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Pinkes Glitzer Feen Einhorn

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Ottilie Wildermuth (1817–1877)

Click here Do you believe that this item violates a copyright? Your recently viewed items and featured recommendations. View or edit your browsing history. Get to Know Us. Not Enabled Word Wise: In addition, methyl groups are excellent reporters of hydrophobic interactions that often make significant thermodynamic contributions to the formation of protein-protein complexes.

In our case we made two modifications to the published experiment. In the holo-FepB experiment, magnetization was expected to transfer from GaEnt by spin diffusion to the selectively protonated methyl groups of FepB involved in ligand binding. Mapping of the affected residues onto the lowest energy holo-FepB structure revealed that all three residues were found within the cleft region between the N- and C-terminal domains Fig. In agreement with the backbone and methyl CSP results, the regions surrounding Val and Ile experienced significant changes to their chemical environment upon ligand binding.

Reverse methyl cross-saturation experiment of the GaEnt-FepB complex. Backbone 15 N relaxation measurements to examine fast ps to ns time scale backbone dynamics were performed on apo- and holo-FepB Fig.

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Overall, apo-FepB appears well ordered i. For this loop, residues —, —, and — are significantly more rigid in the holoprotein Fig. Moreover, this increased order affects residues neighboring Ile, which was identified by methyl cross-saturation as an interface residue with GaEnt. These two regions also undergo conformational changes in the transition from apo- to holo- FepB and appear to have a role in ligand binding. NMR dynamics analysis of apo- red and holo-FepB blue. In C , residues — in the large loop region, which shows the greatest difference in heteronuclear NOE values between apo- and holo-FepB forms, are highlighted.

In particular residues — are less flexible in holo-FepB. Standard deviations of heteronuclear NOE values are indicated. Apo- and holo-FepB data were recorded at a static magnetic field strength of It was found that the average times for apo- and holo-FepB were Furthermore, we analyzed whether the individual N- and C-terminal domain lobes of apo- and holo-FepB tumble independently in solution.

No significant change in correlation time data not shown was observed when the lobes were treated independently, indicating that the lobes move together in solution. Arg in both of the FepD homodimer chains is in a homologous position to Arg from both BtuC homodimer chains, shown previously to be important for interactions with BtuF A comparison of the BtuC loop, which interacts with BtuF, and a similarly positioned FepD surface loop revealed differences in the electrostatic composition Fig. In BtuC, the loops are composed of both basic and acidic amino acids, whereas in FepD the purported FepB-interacting loop is primarily acidic Fig.

In A , conserved Glu residues and positions are shown for apo- yellow and holo-FepB red on the holo-FepB structure. A space-filling format is used to represent the conserved Glu residues and the flexible loop region residues — of apo- white and holo-FepB dark gray.

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In this study, NMR spin relaxation experiments were used to evaluate changes in FepB dynamics in the presence and absence of ligand. This is particularly relevant for PBPs, as opening and closing motions are important for both ligand binding and release Fig. For type I and II PBPs, it has been suggested that the rigidity of the hinge region, which is strongly influenced by the hydrogen bonding network between hinge elements, becomes more ordered upon ligand binding leading to large scale opening-closing motions These movements originate from minor changes e.

This results in a minor displacement of the N-lobe toward the C-lobe but does not lead to any significant domain-closing motions. Moreover, submission of the lowest energy apo- and holo-FepB structures to the Dyndom server 81 did not reveal any dynamic hinge-bending domain motions associated with ligand binding. The N-lobe of both forms of each protein was aligned prior to analysis.

PBPs also experience changes to the interface between their two lobes upon ligand binding. In types I e. In contrast, both the apo and holo forms of type III PBPs have extensive interlobe contacts, and ligand binding appears to produce subtle rearrangements to this interface.

