECTORIES | VARIABLES | PROTEINS | DISCOVERY | Likelihood Functions | Algorithms | Biophysical Phenomena | Protein Conformation | Molecular Dynamics Simulation - statistics & numerical data | Proteins - chemistry | Protein Folding | Electronic data processing | Usage | Statistical methods | Methods | Biological Sciences | Physical Sciences
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6. Full Text Changes in the intrinsic electrocatalytic nature of Na+/K+ ATPase reflect structural changes on ATP-binding: Electrochemical label-free approach
by Vacek, Jan and Zatloukalova, Martina and Havlikova, Marika and Ulrichova, Jitka and Kubala, Martin
Electrochemistry Communications, ISSN 1388-2481, 02/2013, Volume 27, pp. 104 - 107
Chronopotentiometric stripping (CPS) analysis was used to show that transmembrane protein Na /K -ATPase (NKA) structural changes can be observed in the... 
Sodium–potassium pump | Structural changes | Chronopotentiometry | Electroanalysis | Membrane protein | Mercury electrode | Sodium-potassium pump | STRIPPING CHRONOPOTENTIOMETRY | ELECTROCHEMISTRY | METALLOTHIONEIN | CRYSTAL-STRUCTURE | HYDROGEN EVOLUTION | MERCURY-ELECTRODES | CARBON ELECTRODES | CONFORMATIONAL-CHANGES | CYTOPLASMIC HEADPIECE | CALCIUM-PUMP | BOVINE SERUM-ALBUMIN
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7. Full Text Structural changes of envelope proteins during alphavirus fusion
by Xiang, Ye and Kuhn, Richard J and Rossmann, Michael G and Jose, Joyce and Li, Long
Nature, ISSN 0028-0836, 12/2010, Volume 468, Issue 7324, pp. 705 - 708
Alphaviruses are enveloped RNA viruses that have a diameter of about 700 Å and can be lethal human pathogens. Entry of virus into host cells by endocytosis is... 
MEMBRANE-FUSION | PH-DEPENDENT FUSION | SINDBIS VIRUS | DYNAMIC ENVELOPE | CONFORMATIONAL-CHANGE | PRECURSOR | MULTIDISCIPLINARY SCIENCES | SEMLIKI-FOREST-VIRUS | GLYCOPROTEIN | CLASS-II VIRUS | Viral Fusion Proteins - metabolism | Membrane Glycoproteins - metabolism | Receptors, Virus - metabolism | Membrane Glycoproteins - chemistry | Protein Multimerization | Crystallography, X-Ray | Virion - chemistry | Endosomes - metabolism | Virus Internalization | Sindbis Virus - metabolism | Sindbis Virus - chemistry | Viral Fusion Proteins - chemistry | Protein Structure, Quaternary | Viral Envelope Proteins - metabolism | Protein Structure, Tertiary | Cell Line | Membrane Fusion | Models, Molecular | Virion - metabolism | Cryoelectron Microscopy | Animals | Viral Envelope Proteins - chemistry | Hydrophobic and Hydrophilic Interactions | Drosophila melanogaster | Hydrogen-Ion Concentration | RNA viruses | Physiological aspects | Glycoproteins | Research | Structure | Health aspects | Protein binding | Pathology | Virology | Crystal structure
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8. Full Text Global analysis of protein structural changes in complex proteomes
by Feng, Yuehan and De Franceschi, Giorgia and Kahraman, Abdullah and Soste, Martin and Melnik, Andre and Boersema, Paul J and De Laureto, Patrizia Polverino and Nikolaev, Yaroslav and Oliveira, Ana Paula and Picotti, Paola
Nature Biotechnology, ISSN 1087-0156, 10/2014, Volume 32, Issue 10, pp. 1036 - 1044
Changes in protein conformation can affect protein function, but methods to probe these structural changes on a global scale in cells have been lacking. To... 
