The price of flexibility – a case study on septanoses as pyranose mimetics

Sager, Christoph P.; Fiege, Brigitte; Zihlmann, Pascal; Vannam, Raghu; Rabbani, Said; Jakob, R.P.; Preston, Roland C.; Zalewski, Adam; Maier, Timm; Peczuh, Mark W.; Ernst, Beat

doi:10.1039/c7sc04289b

Cited by 33 publications

(40 citation statements)

References 62 publications

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“…However, mannose modification may also affect the on‐rate constant, as observed for the ring extended compound 9 . As shown in the study of Sager et al., septulose 9 (PDB‐code: 5CGB) and pyranoside 1 (PDB‐code: 4XO8) establish an identical H‐bond network with FimH LD . Upon binding to the lectin, the markedly increased flexibility of septulose 9 in solution leads to an entropy penalty due to a loss of conformational freedom upon binding.…”

Section: Resultsmentioning

confidence: 90%

KinITC—One Method Supports both Thermodynamic and Kinetic SARs as Exemplified on FimH Antagonists

Zihlmann

Silbermann

Sharpe

et al. 2018

Chemistry A European J

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Affinity data, such as dissociation constants (K ) or inhibitory concentrations (IC ), are widely used in drug discovery. However, these parameters describe an equilibrium state, which is often not established in vivo due to pharmacokinetic effects and they are therefore not necessarily sufficient for evaluating drug efficacy. More accurate indicators for pharmacological activity are the kinetics of binding processes, as they shed light on the rate of formation of protein-ligand complexes and their half-life. Nonetheless, although highly desirable for medicinal chemistry programs, studies on structure-kinetic relationships (SKR) are still rare. With the recently introduced analytical tool kinITC this situation may change, since not only thermodynamic but also kinetic information of the binding process can be deduced from isothermal titration calorimetry (ITC) experiments. Using kinITC, ITC data of 29 mannosides binding to the bacterial adhesin FimH were re-analyzed to make their binding kinetics accessible. To validate these kinetic data, surface plasmon resonance (SPR) experiments were conducted. The kinetic analysis by kinITC revealed that the nanomolar affinities of the FimH antagonists arise from both (i) an optimized interaction between protein and ligand in the bound state (reduced off-rate constant k ) and (ii) a stabilization of the transition state or a destabilization of the unbound state (increased on-rate constant k ). Based on congeneric ligand modifications and structural input from co-crystal structures, a strong relationship between the formed hydrogen-bond network and k could be concluded, whereas electrostatic interactions and conformational restrictions upon binding were found to have mainly an impact on k .

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Section: Resultsmentioning

confidence: 90%

KinITC—One Method Supports both Thermodynamic and Kinetic SARs as Exemplified on FimH Antagonists

Zihlmann

Silbermann

Sharpe

et al. 2018

Chemistry A European J

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“…⌬S 0 obs (change in entropy) was calculated from the known thermodynamic quantities and further dissected into conformational, mixing, and solvation entropy according to the methodology as described in Ref. 70. A concentration correction factor was included as fitting parameter to account for the uncertainty in determining FimH LD concentration.…”

Section: Isothermal Titration Calorimetry (Itc)mentioning

confidence: 99%

Conformational switch of the bacterial adhesin FimH in the absence of the regulatory domain: Engineering a minimalistic allosteric system

