Opening and closing motions in the periplasmic vitamin B12 binding protein BtuF

BtuF is the periplasmic binding protein (PBP) in the vitamin B(12) uptake system in Escherichia coli where it is associated with the ABC transporter BtuCD. When the ligand binds, PBPs generally display large conformational changes, commonly termed the Venus flytrap mechanism. BtuF belongs to a group of PBPs that, on the basis of crystal structures, does not appear to display such behavior. Using 480 ns multicopy molecular dynamics simulations of apo and holo forms of the protein, we investigate the dynamics of BtuF. We find BtuF to be more flexible than previously assumed, displaying clear opening and closing motions which are more pronounced in the apo form. The protein behavior is compatible with a PBP functional model that postulates a closed conformation for the ligand-bound state, whereas the empty form fluctuates between open and closed conformations. Elastic network normal-mode analysis suggests that all BtuF-like PBPs are capable of similar opening and closing motions. It also makes the typical Venus flytrap domain motions a likely common means of how PBP-ABC transporter interaction could occur.     

Crystal structures of the BtuF periplasmic-binding protein for vitamin B12 suggest a functionally important reduction in protein mobility upon ligand binding

BtuF is the periplasmic binding protein (PBP) for the vitamin B12 transporter BtuCD, a member of the ATP-binding cassette (ABC) transporter superfamily of transmembrane pumps. We have determined crystal structures of Escherichia coli BtuF in the apo state at 3.0 A resolution and with vitamin B12 bound at 2.0 A resolution. The structure of BtuF is similar to that of the FhuD and TroA PBPs and is composed of two alpha/beta domains linked by a rigid alpha-helix. B12 is bound in the "base-on" or vitamin conformation in a wide acidic cleft located between these domains. The C-terminal domain shares structural homology to a B12-binding domain found in a variety of enzymes. The same surface of this domain interacts with opposite surfaces of B12 when comparing ligand-bound structures of BtuF and the homologous enzymes, a change that is probably caused by the obstruction of the face that typically interacts with this domain by the base-on conformation of vitamin B12 bound to BtuF. There is no apparent pseudo-symmetry in the surface properties of the BtuF domains flanking its B12 binding site even though the presumed transport site in the previously reported crystal structure of BtuCD is located in an intersubunit interface with 2-fold symmetry. Unwinding of an alpha-helix in the C-terminal domain of BtuF appears to be part of conformational change involving a general increase in the mobility of this domain in the apo structure compared with the B12-bound structure. As this helix is located on the surface likely to interact with BtuC, unwinding of the helix upon binding to BtuC could play a role in triggering release of B12 into the transport cavity. Furthermore, the high mobility of this domain in free BtuF could provide an entropic driving force for the subsequent release of BtuF required to complete the transport cycle.     

Mechanistic basis of vitamin B12 and cobinamide salvaging by the Vibrio species

Biosynthesis of vitamin B12, which occurs through salvaging pathway or de novo synthesis, is essential for the survival and growth of bacteria. While the mechanism is known for many bacteria, it is elusive yet for diarrhea causing pathogenic bacteria Vibrio cholerae or the other Vibrio species. Sequence analysis using genome databases delineated that majority of the Vibrio species including V. cholerae contain genes required for salvaging cobalamin/cobinamide in aerobic pathway while lack the genes required for de novo synthesis of B12. Fluorescence quenching study showed that VcBtuF, the PBP of putative ABC transporter BtuF-CD of V. cholerae O395 binds cyanocobalamin and dicyanocobinamide with micromolar dissociation constants (K_d). Productive internalization of these nutrients has been established through growth assay. The crystal structure of cyanocobalamin bound VcBtuF has shown that although interactions between cyanocobalamin and VcBtuF are largely similar to E. coli BtuF, VcBtuF possesses a wider binding pocket. MD simulations indicated that in contrast to EcBtuF that executes ‘open-close’ movement, inter-lobe twisting is prevalent in VcBtuF. Although H70, located at the entrance of the substrate binding cleft of VcBtuF, executes swinging motion, it cannot act as ‘closed gate’ to retain cyanocobalamin or cobinamide in the pocket like corresponding residue W66 of EcBtuF. Rather, VcBtuF shows a distinctive phenomenon of heme binding with comparable affinity to B12. Soret shift of heme upon binding with VcBtuF pointed towards involvement of H70 in heme recognition. This may lead to a restricted B12 or cobinamide binding during abundance of heme in the periplasmic space.     

