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  • 1
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    Statistical thermodynamics. Taking a walk on a landscape (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-07-28
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Brooks, C L 3rd -- Onuchic, J N -- Wales, D J -- New York, N.Y. -- Science. 2001 Jul 27;293(5530):612-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. brooks@scripps.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11474087" target="_blank"〉PubMed〈/a〉
    Keywords: Chemistry, Physical ; Computer Simulation ; Entropy ; Glass/*chemistry ; Physicochemical Phenomena ; *Protein Folding ; Proteins/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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  • 2
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    First-principles calculation of the folding free energy of a three-helix bundle protein (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-07-21
    Description: The folding and unfolding of a three-helix bundle protein were explored with molecular-dynamics simulations, cluster analysis, and weighted-histogram techniques. The folding-unfolding process occurs by means of a "folding funnel," in which a uniform and broad distribution of conformational states is accessible outside of the native manifold. This distribution narrows near a transition region and becomes compact within the native manifold. Key thermodynamic steps in folding include initial interactions around the amino-terminal helix-turn-helix motif, interactions between helices I and II, and, finally, the docking of helix III onto the helix I-II subdomain. A metastable minimum in the calculated free-energy surface is observed at approximately 1.5 times the native volume. Folding-unfolding thermodynamics are dominated by the opposing influences of protein-solvent energy, which favors unfolding, and the overall entropy, which favors folding by means of the hydrophobic effect.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Boczko, E M -- Brooks, C L 3rd -- GM48807/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1995 Jul 21;269(5222):393-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7618103" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Computer Graphics ; Helix-Loop-Helix Motifs ; Models, Molecular ; Molecular Sequence Data ; Peptide Fragments/*chemistry ; *Protein Folding ; *Protein Structure, Secondary ; Staphylococcal Protein A/*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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  • 3
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    Ribosome assembly factors prevent premature translation initiation by 40S assembly intermediates (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-08-13
    Description: Ribosome assembly in eukaryotes requires approximately 200 essential assembly factors (AFs) and occurs through ordered events that initiate in the nucleolus and culminate in the cytoplasm. Here, we present the electron cryo-microscopy (cryo-EM) structure of a late cytoplasmic 40S ribosome assembly intermediate from Saccharomyces cerevisiae at 18 angstrom resolution. We obtained cryo-EM reconstructions of preribosomal complexes lacking individual components to define the positions of all seven AFs bound to this intermediate. These late-binding AFs are positioned to prevent each step in the translation initiation pathway. Together, they obstruct the binding sites for initiation factors, prevent the opening of the messenger RNA channel, block 60S subunit joining, and disrupt the decoding site. These redundant mechanisms probably ensure that pre-40S particles do not enter the translation pathway, which would result in their rapid degradation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3402165/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3402165/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Strunk, Bethany S -- Loucks, Cherisse R -- Su, Min -- Vashisth, Harish -- Cheng, Shanshan -- Schilling, Justin -- Brooks, Charles L 3rd -- Karbstein, Katrin -- Skiniotis, Georgios -- P41 RR012255/RR/NCRR NIH HHS/ -- R01 GM086451/GM/NIGMS NIH HHS/ -- R01-GM086451/GM/NIGMS NIH HHS/ -- RR12255/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 2011 Sep 9;333(6048):1449-53. doi: 10.1126/science.1208245. Epub 2011 Aug 11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Chemical Biology Doctoral Program, University of Michigan, Ann Arbor, MI 48109, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21835981" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Cryoelectron Microscopy ; Eukaryotic Initiation Factor-1/chemistry/metabolism ; Eukaryotic Initiation Factor-3/chemistry/metabolism ; Image Processing, Computer-Assisted ; Methyltransferases/chemistry/metabolism ; Models, Molecular ; Nuclear Proteins/chemistry/metabolism ; *Peptide Chain Initiation, Translational ; Protein-Serine-Threonine Kinases/chemistry/metabolism ; RNA, Fungal/genetics/metabolism ; RNA, Messenger/genetics/metabolism ; Ribosomal Proteins/chemistry/metabolism ; Ribosome Subunits, Small, Eukaryotic/chemistry/*metabolism/ultrastructure ; Saccharomyces cerevisiae/chemistry/*genetics/metabolism ; Saccharomyces cerevisiae Proteins/*chemistry/*metabolism
    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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