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  • 1
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    Quantifying sources and sinks of reactive gases in the lower atmosphere using airborne flux observations (2015)
    Wiley
    Details
    Publication Date: 2015-09-30
    Description: Atmospheric composition is governed by the interplay of emissions, chemistry, deposition and transport. Substantial questions surround each of these processes, especially in forested environments with strong biogenic emissions. Utilizing aircraft observations acquired over a forest in the southeast U.S., we calculate eddy covariance fluxes for a suite of reactive gases and apply the synergistic information derived from this analysis to quantify emission and deposition fluxes, oxidant concentrations, aerosol uptake coefficients and other key parameters. Evaluation of results against state-of-the-science models and parameterizations provides insight into our current understanding of this system and frames future observational priorities. As a near-direct measurement of fundamental process rates, airborne fluxes offer a new tool to improve biogenic and anthropogenic emissions inventories, photochemical mechanisms and deposition parameterizations.
    Print ISSN: 0094-8276
    Electronic ISSN: 1944-8007
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 2
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    Protein design of an HIV-1 entry inhibitor (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-03-07
    Description: Human immunodeficiency virus type-1 (HIV-1) membrane fusion is promoted by the formation of a trimer-of-hairpins structure that brings the amino- and carboxyl-terminal regions of the gp41 envelope glycoprotein ectodomain into close proximity. Peptides derived from the carboxyl-terminal region (called C-peptides) potently inhibit HIV-1 entry by binding to the gp41 amino-terminal region. To test the converse of this inhibitory strategy, we designed a small protein, denoted 5-Helix, that binds the C-peptide region of gp41. The 5-Helix protein displays potent (nanomolar) inhibitory activity against diverse HIV-1 variants and may serve as the basis for a new class of antiviral agents. The inhibitory activity of 5-Helix also suggests a strategy for generating an HIV-1 neutralizing antibody response that targets the carboxyl-terminal region of the gp41 ectodomain.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Root, M J -- Kay, M S -- Kim, P S -- P01 GM56552/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2001 Feb 2;291(5505):884-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Whitehead Institute for Biomedical Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA. kimadmin@wi.mit.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11229405" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; *Anti-HIV Agents/chemistry/immunology/metabolism/pharmacology ; Carrier Proteins/*chemistry/metabolism/*pharmacology ; Cell Line ; *Drug Design ; Giant Cells/drug effects ; HIV Antibodies/immunology ; HIV Envelope Protein gp41/chemistry/*metabolism ; HIV-1/*drug effects/physiology ; Humans ; Membrane Fusion/*drug effects ; Molecular Sequence Data ; Neutralization Tests ; Peptide Fragments/chemistry/immunology/metabolism ; *Peptides ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Tumor Cells, Cultured
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 3
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    High-resolution protein design with backbone freedom (1998)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1998-11-20
    Description: Recent advances in computational techniques have allowed the design of precise side-chain packing in proteins with predetermined, naturally occurring backbone structures. Because these methods do not model protein main-chain flexibility, they lack the breadth to explore novel backbone conformations. Here the de novo design of a family of alpha-helical bundle proteins with a right-handed superhelical twist is described. In the design, the overall protein fold was specified by hydrophobic-polar residue patterning, whereas the bundle oligomerization state, detailed main-chain conformation, and interior side-chain rotamers were engineered by computational enumerations of packing in alternate backbone structures. Main-chain flexibility was incorporated through an algebraic parameterization of the backbone. The designed peptides form alpha-helical dimers, trimers, and tetramers in accord with the design goals. The crystal structure of the tetramer matches the designed structure in atomic detail.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Harbury, P B -- Plecs, J J -- Tidor, B -- Alber, T -- Kim, P S -- GM44162/GM/NIGMS NIH HHS/ -- GM48598/GM/NIGMS NIH HHS/ -- GM55758/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1998 Nov 20;282(5393):1462-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Whitehead Institute for Biomedical Research, Howard Hughes Medical Institute and Department of Biology, Massachusetts Institute of Technology, Nine Cambridge Center, Cambridge, MA 02142, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9822371" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Circular Dichroism ; Computer Simulation ; Crystallography, X-Ray ; Dimerization ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; Molecular Weight ; Mutation ; Peptides/chemical synthesis/*chemistry ; *Protein Conformation ; Protein Denaturation ; *Protein Engineering ; *Protein Folding ; Protein Structure, Secondary ; Proteins/chemical synthesis/*chemistry ; Thermodynamics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 4
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    Preferential heterodimer formation by isolated leucine zippers from fos and jun (1989)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1989-08-11
