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 α-helix rather than two or three central β-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 α-helix connecting the two domains imposes greater rigidity on the structure relative to the β-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° upon release of its siderophore. This relatively large motion suggests differences that would allow FhuB to distinguish between ferrichrome-bound and ferrichrome-free FhuD.

[1]  H. Berendsen,et al.  Interaction Models for Water in Relation to Protein Hydration , 1981 .

[2]  H. Berendsen,et al.  A consistent empirical potential for water–protein interactions , 1984 .

[3]  P. Kraulis.  A program to produce both detailed and schematic plots of protein structures , 1991 .

[4]  J. Zou,et al.  Improved methods for building protein models in electron density maps and the location of errors in these models. , 1991, Acta crystallographica. Section A, Foundations of crystallography.

[5]  F. Quiocho,et al.  The 2.3-A resolution structure of the maltose- or maltodextrin-binding protein, a primary receptor of bacterial active transport and chemotaxis. , 1992 .

[6]  F. Quiocho,et al.  Crystallographic evidence of a large ligand-induced hinge-twist motion between the two domains of the maltodextrin binding protein involved in active transport and chemotaxis. , 1992, Biochemistry.

[7]  T. Darden,et al.  Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems , 1993 .

[8]  M H Saier,et al.  Structural, functional, and evolutionary relationships among extracellular solute-binding receptors of bacteria , 1993, Microbiological reviews.

[9]  J. Thompson,et al.  CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.

[10]  D. Svergun,et al.  CRYSOL : a program to evaluate X-ray solution scattering of biological macromolecules from atomic coordinates , 1995 .

[11]  D. van der Spoel,et al.  GROMACS: A message-passing parallel molecular dynamics implementation , 1995 .

[12]  T. Darden,et al.  A smooth particle mesh Ewald method , 1995 .

[13]  F. Quiocho,et al.  Atomic structure and specificity of bacterial periplasmic receptors for active transport and chemotaxis: variation of common themes , 1996, Molecular microbiology.

[14]  S. Mowbray,et al.  Conformational changes of three periplasmic receptors for bacterial chemotaxis and transport: the maltose-, glucose/galactose- and ribose-binding proteins. , 1996, Journal of molecular biology.

[15]  M. Billeter,et al.  MOLMOL: a program for display and analysis of macromolecular structures. , 1996, Journal of molecular graphics.

[16]  E A Merritt,et al.  Raster3D: photorealistic molecular graphics. , 1997, Methods in enzymology.

[17]  D. McRee,et al.  Structure of Haemophilus influenzae Fe+3-binding protein reveals convergent evolution within a superfamily , 1997, Nature Structural Biology.

[18]  F A Quiocho,et al.  Extensive features of tight oligosaccharide binding revealed in high-resolution structures of the maltodextrin transport/chemosensory receptor. , 1997, Structure.

[19]  M. Lawrence,et al.  The crystal structure of pneumococcal surface antigen PsaA reveals a metal-binding site and a novel structure for a putative ABC-type binding protein. , 1998, Structure.

[20]  J. Radolf,et al.  Treponema pallidum TroA is a periplasmic zinc-binding protein with a helical backbone , 1999, Nature Structural Biology.

[21]  K. Nishikawa,et al.  Domain dislocation: a change of core structure in periplasmic binding proteins in their evolutionary history. , 1999, Journal of molecular biology.

[22]  H. Vogel,et al.  The structure of the ferric siderophore binding protein FhuD complexed with gallichrome , 2000, Nature Structural Biology.

[23]  D. McRee,et al.  Crystallographic and biochemical analyses of the metal-free Haemophilus influenzae Fe3+-binding protein. , 2001, Biochemistry.

[24]  J. Claverys.  A new family of high-affinity ABC manganese and zinc permeases. , 2001, Research in microbiology.

[25]  W. Köster.  ABC transporter-mediated uptake of iron, siderophores, heme and vitamin B12. , 2001, Research in microbiology.

[26]  Berk Hess,et al.  GROMACS 3.0: a package for molecular simulation and trajectory analysis , 2001 .

[27]  D. Rees,et al.  The structure of Escherichia coli BtuF and binding to its cognate ATP binding cassette transporter , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[28]  Steven Hayward,et al.  Improvements in the analysis of domain motions in proteins from conformational change: DynDom version 1.50. , 2002, Journal of molecular graphics & modelling.

[29]  H. Vogel,et al.  X-ray Crystallographic Structures of the Escherichia coli Periplasmic Protein FhuD Bound to Hydroxamate-type Siderophores and the Antibiotic Albomycin* , 2002, The Journal of Biological Chemistry.

[30]  Douglas C. Rees,et al.  The E. coli BtuCD Structure: A Framework for ABC Transporter Architecture and Mechanism , 2002, Science.

[31]  J. Radolf,et al.  The Crystal Structure of Zn(II)-Free Treponema pallidum TroA, a Periplasmic Metal-Binding Protein, Reveals a Closed Conformation , 2002, Journal of bacteriology.

[32]  V. Braun,et al.  Iron transport and signaling in Escherichia coli , 2002, FEBS letters.

[33]  Andrew Pang,et al.  Interdomain dynamics and ligand binding: molecular dynamics simulations of glutamine binding protein , 2003, FEBS letters.

[34]  J. Tame,et al.  Crystal Structures of the Liganded and Unliganded Nickel-binding Protein NikA from Escherichia coli* , 2003, Journal of Biological Chemistry.

[35]  John F. Hunt,et al.  Crystal Structures of the BtuF Periplasmic-binding Protein for Vitamin B12 Suggest a Functionally Important Reduction in Protein Mobility upon Ligand Binding* , 2003, The Journal of Biological Chemistry.

[36]  Stefan Fischer,et al.  Molecular dynamics simulation reveals a surface salt bridge forming a kinetic trap in unfolding of truncated Staphylococcal nuclease , 2003, Proteins.

[37]  H. Nikaido.  Molecular Basis of Bacterial Outer Membrane Permeability Revisited , 2003, Microbiology and Molecular Biology Reviews.

[38]  Moe Razaz,et al.  The DynDom Database of Protein Domain Motions , 2003, Bioinform..

[39]  J. H. Crosa,et al.  Iron transport in bacteria , 2004 .

[40]  H. Vogel,et al.  Periplasmic Binding Proteins Involved in Bacterial Iron Uptake , 2004 .

[41]  D Peter Tieleman,et al.  Conformational Transitions Induced by the Binding of MgATP to the Vitamin B12 ATP-binding Cassette (ABC) Transporter BtuCD* , 2004, Journal of Biological Chemistry.