Holo- and apo-bound structures of bacterial periplasmic heme-binding proteins

An essential component of heme transport in Gram-negative bacterial pathogens is the periplasmic protein that shuttles heme between outer and inner membranes. We have solved the first crystal structures of two such proteins, ShuT from Shigella dysenteriae and PhuT from Pseudomonas aeruginosa. Both share a common architecture typical of Class III periplasmic binding proteins. The heme binds in a narrow cleft between the N- and C-terminal binding domains and is coordinated by a Tyr residue. A comparison of the heme-free (apo) and -bound (holo) structures indicates little change in structure other than minor alterations in the heme pocket and movement of the Tyr heme ligand from an "in" position where it can coordinate the heme iron to an "out" orientation where it points away from the heme pocket. The detailed architecture of the heme pocket is quite different in ShuT and PhuT. Although Arg(228) in PhuT H-bonds with a heme propionate, in ShuT a peptide loop partially takes up the space occupied by Arg(228), and there is no Lys or Arg H-bonding with the heme propionates. A comparison of PhuT/ShuT with the vitamin B(12)-binding protein BtuF and the hydroxamic-type siderophore-binding protein FhuD, the only two other structurally characterized Class III periplasmic binding proteins, demonstrates that PhuT/ShuT more closely resembles BtuF, which reflects the closer similarity in ligands, heme and B(12), compared with ligands for FhuD, a peptide siderophore.     

In vitro functional characterization of BtuCD-F, the Escherichia coli ABC transporter for vitamin B12 uptake

BtuCD is an ATP binding cassette (ABC) transporter that facilitates uptake of vitamin B(12) into the cytoplasm of Escherichia coli. The crystal structures of BtuCD and its cognate periplasmic binding protein BtuF have been recently determined. We have now explored BtuCD-F function in vitro, both in proteoliposomes and in various detergents. BtuCD reconstituted into proteoliposomes has a significant basal ATP hydrolysis rate that is stimulated by addition of BtuF and inhibited by sodium ortho-vanadate. When using different detergents to solubilize BtuCD, the basal ATP hydrolysis rate, the ability of BtuF to stimulate hydrolysis, and the extent to which sodium ortho-vanadate inhibits ATP hydrolysis all vary significantly. Reconstituted BtuCD can mediate transport of vitamin B(12) against a concentration gradient when coupled to ATP hydrolysis by BtuD in the liposome lumen and BtuF outside the liposomes. These in vitro studies establish the functional competence of the BtuCD and BtuF preparations used in the crystallographic analyses for both ATPase and transport activities. Furthermore, the tight binding of BtuF to BtuCD under the conditions studied suggests that the binding protein may not dissociate from the transporter during the catalytic cycle, which may be relevant to the mechanisms of other ABC transporter systems.     

Holo‐BtuF stabilizes the open conformation of the vitamin B12 ABC transporter BtuCD

