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1. Full Text Protein activity regulation by conformational entropy
by Tzeng, Shiou-Ru and Kalodimos, Charalampos G
Nature, ISSN 0028-0836, 08/2012, Volume 488, Issue 7410, pp. 236 - 240
How the interplay between protein structure and internal dynamics regulates protein function is poorly understood. Often, ligand binding, post-translational... 
LIGAND-BINDING | MOLECULAR RECOGNITION | DYNAMIC ACTIVATION | NMR-SPECTROSCOPY | MULTIDISCIPLINARY SCIENCES | ESCHERICHIA-COLI | ORDER PARAMETERS | CATABOLITE ACTIVATOR PROTEIN | RELAXATION | RECEPTOR PROTEIN | FREE-ENERGY | Protein Structure, Tertiary | Motion | Models, Molecular | Cyclic AMP Receptor Protein - genetics | Entropy | DNA - metabolism | Cyclic AMP Receptor Protein - metabolism | DNA - chemistry | Cyclic AMP Receptor Protein - chemistry | Time Factors | Nuclear Magnetic Resonance, Biomolecular | Protein Binding | Binding Sites | Proteins | Nuclear magnetic resonance spectroscopy | Usage | Research | Structure | Protein binding | Enzymes | Ligands | Experiments | Compensation
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2. Full Text Dynamic activation of an allosteric regulatory protein
by Tzeng, Shiou-Ru and Kalodimos, Charalampos G
Nature, ISSN 0028-0836, 11/2009, Volume 462, Issue 7271, pp. 368 - 372
Allosteric regulation is used as a very efficient mechanism to control protein activity in most biological processes, including signal transduction,... 
CONFORMATIONAL ENTROPY | ANGSTROM RESOLUTION | NMR-SPECTROSCOPY | MULTIDISCIPLINARY SCIENCES | ESCHERICHIA-COLI | ORDER PARAMETERS | CAMP RECEPTOR PROTEIN | CHEMICAL-EXCHANGE | BINDING PROTEIN | CAP-DNA COMPLEX | ROTATIONAL DIFFUSION | Protein Structure, Tertiary | Cyclic AMP - chemistry | Cyclic AMP Receptor Protein - chemistry | Energy Metabolism | Escherichia coli - metabolism | Models, Molecular | Protein Binding | Escherichia coli Proteins - metabolism | DNA - metabolism | Escherichia coli Proteins - chemistry | Cyclic AMP - metabolism | Cyclic AMP Receptor Protein - metabolism | Usage | Allosteric proteins | Physiological aspects | Nuclear magnetic resonance spectroscopy | Cellular signal transduction | Research | Structure | DNA-ligand interactions | Proteins | Changes | Biochemistry | Entropy | E coli
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3. Full Text Novel roles of camp receptor protein (CRP) in regulation of transport and metabolism of carbon sources
by Shimada, Tomohiro and Fujita, Nobuyuki and Yamamoto, Kaneyoshi and Ishihama, Akira
PLoS ONE, ISSN 1932-6203, 2011, Volume 6, Issue 6, p. e20081
CRP (cAMP receptor protein), the global regulator of genes for carbon source utilization in the absence of glucose, is the best-studied prokaryotic... 
POLYMERASE-ALPHA-SUBUNIT | MOLECULAR CHARACTERIZATION | SIGNAL-TRANSDUCTION | MULTIDISCIPLINARY SCIENCES | ESCHERICHIA-COLI K-12 | TRANSCRIPTION ACTIVATION | CATABOLITE ACTIVATOR PROTEIN | MAJOR FACILITATOR SUPERFAMILY | ABC TRANSPORTERS | PHOSPHOTRANSFERASE SYSTEM | RNA-POLYMERASE | Consensus Sequence | Carbon - metabolism | Oligonucleotide Array Sequence Analysis | Genomics | Escherichia coli Proteins - metabolism | Cyclic AMP Receptor Protein - metabolism | Biological Transport | Cyclic AMP Receptor Protein - chemistry | Escherichia coli - genetics | Base Sequence | Escherichia coli - metabolism | Transcription, Genetic | Escherichia coli Proteins - chemistry | Binding Sites | Cyclic AMP - metabolism | Glucose metabolism | Genes | Escherichia coli | Genetic aspects | Cyclic adenylic acid | Genetic transcription | Transportation policy | Tricarboxylic acid cycle | Regulations | Target recognition | Pyruvic acid | Genomes | Kinases | Phosphatase | Proteins | E coli | Carbon sources | Deoxyribonucleic acid--DNA | Gluconeogenesis | Enzymes | Sequences | Cloning | Cyclic AMP | Glycerol | Operons | RNA polymerase | Metabolism | Gene expression | Carbon | Promoters | Screening | Aerobic respiration | Plasmids | Glycolysis | Regulation | Mutation | Transport | Nanotechnology | Binding sites | Deoxyribonucleic acid | DNA
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4. Full Text Cyclic-AMP and bacterial cyclic-AMP receptor proteins revisited: adaptation for different ecological niches
by Green, Jeffrey and Stapleton, Melanie R and Smith, Laura J and Artymiuk, Peter J and Kahramanoglou, Christina and Hunt, Debbie M and Buxton, Roger S
Current Opinion in Microbiology, ISSN 1369-5274, 2014, Volume 18, Issue 1, pp. 1 - 7
Highlights • E. coli cyclic-AMP receptor protein (CRP) is a paradigm of gene regulation. • Comparison of CRPs reveals differences in their affinity of cAMP. •... 
