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SUMMARY:Dynamics of uninhibited and covalently inhibited cysteine protease
  on non-physiological pH
DTSTART;VALUE=DATE-TIME:20121019T083000Z
DTEND;VALUE=DATE-TIME:20121019T090000Z
DTSTAMP;VALUE=DATE-TIME:20261010T233210Z
UID:indico-contribution-192@indico.ipb.ac.rs
DESCRIPTION:Speakers: Branko J. Drakulić (Department of Chemistry-IChTM\,
  University of Belgrade\, Njegoševa 12\, Belgrade\, Serbia)\nCysteine pro
 teases involved in degradation of proteins\, widespread in plants\, parasi
 tes and vertebrates\, are an important medicinal chemistry target implicat
 ed in the diseases ranging from immunological processes to cancer. Due to 
 conserved cysteine residue in their active site\, unsaturated ketones and 
 their analogs represent one of the major chemotypes used for inhibitors de
 sign [1]. In this communication the dynamics of the papain-like cysteine p
 rotease isolated from the fruit\, uninhibited and inhibited with covalent 
 inhibitor E-64 (Scheme 1)\, on non-physiological pH\, were reported mergin
 g results and experiences from our biochemical and medicinal chemistry lab
 oratories.The aim of our study is to explain some experimental findings. P
 roteins are modeled using similar ones with the known 3D structure\, taken
  from Protein Data Bank [2]. After sequence alignment residues that differ
 entiate templates from the experimental proteins were manually changed. Af
 terward the eventual existence of close contacts\, bumps or similar was ca
 refully checked. The protonation states of the aminoacid residues and the 
 inhibitor ionizable groups were adjusted to pH 1.5\, using empirical funct
 ion [3]. Systems were neutralized with explicit counterions\, than embed i
 n explicit water\, obtaining the sphere having ~ 100 Å radius. Systems un
 der simulations were minimized during 30000 steps\, than heated to 300 K d
 uring 10000 steps. After equilibration\, the 5 ns unconstrained and unbias
 ed molecular dynamics simulation\, on 300 ± 10 K\, were performed on the 
 each system. CHARMm22 force field and Geisteiger charges were used. Electr
 ostatics was treated by Particle Mesh Ewald method. The periodic boundary 
 conditions were applied\, and 12 Å cut-off (8 Å switching)\, with pair l
 ist distances set to 13.5 Å. Each simulation was performed in duplicate\,
  using different random seeds and giving comparable results. The root-mean
 -square deviation of the backbone atoms and the energy profiles of the sys
 tems under the study proved stable\, converged simulation. The movement of
  the loops and the (flexible) inhibitor\, as well as radius of gyration of
  the selected amino-acid side chains was analyzed and conclusion derived o
 n the influence of the covalently bound inhibitors on the dynamics of the 
 enzyme on pH 1.5. All calculations were performed by NAMD 2.8 [4] on the m
 ultimode Linux cluster. For the preparation of the systems\, and analysis 
 of the results VegaZZ 2.4.0 were used [5].\n\nAcknowledgement: The work is
  supported by the European Commission under EU FP7 project HP-SEE\, http:/
 /www.hp-see.eu/.  The Ministry of Education and Science of Serbia support 
 this work. Grants 172035 and 172049.\n\nReferences: [1] Mini-Rev. Med. Che
 m. 7 (2007) 1040\; [2] J. Mol. Biol. 112 (1977) 535\; [3] Proteins 73 (200
 8) 765\; [4] J. Compt. Chem. 26 (2005) 1781\; [5] J. Comp. Aided Mol. Des.
  18 (2004) 167\n\nhttps://events.saifa.rs/event/291/contributions/192/
LOCATION:National Library of Serbia
URL:https://events.saifa.rs/event/291/contributions/192/
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