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  • 1
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    Molecular characterization of helix-loop-helix peptides (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-02-21
    Description: A class of regulators of eukaryotic gene expression contains a conserved amino acid sequence responsible for protein oligomerization and binding to DNA. This structure consists of an arginine- and lysine-rich basic region followed by a helix-loop-helix motif, which together mediate specific binding to DNA. Peptides were prepared that span this motif in the MyoD protein; in solution, they formed alpha-helical dimers and tetramers. They bound to DNA as dimers and their alpha-helical content increased on binding. Parallel and antiparallel four-helix models of the DNA-bound dimer were constructed. Peptides containing disulfide bonds were engineered to test the correctness of the two models. A disulfide that is compatible with the parallel model promotes specific interaction with DNA, whereas a disulfide compatible with the antiparallel model abolishes specific binding. Electron paramagnetic resonance (EPR) measurements of nitroxide-labeled peptides provided intersubunit distance measurements that also supported the parallel model.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Anthony-Cahill, S J -- Benfield, P A -- Fairman, R -- Wasserman, Z R -- Brenner, S L -- Stafford, W F 3rd -- Altenbach, C -- Hubbell, W L -- DeGrado, W F -- GM13731/GM/NIGMS NIH HHS/ -- GM14321/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1992 Feb 21;255(5047):979-83.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biotechnology Department, DuPont Merck Pharmaceutical Co., Wilmington, DE 19880-0328.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1312255" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Binding Sites ; Circular Dichroism ; DNA-Binding Proteins/*chemistry ; Disulfides ; Electron Spin Resonance Spectroscopy ; Enhancer Elements, Genetic ; Gene Expression Regulation ; Humans ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Regulatory Sequences, Nucleic Acid ; Sequence Alignment ; Transcription Factors/*chemistry
    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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  • 2
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    Protein design, a minimalist approach (1989)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1989-02-03
    Description: The question of how the amino acid sequence of a protein specifies its three-dimensional structure remains to be answered. Proteins are so large and complex that it is difficult to discern the features in their sequences that contribute to their structural stability and function. One approach to this problem is de novo design of model proteins, much simpler than their natural counterparts, yet containing sufficient information in their sequences to specify a given function (for example, folding in aqueous solution, folding in membranes, or formation of ion channels). Designed proteins provide simple model systems for understanding protein structure and function.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉DeGrado, W F -- Wasserman, Z R -- Lear, J D -- New York, N.Y. -- Science. 1989 Feb 3;243(4891):622-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉E. I. du Pont de Nemours & Company, Central Research and Development Department, Wilmington, DE 19898.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2464850" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Ion Channels ; Macromolecular Substances ; Models, Molecular ; Protein Conformation ; *Proteins ; Solubility ; Structure-Activity Relationship ; Tropomyosin ; Water
    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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    Synthetic amphiphilic peptide models for protein ion channels (1988)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1988-05-27
    Description: Ion channel proteins are important for the conduction of ions across biological membranes. Recent analyses of their sequences have suggested that they are composed of bundles of alpha-helices that associate to form ion-conducting channels. To gain insight into the mechanisms by which alpha-helices can aggregate and conduct ions, three model peptides containing only leucine and serine residues were synthesized and characterized. A 21-residue peptide, H2N-(Leu-Ser-Ser-Leu-Leu-Ser-Leu)3-CONH2, which was designed to be a membrane-spanning amphiphilic alpha-helix, formed well-defined ion channels with ion permeability and lifetime characteristics resembling the acetylcholine receptor. In contrast, a 14-residue version of this peptide, which was too short to span the phospolipid bilayer as an alpha-helix, failed to form discrete, stable channels. A third peptide, H2N-(Leu-Ser-Leu-Leu-Leu-Ser-Leu)3-CONH2, in which one serine per heptad repeat was replaced by leucine, produced proton-selective channels. Computer graphics and energy minimization were used to create molecular models that were consistent with the observed properties of the channels.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lear, J D -- Wasserman, Z R -- DeGrado, W F -- New York, N.Y. -- Science. 1988 May 27;240(4856):1177-81.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Central Research and Development Department, E. I. du Pont de Nemours and Company, Wilmington, DE 19898.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2453923" target="_blank"〉PubMed〈/a〉
    Keywords: Computer Graphics ; Electric Conductivity ; *Ion Channels ; Leucine ; *Membrane Proteins ; Models, Chemical ; Models, Molecular ; Peptides/chemical synthesis ; Protons ; Serine
    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
