Molecular mechanics modelling of siderophores

Molecular dynamics simulations of the bacterial outer membrane protein FhuA: a comparative study of the ferrichrome-free and bound states

FhuA is one of the more complex members of the superfamily of bacterial outer membrane proteins. Its primary function is to provide a binding site on the outer membrane surface for siderophores, such as ferrichrome, and subsequently to facilitate their energy-dependent transport across the membrane, presumably powered by the TonB-ExbBD protein complex that resides in the cytoplasmic membrane. Crystal structures of FhuA with and without a bound ferrichrome molecule have provided some clues as to the initial stages of the siderophore transport mechanism. In the current study, we have employed 10-ns duration molecular dynamics simulations of FhuA and of the FhuA-ferrichrome complex, both embedded in a phospholipid bilayer, to probe the short timescale dynamics of this integral membrane protein, and to explore possible mechanistic implications of this dynamic behavior. Analysis of the dynamics of the protein suggests that the extracellular loops move as relatively rigid entities relative to the transmembrane beta-barrel. Comparison of the two simulations (with and without bound ferrichrome) revealed some ligand-induced changes in loop mobility. Specifically, loop L8 appears to be involved in a mechanism whereby the binding site is gated closed upon ligand binding. Analysis of the dynamics of water molecules within the core of the FhuA protein provided no evidence for a water-permeable protopore through which the ferrichrome might pass without a major perturbation of the FhuA protein. Overall, these simulations support the proposal that binding of ferrichrome initiates a signaling mechanism that ultimately leads to the TonB-mediated partial or total removal of the core domain from the beta-barrel, thus opening up a permeable pore. These simulations are among the longest that have been performed on a complex membrane protein. However, a simple analysis of sampling reveals that the description of protein motions is far from complete.

Structural criteria for the rational design of selective ligands. 3. Quantitative structure-stability relationship for iron(III) complexation by tris-catecholamide siderophores

We present an extended MM3 model for catecholamide ligands and their Fe(3+) complexes and the application of this model to understand how ligand architecture effects Fe(3+) binding affinity. Force field parameters were fit to geometries and energies from electronic structure calculations, and to crystal structure data. Optimized geometries are reported for phenol, acetamide, the phenol-phenol dimer, the acetamide-phenol dimer, and N-methylsalicylamide (HMSA) at the BLYP/DZVP2/A2 level of theory. Optimized geometries and relative energies are reported for the pseudo-octahedral ground state and the trigonal planar transition state of [Fe(CAT)(3)](3)(-) at the VWN/DZVP2/A1 level of theory. The MM3 model is validated by comparison of calculated structures with crystal structures containing 1,2-dihydroxybenzene (H(2)CAT) and 2,3-dihydroxy-N-methylbenzamide (H(2)MBA) fragments, crystal structures of [Fe(CAT)(3)](3)(-) and tris-catecholamide Fe(3+) complexes, and comparison of MM3 (6.8 kcal/mol) and VWN (5.9 kcal/mol) barriers for intramolecular octahedral inversion in [Fe(CAT)(3)](3)(-). The MM3 model also rationalizes the higher inversion barrier (14 to 18 kcal/mol) reported for [Ga(N,N-diisopropylterephthalamide)(3)](3)(-) ([Ga(DIPTA)(3)](3)(-)). Conformational searches were performed on enterobactin (H(6)ENT), 1,3,5-tris(2,3-dihydroxybenzamidomethyl)-2,4,6-triethylbenzene (H(6)EMECAM), 1,3,5-tris(2,3-dihydroxybenzamidomethyl)-2,4,6-trimethylbenzene (H(6)MMECAM), 1,3,5-tris(2,3-dihydroxybenzamidomethyl)benzene (H(6)MECAM), and 1,5,9-N,N',N' '-tris(2,3-dihydroxybenzoyl)cyclotriazatridecane (H(6)-3,3,4-CYCAM) and Fe(3+) complexes with each of these ligands. A conformational search also was done on the Fe(3+) complex with the 2,2',2' '-tris(2,3-dihydroxybenzamido)triethylammonium cation (H(7)TRENCAM(+)). The relationship between calculated steric energies and measured thermodynamic quantities is discussed, and linear correlations between formation constants and steric energy differences are reported. Extrapolation to zero strain predicts formation constants 8 +/- 5 orders of magnitude higher than that exhibited by ENT (10(49)) are possible. This prediction is supported by a formation constant of 10(63) estimated from the formation constant of [Fe(2,3-dihydroxy-N,N-dimethylbenzamide)(3)](3)(-) ([Fe(DMBA)(3)](3)(-)) by considering the entropic consequences of connecting three DMBA ligands to a rigid backbone. Structural criteria for the identification of improved tris-catecholate ligand architectures are presented.