Pathology | MYCOBACTERIUM-TUBERCULOSIS | DNA-BINDING | GENE | PSEUDOMONAS-PUTIDA | ESCHERICHIA-COLI | TRANSCRIPTION ACTIVATION | CATABOLITE ACTIVATOR PROTEIN | MICROBIOLOGY | CRP REGULATOR | ADENYLATE-CYCLASE | CAMP LEVELS | Pseudomonas putida - genetics | Stress, Physiological | Cyclic AMP Receptor Protein - metabolism | Pseudomonas putida - physiology | Pseudomonas putida - metabolism | Escherichia coli - genetics | Escherichia coli - metabolism | Mycobacterium tuberculosis - physiology | Gene Expression Regulation, Bacterial | Cyclic AMP - metabolism | Escherichia coli - physiology | Mycobacterium tuberculosis - metabolism | Mycobacterium tuberculosis - genetics | Niche (Ecology) | Analysis
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5. Full Text Structural Basis for cAMP-Mediated Allosteric Control of the Catabolite Activator Protein
by Nataliya Popovych and Shiou-Ru Tzeng and Marco Tonelli and Richard H. Ebright and Charalampos G. Kalodimos and Peter H. von Hippel
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 4/2009, Volume 106, Issue 17, pp. 6927 - 6932
The cAMP-mediated allosteric transition in the catabolite activator protein (CAP; also known as the cAMP receptor protein, CRP) is a textbook example of... 
Proteins | Chemical equilibrium | Salts | Hydrogen bonds | Allosteric regulation | DNA | Biochemistry | Dimers | Cyclic AMP receptor protein | Crystal structure | NMR structure | cAMP binding | Gene regulation | Protein NMR | protein NMR | CRYSTAL-STRUCTURE | MULTIDISCIPLINARY SCIENCES | ESCHERICHIA-COLI | CONFORMATIONAL CHANGE | allosteric regulation | CAP-DNA COMPLEX | GLOBAL FOLD | TRANSCRIPTIONAL REGULATOR | ANGSTROM RESOLUTION | NMR | CYCLIC-NUCLEOTIDE BINDING | gene regulation | AMP RECEPTOR PROTEIN | Apoproteins - chemistry | Protein Structure, Tertiary | Protein Structure, Secondary | Allosteric Regulation | Models, Molecular | Cyclic AMP Receptor Protein - genetics | DNA - metabolism | Cyclic AMP Receptor Protein - metabolism | DNA - chemistry | Phenotype | Cyclic AMP - chemistry | Cyclic AMP Receptor Protein - chemistry | Cyclic GMP - metabolism | Cyclic GMP - chemistry | Protein Structure, Quaternary | Apoproteins - genetics | Nuclear Magnetic Resonance, Biomolecular | Protein Binding | Cyclic AMP - metabolism | Apoproteins - metabolism | Cyclic adenylic acid | Research | Properties | Structure | Protein binding | Biological Sciences
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6. Full Text Dynamically driven protein allostery
by Popovych, Nataliya and Sun, Shangjin and Ebright, Richard H and Kalodimos, Charalampos G
Nature Structural and Molecular Biology, ISSN 1545-9993, 09/2006, Volume 13, Issue 9, pp. 831 - 838
Allosteric interactions are typically considered to proceed through a series of discrete changes in bonding interactions that alter the protein conformation.... 
