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10.1080/07391102.2013.869660 http://scihub22266oqcxt.onion/10.1080/07391102.2013.869660 C4915731!4915731 !24417415     free     free     free Warning: file_get_contents(https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=24417415 &cmd=llinks): Failed to open stream: HTTP request failed! 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Molecular recognition mechanism of peptide chain bound to the tRNA(Lys3) anticodon loop in silico |pdf=|usr=}}{{24417415 }} gab.com Text Molecular recognition mechanism of peptide chain bound to the tRNA(Lys3) anticodon loop in silico JO: J Biomol Struct Dyn http://www.kidney.de/pget.php?&tw=1&pmid=24417415 #FOAvip The mechanism by which proteins recognize and bind the post-transcriptional modifications of RNAs is unknown, yet these interactions play important functions in biology. Atomistic molecular dynamics simulations were performed to examine the folding of the model peptide chain -RVTHHAFLGAHRTVG- and the complex formed by the folded peptide with the native anticodon stem and loop of the human tRNA(Lys3) (hASL(Lys3)) in order to explore the binding mechanism. By analyzing and comparing two folded conformations of this peptide obtained from the folding simulation, we found that the van der Waals (VDW) energy is necessary for the thermal stability of the peptide, and the charge-charge (ELE?+?EGB) energy is crucial for determining the three-dimensional folded structure of the peptide backbone. Subsequently, two conformations of the peptide were employed to investigate their binding behaviors to hASL(Lys3). The metastable folded peptide was found to bind to hASL(Lys3) much easier than the stable folded peptide in the binding simulations. An energetic analysis reveals that the VDW energy favors the binding, whereas the ELE?+?EGB energies disfavor the binding. Arginines on the peptide preferentially attract the phosphate backbone via the inter-chain ELE?+?EGB interaction, significantly contributing to the binding affinity. The hydrophobic phenylalanine interacts with the anticodon loop of hASL(Lys3) via the inter-chain VDW interaction, significantly contributing to the binding specificity. Twit Text FOAVip Molecular recognition mechanism of peptide chain bound to the tRNA(Lys3) anticodon loop in silico ????J Biomol Struct Dyn http://www.kidney.de/pget.php?&tw=1&pmid=24417415 #FOAvip Twit Text # Free Paper on # # # # # LINK http://www.kidney.de/pget.php?&tw=1&pmid=24417415 #FOAvip English Wikipedia <ref>{{Cite pmid|24417415 }}</ref> Molecular recognition mechanism of peptide chain bound to the tRNA(Lys3) anticodon loop in silico #MMPMID24417415 Xiao X ; Agris PF ; Hall CK J Biomol Struct Dyn 2015[]; 33 (1 ): 14-27 PMID24417415 show ga The mechanism by which proteins recognize and bind the post-transcriptional modifications of RNAs is unknown, yet these interactions play important functions in biology. Atomistic molecular dynamics simulations were performed to examine the folding of the model peptide chain -RVTHHAFLGAHRTVG- and the complex formed by the folded peptide with the native anticodon stem and loop of the human tRNA(Lys3) (hASL(Lys3)) in order to explore the binding mechanism. By analyzing and comparing two folded conformations of this peptide obtained from the folding simulation, we found that the van der Waals (VDW) energy is necessary for the thermal stability of the peptide, and the charge-charge (ELE?+?EGB) energy is crucial for determining the three-dimensional folded structure of the peptide backbone. Subsequently, two conformations of the peptide were employed to investigate their binding behaviors to hASL(Lys3). The metastable folded peptide was found to bind to hASL(Lys3) much easier than the stable folded peptide in the binding simulations. An energetic analysis reveals that the VDW energy favors the binding, whereas the ELE?+?EGB energies disfavor the binding. Arginines on the peptide preferentially attract the phosphate backbone via the inter-chain ELE?+?EGB interaction, significantly contributing to the binding affinity. The hydrophobic phenylalanine interacts with the anticodon loop of hASL(Lys3) via the inter-chain VDW interaction, significantly contributing to the binding specificity. |*Computer Simulation [MESH] |Algorithms [MESH] |Amino Acid Sequence [MESH] |Amino Acids/chemistry/metabolism [MESH] |Anticodon/chemistry/genetics/*metabolism [MESH] |Humans [MESH] |Models, Molecular [MESH] |Molecular Sequence Data [MESH] |Nucleic Acid Conformation [MESH] |Peptides/chemistry/*metabolism [MESH] |Phenylalanine/chemistry/metabolism [MESH] |Protein Binding [MESH] |Protein Folding [MESH] |Protein Structure, Secondary [MESH] |Protein Structure, Tertiary [MESH] |RNA, Transfer, Lys/chemistry/*metabolism [MESH] |Static Electricity [MESH]Molecular recognition mechanism of peptide chain bound to the tRNA(Lys(epmc).pdf DeepDyve Pubget Overpricing