Allosteric Coupling in the Bacterial Adhesive Protein FimH

Rodriguez, Victoria B.; Kidd, Brian; Interlandi, Gianluca; Tchesnokova, Veronika; Sokurenko, Evgeni V.; Thomas, Wendy E.

doi:10.1074/jbc.m113.461376

Cited by 37 publications

(69 citation statements)

References 56 publications

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“…The conformational fluctuations of the two binding sites were weakly correlated to each other. These observations are consistent with a recent mutagenesis study that also showed weak conformational coupling between the two distal regions 15. The centrally located large β sheet was found here to have the characteristics of a soft spring indicated by the Guassian distribution of a dihedral angle that describes its twisting motion.…”

Section: Discussionsupporting

confidence: 93%

“…This indicates that the conformational transition is propagated across the lectin domain mainly through twisting of the large β sheet, which has the greatest effect on the clamp and swing loops. In contrast, other elements that lie between the regulatory and active sites, like the bulge‐helix segment that are known to be part of the allosteric pathway,15 do not demonstrate any involvement in propagation between the distal sites in our study, and instead may stabilize the two distinct conformations of the regulatory region.…”

Section: Discussioncontrasting

confidence: 89%

“…4(a,b) and Table 3 and a previous publication by us15]. In contrast, the simulations of the low affinity state in complex with mannose presented only five persistent hydrogen bonds, which are a subset of the six observed in high affinity.…”

Section: Resultsmentioning

confidence: 59%

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Mechanism of allosteric propagation across a β‐sheet structure investigated by molecular dynamics simulations

Interlandi

Thomas

2016

Proteins

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The bacterial adhesin FimH consists of an allosterically regulated mannose‐binding lectin domain and a covalently linked inhibitory pilin domain. Under normal conditions, the two domains are bound to each other, and FimH interacts weakly with mannose. However, under tensile force, the domains separate and the lectin domain undergoes conformational changes that strengthen its bond with mannose. Comparison of the crystallographic structures of the low and the high affinity state of the lectin domain reveals conformational changes mainly in the regulatory inter‐domain region, the mannose binding site and a large β sheet that connects the two distally located regions. Here, molecular dynamics simulations investigated how conformational changes are propagated within and between different regions of the lectin domain. It was found that the inter‐domain region moves towards the high affinity conformation as it becomes more compact and buries exposed hydrophobic surface after separation of the pilin domain. The mannose binding site was more rigid in the high affinity state, which prevented water penetration into the pocket. The large central β sheet demonstrated a soft spring‐like twisting. Its twisting motion was moderately correlated to fluctuations in both the regulatory and the binding region, whereas a weak correlation was seen in a direct comparison of these two distal sites. The results suggest a so called “population shift” model whereby binding of the lectin domain to either the pilin domain or mannose locks the β sheet in a rather twisted or flat conformation, stabilizing the low or the high affinity state, respectively. Proteins 2016; 84:990–1008. © 2016 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.

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Section: Discussionsupporting

confidence: 93%

Section: Discussioncontrasting

confidence: 89%

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Mechanism of allosteric propagation across a β‐sheet structure investigated by molecular dynamics simulations

Interlandi

Thomas

2016

Proteins

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“…Most bonds between K12 and man-BSA last under 1 s, and a small fraction are much longer lived, demonstrating that K12 can bind to mannose in both the inactive and active states (20). The structure of the short-lived inactive bound state is not known, but mutational studies suggest weak, or sequential, allosteric coupling, in which the clamp loop closes transiently around mannose and the regulatory region remains compressed (27). FimH forms catch bonds because mechanical force induces the elongated state of the regulatory region, which stabilizes the closed form of the clamp loop (20,28).…”

Section: Significancementioning

confidence: 99%

“…FimH forms catch bonds because mechanical force induces the elongated state of the regulatory region, which stabilizes the closed form of the clamp loop (20,28). Many variants of FimH have been either engineered or discovered in clinical isolates that increase binding to mannose in static conditions (27,29,30) by destabilizing the inactive state relative to the active state (27). Evolution selects against these mutations (30,31), which strongly suggests that the inactive state provides a functional advantage in vivo, but the mechanism for this advantage remains unknown.…”