CONFORMATIONAL ENTROPY | DOMAIN | LIGAND-BINDING | NMR-SPECTROSCOPY | BIOCHEMISTRY & MOLECULAR BIOLOGY | RELAXATION | CELL BIOLOGY | NEGATIVE COOPERATIVITY | BIOPHYSICS | DNA | AMP RECEPTOR PROTEIN | SITES | COMMUNICATION | Cyclic AMP Receptor Protein - chemistry | Protein Structure, Secondary | Models, Biological | Allosteric Regulation | Escherichia coli - metabolism | Nuclear Magnetic Resonance, Biomolecular | Protein Binding | Entropy | Protein Subunits - chemistry | Cyclic AMP - metabolism | Cyclic AMP Receptor Protein - metabolism | Proteins | Physiological aspects | Research | Structure | Methods | Proteomics | Molecular biology | Binding sites
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7. Full Text Origins of specificity in protein-DNA recognition
by Rohs, Remo and Jin, Xiangshu and West, Sean M and Joshi, Rohit and Honig, Barry and Mann, Richard S
Annual Review of Biochemistry, ISSN 0066-4154, 07/2010, Volume 79, Issue 1, pp. 233 - 269
Specific interactions between proteins and DNA are fundamental to many biological processes. In this review, we provide a revised view of protein-DNA... 
indirect readout | protein-DNA binding | direct readout | narrow minor groove | DNA shape recognition | DNA base recognition | REPRESSOR-OPERATOR COMPLEX | MOLECULAR-STRUCTURE | BIOCHEMISTRY & MOLECULAR BIOLOGY | STRUCTURAL BASIS | FINGER-DNA | INTEGRATION HOST FACTOR | ENDONUCLEASE I-TEVI | B-DNA | CO-CRYSTAL STRUCTURE | MINOR-GROOVE-BINDING | TRANSCRIPTION FACTOR | Repressor Proteins - chemistry | Crystallography, X-Ray | DNA - metabolism | DNA-Binding Proteins - chemistry | Cyclic AMP Receptor Protein - metabolism | Viral Regulatory and Accessory Proteins - metabolism | DNA-Binding Proteins - metabolism | DNA - chemistry | Cyclic AMP Receptor Protein - chemistry | Base Sequence | Nucleic Acid Conformation | Repressor Proteins - metabolism | Viral Regulatory and Accessory Proteins - chemistry | Proteins | DNA testing | Structure | DNA-ligand interactions | Analysis | Methods | Direct readout | DNA kinks | A-DNA | Protein-DNA binding | Narrow minor groove | Indirect readout | Z-DNA | DNA bending
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8. Full Text C‐terminal dimerization of apo‐cyclic AMP receptor protein validated in solution
by Sim, Dae‐Won and Choi, Jae Wan and Kim, Ji‐Hun and Ryu, Kyoung‐Seok and Kim, Myeongkyu and Yu, Hee‐Wan and Jo, Ku‐Sung and Kim, Eun‐Hee and Seo, Min‐Duk and Jeon, Young Ho and Lee, Bong‐Jin and Kim, Young Pil and Won, Hyung‐Sik
FEBS Letters, ISSN 0014-5793, 04/2017, Volume 591, Issue 7, pp. 1064 - 1070
Although cyclic AMP receptor protein (CRP) has long served as a typical example of effector‐mediated protein allostery, mechanistic details into its regulation... 
NMR spectroscopy | protein allostery | cyclic AMP receptor protein | CRP | DNA-BINDING | CRYSTAL-STRUCTURE | BIOCHEMISTRY & MOLECULAR BIOLOGY | ESCHERICHIA-COLI | RESOLUTION | ACTIVATOR PROTEIN | IDENTIFICATION | ALLOSTERIC TRANSITION | CELL BIOLOGY | CAP | BIOPHYSICS | CAMP | Apoproteins - chemistry | Recombinant Proteins - metabolism | Amino Acid Sequence | Magnetic Resonance Spectroscopy | Protein Structure, Secondary | Protein Multimerization | Models, Molecular | Recombinant Proteins - chemistry | Escherichia coli Proteins - metabolism | Cyclic AMP Receptor Protein - genetics | Cyclic AMP Receptor Protein - metabolism | Solutions - chemistry | Cyclic AMP - chemistry | Cyclic AMP Receptor Protein - chemistry | Apoproteins - genetics | Escherichia coli Proteins - genetics | Protein Binding | Protein Domains | Escherichia coli Proteins - chemistry | Circular Dichroism | Cyclic AMP - metabolism | Apoproteins - metabolism
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9. Full Text Crosstalk of Escherichia coli FadR with Global Regulators in Expression of Fatty Acid Transport Genes
by Feng, Youjun and Cronan, John E
PLoS ONE, ISSN 1932-6203, 09/2012, Volume 7, Issue 9, p. e46275
Escherichia coli FadR plays two regulatory roles in fatty acid metabolism. FadR represses the fatty acid degradation (fad) system and activates the unsaturated... 