    Description: The products of the nuclear oncogenes fos and jun are known to form heterodimers that bind to DNA and modulate transcription. Both proteins contain a leucine zipper that is important for heterodimer formation. Peptides corresponding to these leucine zippers were synthesized. When mixed, these peptides preferentially form heterodimers over homodimers by at least 1000-fold. Both homodimers and the heterodimer are parallel alpha helices. The leucine zipper regions from Fos and Jun therefore correspond to autonomous helical dimerization sites that are likely to be short coiled coils, and these regions are sufficient to determine the specificity of interaction between Fos and Jun. The Fos leucine zipper forms a relatively unstable homodimer. Instability of homodimers provides a thermodynamic driving force for preferential heterodimer formation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉O'Shea, E K -- Rutkowski, R -- Stafford, W F 3rd -- Kim, P S -- RR05711/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 1989 Aug 11;245(4918):646-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Whitehead Institute for Biomedical Research, Cambridge, MA 02142.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2503872" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Circular Dichroism ; *DNA-Binding Proteins ; Disulfides ; *Leucine ; Macromolecular Substances ; Molecular Sequence Data ; Peptide Fragments/chemical synthesis ; Protein Conformation ; *Proto-Oncogene Proteins ; Proto-Oncogene Proteins c-fos ; Proto-Oncogene Proteins c-jun ; *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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  • 5
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    Sequence requirements for coiled-coils: analysis with lambda repressor-GCN4 leucine zipper fusions (1990)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1990-12-07
    Description: A genetic system was developed in Escherichia coli to study leucine zippers with the amino-terminal domain of bacteriophage lambda repressor as a reporter for dimerization. This system was used to analyze the importance of the amino acid side chains at eight positions that form the hydrophobic interface of the leucine zipper dimer from the yeast transcriptional activator, GCN4. When single amino acid substitutions were analyzed, most functional variants contained hydrophobic residues at the dimer interface, while most nonfunctional sequence variants contained strongly polar or helix-breaking residues. In multiple randomization experiments, however, many combinations of hydrophobic residues were found to be nonfunctional, and leucines in the heptad repeat were shown to have a special function in leucine zipper dimerization.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hu, J C -- O'Shea, E K -- Kim, P S -- Sauer, R T -- AI15706/AI/NIAID NIH HHS/ -- GM11117/GM/NIGMS NIH HHS/ -- GM44162/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1990 Dec 7;250(4986):1400-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Massachusetts Institute of Technology, Cambridge 02139.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2147779" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacteriophage lambda/*genetics ; DNA-Binding Proteins/*genetics ; Escherichia coli/*genetics ; Fungal Proteins/*genetics ; Genetic Variation ; Leucine Zippers/*genetics ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Phenotype ; Protein Conformation ; *Protein Kinases ; Random Allocation ; Recombinant Fusion Proteins/metabolism ; *Saccharomyces cerevisiae Proteins ; Transcription Factors/*genetics
    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
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    Evidence that the leucine zipper is a coiled coil (1989)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1989-01-27
    Description: Recently, a hypothetical structure called a leucine zipper was proposed that defines a new class of DNA binding proteins. The common feature of these proteins is a region spanning approximately 30 amino acids that contains a periodic repeat of leucines every seven residues. A peptide corresponding to the leucine zipper region of the yeast transcriptional activator GCN4 was synthesized and characterized. This peptide associates in the micromolar concentration range to form a very stable dimer of alpha helices with a parallel orientation. Although some features of the leucine zipper model are supported by our experimental data, the peptide has the characteristics of a coiled coil.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉O'Shea, E K -- Rutkowski, R -- Kim, P S -- New York, N.Y. -- Science. 1989 Jan 27;243(4890):538-42.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Whitehead Institute for Biomedical Research, Cambridge, MA 02142.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2911757" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Chromatography, High Pressure Liquid ; Circular Dichroism ; DNA/metabolism ; *DNA-Binding Proteins ; Disulfides ; *Fungal Proteins ; *Leucine ; Macromolecular Substances ; Molecular Sequence Data ; Peptide Fragments ; Protein Conformation ; *Protein Kinases ; Repetitive Sequences, Nucleic Acid ; *Saccharomyces cerevisiae Proteins ; *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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  • 7
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    Sequence-specific DNA binding by a short peptide dimer (1990)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1990-08-17