Structural differences that arise from changes to the intermolecular interactions at this region were evaluated by assessing the interlobe SASA Table 2 Changes to the interlobe interface during the transition between apo and holo forms appears to be important in some type III PBPs for accommodating the structural changes associated with ligand binding, and they could have a role in regulating the opening-closing domain motions. Interestingly, apo-BtuF extracted from the complex with its ABC transporter BtuCD experiences a decrease in interlobe SASA, indicating that its lobes are spread further apart in complex with the transporter than the isolated apo form.

The notable exception is BtuF, which 20 experiences an expansion of its binding pocket upon cyanocobalamin interaction Table 2.

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An increase or reduction in binding pocket SASA is related to the size of the ligand, the depth of binding, and structural features of the protein. Interestingly, Arg is part of a structural insert residues 72—78 that is absent in ViuP Fig. Although two of three basic coordinating residues differ between FepB and ViuP, there exists significant similarity in their binding pocket composition.

CeuE and YclQ and also use a Tyr residue to help coordinate ligand binding. Taken together, our NMR data strongly suggest that FepB possesses a ligand binding pocket similar to that of ViuP, with the primary difference being residues 72—78, which provide a coordinating residue i. A structure-based sequence alignment of PBPs that bind catecholate-type siderophores. Numbering based on alignment position and residue numbers are shown above and on the right of the sequences, respectively. The sequence alignment was constructed using 3D-Coffee From our NMR relaxation experiments, the flexible loop region — in apo-FepB becomes more ordered upon ligand binding.

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This increased rigidity likely originates from direct interactions with GaEnt, as observed with Ile Fig. The movement and direct involvement of C-lobe loop residues in ligand binding has been observed previously for the type III substrate-binding proteins HtsA 90 and SirA 91 from Staphylococcus aureus. B-factor analysis of ViuP suggests that it may also possess a flexible C-lobe loop region residues — , which becomes more rigid upon ligand binding but does not change position.

This structure confirms our ligand binding findings and shows that Arg, Arg, and Arg are the basic trio of residues involved in FeEnt coordination and that the methyl groups of Val, Val, and Ile contribute to ligand binding. The apo FepB crystal structure remains elusive, which is required for understanding the binding mode and mechanism of FeEnt recognition. This interaction is characterized by salt-bridge contacts formed between conserved acidic residues at the apices of each PBP lobe and basic residues on the periplasmic exposed surface of the transporter 8.

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The movement of Glu appears to be related to the ordering of residues within the large loop region residues — of FepB, which occurs upon ligand binding and may help to position Glu for contact with FepD. Interestingly, homology modeling of FepD reveals the presence of acidic loops that would be in position to interact with the predominantly basic ordered loop and binding pocket of FepB to potentially disrupt FeEnt binding in a similar manner as thought to be the case for cyanocobalamin release and BtuF-BtuCD Fig. This result also points to an important role for protein dynamics in PBP-transporter interactions and suggests a mechanism through which FepD can trigger release of FeEnt from FepB, despite its strong ligand binding affinity.

In this study, the mapping of siderophore binding to FepB by a modified reverse methyl-cross saturation NMR experiment was particularly effective in highlighting residues that make hydrophobic contacts with the ligand; this is an effective technique that can be applied to other studies of PBP-ligand interactions. C-lobe loop dynamics were shown to have a significant role in ligand binding in FepB, which highlights the usefulness of our solution NMR approach to studying PBPs.

For regions —, —, and 77—81 within the larger region of residues 70—94 of FepB, the movement of these loops is expected to provide critical contacts with the ligand. The additional flexibility of PBPs as suggested by this study of FepB is likely also important for ligand dissociation.

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The role of protein dynamics in ligand release from the PBP to its cognate cytoplasmic membrane ABC transporter is currently not well understood. As suggested by the more open BtuF structure in complex with its cytoplasmic membrane ABC transporter, BtuCD, protein dynamics may play an important role in enabling the C-lobe of BtuF to pivot and spread apart leading to release of cyanocobalamin We are grateful to the late Dr. Peter Tieleman for the use of the cluster computing resources in calculating the FepB structures. We also thank Dr. Hiroaki Ishida for helpful discussions and testing of the methyl cross-saturation experiments and Dr.