    Electronic Resource
    Electronic Resource
    Molecular orbital theory of the electronic structure of organic compounds. 28. Geometries and energies of singlet and triplet states of the C3H2 hydrocarbons (1976)
    s.l. : American Chemical Society
    Journal of the American Chemical Society 98 (1976), S. 4378-4383 
    Details
    ISSN: 1520-5126
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/ja00431a005
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  • 5
    Electronic Resource
    Electronic Resource
    Block Copolymer Theory. 4. Narrow Interphase Approximation (1976)
    s.l. : American Chemical Society
    Macromolecules 9 (1976), S. 879-888 
    Details
    ISSN: 1520-5835
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/ma60054a001
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  • 6
    Electronic Resource
    Electronic Resource
    Block Copolymer Theory. 5. Spherical Domains (1978)
    s.l. : American Chemical Society
    Macromolecules 11 (1978), S. 960-966 
    Details
    ISSN: 1520-5835
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/ma60065a023
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  • 7
    Electronic Resource
    Electronic Resource
    Block Copolymer Theory. 6. Cylindrical Domains (1980)
    s.l. : American Chemical Society
    Macromolecules 13 (1980), S. 994-998 
    Details
    ISSN: 1520-5835
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/ma60076a044
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  • 8
    Electronic Resource
    Electronic Resource
    Brownian Dynamics Study of Polymer Conformational Transitions± (1980)
    s.l. : American Chemical Society
    Macromolecules 13 (1980), S. 526-533 
    Details
    ISSN: 1520-5835
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/ma60075a011
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  • 9
    Electronic Resource
    Electronic Resource
    Computer simulation of biological interactions and reactivity (1988)
    Springer
    Journal of computer aided molecular design 1 (1988), S. 313-322 
    Details
    ISSN: 1573-4951
    Keywords: Electron transfer ; Ion channel ; Micelle ; Molecular dynamics ; Cytochrome c
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary Computer simulations of molecular motion provide a useful tool for analyzing dynamic aspects of macromolecular structure and function. In many cases, simulations can be compared to experimental results that provide an average estimate of molecular flexibility. For example, variations in computed molecular motions in different regions of a protein structure can be compared to refined B-values obtained from X-ray crystallographic refinement. Such comparisons both provide a detailed view of the motions responsible for crystalline disorder, and allow an evaluation of how crystal packing affects mobility of groups on the protein surface. In these applications, dynamics simulations provide a means of regenerating the temporal dimension of a structure whose average behavior is experimentally well defined in the crystal lattice. An additional benefit of the detailed and instantaneous view of molecular flexibility offered by simulation methods lies in its potential for exploring infrequent structural fluctuations or dynamic states of molecular association that cannot be examined in detail by X-ray methods, but are suggested on the basis of alternative structural information. For example, studies of the effects of surface chemical modifications on interacting proteins can produce information concerning the sites, if not the exact details, of the intermolecular interactions. The present work describes some applications of molecular dynamics methods to the study of large molecular aggregates whose dynamic properties thus far have precluded detailed structural descriptions. These include simulations of an electrostatically associated electron transfer complex between cytochromes c and b5, some model systems for trans-membrane ion channels, and a phospholipid micelle.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01677279
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  • 10
    Electronic Resource
    Electronic Resource
    A molecular dynamics investigation of the elastomeric restoring force in elastin (1990)
    New York : Wiley-Blackwell
    Biopolymers 29 (1990), S. 1613-1631 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A repetitive polypentapeptide organized as a connected chain of β-bends is believed to be an important structural element of elastin, the major elastomer in biological systems. Molecular dynamics simulations were carried out on hydrated polymers of (Val-Pro-Gly-Val-Gly)18 at various extensions. Analysis of the fluctuations of backbone angles in relaxed elastin showed that particularly large-amplitude torsional motions occur in φ and ψ angles of residues connecting sequentially adjacent hairpin bends. Many such motions reflect peptide plane librations that result from anticorrelated crankshaft rotations of ψi and φi+1. These effects were much reduced in stretched polymer models. The conformational entropy of relaxed and stretched elastin models was estimated using a treatment due to Meirovitch, and gave a calculated decrease in entropy of about 1 cal/mol deg when the polymer was stretched to 1.75 times its original length. There are large changes in solvent-accessible surface area during the intitial stages of elastin stretching. Collectively these results suggest that hydrophobic interactions make contributions to elastin entropy at low extensions, but that librational mechanisms make large contributions to the elastic restoring force at longer extensions.
    Additional Material: 10 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360291211
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