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Sökning: WFRF:(Ryde Ulf) > Engelska

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1.
  • Diehl, Carl, et al. (författare)
  • Protein Flexibility and Conformational Entropy in Ligand Design Targeting the Carbohydrate Recognition Domain of Galectin-3.
  • 2010
  • Ingår i: Journal of the American Chemical Society. - The American Chemical Society. - 1520-5126. ; 132, s. 14577-14589
  • Tidskriftsartikel (refereegranskat)abstract
    • Rational drug design is predicated on knowledge of the three-dimensional structure of the protein-ligand complex and the thermodynamics of ligand binding. Despite the fundamental importance of both enthalpy and entropy in driving ligand binding, the role of conformational entropy is rarely addressed in drug design. In this work, we have probed the conformational entropy and its relative contribution to the free energy of ligand binding to the carbohydrate recognition domain of galectin-3. Using a combination of NMR spectroscopy, isothermal titration calorimetry, and X-ray crystallography, we characterized the binding of three ligands with dissociation constants ranging over 2 orders of magnitude. (15)N and (2)H spin relaxation measurements showed that the protein backbone and side chains respond to ligand binding by increased conformational fluctuations, on average, that differ among the three ligand-bound states. Variability in the response to ligand binding is prominent in the hydrophobic core, where a distal cluster of methyl groups becomes more rigid, whereas methyl groups closer to the binding site become more flexible. The results reveal an intricate interplay between structure and conformational fluctuations in the different complexes that fine-tunes the affinity. The estimated change in conformational entropy is comparable in magnitude to the binding enthalpy, demonstrating that it contributes favorably and significantly to ligand binding. We speculate that the relatively weak inherent protein-carbohydrate interactions and limited hydrophobic effect associated with oligosaccharide binding might have exerted evolutionary pressure on carbohydrate-binding proteins to increase the affinity by means of conformational entropy.
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2.
  • Kadhirvel, Saraboji, et al. (författare)
  • The Carbohydrate-Binding Site in Galectin-3 Is Preorganized To Recognize a Sugarlike Framework of Oxygens: Ultra-High-Resolution Structures and Water Dynamics
  • 2012
  • Ingår i: Biochemistry. - The American Chemical Society. - 0006-2960. ; 51:1, s. 296-306
  • Tidskriftsartikel (refereegranskat)abstract
    • The recognition of carbohydrates by proteins is a fundamental aspect of communication within and between living cells. Understanding the molecular basis of carbohydrate-protein interactions is a prerequisite for the rational design of synthetic ligands. Here we report the high- to ultrahigh-resolution crystal structures of the carbohydrate recognition domain of galectin-3 (Gal3C) in the ligand-free state (1.08 angstrom at 100 K, 1.25 angstrom at 298 K) and in complex with lactose (0.86 angstrom) or glycerol (0.9 angstrom). These structures reveal striking similarities in the positions of water and carbohydrate oxygen atoms in all three states, indicating that the binding site of Gal3C is preorganized to coordinate oxygen atoms in an arrangement that is nearly optimal for the recognition of beta-galactosides. Deuterium nuclear magnetic resonance (NMR) relaxation dispersion experiments and molecular dynamics simulations demonstrate that all water molecules in the lactose-binding site exchange with bulk water on a time scale of nanoseconds or shorter. Nevertheless, molecular dynamics simulations identify transient water binding at sites that agree well with those observed by crystallography, indicating that the energy landscape of the binding site is maintained in solution. All heavy atoms of glycerol are positioned like the corresponding atoms of lactose in the Gal3C complexes. However, binding of glycerol to Gal3C is insignificant in solution at room temperature, as monitored by NMR spectroscopy or isothermal titration calorimetry under conditions where lactose binding is readily detected. These observations make a case for protein cryo-crystallography as a valuable screening method in fragment-based drug discovery and further suggest that identification of water sites might inform inhibitor design.
3.
  • Lecerof, David, et al. (författare)
  • Metal binding to Bacillus subtilis ferrochelatase and interaction between metal sites.
