Probing the influence of local coordination environment on the properties of Fe-type nitrile hydratase model complexes

A series of four structurally related cis-dithiolate-ligated Fe(III) complexes, [Fe(III)(DITpy)2]Cl (1), [Fe(III)(DITIm)2]Cl (2), [Fe(III)(ADIT)2]Cl (3), and [Fe(III)(AMIT)2]Cl (4), are described. The structural characterization of 3 as well as the spectroscopic properties of 3 and 4 has been previously reported. Crystal data for 1, 2, and 4 are as follows: 1.3H2O crystallizes in the orthorhombic space group Pca2(1) with a = 19.800(4) A, b = 18.450(4) A, c = 14.800(3) A, and Z = 8. 2.(1/2)EtOH.1/2H2O crystallizes in the monoclinic space group Cc with a = 24.792(4) A, b = 14.364(3) A, c = 17.527(3) A, beta = 124.91(2) degrees, and Z = 8. 4 crystallizes in the triclinic space group P1 with a = 8.0152(6) A, b = 10.0221(8) A, c = 11.8384(10) A, alpha = 73.460(3) degrees, beta = 71.451(5) degrees, gamma = 72.856(4) degrees, and Z = 2. Complexes 1-4 share a common S2N4 coordination environment that consists of two cis-thiolates, two trans-imines, and two cis-terminal nitrogen donors: Nterm = pyridine (1), imidazole (2), and primary amine (3 and 4). The crystallographically determined mean Fe-S bond distances in 1-4 range from 2.196 to 2.232 A and are characteristic of low-spin Fe(III)-thiolate complexes. The low-spin S = 1/2 ground state was confirmed by both EPR and magnetic susceptibility measurements. The electronic spectra of these complexes are characterized by broad absorption bands centered near approximately 700 nm that are consistent with ligand-to-metal charge-transfer (CT) bands. The complexes were further characterized by cyclic voltammetry measurements, and all possess highly negative Fe(III)/Fe(II) redox couples ( approximately -1 V vs SCE, saturated calomel electrode) indicating that alkyl thiolate donors are effective at stabilizing Fe(III) centers. Both the redox couple and the 700 nm band in the visible spectra show solvent-dependent shifts that are dependent upon the H-bonding ability of the solvent. The implications of these results with respect to the active site of the iron-containing nitrile hydratases are also discussed.     

Representing receptor flexibility in ligand docking through relevant normal modes

Inspired by the current representation of the ligand-receptor binding process, a normal-mode-based methodology is presented to incorporate receptor flexibility in ligand docking and virtual screening. However, the systematic representation of the deformation space grows geometrically with the number of modes, and furthermore, midscale loop rearrangements like those found in protein kinase binding pockets cannot be accounted for with the first lowest-frequency modes. We thus introduced a measure of relevance of normal modes on a given region of interest and showed that only very few modes in the low-frequency range are necessary and sufficient to describe loop flexibility in cAMP-dependent protein kinase. We used this approach to generate an ensemble of representative receptor backbone conformations by perturbing the structure along a combination of relevant modes. Each ensemble conformation is complexed with known non-native binders to optimize the position of the binding-pocket side chains through a full flexible docking procedure. The multiple receptor conformations thus obtained are used in a small-scale virtual screening using receptor ensemble docking. We evaluated this algorithm on holo and apo structures of cAMP-dependent protein kinase that exhibit backbone rearrangements on two independent loop regions close to the binding pocket. Docking accuracy is improved, since the ligands considered in the virtual screening docked within 1.5 A to at least one of the structures. The discrimination between binders and nonbinders is also enhanced, as shown by the improvement of the enrichment factor. This constitutes a new step toward the systematic integration of flexible ligand-flexible receptor docking tools in structure-based drug discovery.     

