Insights into the structure of the PmrD protein with molecular dynamics simulations (Journal article)

Tatsis, V. A./ Tsoulos, I. G./ Krinas, C. S./ Alexopoulos, C./ Stavrakoudis, A.


Resistance to cationic antimicrobial peptide polymyxin B from Gram-negative bacteria is accomplished by two-component systems (TCSs), protein complexes PmrA/PmrB and PhoP/PhoQ. PmrD is the first protein identified to mediate the connectivity between two TCSs. The 3D structure of PmrD has been recently solved by NMR and its unique fold was revealed. Here, a molecular dynamics study is presented started from the NMR structure. Numerous hydrophobic and electrostatic interactions were identified to contribute to PmrD's 3D stability. Moreover, the mobility of the five loops that connect the protein's six beta-strands has been explored. Solvent-accessible surface area calculation revealed that a Leucine-rich hydrophobic cluster of the protein stabilized the protein's structure. (C) 2009 Elsevier B.V. All rights reserved.
Institution and School/Department of submitter: Πανεπιστήμιο Ιωαννίνων. Σχολή Οικονομικών και Κοινωνικών Επιστημών. Τμήμα Οικονομικών Επιστημών
Keywords: beta-barrel,computer simulation,leucine-rich hydrophobic cluster,molecular dynamics,polymyxin resistance,pmrd,peptide,water,orientation,system,force,ewald
URI: http://olympias.lib.uoi.gr/jspui/handle/123456789/11176
ISSN: 0141-8130
Link: <Go to ISI>://000266712500003
Appears in Collections:Άρθρα σε επιστημονικά περιοδικά ( Ανοικτά)

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