  • 2003
  • Ingår i: Journal of Biological Inorganic Chemistry. - Springer. - 1432-1327. ; 8:4, s. 452-458
  • Tidskriftsartikel (refereegranskat)abstract
    • Ferrochelatase, the terminal enzyme in heme biosynthesis, catalyses metal insertion into protoporphyrin IX. The location of the metal binding site with respect to the bound porphyrin substrate and the mode of metal binding are of central importance for understanding the mechanism of porphyrin metallation. In this work we demonstrate that Zn2+, which is commonly used as substrate in assays of the ferrochelatase reaction, and Cd2+, an inhibitor of the enzyme, bind to the invariant amino acids His183 and Glu264 and water molecules, all located within the porphyrin binding cleft. On the other hand, Mg2+, which has been shown to bind close to the surface at 7 Å from His183, was largely absent from its site. Activity measurements demonstrate that Mg2+ has a stimulatory effect on the enzyme, lowering KM for Zn2+ from 55 to 24 µM. Changing one of the Mg2+ binding residues, Glu272, to serine abolishes the effect of Mg2+. It is proposed that prior to metal insertion the metal may form a sitting-atop (SAT) complex with the invariant His-Glu couple and the porphyrin. Metal binding to the Mg2+ site may stimulate metal release from the protein ligands and its insertion into the porphyrin.
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4.
  • Andrejic, Milica, et al. (författare)
  • Coupled-Cluster Interaction Energies for 200-Atom Host-Guest Systems
  • 2014
  • Ingår i: ChemPhysChem. - John Wiley & Sons. - 1439-7641. ; 15:15, s. 3270-3281
  • Tidskriftsartikel (refereegranskat)abstract
    • We have developed a method to calculate interaction energies of large systems (such as host-guest or even protein-ligand systems) at the local coupled-cluster with singles, doubles, and perturbative triples level, and with extrapolation to the limit of a complete basis set. The method is based on the polarizable multipole interactions with supermolecular pairs molecular fractionation approach, which combines a pairwise quantum-mechanical evaluation of the short-range interactions with a polarizable multipole treatment of many-body effects. The method is tested for nine guest molecules binding to an octa-acid host (in total 198-207 atoms), as part of the SAMPL4 blind challenge. From the test calculations, the accuracy of the approach is found to be 10 kJ mol(-1) or better. Comparison with dispersion-corrected density functional theory reveals that the latter underestimates the dispersion contribution for this type of system, which leads to a difference in the ranking of the ligands.
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6.
  • Ballmann, Joachim, et al. (författare)
  • Secondary bonding interactions in biomimetic [2Fe-2S] clusters
  • 2008
  • Ingår i: Inorganic Chemistry. - The American Chemical Society. - 1520-510X. ; 47:5, s. 1586-1596
  • Tidskriftsartikel (refereegranskat)abstract
    • A series of synthetic [2Fe-2S] complexes with terminal thiophenolate ligands and tethered ether or thioether moieties has been prepared and investigated in order to provide models for the potential interaction of additional donor atoms with the Fe atoms in biological [2Fe-2S] clusters. X-ray crystal structures have been determined for six new complexes that feature appended Et (1(C)), OMe (1(O)), or SMe (1(S)) groups, or with a methylene group (2(C)), an ether-O (2(O)), or an thioether-S (2(S)) linking two aryl group. The latter two systems provide a constrained chelate arrangement that induces secondary bonding interactions with the ether-O and thioether-S, which is confirmed by density functional theory (DFT) calculations that also reveal significant spin density on those fifth donor atoms. Structural consequences of the secondary bonding interactions are analyzed in detail, and effects on the spectroscopic and electronic properties are probed by UV-vis, Mossbauer, and H-1 NMR spectroscopy, as well by SQUID measurements and cyclic voltammetry. The potential relevance of the findings for biological [2Fe-2S] sites is considered.
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7.
  • Bruschi, Maurizio, et al. (författare)
  • A DFT investigation on structural and redox properties of a synthetic Fe6S6 assembly closely related to the [FeFe]-hydrogenases active site
  • 2008
  • Ingår i: Comptes Rendus. Chimie. - Elsevier. - 1631-0748. ; 11:8, s. 834-841
  • Tidskriftsartikel (refereegranskat)abstract
    • In the present contribution, a density functional theory (DFT) investigation is described regarding a recently synthesized Fe6S6 complex - see C. Tard, X. Liu, S.K. Ibrahim, M. Bruschi, L. De Gioia, S.C. Davies, X. Yang, L.-S. Wang, G. Sawers, C.J. Pickett, Nature 433 (2005) 610 - that is structurally and functionally related to the [FeFe]-hydrogenases active site (the so-called H-cluster, which includes a binuclear subsite directly involved in catalysis and an Fe4S4 cubane). The analysis of relative stabilities and atomic charges of different isomers evidenced that the structural and redox properties of the synthetic assembly are significantly different from those of the enzyme active site. A comparison between the hexanuclear cluster and simpler synthetic diiron models is also described; the results of such a comparison indicated that the cubane moiety can favour the stabilization of the cluster in a structure closely resembling the H-cluster geometry when the synthetic Fe6S6 complex is in its dianionic state. However, the opposite effect is observed when the synthetic cluster is in its monoanionic form.