YEAST | LIMITED PROTEOLYSIS | CONFORMATIONAL-CHANGES | MOLTEN GLOBULE | PHOSPHORYLATION | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | SECONDARY STRUCTURE | SCALE | SACCHAROMYCES-CEREVISIAE | MASS-SPECTROMETRY | TARGETED PROTEOMICS | Fructosediphosphates | Amino Acid Sequence | Peptide Fragments | Molecular Sequence Data | Proteins - analysis | Proteome - analysis | Proteome - chemistry | Trypsin | Proteolysis | Mass Spectrometry | Prions | Protein Conformation | Amyloid | Proteins - chemistry | Proteomics - methods | Proteins | Protein research | Research | Structure | Conformation | Data analysis | Cells | Proteomics
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9. Full Text Pathogenic Mutations Induce Partial Structural Changes in the Native β‑Sheet Structure of Transthyretin and Accelerate Aggregation
by Lim, Kwang Hun and Dasari, Anvesh K. R and Ma, Renze and Hung, Ivan and Gan, Zhehong and Kelly, Jeffery W and Fitzgerald, Michael C
Biochemistry, ISSN 0006-2960, 09/2017, Volume 56, Issue 36, pp. 4808 - 4818
Amyloid formation of natively folded proteins involves global and/or local unfolding of the native state to form aggregation-prone intermediates. Here we... 
SOLID-STATE NMR | WILD-TYPE TRANSTHYRETIN | SPECTROSCOPY | THERMODYNAMIC ANALYSIS | BIOCHEMISTRY & MOLECULAR BIOLOGY | CONFORMATIONAL FLEXIBILITY | INTERMEDIATE | MOLECULAR-DYNAMICS SIMULATIONS | MEMBRANE-PROTEINS | SUBUNIT INTERFACE | AMYLOID FIBRIL FORMATION | Gene Expression | Magnetic Resonance Spectroscopy | Oxidation-Reduction | Time Factors | Escherichia coli - metabolism | Models, Molecular | Protein Binding | Protein Conformation | Prealbumin - chemistry | Mutation | Circular Dichroism | Protein Folding | Chemical reactions | Nuclear magnetic resonance spectroscopy | Usage | Research | Gene mutations | PDSD | Solid-state NMR | TTR | amyloidosis | L55P | SPROX | mass spectrometry | Amyloid | V30M | misfolding
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10. Full Text Structural changes of 2,2′-azobis(2-amidinopropane) dihydrochloride (AAPH) treated shrimp tropomyosin decrease allergenicity
by Lv, Liangtao and Lin, Hang and Lin, Hong and Li, Zhenxing and Nayak, Balunkeswar and Ahmed, Ishfaq and Tian, Shenglan and Chen, Guanzhi and Zhao, Jinxia
Food Chemistry, ISSN 0308-8146, 02/2019, Volume 274, pp. 547 - 557
The aim of this study was to analyze the effect of AAPH on the conformational structure and allergenicity of shrimp tropomyosin (TM). The structure of AAPH-TM... 
Shrimp tropomyosin | Protein oxidation | Allergenicity | AAPH | DL-lysine (PubChem CID: 866) | L-leucine (PubChem CID: 6106) | 1-Anilino-8-naphthalene-sulfonate (PubChem CID: 1369) | 3,3′,5,5′-Tetramethylbenzidine (PubChem CID: 41206) | Acrylamide (PubChem CID: 6579) | Brilliant Blue R (PubChem CID: 61365) | DL-Dithiothreitol (PubChem CID: 446094) | IGE BINDING-CAPACITY | HIGH-PRESSURE | FOOD SCIENCE & TECHNOLOGY | CROSS-LINKING | HEAT-TREATMENT | METAPENAEUS-ENSIS TROPOMYOSIN | NUTRITION & DIETETICS | CONFORMATIONAL STRUCTURE | EGG-WHITE | OXIDATIVE MODIFICATION | CHEMISTRY, APPLIED | SOY-PROTEIN | POTENTIAL ALLERGENICITY | Animals | Allergens - immunology | Tropomyosin - immunology | Allergens - chemistry | Mice | Penaeidae - chemistry | Tropomyosin - chemistry | Amidines - chemistry | Shellfish - analysis | Immunoglobulin E - chemistry | Penaeidae - immunology | Index Medicus
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11. Full Text Helix-helix inversion of an optically-inactive pi-conjugated foldamer triggered by concentration changes of a single enantiomeric guest leading to a change in the helical stability
by Liu, LJ and Ousaka, N and Horie, M and Mamiya, F and Yashima, E
CHEMICAL COMMUNICATIONS, ISSN 1359-7345, 2016, Volume 52, Issue 79, pp. 11752 - 11755
A preferred-handed helicity induced in an optically-inactive poly(phenyleneethynylene)-based foldamer bearing carboxylic acid pendants upon complexation with a... 
