Insights into the structure of the PmrD protein with molecular dynamics simulations.
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.
Tatsis
Vasileios A
VA
Department of Information and Telecommunications Engineering, University of West Macedonia, Kozani, Greece.
Tsoulos
Ioannis G
IG
Krinas
Christos S
CS
Alexopoulos
Charalampos
C
Stavrakoudis
Athanassios
A
D004926:Escherichia coli; D029968:Escherichia coli Proteins / Q000737:chemistry*; D057927:Hydrophobic and Hydrophilic Interactions; D008958:Models, Molecular; D055550:Protein Stability; D017433:Protein Structure, Secondary; D055672:Static Electricity; D013499:Surface Properties
D029968:Escherichia coli Proteins; C523605:PmrD protein, E coli