Computing phenomenologic Adair-Klotz constants from microscopic MWC parameters

<p>Abstract</p> <p>Background</p> <p>Modellers using the MWC allosteric framework have often found it difficult to validate their models. Indeed many experiments are not conducted with the notion of alternative conformations in mind and therefore do not (or cannot) measure relevant microscopic constant and parameters. Instead, experimentalists widely use the Adair-Klotz approach in order to describe their experimental data.</p> <p>Results</p> <p>We propose a way of computing apparent Adair-Klotz constants from microscopic association constants and allosteric parameters of a generalised concerted model with two different states (<it>R </it>and <it>T</it>), with an arbitrary number of non-equivalent ligand binding sites. We apply this framework to compute Adair-Klotz constants from existing models of calmodulin and hemoglobin, two extreme cases of the general framework.</p> <p>Conclusion</p> <p>The validation of computational models requires methods to relate model parameters to experimentally observable quantities. We provide such a method for comparing generalised MWC allosteric models to experimentally determined Adair-Klotz constants.</p

Cooperative Binding

Molecular binding is an interaction between molecules that results in a stable association between those molecules. Cooperative binding occurs if the number of binding sites of a macromolecule that are occupied by a specific type of ligand is a nonlinear function of this ligand’s concentration. This can be due, for instance, to an affinity for the ligand that depends on the amount of ligand bound. Cooperativity can be positive (supralinear) or negative (infralinear). Cooperative binding is most often observed in proteins, but nucleic acids can also exhibit cooperative binding, for instance of transcription factors. Cooperative binding has been shown to be the mechanism underlying a large range of biochemical and physiological processes

Modulation of calmodulin lobes by different targets: an allosteric model with hemiconcerted conformational transitions

Calmodulin, the ubiquitous calcium-activated second messenger in eukaryotes, is an extremely versatile molecule involved in many biological processes: muscular contraction, synaptic plasticity, circadian rhythm, and cell cycle, among others. The protein is structurally organised into two globular lobes, joined by a flexible linker. Calcium modulates calmodulin activity by favoring a conformational transition of each lobe from a closed conformation to an open conformation. Most targets have a strong preference for one conformation over the other, and depending on the free calcium concentration in a cell, particular sets of targets will preferentially interact with calmodulin. In turn, targets can increase or decrease the calcium affinity of the calmodulin molecules to which they bind. Interestingly, experiments with the tryptic fragments showed that most targets have a much lower affinity for the N-lobe than for the C-lobe. Hence, the latter predominates in the formation of most calmodulin-target complexes. We showed that a relatively simple allosteric mechanism, based the classic MWC model, can capture the observed modulation of both the isolated C-lobe, and intact calmodulin, by individual targets. Moreover, our model can be naturally extended to study how the calcium affinity of a single pool of calmodulin is modulated by a mixture of competing targets in vivo

Supramolekulární komplexy oxoporfyrinogenů s organickými molekulami

Title: Supramolecular complexes of oxoporphyrinogens with organic molecules Author: Václav Březina Department: Department of Macromolecular Physics Supervisor: doc. RNDr. Lenka Hanyková, Dr., Department of Macromolecular Physics Abstract: Oxoporphyrinogens are flat macrocyclic molecules possessing binding and protonation sites, and capable of light absorption in the visible region. These properties are prerequisites for a colori- metric molecular sensor, i.e. a specific detector of other molecules in the sample. In this work, we studied chromic properties of three oxoporphyrinogens, OxP and its partially (Bz2OxP) and fully (Bz4OxP) N-benzylated derivatives. Their colorimetric response to organic acids is caused by protonation and subsequent formation of supramolecular host-guest complex. We have shown that colorimetric sensitivity is highest for OxP and gradually weakens for Bz2OxP and Bz4OxP since the N-benzylation blocks the central binding sites, decreasing binding affinity of the ox- oporphyrinogens. Furthermore, solvatochromic response of the oxoporphyrinogens to varying solvent polarity showed similar sensitivity decrease in Bz2OxP and Bz4OxP. The chromic and binding properties were studied by UV/vis and NMR spectroscopy, host-guest binding models were applied to describe the formation of...Oxoporfyrinogeny, ploché makrocyklické molekuly, na sebe dokáží navázat kyseliny či jiné látky a zároveň pohlcují světlo ve viditelném oboru. Tyto vlastnosti jsou předpokladem pro molekulární kolorimetrický senzor, detekující přítomnost konkrétních látek ve vzorku. V této práci jsme studovali chromismus tří oxoporfyrinogenů, OxP a jeho částečně (Bz2OxP) a úplně (Bz4OxP) N-benzylovaných derivátů. Jejich kolorimetrická odezva na organické kyseliny je způsobena protonací a následnou tvorbou supramolekulárního "host-guest" komplexu. Vysoká citlivost OxP na přítomnost kyseliny se postupně snižuje u Bz2OxP a Bz4OxP, neboť N-benzylace blokuje centrální vazebná místa a tím se snižuje vazebná afinita oxoporfyrinogenů. Kromě toho byla pozorována solvatochromická odezva oxoporfyrinogenů na měnící se polaritu rozpouštědla, kde se ukázala podobně snížená citlivost u Bz2OxP a Bz4OxP. Ke studiu chromismu a vazebných vlastností byly použity UV/vis a NMR spektroskopie, tvorba komplexů oxoporfyrinogen-kyselina byla popsána vazebnými modely typu "host-guest". Přítomnost chemické výměny v NMR spektrech protonovaného OxP a Bz2OxP ukázala na přítomnost několika dynamických procesů, mimo jiné prototropní tautomerizace (tj. změna místa protonace) nebo rotace objemných postranních skupin v Bz2OxP. Tyto procesy byly v NMR...Department of Macromolecular PhysicsKatedra makromolekulární fyzikyFaculty of Mathematics and PhysicsMatematicko-fyzikální fakult