Die Bildung von [(tBu)2P]2P?P[P(tBu)2]2 aus LiP[P(tBu)2]2 und 1,2-Dibromethan. Die Thermolyse von tBu2P?PP(Br)tBu2

[(tBu)₂P]₂P? P[P(tBu)₂]₂ from LiP[P(tBu)₂]₂ and 1,2-Dibromomethane. Pyrolysis of tBu₂P? P?P(Br)tBu₂ All products of the reaction of [tBu₂P]₂PLi 1 with 1,2-dibromoethane 2 were investigated. Already at ?70°C tBu₂P? P?P(Br)tBu₂ 3 as main product and [tBu₂P]₂PBr 4 are formed. Only with an excess of 1 also [tBu₂P]P? P[P(tBu)₂]₂ 5 is obtained. Warming of a pure solution of 3 in toluene from ?70°C to ?30°C leads to 4 , and at 20°C tBu₂PBr and the cyclophosphanes P₄[P(tBu)₂]₄ and P₃[P(tBu)₂]₃ are observed. 5 does not result from 3 , it's rather a byproduct from the reaction of 1 with 4 . Also the ylide 3 and 1 yields 5 .     

The nonlinear vibration analysis of a clamped-clamped beam by a reduced multibody method

The nonlinear response characteristics for a dynamic system with a geometric nonlinearity is examined using a multibody dynamics method. The planar system is an initially straight clamped-clamped beam subject to high frequency excitation in the vicinity of its third natural mode. The model includes a pre-applied static axial load, linear bending stiffness and a cubic in-plane stretching force. Constrained flexibility is applied to a multibody method that lumps the beam into N elements for three substructures subjected to the nonlinear partial differential equation of motion and N-1 linear modal constraints. This procedure is verified by d'Alembert's principle and leads to a discrete form of Galerkin's method. A finite difference scheme models the elastic forces. The beam is tuned by the axial force to obtain fourth order internal resonance that demonstrates bimodal and trimodal responses in agreement with low and moderate excitation test results. The continuous Galerkin method is shown to generate results conflicting with the test and multibody method. A new checking function based on Gauss' principle of least constraint is applied to the beam to minimize modal constraint error.     

Cyclodextrin knowledgebase a web-based service managing CD-ligand complexation data

Cyclodextrins are cyclic oligosaccharides that are able to form water-soluble inclusion complexes with small molecules. Because of their complexing ability, they are widely applied in food, pharmaceutical and chemical industries. In this paper we describe the development of a free web-service, Cyclodextrin KnowledgeBase: (http://www.cyclodextrin.net). The database contains four modules: the Publication, Interaction, Chirality and Analysis Modules. In the Publication Module, almost 50,000 publication details are collected that can be retrieved by text search. In the Interaction and Chirality Modules relevant literature data on cyclodextrin complexation and chiral recognition are collected that can be retrieved by both text and structural searches. Moreover, in the Analysis Module, the geometries of small molecule-cyclodextrin complexes can be predicted using molecular docking tools in order to explore the structures and interaction energies of the inclusion complexes. Complex geometry prediction is made possible by the built-in database of 95 cyclodextrin derivatives, where the 3D structures as well as the partial charges are calculated and stored for further utilization. The use of the database is demonstrated by several examples.     

Front propagation in the bromate-sulfite-ferrocyanide-aluminum (III) system: Autocatalytic front in a buffer system

We study the propagation of pH fronts in a narrow, pseudo-one-dimensional strip of gel containing bromate, sulfite, ferrocyanide and aluminum ions. The front propagation speed v decreases with [ Al³⁺] as , where c is a constant. We determine the diffusion coefficients of protons and ferricyanide ions and find that Al(OH)₃ loaded in agarose or acrylamide gels binds protons reversibly, thereby slowing the propagating fronts without significantly affecting the diffusion of ferricyanide ions. We present a model that qualitatively reproduces the experimental behavior, and we suggest some general principles governing autocatalytic fronts in buffered systems.     