SENSE INVERSION | SCREW-SENSE | MAIN-CHAIN | CONFORMATIONAL-CHANGE | CIRCULAR-DICHROISM | PHENYLENE ETHYNYLENE OLIGOMERS | MACROMOLECULAR HELICITY | POLY(PHENYLACETYLENE)S BEARING | CHAIN-LENGTH DEPENDENCE | CHIRAL AMPLIFICATION | CHEMISTRY, MULTIDISCIPLINARY | Complexation | Diamines | Stability | Inversions | Helices | Carboxylic acids | Helicity | Bearing
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12. Full Text Protonation and pK changes in protein-ligand binding
by Onufriev, Alexey V and Alexov, Emil
Quarterly Reviews of Biophysics, ISSN 0033-5835, 05/2013, Volume 46, Issue 2, pp. 181 - 209
Formation of protein-ligand complexes causes various changes in both the receptor and the ligand. This review focuses on changes in pK and protonation states... 
ELECTROSTATIC INTERACTIONS | FREE-ENERGY CALCULATIONS | PK(A) VALUES | IONIZATION STATES | CONFORMATIONAL-CHANGES | BIOPHYSICS | HYDROGEN-BOND | CATALYTIC ASPARTYL GROUPS | PH MOLECULAR-DYNAMICS | HIV-1 PROTEASE | IONIZABLE GROUPS | Protons | Proteins - metabolism | Humans | Protein Binding | Ligands | Molecular Docking Simulation | Hydrogen-Ion Concentration | Proteins | Biophysics | Molecular biology | Binding sites | Drugs | Binding | Computation | Ionization | Binding energy | Protonation | Optimization
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13. Full Text Conformational changes in G‐protein‐coupled receptors—the quest for functionally selective conformations is open
by Hoffmann, C and Zürn, A and Bünemann, M and Lohse, M J
British Journal of Pharmacology, ISSN 0007-1188, 03/2008, Volume 153, Issue S1, pp. S358 - S366
The G‐protein‐coupled receptors (GPCRs) represent one the largest families of drug targets. Upon agonist binding a receptor undergoes conformational... 
G‐protein‐coupled receptors | conformational changes | FRET | 7‐TM | FlAsH‐EDT2 | functional selectivity | FlAsH-EDT | Conformational changes | 7-TM | Functional selectivity | G-protein-coupled receptors | BETA ADRENERGIC-RECEPTOR | TOGGLE SWITCH MODEL | RESONANCE ENERGY-TRANSFER | PARTIAL AGONISM | MUSCARINIC ACETYLCHOLINE-RECEPTOR | TRANSMEMBRANE DOMAINS III | GREEN FLUORESCENT PROTEIN | OPIOID RECEPTOR | PHARMACOLOGY & PHARMACY | FlAsH-EDT2 | DISULFIDE CROSS-LINKING | LIVING CELLS | Humans | Receptor, Muscarinic M3 - drug effects | Receptor, Muscarinic M3 - chemistry | Chelating Agents - pharmacology | Receptors, Adrenergic, beta-2 - drug effects | Receptors, Adrenergic, beta-2 - chemistry | Receptors, Drug - chemistry | Animals | Receptors, Drug - drug effects | Fluorescence Resonance Energy Transfer | Protein Conformation | Rhodopsin - drug effects | Receptors, G-Protein-Coupled - drug effects | Receptors, G-Protein-Coupled - chemistry | Rhodopsin - chemistry | Review
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