Section: Significancementioning

confidence: 99%

Inactive conformation enhances binding function in physiological conditions

Yakovenko

Tchesnokova

Sokurenko

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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Many receptors display conformational flexibility, in which the binding pocket has an open inactive conformation in the absence of ligand and a tight active conformation when bound to ligand. Here we study the bacterial adhesin FimH to address the role of the inactive conformation of the pocket for initiating binding by comparing two variants: a wild-type FimH variant that is in the inactive state when not bound to its target mannose, and an engineered activated variant that is always in the active state. Not surprisingly, activated FimH has a longer lifetime and higher affinity, and bacteria expressing activated FimH bound better in static conditions. However, bacteria expressing wild-type FimH bound better in flow. It is now known that few proteins recognize ligands through a lock and key mechanism, in which the binding pocket is in essentially the same conformation whether or not ligand is bound. Instead, the conformation of the binding pocket is usually dynamic. Conformational dynamics have many functions for receptors as well as enzymes, so for simplicity, we will use the term ligand to describe substrates and products as well as molecules that are not changed by binding. For allosteric proteins, an obvious function of conformational changes in the pocket is to allow regulation of ligand binding by an allosteric effector. For other proteins, flexibility in the binding pocket allows proteins to bind structurally distinct ligands (1), which may in turn facilitate evolution of new structures and functions (2, 3). In many cases, the inactive conformation of the pocket is relatively loose, and the active conformation tightens around the ligand, often due to the closing of a hinge (4) between two domains, or loops that are described as a gate (e.g., refs. 5-7) or a lid (e.g., refs. 8-11) because they close over the ligand in binding pocket. The ability of the pocket to close around different ligands can contribute to specificity (5). Switching to the inactive state of the receptor dramatically increases the dissociation rate, so pocket dynamics controls the residence time of ligands (4, 12), and thus the catalytic rate of most enzymes (3). The importance of the inactive state to association rates is less clear; inactive states have been shown have lower (4, 12), similar (13), or higher (14) association rates relative to the active state, and the functional importance of the differences is unclear.We hypothesize that inactive states can have faster ligand association rates, and that this is important for nonequilibrium processes, where the kinetics, or rates, of individual steps are more important than overall affinity because the process does not reach equilibrium. An example of a nonequilibrium process is cell adhesion. Because adhesive receptors bind to ligands that are anchored to other cells or surfaces, the adhesive bonds are subjected to tensile mechanical force due to cytoskeletal contraction, fluidflow-induced drag forces, or other stresses. This tensile force can only be applied between receptor and lig...

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The Tyrosine Gate of the Bacterial Lectin FimH: A Conformational Analysis by NMR Spectroscopy and X‐ray Crystallography

et al. 2015

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Urinary tract infections caused by uropathogenic E. coli are among the most prevalent infectious diseases. The mannose-specific lectin FimH mediates the adhesion of the bacteria to the urothelium, thus enabling host cell invasion and recurrent infections. An attractive alternative to antibiotic treatment is the development of FimH antagonists that mimic the physiological ligand. A large variety of candidate drugs have been developed and characterized by means of in vitro studies and animal models. Here we present the X-ray co-crystal structures of FimH with members of four antagonist classes. In three of these cases no structural data had previously been available. We used NMR spectroscopy to characterize FimH-antagonist interactions further by chemical shift perturbation. The analysis allowed a clear determination of the conformation of the tyrosine gate motif that is crucial for the interaction with aglycone moieties and was not obvious from X-ray structural data alone. Finally, ITC experiments provided insight into the thermodynamics of antagonist binding. In conjunction with the structural information from X-ray and NMR experiments the results provide a mechanism for the often-observed enthalpy-entropy compensation of FimH antagonists that plays a role in fine-tuning of the interaction.

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Allosteric Coupling in the Bacterial Adhesive Protein FimH

Cited by 37 publications

References 56 publications

Mechanism of allosteric propagation across a β‐sheet structure investigated by molecular dynamics simulations

Mechanism of allosteric propagation across a β‐sheet structure investigated by molecular dynamics simulations

Inactive conformation enhances binding function in physiological conditions

The Tyrosine Gate of the Bacterial Lectin FimH: A Conformational Analysis by NMR Spectroscopy and X‐ray Crystallography

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