2005 drug complexes and probing helical propensity of amino acid

2005 drug complexes and probing helical propensity of amino acid

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Application of steered molecular dynamics (SMD) to study DNA–drug complexes and probing helical propensity of amino acids This article has been downloaded from IOPscience. Please scroll down to see the full text article. 2005 J. Phys.: Condens. Matter 17 S1627 (http://iopscience.iop.org/0953-8984/17/18/018) Download details: IP Address: 217.131.9.117 The article was downloaded on 20/10/2010 at 20:01 Please note that terms and conditions apply. View the table of contents for this issue, or go to the journal homepage for more Home Search Collections Journals About Contact us My IOPscience
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INSTITUTE OF PHYSICS PUBLISHING JOURNAL OF PHYSICS: CONDENSED MATTER J. Phys.: Condens. Matter 17 (2005) S1627–S1640 doi:10.1088/0953-8984/17/18/018 Application of steered molecular dynamics (SMD) to study DNA–drug complexes and probing helical propensity of amino acids MarekOrzechowski 1 and Piotr Cieplak 2 1 Faculty of Chemistry, Warsaw University, 1 Pasteura Street, Warsaw, 02-093, Poland 2 Accelrys Incorporated, 9685 Scranton Road, San Diego, CA 92121, USA E-mail: morzech@tiger.chem.uw.edu.pl and pcieplak@accelrys.com Received 26 October 2004, in ±nal form 26 October 2004 Published 22 April 2005 Online at stacks.iop.org/JPhysCM/17/S1627 Abstract We present the preliminary results of two computer experiments involving the application of an externalforce to molecularsystems. In the ±rst experimentwe simulated the process of pulling out a simple intercalator, the 9-aminoacridine molecule, from its complex with a short DNA oligonucleotide in aqueous solution. Removing a drug from the DNA is assumed to be an opposite process to the complex formation. The force and energy pro±les suggest that formation of the DNA–9-aminoacridinecomplex is preferred when the acridine approaches the DNA from the minor groove rather than the major groove side. For a given mode of pulling the intercalation process is also shown to be nucleotide sequence dependent. In another computer experiment we performed a series of molecular dynamics simulations for stretching short, containing 15 amino acids, helical polypeptides in aqueous solution using an external force. The purpose of these simulations is to check whether this type of approach is sensitive enough to probe the sequence dependent helical propensity of short polypeptides. 1. Introduction Recently, the rapid development of modern experimental techniques suchasthe AFM (atomic force microscope) or so-called optical tweezers has enabled the direct manipulation of a single molecule on the atomic level. Such techniques are mainly applied to biologically important molecules of living organisms. The ability to manipulate large molecules on an atomic scale has encouraged experimentalists to reproduce biological phenomena such as strand separation in double stranded DNA [1, 2], stretching DNAs and RNAs [3–5], complex formation between various proteins and ligands [6–8], as well as stretching elastic proteins such as titin [9, 10].
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2005 drug complexes and probing helical propensity of amino acid

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