While there is evidence that other ABC transporters can tell between empty and loaded substrate binding protein, reconstitution experiments suggest otherwise for the Escherichia coli vitamin B12 importer BtuCD‐F. Here, we address the question of BtuCD‐F substrate sensitivity in a combined protein–protein docking and molecular dynamics simulation approach. Starting from the BtuCD and holo‐BtuF crystal structures, we model two holo‐BtuCD‐F docking complexes differing by a 180° orientation of BtuF. One of these is similar to the apo‐BtuCD‐F crystal structure. Both docking complexes were embedded in a lipid/water environment to investigate their dynamics and BtuCD's conformational response to the presence and absence of BtuF, vitamin B12, and Mg‐ATP in a series of 28 independent MD simulations. We find holo‐BtuF stabilizing the open conformation of BtuCD, whereas the transporter begins to close again when BtuF or vitamin B12 is removed—suggesting BtuCD‐F is capable of substrate sensitivity. We identified BtuC transmembrane helices 3 and 5, the L‐loops and the adjacent helices comprised of BtuC residues 170–180 as hotspots of conformational change. We propose the latter to act as substrate sensors. BtuF‐Trp44 appears to act as a lid on the vitamin B12 binding cleft in BtuF X‐ray structures and protrudes into the BtuCD transport channel in one of our simulations, which might represent an initial step in vitamin B12 uptake. On an average, we observe subunit motions where the nucleotide binding domains approach each other while the transmembrane domains display an opening trend toward the periplasm. Proteins 2010. © 2009 Wiley‐Liss, Inc.     

Characterization of the periplasmic heme-binding protein shut from the heme uptake system of Shigella dysenteriae

The heme uptake systems by which bacterial pathogens acquire and utilize heme have recently been described. Such systems may utilize heme directly from the host's hemeproteins or via a hemophore that sequesters and transports heme to an outer membrane receptor and subsequently to the translocating proteins by which heme is further transported into the cell. However, little is known of the heme binding and release mechanisms that facilitate the uptake of heme into the pathogenic organism. As a first step toward elucidating the molecular level events that drive heme binding and release, we have undertaken a spectroscopic and mutational study of the first purified periplasmic heme-binding protein (PBP), ShuT from Shigella dysenteriae. On the basis of sequence identity, the ShuT protein is most closely related to the class of PBPs typified by the vitamin B(12) (BtuF) and iron-hydroxamate (FhuD) PBPs and is a monomeric protein having a molecular mass of 28.5 kDa following proteolytic processing of the periplasmic signaling peptide. ShuT binds one b-type heme per monomer with high affinity and bears no significant homology with other known heme proteins. The resonance Raman, MCD, and UV-visible spectra of WT heme-ShuT are consistent with a five-coordinate high spin heme having an anionic O-bound proximal ligand. Site-directed ShuT mutants of the absolutely conserved Tyr residues, Tyr-94 (Y94A) and Tyr-228 (Y228F), which are found in all putative periplasmic heme-binding proteins, were subjected to UV-visible, resonance Raman, and MCD spectroscopic investigations of heme coordination environment and rates of heme release. The results of these experiments confirmed Tyr-94 as the only axial heme ligand and Tyr-228 as making a significant contribution to the stability of heme-loaded ShuT, albeit without directly interacting with the heme iron.     

Comparison of selenium level and glutathione peroxidase activity in tissues of vitamin B6-deficient rats fed sodium selenite or DL-selenomethionine

