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David M. Smith Div. Org. Chem. and Biochem., Institut Ruđer Bošković, Zagreb

On the Characterization of Specific Interactions between Sense and Complementary Peptides: An Investigation Using Replica-Exchange Molecular Dynamics. David M. Smith Div. Org. Chem. and Biochem., Institut Ruđer Bošković, Zagreb. The System. Ace-Tyr-Gly-Gly-Phe-Met-Nme.

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David M. Smith Div. Org. Chem. and Biochem., Institut Ruđer Bošković, Zagreb

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  1. On the Characterization of Specific Interactions between Sense and Complementary Peptides: An Investigation Using Replica-Exchange Molecular Dynamics David M. Smith Div. Org. Chem. and Biochem., Institut Ruđer Bošković, Zagreb

  2. The System Ace-Tyr-Gly-Gly-Phe-Met-Nme Ace-Ile-Pro-Pro-Lys-Tyr-Nme Croat. Chem. Acta.1998, 71, 591

  3. A modern solution is to construct several replica simulations with different temperatures and allow them to exchange according to: Replica Exchange Dynamics Single simulations, especially in explicit solvent, are prone to become trapped in potential energy minima Increasing the temperature can facilitate barrier crossings but can lead to irrelevant results

  4. Replica Exchange Dynamics 16 replicas simulated for 10 ns each, implying 160ns in total. The temperatures range between 275K and 400K such that P≈0.2.

  5. Analysis: Structural Properties Separation of the centres of mass of the two peptides

  6. Sense Peptide N → Tyr-Gly-Gly-Phe-Met → C Translation Sense mRNA (+) 5’ → UAU-CCC-GGC-UUC-AUG → 3’ Transcription Complementary DNA 3’ ← ATA-CCC-CCG-AAG-TAC ← 5’ Sense DNA 5’ → TAT-GGG-GGC-TTC-ATG → 3’ Complementary mRNA (-) 3’ ← AUA-CCC-CCG-AAG-UAC ← 5’ C ← Ile-Pro-Ala-Glu-His ← N Complementary Peptide Complementary Peptides: What are they ? ChemBioChem.2002, 3, 136

  7. Some Mekler-Idlis Pairs Sense Complementary Sense Complementary Cys Arg Gly Ser Ser Ala Thr Pro Ala Gly Trp Gly Arg Arg Cys Agr Gly Ser Pro Thr Biophyzika.1969, 14, 581

  8. Sense Peptide N → Tyr-Gly-Gly-Phe-Met → C Sense mRNA (+) 5’ → UAU-CCC-GGC-UUC-AUG → 3’ Complementary DNA 3’ ← ATA-CCC-CCG-AAG-TAC ← 5’ Sense DNA 5’ → TAT-GGG-GGC-TTC-ATG → 3’ Complementary mRNA (-) 3’ → AUA-CCC-CCG-AAG-UAC →5’ N → Ile-Pro-Pro-Lys-Tyr →C Complementary Peptide An Alternative Definition of Complementary Peptides: Pro. Nat. Acad. Sci.1985, 82, 1372

  9. Some Root-Bernstein Pairs Sense Complementary Sense Complementary Arg Arg Arg Arg Pro Pro Pro Pro Ala Gly Gly Gly Gly Gly Cys Cys Trp stop Pro Thr J. Theor. Biol.1983, 100, 99

  10. Bonds Angles Dihedrals Van der Waals Electrostatic Implicit Solvation (Non Elec.) Implicit Solvation (Elec.) Molecular Dynamics: The Force Field

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