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  • 1
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2011-10-29
    Description: An outstanding challenge in the field of molecular biology has been to understand the process by which proteins fold into their characteristic three-dimensional structures. Here, we report the results of atomic-level molecular dynamics simulations, over periods ranging between 100 mus and 1 ms, that reveal a set of common principles underlying the folding of 12 structurally diverse proteins. In simulations conducted with a single physics-based energy function, the proteins, representing all three major structural classes, spontaneously and repeatedly fold to their experimentally determined native structures. Early in the folding process, the protein backbone adopts a nativelike topology while certain secondary structure elements and a small number of nonlocal contacts form. In most cases, folding follows a single dominant route in which elements of the native structure appear in an order highly correlated with their propensity to form in the unfolded state.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lindorff-Larsen, Kresten -- Piana, Stefano -- Dror, Ron O -- Shaw, David E -- New York, N.Y. -- Science. 2011 Oct 28;334(6055):517-20. doi: 10.1126/science.1208351.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉D. E. Shaw Research, New York, NY 10036, USA. kresten.lindorff-larsen@DEShawResearch.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22034434" target="_blank"〉PubMed〈/a〉
    Keywords: Kinetics ; Molecular Dynamics Simulation ; Protein Conformation ; *Protein Folding ; Protein Structure, Secondary ; Proteins/*chemistry ; Thermodynamics
    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: 2012-02-24
    Description: Acetylcholine, the first neurotransmitter to be identified, exerts many of its physiological actions via activation of a family of G-protein-coupled receptors (GPCRs) known as muscarinic acetylcholine receptors (mAChRs). Although the five mAChR subtypes (M1-M5) share a high degree of sequence homology, they show pronounced differences in G-protein coupling preference and the physiological responses they mediate. Unfortunately, despite decades of effort, no therapeutic agents endowed with clear mAChR subtype selectivity have been developed to exploit these differences. We describe here the structure of the G(q/11)-coupled M3 mAChR ('M3 receptor', from rat) bound to the bronchodilator drug tiotropium and identify the binding mode for this clinically important drug. This structure, together with that of the G(i/o)-coupled M2 receptor, offers possibilities for the design of mAChR subtype-selective ligands. Importantly, the M3 receptor structure allows a structural comparison between two members of a mammalian GPCR subfamily displaying different G-protein coupling selectivities. Furthermore, molecular dynamics simulations suggest that tiotropium binds transiently to an allosteric site en route to the binding pocket of both receptors. These simulations offer a structural view of an allosteric binding mode for an orthosteric GPCR ligand and provide additional opportunities for the design of ligands with different affinities or binding kinetics for different mAChR subtypes. Our findings not only offer insights into the structure and function of one of the most important GPCR families, but may also facilitate the design of improved therapeutics targeting these critical receptors.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3529910/" 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/PMC3529910/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kruse, Andrew C -- Hu, Jianxin -- Pan, Albert C -- Arlow, Daniel H -- Rosenbaum, Daniel M -- Rosemond, Erica -- Green, Hillary F -- Liu, Tong -- Chae, Pil Seok -- Dror, Ron O -- Shaw, David E -- Weis, William I -- Wess, Jurgen -- Kobilka, Brian K -- GM56169/GM/NIGMS NIH HHS/ -- NS028471/NS/NINDS NIH HHS/ -- R01 GM083118/GM/NIGMS NIH HHS/ -- R01 NS028471/NS/NINDS NIH HHS/ -- Intramural NIH HHS/ -- England -- Nature. 2012 Feb 22;482(7386):552-6. doi: 10.1038/nature10867.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 279 Campus Drive, Stanford, California 94305, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22358844" target="_blank"〉PubMed〈/a〉
    Keywords: Acetylcholine/chemistry/metabolism ; Allosteric Site ; Animals ; COS Cells ; Crystallization ; Crystallography, X-Ray ; Kinetics ; Ligands ; Models, Molecular ; Molecular Dynamics Simulation ; Radioligand Assay ; Rats ; Receptor, Muscarinic M3/*chemistry/*metabolism ; Scopolamine Derivatives/chemistry/metabolism ; Substrate Specificity ; Tiotropium Bromide
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 3
    Publication Date: 2010-10-16
    Description: Molecular dynamics (MD) simulations are widely used to study protein motions at an atomic level of detail, but they have been limited to time scales shorter than those of many biologically critical conformational changes. We examined two fundamental processes in protein dynamics--protein folding and conformational change within the folded state--by means of extremely long all-atom MD simulations conducted on a special-purpose machine. Equilibrium simulations of a WW protein domain captured multiple folding and unfolding events that consistently follow a well-defined folding pathway; separate simulations of the protein's constituent substructures shed light on possible determinants of this pathway. A 1-millisecond simulation of the folded protein BPTI reveals a small number of structurally distinct conformational states whose reversible interconversion is slower than local relaxations within those states by a factor of more than 1000.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shaw, David E -- Maragakis, Paul -- Lindorff-Larsen, Kresten -- Piana, Stefano -- Dror, Ron O -- Eastwood, Michael P -- Bank, Joseph A -- Jumper, John M -- Salmon, John K -- Shan, Yibing -- Wriggers, Willy -- New York, N.Y. -- Science. 2010 Oct 15;330(6002):341-6. doi: 10.1126/science.1187409.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉D. E. Shaw Research, 120 West 45th Street, New York, NY 10036, USA. David.Shaw@DEShawResearch.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20947758" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Substitution ; Aprotinin/*chemistry ; Computational Biology ; Computers ; Kinetics ; Microfilament Proteins/chemistry ; Models, Molecular ; *Molecular Dynamics Simulation ; Mutant Proteins/chemistry ; *Protein Conformation ; *Protein Folding ; Protein Structure, Tertiary ; Proteins/*chemistry ; Solvents ; Thermodynamics
    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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