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10.1016/bs.mie.2016.05.027 http://scihub22266oqcxt.onion/10.1016/bs.mie.2016.05.027 C5492730!5492730 !27497176     free     free     free Deprecated: Implicit conversion from float 211.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Deprecated: Implicit conversion from float 211.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Deprecated: Implicit conversion from float 211.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Warning: imagejpeg(C:\Inetpub\vhosts\kidney.de\httpdocs\phplern\27497176 .jpg): Failed to open stream: No such file or directory in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 117       Methods+Enzymol 2016 ; 578 (ä): 429-47 Nephropedia Template TP {{tp|p=27497176 |t=2016. Detecting Allosteric Networks Using Molecular Dynamics Simulation |pdf=|usr=}}{{27497176 }} gab.com Text Detecting Allosteric Networks Using Molecular Dynamics Simulation JO: Methods Enzymol http://www.kidney.de/pget.php?&tw=1&pmid=27497176 #FOAvip Allosteric networks allow enzymes to transmit information and regulate their catalytic activities over vast distances. In principle, molecular dynamics (MD) simulations can be used to reveal the mechanisms that underlie this phenomenon; in practice, it can be difficult to discern allosteric signals from MD trajectories. Here, we describe how MD simulations can be analyzed to reveal correlated motions and allosteric networks, and provide an example of their use on the coagulation enzyme thrombin. Methods are discussed for calculating residue-pair correlations from atomic fluctuations and mutual information, which can be combined with contact information to identify allosteric networks and to dynamically cluster a system into highly correlated communities. In the case of thrombin, these methods show that binding of the antagonist hirugen significantly alters the enzyme's correlation landscape through a series of pathways between Exosite I and the catalytic core. Results suggest that hirugen binding curtails dynamic diversity and enforces stricter venues of influence, thus reducing the accessibility of thrombin to other molecules. Twit Text FOAVip Detecting Allosteric Networks Using Molecular Dynamics Simulation ????Methods Enzymol http://www.kidney.de/pget.php?&tw=1&pmid=27497176 #FOAvip Twit Text # Free Paper on # # # # # LINK http://www.kidney.de/pget.php?&tw=1&pmid=27497176 #FOAvip English Wikipedia <ref>{{Cite pmid|27497176 }}</ref> Detecting Allosteric Networks Using Molecular Dynamics Simulation #MMPMID27497176 Bowerman S ; Wereszczynski J Methods Enzymol 2016[]; 578 (ä): 429-47 PMID27497176 show ga Allosteric networks allow enzymes to transmit information and regulate their catalytic activities over vast distances. In principle, molecular dynamics (MD) simulations can be used to reveal the mechanisms that underlie this phenomenon; in practice, it can be difficult to discern allosteric signals from MD trajectories. Here, we describe how MD simulations can be analyzed to reveal correlated motions and allosteric networks, and provide an example of their use on the coagulation enzyme thrombin. Methods are discussed for calculating residue-pair correlations from atomic fluctuations and mutual information, which can be combined with contact information to identify allosteric networks and to dynamically cluster a system into highly correlated communities. In the case of thrombin, these methods show that binding of the antagonist hirugen significantly alters the enzyme's correlation landscape through a series of pathways between Exosite I and the catalytic core. Results suggest that hirugen binding curtails dynamic diversity and enforces stricter venues of influence, thus reducing the accessibility of thrombin to other molecules. |*Molecular Dynamics Simulation [MESH] |Allosteric Regulation [MESH] |Allosteric Site [MESH] |Catalytic Domain [MESH] |Chlorides/chemistry [MESH] |Heparin/chemistry [MESH] |Hirudins/*chemistry [MESH] |Humans [MESH] |Peptide Fragments/*chemistry [MESH] |Protein Binding [MESH] |Protein Conformation, alpha-Helical [MESH] |Protein Conformation, beta-Strand [MESH] |Protein Interaction Domains and Motifs [MESH] |Sodium/chemistry [MESH] |Thrombin/*chemistry [MESH]Detecting Allosteric Networks Using Molecular Dynamics Simulation (epmc).pdf DeepDyve Pubget Overpricing