    Description: A recently described class of DNA binding proteins is characterized by the "bZIP" motif, which consists of a basic region that contacts DNA and an adjacent "leucine zipper" that mediates protein dimerization. A peptide model for the basic region of the yeast transcriptional activator GCN4 has been developed in which the leucine zipper has been replaced by a disulfide bond. The 34-residue peptide dimer, but not the reduced monomer, binds DNA with nanomolar affinity at 4 degrees C. DNA binding is sequence-specific as judged by deoxyribonuclease I footprinting. Circular dichroism spectroscopy suggests that the peptide adopts a helical structure when bound to DNA. These results demonstrate directly that the GCN4 basic region is sufficient for sequence-specific DNA binding and suggest that a major function of the GCN4 leucine zipper is simply to mediate protein dimerization. Our approach provides a strategy for the design of short sequence-specific DNA binding peptides.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Talanian, R V -- McKnight, C J -- Kim, P S -- GM13665/GM/NIGMS NIH HHS/ -- GM44162/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1990 Aug 17;249(4970):769-71.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Whitehead Institute for Biomedical Research, Nine Cambridge Center, MA 02142.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2389142" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Base Sequence ; Binding Sites ; Circular Dichroism ; DNA/*metabolism ; DNA-Binding Proteins/*metabolism ; Deoxyribonuclease I ; Disulfides ; Fungal Proteins/*metabolism ; Leucine ; Macromolecular Substances ; Molecular Sequence Data ; Peptides/*metabolism ; Protein Conformation ; *Protein Kinases ; *Saccharomyces cerevisiae Proteins ; Transcription Factors/*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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  • 8
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    X-ray structure of the GCN4 leucine zipper, a two-stranded, parallel coiled coil (1991)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1991-10-25
    Description: The x-ray crystal structure of a peptide corresponding to the leucine zipper of the yeast transcriptional activator GCN4 has been determined at 1.8 angstrom resolution. The peptide forms a parallel, two-stranded coiled coil of alpha helices packed as in the "knobs-into-holes" model proposed by Crick in 1953. Contacts between the helices include ion pairs and an extensive hydrophobic interface that contains a distinctive hydrogen bond. The conserved leucines, like the residues in the alternate hydrophobic repeat, make side-to-side interactions (as in a handshake) in every other layer of the dimer interface. The crystal structure of the GCN4 leucine zipper suggests a key role for the leucine repeat, but also shows how other features of the coiled coil contribute to dimer formation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉O'Shea, E K -- Klemm, J D -- Kim, P S -- Alber, T -- GM 44162/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1991 Oct 25;254(5031):539-44.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Cambridge, MA 02142.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1948029" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Computer Simulation ; DNA-Binding Proteins/*chemistry ; Fungal Proteins/*chemistry ; Hydrogen Bonding ; *Leucine Zippers ; Macromolecular Substances ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; *Protein Kinases ; *Saccharomyces cerevisiae Proteins ; Transcription Factors/*chemistry ; X-Ray Diffraction
    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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  • 9
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    Internal stark effect measurement of the electric field at the amino terminus of an alpha helix (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-08-14
    Description: The strengths of electrostatic interactions in biological molecules are difficult to calculate or predict because they occur in complicated, inhomogeneous environments. The electric field at the amino terminus of an alpha helix in water has been determined by measuring the shift in the absorption band for a covalently attached, neutral probe molecule with an electric dipole moment difference between the ground and excited electronic states (an internal Stark effect). The field at the interface between the helix and the solvent is found to be an order of magnitude stronger than expected from the dielectric properties of bulk water. Furthermore, although the total electric dipole moment of the helix increases with length, the electric field at the amino terminus does not.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lockhart, D J -- Kim, P S -- New York, N.Y. -- Science. 1992 Aug 14;257(5072):947-51.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Massachusetts Institute of Technology, Nine Cambridge Center 02142.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1502559" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Amino Acids/*chemistry ; Electrochemistry ; Models, Molecular ; Molecular Sequence Data ; Peptides/*chemistry ; *Protein Conformation ; Proteins/*chemistry ; Spectrophotometry, Ultraviolet ; Water
    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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  • 10
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    Reexamination of the folding of BPTI: predominance of native intermediates (1991)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1991-09-20
    Description: Bovine pancreatic trypsin inhibitor (BPTI) continues to be the only protein for which a detailed pathway of folding has been described. Previous studies led to the conclusion that nonnative states are well populated in the oxidative folding of BPTI. This conclusion has broadly influenced efforts to understand protein folding. The population of intermediates present during the folding of BPTI has been reexamined by modern separation techniques. It was found that all well-populated folding intermediates contain only native disulfide bonds. These data emphasize the importance of native protein structure for understanding protein folding.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Weissman, J S -- Kim, P S -- GM 41307/GM/NIGMS NIH HHS/ -- RR 05927/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 1991 Sep 20;253(5026):1386-93.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Whitehead Institute for Biomedical Research, Cambridge, MA 02142.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1716783" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Aprotinin/*chemistry ; Chromatography, High Pressure Liquid ; Disulfides/analysis ; Indicators and Reagents ; Models, Structural ; Molecular Sequence Data ; Peptide Fragments/isolation & purification ; Protein Conformation
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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