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  • 1
    Publication Date: 2001-03-27
    Description: Protein actions are usually discussed in terms of static structures, but function requires motion. We find a strong correlation between phosphorylation-driven activation of the signaling protein NtrC and microsecond time-scale backbone dynamics. Using nuclear magnetic resonance relaxation, we characterized the motions of NtrC in three functional states: unphosphorylated (inactive), phosphorylated (active), and a partially active mutant. These dynamics are indicative of exchange between inactive and active conformations. Both states are populated in unphosphorylated NtrC, and phosphorylation shifts the equilibrium toward the active species. These results support a dynamic population shift between two preexisting conformations as the underlying mechanism of activation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Volkman, B F -- Lipson, D -- Wemmer, D E -- Kern, D -- GM62117/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2001 Mar 23;291(5512):2429-33.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉National Magnetic Resonance Facility at Madison (NMRFAM), Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11264542" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Regulation ; *Bacterial Proteins ; Binding Sites ; DNA-Binding Proteins/*chemistry/genetics/*metabolism ; Models, Molecular ; Motion ; Mutation ; Nuclear Magnetic Resonance, Biomolecular ; PII Nitrogen Regulatory Proteins ; Phosphorylation ; *Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Signal Transduction ; Time ; *Trans-Activators ; *Transcription Factors
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 2
    Publication Date: 1991-05-10
    Description: Methylamine dehydrogenase (MADH), an alpha 2 beta 2 enzyme from numerous methylotrophic soil bacteria, contains a novel quinonoid redox prosthetic group that is covalently bound to its small beta subunit through two amino acyl residues. A comparison of the amino acid sequence deduced from the gene sequence of the small subunit for the enzyme from Methylobacterium extorquens AM1 with the published amino acid sequence obtained by the Edman degradation method, allowed the identification of the amino acyl constituents of the cofactor as two tryptophyl residues. This information was crucial for interpreting 1H and 13C nuclear magnetic resonance, and mass spectral data collected for the semicarbazide- and carboxymethyl-derivatized bis(tripeptidyl)-cofactor of MADH from bacterium W3A1. The cofactor is composed of two cross-linked tryptophyl residues. Although there are many possible isomers, only one is consistent with all the data: The first tryptophyl residue in the peptide sequence exists as an indole-6,7-dione, and is attached at its 4 position to the 2 position of the second, otherwise unmodified, indole side group. Contrary to earlier reports, the cofactor of MADH is not 2,7,9-tricarboxypyrroloquinoline quinone (PQQ), a derivative thereof, or pro-PQQ. This appears to be the only example of two cross-linked, modified amino acyl residues having a functional role in the active site of an enzyme, in the absence of other cofactors or metal ions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉McIntire, W S -- Wemmer, D E -- Chistoserdov, A -- Lidstrom, M E -- GM 36296/GM/NIGMS NIH HHS/ -- HL 16251/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 1991 May 10;252(5007):817-24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Veterans Affairs Medical Center, San Francisco, CA 94121.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2028257" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Dipeptides/*chemistry ; Gram-Negative Aerobic Bacteria/enzymology ; Magnetic Resonance Spectroscopy ; Mass Spectrometry ; Molecular Sequence Data ; Oxidation-Reduction ; Oxidoreductases Acting on CH-NH Group Donors/*chemistry ; Quinones/*chemistry ; Tryptophan/chemistry
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 3
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1994-10-28
    Description: A four-ring tripeptide containing alternating imidazole and pyrrole carboxamides specifically binds six-base pair 5'-(A,T)GCGC(A,T)-3' sites in the minor groove of DNA. The designed peptide has a specificity completely reversed from that of the tripyrrole distamycin, which binds A,T sequences. Structural studies with nuclear magnetic resonance revealed that two peptides bound side-by-side and in an antiparallel orientation in the minor groove. Each of the four imidazoles in the 2:1 ligand-DNA complex recognized a specific guanine amino group in the GCGC core through a hydrogen bond. Targeting a designated four-base pair G.C tract by this synthetic ligand supports the generality of the 2:1 peptide-DNA motif for sequence-specific minor groove recognition of DNA.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Geierstanger, B H -- Mrksich, M -- Dervan, P B -- Wemmer, D E -- GM-27681/GM/NIGMS NIH HHS/ -- GM-43129/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1994 Oct 28;266(5185):646-50.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Graduate Group in Biophysics, University of California, Berkeley 94720.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7939719" target="_blank"〉PubMed〈/a〉