Rabbani

Fiege

Eriş

et al. 2018

Journal of Biological Chemistry

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Edited by Wolfgang Peti For many biological processes such as ligand binding, enzymatic catalysis, or protein folding, allosteric regulation of protein conformation and dynamics is fundamentally important. One example is the bacterial adhesin FimH, where the C-terminal pilin domain exerts negative allosteric control over binding of the N-terminal lectin domain to mannosylated ligands on host cells. When the lectin and pilin domains are separated under shear stress, the FimH-ligand interaction switches in a so-called catch-bond mechanism from the low-to high-affinity state. So far, it has been assumed that the pilin domain is essential for the allosteric propagation within the lectin domain that would otherwise be conformationally rigid. To test this hypothesis, we generated mutants of the isolated FimH lectin domain and characterized their thermodynamic, kinetic, and structural properties using isothermal titration calorimetry, surface plasmon resonance, nuclear magnetic resonance, and X-ray techniques. Intriguingly, some of the mutants mimicked the conformational and kinetic behaviors of the full-length protein and, even in absence of the pilin domain, conducted the cross-talk between allosteric sites and the mannoside-binding pocket. Thus, these mutants represent a minimalistic allosteric system of FimH, useful for further mechanistic studies and antagonist design. The authors declare that they have no conflicts of interest with the contents of this article. This article contains Figs. S1-S11, Tables S1-S2, supporting Extended Experimental procedures, and supporting Refs. 1-5. The atomic coordinates and structure factors (code 5MCA) have been deposited in the Protein Data Bank (http://wwpdb.org/).

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“…The major conformational states observed for the lectin domain are one with a wide mannose binding site, another with a narrow site around the ligand, and a third intermediate conformation. The major conformations of the lectin domains have been variously labeled as “elongated” and “compressed,” “open” and “closed,” “low affinity” and “high affinity,” “R” and “T” states, and “loose” and “tight” . Adjectives describing the ligand binding site (“wide” and “narrow”) will be used here as labels for the major domain conformations.…”

Section: Introductionmentioning

confidence: 99%

“…The and "high affinity," 10 "R" and "T" states, 11 and "loose" and "tight". 12 Adjectives describing the ligand binding site ("wide" and "narrow") will be used here as labels for the major domain conformations. The "intermediate" structures (see below) complicate attempts to correlate wide and narrow mannose binding sites with the lectin domain conformations, but the "wide" and "narrow" labels for the domain conformations will be applied to the major conformations.…”

Section: Introductionmentioning

confidence: 99%

RMSD analysis of structures of the bacterial protein FimH identifies five conformations of its lectin domain

et al. 2019

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FimH is a bacterial adhesin protein located at the tip of Escherichia coli fimbria that functions to adhere bacteria to host cells. Thus, FimH is a critical factor in bacterial infections such as urinary tract infections and is of interest in drug development. It is also involved in vaccine development and as a model for understanding shear‐enhanced catch bond cell adhesion. To date, over 60 structures have been deposited in the Protein Data Bank showing interactions between FimH and mannose ligands, potential inhibitors, and other fimbrial proteins. In addition to providing insights about ligand recognition and fimbrial assembly, these structures provide insights into conformational changes in the two domains of FimH that are critical for its function. To gain further insights into these structural changes, we have superposed FimH's mannose binding lectin domain in all these structures and categorized the structures into five groups of lectin domain conformers using RMSD as a metric. Many structures also include the pilin domain, which anchors FimH to the fimbriae and regulates the conformation and function of the lectin domain. For these structures, we have also compared the relative orientations of the two domains. These structural analyses enhance our understanding of the conformational changes associated with FimH ligand binding and domain‐domain interactions, including its catch bond behavior through allosteric action of force in bacterial adhesion.

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The price of flexibility – a case study on septanoses as pyranose mimetics

Abstract: Interacting with lectins, mannose can be mimicked with seven-membered ring analogues but at the price of a substantial entropy penalty.

Cited by 33 publications

References 62 publications

KinITC—One Method Supports both Thermodynamic and Kinetic SARs as Exemplified on FimH Antagonists

KinITC—One Method Supports both Thermodynamic and Kinetic SARs as Exemplified on FimH Antagonists

Conformational switch of the bacterial adhesin FimH in the absence of the regulatory domain: Engineering a minimalistic allosteric system

RMSD analysis of structures of the bacterial protein FimH identifies five conformations of its lectin domain

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