DNA-BINDING | BIOSYNTHESIS | MULTIDISCIPLINARY SCIENCES | GROWTH | DEGRADATION | SYNTHETASE | EXCISION | RECEPTOR PROTEIN | REPRESSOR | TRANSCRIPTION FACTOR | ACYL-COENZYME | Protein Kinases - metabolism | Protein Kinases - genetics | Coenzyme A Ligases - genetics | Cyclic AMP Receptor Protein - genetics | Cyclic AMP Receptor Protein - metabolism | Oxygen - metabolism | Coenzyme A Ligases - metabolism | Regulon | Fatty Acid Transport Proteins - metabolism | Biological Transport | Escherichia coli - metabolism | Transcription, Genetic | Membrane Proteins - metabolism | Binding Sites | Cyclic AMP - metabolism | Fatty Acids - metabolism | Bacterial Outer Membrane Proteins - genetics | Repressor Proteins - metabolism | Promoter Regions, Genetic | Oxidation-Reduction | Signal Transduction | Membrane Proteins - genetics | Bacterial Proteins - genetics | Repressor Proteins - genetics | Escherichia coli Proteins - metabolism | Bacterial Outer Membrane Proteins - metabolism | Escherichia coli - genetics | Escherichia coli Proteins - genetics | Protein Binding | Bacterial Proteins - metabolism | Gene Expression Regulation, Bacterial | Fatty Acid Transport Proteins - genetics | Fatty acid metabolism | Crosstalk | Analysis | Escherichia coli | Physiological aspects | Cyclic adenylic acid | Research | Genetic transcription | Enzymes | Regulators | Transcription | Genes | Cyclic AMP | Chains | Biosynthesis | Glucose | Metabolism | Gene expression | Fatty acids | Flavin-adenine dinucleotide | Proteins | FADD protein | E coli | Plasmids | Oxidation | In vivo methods and tests | Transport | Binding sites
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10. Electrophoretic mobility shift assay (EMSA) for detecting protein-nucleic acid interactions
by Hellman, Lance M and Fried, Michael G
Nature Protocols, ISSN 1754-2189, 08/2007, Volume 2, Issue 8, pp. 1849 - 1861
The gel electrophoresis mobility shift assay (EMSA) is used to detect protein complexes with nucleic acids. It is the core technology underlying a wide range... 
DNA-BINDING | POLYACRYLAMIDE-GEL ELECTROPHORESIS | REPRESSOR-OPERATOR INTERACTION | ANALYTICAL ULTRACENTRIFUGATION | NITROCELLULOSE FILTER-BINDING | BIOCHEMICAL RESEARCH METHODS | LAC REPRESSOR | O-6-ALKYLGUANINE-DNA ALKYLTRANSFERASE | LACTOSE PROMOTER | CYCLIC-AMP RECEPTOR | RNA-POLYMERASE | Promoter Regions, Genetic | Humans | O-Methylguanine-DNA Methyltransferase - metabolism | Lac Repressors | DNA-Binding Proteins - analysis | Escherichia coli Proteins - metabolism | Lac Operon - genetics | Cyclic AMP Receptor Protein - metabolism | DNA-Binding Proteins - metabolism | Transcription Factors - metabolism | Electrophoretic Mobility Shift Assay - methods | Escherichia coli - genetics | Escherichia coli - metabolism | Bacterial Proteins - metabolism | RNA-Binding Proteins - analysis | Repressor Proteins - metabolism
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11. Full Text Theoretical analysis of inducer and operator binding for cyclic-AMP receptor protein mutants
by Einav, Tal and Duque, Julia and Phillips, Rob
PLoS ONE, ISSN 1932-6203, 09/2018, Volume 13, Issue 9, p. e0204275
Allosteric transcription factors undergo binding events at inducer binding sites as well as at distinct DNA binding domains, and it is difficult to disentangle... 
ALLOSTERIC REGULATION | CONFORMATIONAL-CHANGES | MODELS | GENE | DNA | MULTIDISCIPLINARY SCIENCES | SINGLE-SITE MUTATIONS | ESCHERICHIA-COLI | REGULATORY PROTEIN | ACTIVATOR PROTEIN | PROMOTER | Allosteric Regulation | Escherichia coli Proteins - metabolism | Cyclic AMP Receptor Protein - genetics | Models, Statistical | Cyclic AMP Receptor Protein - metabolism | Algorithms | Cyclic AMP Receptor Protein - chemistry | Escherichia coli - genetics | Escherichia coli - metabolism | Escherichia coli Proteins - genetics | Protein Domains | Protein Conformation | Mutation | Escherichia coli Proteins - chemistry | Gene Expression Regulation, Bacterial | Binding Sites | Usage | Allosteric proteins | Analysis | DNA binding proteins | Genetic transcription | Gene expression | Protein binding | Transcription factors | Nuclear magnetic resonance--NMR | Statistical analysis | Parameters | AMP | Data processing | Theoretical analysis | Biochemistry | Physics | Bacteriology | Mutants | Domains | Proteins | Allosteric properties | E coli | Ligands | Mathematical models | Molecular biology | Binding sites | Deoxyribonucleic acid--DNA | Structure-function relationships | Deoxyribonucleic acid | Nuclear magnetic resonance | NMR
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