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8.
  • Bruschi, Maurizio, et al. (författare)
  • Functionally Relevant Interplay between the Fe(4)S(4) Cluster and CN(-) Ligands in the Active Site of [FeFe]-Hydrogenases.
  • 2010
  • Ingår i: Journal of the American Chemical Society. - The American Chemical Society. - 1520-5126. ; 132:14, s. 4992-4992
  • Tidskriftsartikel (refereegranskat)abstract
    • [FeFe]-hydrogenases are highly efficient H(2)-evolving metalloenzymes that include cyanides and carbonyls in the active site. The latter is an Fe(6)S(6) cluster (the so-called H-cluster) that can be subdivided into a binuclear portion carrying the CO and CN(-) groups and a tetranuclear subcluster. The fundamental role of cyanide ligands in increasing the basicity of the H-cluster has been highlighted previously. Here a more subtle but crucial role played by the two CN(-) ligands in the active site of [FeFe]-hydrogenases is disclosed. In fact, QM/MM calculations on all-atom models of the enzyme from Desulfovibrio desulfuricans show that the cyanide groups fine-tune the electronic and redox properties of the active site, affecting both the protonation regiochemistry and electron transfer between the two subclusters of the H-cluster. Despite the crucial role of cyanides in the protein active site, the currently available bioinspired electrocatalysts generally lack CN(-) groups in order to avoid competition between the latter and the catalytic metal centers for proton binding. In this respect, we show that a targeted inclusion of phosphine ligands in hexanuclear biomimetic clusters may restore the electronic and redox features of the wild-type H-cluster.
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9.
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10.
  • Caldararu, Octav, et al. (författare)
  • Binding free energies in the SAMPL5 octa-acid host–guest challenge calculated with DFT-D3 and CCSD(T)
  • 2016
  • Ingår i: Journal of Computer-Aided Molecular Design. - Kluwer. - 0920-654X.
  • Tidskriftsartikel (refereegranskat)abstract
    • We have tried to calculate the free energy for the binding of six small ligands to two variants of the octa-acid deep cavitand host in the SAMPL5 blind challenge. We employed structures minimised with dispersion-corrected density-functional theory with small basis sets and energies were calculated using large basis sets. Solvation energies were calculated with continuum methods and thermostatistical corrections were obtained from frequencies calculated at the HF-3c level. Care was taken to minimise the effects of the flexibility of the host by keeping the complexes as symmetric and similar as possible. In some calculations, the large net charge of the host was reduced by removing the propionate and benzoate groups. In addition, the effect of a restricted molecular dynamics sampling of structures was tested. Finally, we tried to improve the energies by using the DLPNO–CCSD(T) approach. Unfortunately, results of quite poor quality were obtained, with no correlation to the experimental data, systematically too positive affinities (by ~50 kJ/mol) and a mean absolute error (after removal of the systematic error) of 11–16 kJ/mol. DLPNO–CCSD(T) did not improve the results, so the accuracy is not limited by the energy function. Instead, four likely sources of errors were identified: first, the minimised structures were often incorrect, owing to the omission of explicit solvent. They could be partly improved by performing the minimisations in a continuum solvent with four water molecules around the charged groups of the ligands. Second, some ligands could bind in several different conformations, requiring sampling of reasonable structures. Third, there is an indication the continuum-solvation model has problems to accurately describe the binding of both the negatively and positively charged guest molecules. Fourth, different methods to calculate the thermostatistical corrections gave results that differed by up to 30 kJ/mol and there is an indication that HF-3c overestimates the entropy term. In conclusion, it is a challenge to calculate binding affinities for this octa-acid system with quantum–mechanical methods.
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