Molecular dynamics simulations of the periplasmic ferric-hydroxamate binding protein FhuD.
FhuD is a periplasmic binding protein (PBP) that, under iron-limiting conditions, transports various hydroxamate-type siderophores from the outer membrane receptor (FhuA) to the inner membrane ATP-binding cassette transporter (FhuBC). Unlike many other PBPs, FhuD possesses two independently folded domains that are connected by an alpha-helix rather than two or three central beta-strands. Crystal structures of FhuD with and without bound gallichrome have provided some insight into the mechanism of siderophore binding as well as suggested a potential mechanism for FhuD binding to FhuB. Since the alpha-helix connecting the two domains imposes greater rigidity on the structure relative to the beta-strands in other 'classical' PBPs, these structures reveal no large conformational change upon binding a hydroxamate-type siderophore. Therefore, it is difficult to explain how the inner membrane transporter FhuB can distinguish between ferrichrome-bound and ferrichrome-free FhuD. In the current study, we have employed a 30 ns molecular dynamics simulation of FhuD with its bound siderophore removed to explore the dynamic behavior of FhuD in the substrate-free state. The MD simulation suggests that FhuD is somewhat dynamic with a C-terminal domain closure of 6 degrees upon release of its siderophore. This relatively large motion suggests differences that would allow FhuB to distinguish between ferrichrome-bound and ferrichrome-free FhuD.
Krewulak
Karla D
KD
Structural Biology Research Group, Department of Biological Sciences, University of Calgary, 2500 University Drive N.W, Alberta, Canada T2N 1N4.
Shepherd
Craig M
CM
Vogel
Hans J
HJ
D000595:Amino Acid Sequence; D001425:Bacterial Outer Membrane Proteins / Q000737:chemistry; D001692:Biological Transport; D018360:Crystallography, X-Ray; D004926:Escherichia coli / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000737:chemistry / Q000378:metabolism / Q000502:physiology*; D005291:Ferrichrome / Q000031:analogs & derivatives / Q000737:chemistry; D026901:Membrane Transport Proteins / Q000737:chemistry / Q000378:metabolism / Q000502:physiology*; D008958:Models, Molecular; D008968:Molecular Conformation; D008969:Molecular Sequence Data; D033902:Periplasmic Binding Proteins / Q000737:chemistry / Q000378:metabolism / Q000502:physiology*; D011485:Protein Binding; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011991:Receptors, Virus / Q000737:chemistry; D017386:Sequence Homology, Amino Acid; D017262:Siderophores / Q000737:chemistry; D013379:Substrate Specificity; D013997:Time Factors
D001425:Bacterial Outer Membrane Proteins; D029968:Escherichia coli Proteins; C050900:FhuA protein, E coli; D026901:Membrane Transport Proteins; D033902:Periplasmic Binding Proteins; D011991:Receptors, Virus; D017262:Siderophores; C069968:fhuB protein, E coli; C069969:fhuD protein, E coli; D005291:Ferrichrome; C407026:gallichrome