The effect of vitamin B₆ on the levels of tissue selenium (Se) and glutathione peroxidase (GSH-Px) was studied. Male Wistar 4-week-old rats were fed a vitamin B₆-Se-deficient basal diet for 2 weeks, then divided into 10 groups of five or six rats and fed their respective diets for 4 weeks. The experimental design was a 2×2×2 factorial with two levels of vitamin B₆, two forms of Se, and two levels of Se, plus two extra groups (vitamin B₆-supplemented and deficient without Se). Vitamin B₆ was 0 and 250 μg pyridoxine-HCl/100 g of diet; Se forms were Na₂SeO₃ and DL-selenomethionine; Se levels were 0.5 and 5.0 mg Se/kg of diet. Regardless of form or level of Se, vitamin B₆-deficient rats had lower body weights and organ weights than vitamin B₆-supplemented rats. At 5.0 mg Se/kg of diet, Na₂SeO₃ caused a further depression. Vitamin B₆ deficiency resulted in a higher Se level and GSH-Px activity in plasma of rats fed selenomethionine. However, Se content an GSH-Px activity in erythrocytes were significantly elevated in vitamin B₆-supplemented rats compared with vitamin B₆-deficient rats. Se levels in muscle and heart were significantly lower in vitamin B₆-deficient groups fed Na₂SeO₃ than in vitamin B₆-supplemented groups. Vitamin B₆-deficient rats fed selenomethionine had higher Se levels in muscle, heart, spleen, liver, and kidneys than vitamin B₆-supplemented rats. Activity of GSH-Px in muscle, heart, and spleen was significantly lower in vitamin B₆-deficient groups than in vitamin B₆-supplemented groups, regardless of form of Se. A significant decrease of GSH-Px in liver was observed in vitamin B₆-deficient rats fed selenomethionine compared with vitamin B₆-supplemented rats, whereas no significant decrease was observed in those fed Na₂SeO₃. These results suggest that vitamin B₆ is involved in the distribution and transportation of Se in body and the metabolism of selenomethionine in liver.     

Asymmetric states of vitamin B₁₂ transporter BtuCD are not discriminated by its cognate substrate binding protein BtuF

BtuCD is an ABC transporter catalyzing the uptake of vitamin B₁₂ across the Escherichia coli inner membrane. A previously reported X-ray structure of BtuCD in complex with the periplasmic vitamin B₁₂-binding protein BtuF revealed asymmetry of the transmembrane BtuC subunits. The functional relevance of this asymmetry has remained uncertain. Here we report the X-ray structure of a catalytically impaired BtuCD mutant in complex with BtuF, where the BtuC subunits adopt a distinct asymmetric conformation. The structure suggests that BtuF does not discriminate between, or impose, asymmetric conformations of BtuCD. It also explains the conformational disorder observed in BtuCDF crystals.Structured summary of protein interactionsBtuF, BtuD and BtuC physically interact by X-ray crystallography (View interaction)     

Molecular dynamics simulations of the bacterial periplasmic heme binding proteins ShuT and PhuT

ShuT and PhuT are two periplasmic heme binding proteins that shuttle heme between the outer and inner membranes of the Gram-negative bacteria. Periplasmic binding proteins (PBPs) generally exhibit considerable conformational changes during the ligand binding process, whereas ShuT and PhuT belong to a class of PBPs that do not show such behavior based on their apo and holo crystal structures. By employing a series of molecular dynamic simulations on the ShuT and the PhuT, the dynamics and functions of the two PBPs were investigated. Through monitoring the distance changes between the two conserved glutamates of ShuT and PhuT, it was found the two PBPs were more flexible than previously assumed, exhibiting obvious opening-closing motions which were more remarkable in the apo runs of ShuT. Based on the results of the domain motion analysis, large scale conformational transitions were found in all apo runs of ShuT and PhuT, hinting that the domain motions of the two PBPs may be intrinsic. On the basis of the results of the principle component analysis, distinct opening-closing and twisting motion tendencies were observed not only in the apo, but also in the holo simulations of the two PBPs. The Gaussian network model was applied in order to analyze the hinge bending regions. The most important bending regions of ShuT and PhuT are located around the midpoints of their respective connecting helixes. Finally, the flexibilities and the details of the simulations of ShuT and PhuT were discussed. Characterized by the remarkably large flexibilities, the loop constituted by Ala 169, Gly170 and Gly171 of ShuT and the beta-turn constituted by Ala176, Gly177 and Gly178 of PhuT may be important for the functions of the two PBPs. Furthermore, the Asn254 of ShuT and the Arg228 of PhuT may be indispensable for the binding or unbinding of heme, since it is involved in the important hydrogen bonding to the propionate side-chains of heme.     