    Keywords: Base Composition ; Base Sequence ; Computer Graphics ; DNA/chemistry/*metabolism ; Drug Design ; Hydrogen Bonding ; Imidazoles/chemical synthesis/*chemistry/metabolism ; Ligands ; Magnetic Resonance Spectroscopy ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Oligodeoxyribonucleotides/chemistry/metabolism ; Oligopeptides/chemical synthesis/*chemistry/metabolism ; Protein Conformation ; Pyrroles/chemical synthesis/*chemistry/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 4
    Publication Date: 2006-10-21
    Description: A magnetic resonance approach is presented that enables high-sensitivity, high-contrast molecular imaging by exploiting xenon biosensors. These sensors link xenon atoms to specific biomolecular targets, coupling the high sensitivity of hyperpolarized nuclei with the specificity of biochemical interactions. We demonstrated spatial resolution of a specific target protein in vitro at micromolar concentration, with a readout scheme that reduces the required acquisition time by 〉3300-fold relative to direct detection. This technique uses the signal of free hyperpolarized xenon to dramatically amplify the sensor signal via chemical exchange saturation transfer (CEST). Because it is approximately 10,000 times more sensitive than previous CEST methods and other molecular magnetic resonance imaging techniques, it marks a critical step toward the application of xenon biosensors as selective contrast agents in biomedical applications.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schroder, Leif -- Lowery, Thomas J -- Hilty, Christian -- Wemmer, David E -- Pines, Alexander -- New York, N.Y. -- Science. 2006 Oct 20;314(5798):446-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of California, Berkeley, CA 94720, USA. dewemmer@lbl.gov〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17053143" target="_blank"〉PubMed〈/a〉
    Keywords: Avidin ; *Biosensing Techniques ; Biotin ; Contrast Media ; Magnetic Resonance Imaging/*methods ; Magnetic Resonance Spectroscopy/*methods ; Microspheres ; Sensitivity and Specificity ; Sepharose ; Time Factors ; *Xenon Isotopes
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 5
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1987-12-18
    Description: One- and two-dimensional nuclear magnetic resonance (NMR) methods were used to determine a three-dimensional model of an eight-base-pair DNA fragment (d-GGGTACCC) cross-linked with psoralen in solution. Two-dimensional nuclear Overhauser effect experiments were used to assign the spectrum and estimate distances for 171 proton pairs in the cross-linked DNA. The NMR-derived model shows a 53 degree bend into the major groove that occurs primarily at the site of drug addition and a 56 degree unwinding that spans the eight-base-pair duplex.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tomic, M T -- Wemmer, D E -- Kim, S H -- GM 31616/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1987 Dec 18;238(4834):1722-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of California, Berkeley 94720.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3686011" target="_blank"〉PubMed〈/a〉
    Keywords: Base Composition ; *Cross-Linking Reagents ; *Dna ; Magnetic Resonance Spectroscopy/methods ; *Methoxsalen ; Models, Molecular ; Nucleic Acid Conformation ; *Oligodeoxyribonucleotides ; *Thymine
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 6
    Electronic Resource
    Electronic Resource
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 24 (1995), S. 463-493 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Type of Medium: Electronic Resource
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  • 7
    Electronic Resource
    Electronic Resource
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Physical Chemistry 46 (1995), S. 139-168 
    ISSN: 0066-426X
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
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  • 8
    Electronic Resource
    Electronic Resource
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Physical Chemistry 36 (1985), S. 105-137 
    ISSN: 0066-426X
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
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  • 9
    Electronic Resource
    Electronic Resource
    s.l. : American Chemical Society
    Journal of the American Chemical Society 110 (1988), S. 5668-5671 
    ISSN: 1520-5126
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 10
    Electronic Resource
    Electronic Resource
    s.l. : American Chemical Society
    Journal of the American Chemical Society 103 (1981), S. 28-33 
    ISSN: 1520-5126
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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