Investigating the Non-globular Proteins of the Canonical Wnt Signalling Pathway

The canonical Wnt pathway is a vitally important signalling pathway that plays an important role in cell proliferation, differentiation and fate decisions in embryonic development and in the maintenance of adult tissues. The twelve Armadillo (ARM) repeat-containing protein beta-catenin acts as the signal transducer in this pathway and is continuously degraded in the cytosol by the beta-catenin destruction complex (BDC). Upon receiving the Wnt signal the BDC is inactivated, allowing beta-catenin to accumulate in the cytosol and be transported to the nucleus where it binds to the TCF/LEF family of transcription factors, inducing the expression of cell cycle promotor genes. In this Thesis I describe investigations into the roles of leucine-rich repeat kinase 2 (LRRK2) and the transcription factor TCF7L2 within this signalling pathway. LRRK2 is a large multi-domain protein with strong links to Parkinson’s disease and suggested to play a role in inactivating the BDC in response to the Wnt signal. A recent paper proposed that the previously uncharacterised regions of LRRK2 contain a series of tandem repeat sub-domains. I began an investigation into these sub-domains but I was unable to produce soluble protein constructs despite the use of a range of common techniques, and so I was forced to conclude this project early. The main body of this thesis focuses on the interaction between the intrinsically disordered TCF7L2 and the repeat protein beta-catenin, a very long interface of approximately 4800 Å2 that spans from the third to the eleventh ARM repeat of beta-catenin and residues 12 to 50 of TCF7L2, as determined by X-ray crystal structures. First, a fluorescence reporter system for the binding interaction was developed and used to determine the kinetic rate constants for the association and dissociation of the wild-type construct using stopped-flow fluorescence spectroscopy and time-dependent fluorescence spectroscopy. It was found that association of TCF7L2 and beta-catenin was rapid (7.3 ± 0.1 x107 M-1s-1) with only a single phase was observed, whereas dissociation was biphasic and slow (5.7 ± 0.4 x10-4 s-1, 15.2 ± 2.8 x10-4 s-1). Using either of these two dissociation rate constants the calculated Kd value obtained is much lower than the values previously reported in the literature (8 ± 1 / 20 ± 2 pM compared with 16 nM). This reporter system was then used to investigate the striking variability between three crystal structures previously obtained for the TCF7L2-beta-catenin complex, in which different regions of TCF7L2 show different elements of secondary structure. Mutational analysis revealed that the interface residues on TCF7L2 identified in these structures make little or no contribution to the overall binding affinity, pointing to a transient nature of these contact in solution and suggesting that the observed differences between the structures are due to differences in crystal packing. Further experiments into the effect of osmolarity on the binding equilibrium and kinetics supported this conclusion and suggest a change in the association/dissociation mechanism as a function of ionic strength. Lastly, further mutational analysis of TCF7L2 revealed two regions that contribute particularly strongly to the binding kinetics, suggesting that TCF7L2-beta-catenin assembly proceeds via a two-site avidity mechanism. Some of the most destabilising variants display two additional dissociation phases, indicating the presence of an alternative dissociation pathway that is inaccessible to the wild-type. In summary, the results presented here provide insights into the kinetics of molecular recognition of a long intrinsically disordered region with an extended repeat protein surface, a process shown to involve multiple routes with multiple steps in each

Theoretical-experimental study on protein-ligand interactions based on thermodynamics methods, molecular docking and perturbation models

The current doctoral thesis focuses on understanding the thermodynamic events of protein-ligand interactions which have been of paramount importance from traditional Medicinal Chemistry to Nanobiotechnology. Particular attention has been made on the application of state-of-the-art methodologies to address thermodynamic studies of the protein-ligand interactions by integrating structure-based molecular docking techniques, classical fractal approaches to solve protein-ligand complementarity problems, perturbation models to study allosteric signal propagation, predictive nano-quantitative structure-toxicity relationship models coupled with powerful experimental validation techniques. The contributions provided by this work could open an unlimited horizon to the fields of Drug-Discovery, Materials Sciences, Molecular Diagnosis, and Environmental Health Sciences