Characterization of the B2 receptor and activity of bradykinin analogs in SHP-77 cell line by Cytosensor microphysiometer

The Cytosensor microphysiometer device (Molecular Devices, Sunnyvale, CA) is capable of measuring the rate at which cells acidify their environment in response to ligand–receptor binding. By measuring the extracellular acidification response (ECAR) we characterized some aspects of ligand–B₂ receptor interaction in SHP-77 cell line. SHP-77 cells maximally acidified their environment within 30 s after the exposure to bradykinin (BK) or the BK agonist, B9972, with the maximum effect seen at a ligands concentration of 1 μM. Fetal bovine serum (FBS) modulated the binding of BK or B9972, showing that B9972 is a partial agonist. In addition, the binding of BK agonist or antagonist to the B₂ receptor showed different ECAR and different interaction with other intracellular and plasma membrane proteins. Our microphysiometrical results showed that two parameters, antagonist binding affinity (pD₂) and antagonist potency (pIC₅₀) are required to characterize BK antagonist activity for the B₂ receptor in the SHP-77 cell line. The previously used parameter of B₂ antagonist activity, pA₂, had high variation and poor correlation with the inhibition of SHP-77 cell growth in vitro and suppression of tumor growth when SHP-77 cells were injected to mice. Our results permit us to conclude that BK agonists and antagonists differ in their interactions with the B₂ receptor and consequently elicit different cell responses. Based on our results, we have developed a new microphysiometrical assay for analyzing the activity of BK agonists and antagonist in SHP-77 cells, which may facilitate the discovery of new potent anticancer drugs.     

透明颤菌vgb基因在脱氮假单胞菌中的表达及对维生素B12合成的碳中心代谢流分析

在为维生素B₁₂生产菌株脱氮假单胞菌确立合适的接合转移操作条件的基础上,通过单交换的方式,将vgb基因整合到脱氮假单胞菌染色体上,获得了vgb重组菌株Pvgb-16,并通过¹³C同位素标记实验,探索VHb蛋白对脱氮假单胞菌碳中心代谢流变化和维生素B₁₂合成的影响。研究结果表明,在相同的供氧条件下,vgb重组菌株Pvgb-16拥有更高的比生长速率和比产物合成速率,与出发菌株相比分别提升了22%和52%。碳代谢通量分布分析表明,vgb重组菌株Pvgb-16的PP途径改善,提升了NADPH合成通量;甘氨酸由甜菜碱合成的通量上升,促进了前体物质氨基乙酰丙酸的合成,进一步加速维生素B₁₂的合成。总体来看,含vgb基因的重组菌株与出发菌株相比在促进菌体的生长、维生素B₁₂的合成速率及得率上都有显著效果,对进一步的发酵生产应用研究具有重要意义。     

The Role of Vitamin B12 Binding In the Uptake of the Vitamin By Euglena Gracilis

The uptake of [⁵⁷Co]B₁₃ (cyanocobalamin) by Euglena gracilis strain Z (ATCC 12716) occurred in 2 distinct phases-an initial rapid phase followed by a slower secondary phase. This secondary phase appeared after the saturation of the binding sites involved in the initial rapid phase and was energy-dependent and completely inhibited by 2,4-dinitrophenot, KCN and sodium azide. the subcellular localization of labeled cyanocobalamin taken up by the cell was mostly contained in the chloroplast fraction. the time course and the saturation kinetics of B₁₂ uptake by purified chloroplast fraction indicated that this fraction and the intact cell had a similar affinity for the vitamin B₁₂. This suggested that the chloroplasts contained the binding sites for vitamin ₁₂ and might regulate the uptake process in the intact cell. the kinetic properties of the overall ₁₂ uptake mechanism suggested that the initial phase represent the binding of vitamin ₁₂ to the available sites on the chloroplast. the secondary phase may represent the de novo synthesis of new binding sites.     