Equilibrium and formation/dissociation kinetics of some Ln(III)PCTA complexes

The protonation constants () of 3,6,9,15-tetraazabicyclo[9.3.1]pentadeca-1(15),11,13-triene-3,6,9-triacetic acid (PCTA) and stability constants of complexes formed between this pyridine-containing macrocycle and several different metal ions have been determined in 1.0 M KCl at 25 degrees C and compared to previous literature values. The first protonation constant was found to be 0.5-0.6 log units higher than the value reported previously, and a total of five protonation steps were detected (log = 11.36, 7.35, 3.83, 2.12, and 1.29). The stability constants of complexes formed between PCTA and Mg2+, Ca2+, Cu2+, and Zn2+ were also somewhat higher than those previously reported, but this difference could be largely attributed to the higher first protonation constant of the ligand. Stability constants of complexes formed between PCTA and the Ln3+ series of ions and Y3+ were determined by using an "out-of-cell" potentiometric method. These values ranged from log K = 18.15 for Ce(PCTA) to log K = 20.63 for Yb(PCTA), increasing along the Ln series in proportion to decreasing Ln3+ cation size. The rates of complex formation for Ce(PCTA), Eu(PCTA), Y(PCTA), and Yb(PCTA) were followed by conventional UV-vis spectroscopy in the pH range 3.5-4.4. First-order rate constants (saturation kinetics) obtained for different ligand-to-metal ion ratios were consistent with the rapid formation of a diprotonated intermediate, Ln(H(2)PCTA)(2+). The stabilities of the intermediates as determined from the kinetic data were 2.81, 3.12, 2.97, and 2.69 log K units for Ce(H(2)PCTA), Eu(H(2)PCTA), Y(H(2)PCTA), and Yb(H(2)PCTA), respectively. Rearrangement of these intermediates to the fully chelated complexes was the rate-determining step, and the rate constant (k(r)) for this process was found to be inversely proportional to the proton concentration. The formation rates (k(OH)) increased with a decrease in the lanthanide ion size [9.68 x 10(7), 1.74 x 10(8), 1.13 x 10(8), and 1.11 x 10(9) M(-1) s(-1) for Ce(PCTA), Eu(PCTA), Y(PCTA), and Yb(PCTA), respectively]. These data indicate that the Ln(PCTA) complexes exhibit the fastest formation rates among all lanthanide macrocyclic ligand complexes studied to date. The acid-catalyzed dissociation rates (k1) varied with the cation from 9.61 x 10(-4), 5.08 x 10(-4), 1.07 x 10(-3), and 2.80 x 10(-4) M(-1) s(-1) for Ce(PCTA), Eu(PCTA), Y(PCTA), and Yb(PCTA), respectively.     

A functional model for the cysteinate-ligated non-heme iron enzyme superoxide reductase (SOR)

Superoxide reductases (SORs) are cysteine-ligated, non-heme iron enzymes that reduce toxic superoxide radicals (O2-). The functional role of the trans cysteinate, as well as the mechanism by which SOR reduces O2-, is unknown. Herein is described a rare example of a functional metalloenzyme analogue, which catalytically reduces superoxide in a proton-dependent mechanism, via a trans thiolate-ligated iron-peroxo intermediate, the first example of its type. Acetic-acid-promoted H2O2 release, followed by Cp2Co reduction, regenerates the active Fe(II) catalyst. The thiolate ligand and its trans positioning relative to the substrate are shown to contribute significantly to the catalyst's function, by lowering the redox potential, changing the spin state, and dramatically lowering the nuFe-O stretching frequency well-below that of any other reported iron-peroxo, while leaving nuO-O high, so as to favor superoxide reduction and Fe-O, as opposed to O-O, bond cleavage. Thus we provide critical insight into the relationship between the SOR structure and its function, as well as important benchmark parameters for characterizing highly unstable thiolate-ligated iron-peroxo intermediates.