Multiple mechanisms of membrane anchoring of Escherichia coli penicillin-binding proteins

Abstract: The major penicillin-binding proteins (PBPs) of Escherichia coli play vital roles in cell wall biosynthesis and are located in the inner membrane. The high M _r PBPs 1A, 1B, 2 and 3 are essential bifunctional transglycosylases/transpeptidases which are thought to be type II integral inner membrane proteins with their C-terminal enzymatic domains projecting into the periplasm. The low M _r PBP4 is a DD-carboxypeptidase/endopeptidase, whereas PBPs 5 and are DD-carboxypeptidases. All three low M _r , PBPs act in the modification of peptidoglycan to allow expansion of the sacculus and are thought to be periplasmic proteins attached with varying affinities to the inner membrane via C-terminal amphiphilic α-helices. It is possible that the PBPs and other inner membrane proteins form a peptidoglycan synthesizing complex to coordinate their activities.     

Identification of the Periplasmic Cobalamin-Binding Protein BtuF of Escherichia coli

Cells of Escherichia coli take up vitamin B(12) (cyano-cobalamin [CN-Cbl]) and iron chelates by use of sequential active transport processes. Transport of CN-Cbl across the outer membrane and its accumulation in the periplasm is mediated by the TonB-dependent transporter BtuB. Transport across the cytoplasmic membrane (CM) requires the BtuC and BtuD proteins, which are most related in sequence to the transmembrane and ATP-binding cassette proteins of periplasmic permeases for iron-siderophore transport. Unlike the genetic organization of most periplasmic permeases, a candidate gene for a periplasmic Cbl-binding protein is not linked to the btuCED operon. The open reading frame termed yadT in the E. coli genomic sequence is related in sequence to the periplasmic binding proteins for iron-siderophore complexes and was previously implicated in CN-Cbl uptake in SALMONELLA: The E. coli yadT product, renamed BtuF, is shown here to participate in CN-Cbl uptake. BtuF protein, expressed with a C-terminal His(6) tag, was shown to be translocated to the periplasm concomitant with removal of a signal sequence. CN-Cbl-binding assays using radiolabeled substrate or isothermal titration calorimetry showed that purified BtuF binds CN-Cbl with a binding constant of around 15 nM. A null mutation in btuF, but not in the flanking genes pfs and yadS, strongly decreased CN-Cbl utilization and transport into the cytoplasm. The growth response to CN-Cbl of the btuF mutant was much stronger than the slight impairment previously described for btuC, btuD, or btuF mutants. Hence, null mutations in btuC and btuD were constructed and revealed that the btuC mutant had a strong impairment similar to that of the btuF mutant, whereas the btuD defect was less pronounced. All mutants with defective transport across the CM gave rise to frequent suppressor variants which were able to respond at lower levels of CN-Cbl but were still defective in transport across the CM. These results finally establish the identity of the periplasmic binding protein for Cbl uptake, which is one of few cases where the components of a periplasmic permease are genetically separated.     

The conformational coupling and translocation mechanism of vitamin B12 ATP-binding cassette transporter BtuCD

ATP-binding cassette transporter BtuCD mediating vitamin B₁₂ uptake in Escherichia coli couples the energy of ATP hydrolysis to the translocation of vitamin B₁₂ across the membrane into the cell. Elastic normal mode analysis of BtuCD demonstrates that the simultaneous substrate trapping at periplasmic cavity and ATP binding at the ATP-binding cassette (BtuD) dimer proceeds readily along the lowest energy pathway. The transport power stroke is attributed to ATP-hydrolysis-induced opening of the nucleotide-binding domain dimer, which is coupled to conformational rearrangement of transmembrane domain (BtuC) helices leading to the closing at the periplasmic side and opening at the cytoplasmic gate. Simultaneous hydrolysis of two ATP is supported by the fact that antisymmetric movement of BtuD dimer implying alternating hydrolysis cannot induce effective conformational change of the translocation pathway. A plausible mechanism of translocation cycle is proposed in which the possible effect of the association of periplasmic binding protein BtuF to the transporter is also considered.     

Molecular dynamics simulations of the conformational changes of the glutamate receptor ligand-binding core in the presence of glutamate and kainate

Excitatory synaptic transmission is mediated by ionotropic glutamate receptors (iGluRs) through the induced transient opening of transmembrane ion channels. The three-dimensional structure of the extracellular ligand-binding core of iGluRs shares the overall features of bacterial periplasmic binding proteins (PBPs). In both families of proteins, the ligand-binding site is arranged in two domains separated by a cleft and connected by two peptide stretches. PBPs undergo a typical hinge motion of the two domains associated with ligand binding that leads to a conformational change from an open to a closed form. The common architecture suggests a similar closing mechanism in the ligand-binding core of iGluRs induced by the binding of specific agonists. Starting from the experimentally determined kainate-bound closed form of the S1S2 GluR2 construct, we have studied by means of molecular dynamics simulations the opening motion of the ligand-binding core in the presence and in the absence of both glutamate and kainate. Our results suggest that the opening/closing interdomain hinge motions are coupled to conformational changes in the insertion region of the transmembrane segments. These changes are triggered by the interaction of the agonists with the essential Glu 209 residue. A plausible mechanism for the coupling of agonist binding to channel gating is discussed.     

Dynamics and function in a bacterial ABC transporter: simulation studies of the BtuCDF system and its components

ABC transporters are integral membrane proteins which couple the energy of ATP hydrolysis to the translocation of solutes across cell membranes. BtuCD is a approximately 1100-residue protein found in the inner membrane of Gram-negative bacteria which transports vitamin B12. Vitamin B12 is bound in the periplasm by BtuF, which delivers the solute to the periplasmic entrance of the transporter protein complex BtuCD. Molecular dynamics simulations of the BtuCD and BtuCDF complexes (in a lipid bilayer) and of the isolated BtuD and BtuF proteins (in water) have been used to explore the conformational dynamics of this complex transport system. Overall, seven simulations have been performed, with and without bound ATP, corresponding to a total simulation time of 0.1 micros. Binding of ATP drives closure of the nucleotide-binding domains (NBDs) in BtuD in a symmetrical fashion, but not in BtuCD. It seems that ATP constrains the flexibility of the NBDs in BtuCD such that their closure may only occur upon binding of BtuF to the complex. Upon introduction of BtuF, and concomitant with NBD association, one ATP-binding site displays a closure, while the opposite site remains relatively unchanged. This asymmetry may reflect an initial step in the "alternating hydrolysis" mechanism and is consistent with measurements of nucleotide-binding stoichiometries. Principal components analysis of the simulation of BtuCD reveals motions that are comparable to those suggested in current transport models.     

Modelling of steric structure of a periplasmic molecular chaperone Caf1M of Yersinia pestis, a prototype member of a subfamily with characteristic structural and functional features

Abstract Steric structure of Caf1M, a periplasmic molecular chaperone of Yersinia pestis , was reconstructed by computer modelling based on a statistically significant primary structure homology between Caf1M and PapD protein from Escherichia coli , and using the known atomic coordinates obtained by the X-ray crystallography for PapD. In the three-dimensional model of Caf1M an accessory sequence between F1 and G1 β-strands (as compared to PapD) can form a strain-specific part of the binding pocket of surface organell subunits. This accessory sequence decreases the depth of the binding pocket. The characteristic structural feature of the subfamily of periplasmic molecular chaperones with the accessory sequence (Caf1M subfamily) is the existence of exposed to a solvent Cys residues in F1 and G1 β-strands which can form disulfide bond in the putative binding pocket. The characteristic functional feature of Caf1M subfamily is the chaperoning of more simple compositions of virulence-associated surface organells (in the case of Y. pestis a capsule consists of only F1 protein). Highly conserved R₈₂ and D₉₃, located at the domain surface remote from the putative subunit binding pocket, can participate in direct contacts with the conserved portion of molecular usher proteins.