Transition structure selectivity in enzyme catalysis: a QM/MM study of chorismate mutase

Two different transition structures (TSs) have been located and characterized for the chorismate conversion to prephenate in Bacillus subtilis chorismate mutase by means of hybrid quantum-mechanical/molecular-mechanical (QM/MM) calculations. GRACE software, combined with an AM1/CHARMM24/TIP3P potential, has been used involving full gradient relaxation of the position of ca. 3300 atoms. These TSs have been connected with their respective reactants and products by the intrinsic reaction coordinate (IRC) procedure carried out in the presence of the protein environment, thus obtaining for the first time a realistic enzymatic reaction path for this reaction. Similar QM/MM computational schemes have been applied to study the chemical reaction solvated by ca. 500 water molecules. Comparison of these results together with gas phase calculations has allowed understanding of the catalytic efficiency of the protein. The enzyme stabilizes one of the TSs (TS_OHout) by means of specific hydrogen bond interactions, while the other TS (TS_OHin) is the preferred one in vacuum and in water. The enzyme TS is effectively more polarized but less dissociative than the corresponding solvent and gas phase TSs. Electrostatic stabilization and an intramolecular charge-transfer process can explain this enzymatically induced change. Our theoretical results provide new information on an important enzymatic transformation and the key factors responsible for efficient selectivity are clarified. Received: 25 March 2000 / Accepted: 7 August 2000 / Published online: 23 November 2000     

Rational Design of Heat‐Set and Specific‐Ion‐Responsive Supramolecular Hydrogels Based on the Hofmeister Effect

Smart supramolecular hydrogels have been prepared from a bolaamphiphilic L ‐valine derivative in aqueous solutions of different salts. The hydrogels respond selectively to different ions and are either reinforced or weakened. In one case, in contrast to conventional systems, the hydrogels are formed upon heating of the system. The use of the hydrogels in the controlled release of an entrapped dye is described as a proof of the potential applications of these systems. The responsive hydrogels were rationally designed by taking into account the noticeable effect of different ions from the Hofmeister series in the solubility of the hydrogelator, which was assessed by using NMR experiments. On the one hand, kosmotropic anions such as sulfate produce a remarkable solubility decrease in the gelator, which is associated with gel reinforcement, as measured by rheological experiments. On the other hand, chaotropic species such as perchlorate weaken the gel. A dramatic effect was observed in the presence of guanidinium chloride, which boosted the solubility of the gelator, in accordance with its chaotropic behaviour reported in protein science. In this case, a direct interaction of the guanidinium species with the carbonyl groups of the hydrogelator is detected by ¹³C NMR spectroscopy. The weakening of this interaction upon a temperature increase allows for the preparation of heat‐set hydrogelating systems.     

Cation‐Directed Dimeric versus Tetrameric Assemblies of Lanthanide‐Stabilized Dilacunary Keggin Tungstogermanates

Reaction of mid‐ to late lanthanide ions with GeO₂ and Na₂WO₄ in NaOAc buffer results in a library of [Ln₂(GeW₁₀O₃₈)]^6? clusters ( Ln₂ ), which consist of dilacunary Keggin fragments stabilized by the insertion of 4f atoms in the vacant sites and show the ability to undergo cation‐directed self‐assembly processes. In the presence of Na⁺, two β‐ Ln₂ subunits assemble by means of Ln‐O(WO₅)‐Ln bridges to form the chiral [Ln₄(H₂O)₆(β‐GeW₁₀O₃₈)₂]^12? dimeric anions (ββ‐ Ln₄ , Ln=Gd, Tb, Dy, Ho, Er, Tm, Yb, Lu). When Cs⁺ is present, two Ln₄ ‐like dimers further assemble into the [{Ln₄(H₂O)₅(GeW₁₀O₃₈)₂}₂]^24? species ( Ln₈ , Ln=Ho, Er, Tm, Yb, Lu). Two types of tetramers coexist in the solid state: One shows a full ββ‐ Ln₈ architecture, whereas the other one is a mixed αβ‐ Ln₈ assembly in which each β‐subunit is linked to its corresponding α‐ Ln₂ derivative. Regardless of differences in isomeric forms and the relative arrangement of Ln₂ subunits, all anions display virtually identical {Ln₄} cores as a common structural feature. A combination of ESI mass spectrometry and ¹⁸³W NMR spectroscopy experiments indicates that Ln₈ tetramers fragment into Ln₄ dimers upon dissolution, which undergo partial dissociation into Ln₂ monomers and slow dimer/monomer equilibration. This is most likely followed by β‐to‐α isomerization of Ln₂ clusters with consequent reassembly, as indicated by isolation of three additional αα‐ Ln₄ derivatives. Magnetic and photoluminescence properties in the Na ‐ββ‐ Ln₄ series are also discussed.     

Tight and Selective Caging of Chloride Ions by a Pseudopeptidic Host

The selective molecular recognition of chloride versus similar anions is a continuous challenge in supramolecular chemistry. We have designed and prepared a simple pseudopeptidic cage ( 1 a ) that defines a cavity suitable for the tight encapsulation of chloride. The interaction of the protonated form of 1 a with different inorganic anions was studied in solution by ¹H NMR spectroscopy and ESI‐MS, and in the solid state by X‐ray diffraction. The solution binding data showed that the association constants of 1 a to chloride are more than two orders of magnitude higher than to any other tested inorganic anion. Remarkably, 1 a displayed a high selectivity for chloride over other closely related halides such as bromide (selectivity=111), iodide (selectivity=719), and fluoride (selectivity >1000). Binding experiments (¹H NMR spectroscopy and ESI‐MS) suggested that 1 a has a high‐affinity (inner) binding site and an additional low‐affinity (external) binding site. The supramolecular complexes with F^?, Cl^?, and Br^? have been also characterized by the X‐ray diffraction of the corresponding [ 1 a? nHX] crystalline salts. The structural data show that the chloride anion is tightly encapsulated within the host, in a binding site defined by a very symmetric array of electrostatic H‐bonds. For the fluoride salt, the size of the cage cavity is too large and is occupied by a water molecule, which fits inside the cage efficiently competing with F^?. In the case of the bigger bromide, the mismatch of the anion inside the cage caused a geometrical distortion of the host and thus a large energetic penalty for the interaction. This minimalistic pseudopeptidic host represents a unique example of the construction of a simple well‐defined binding pocket that allows the highly selective molecular recognition of a challenging substrate.     

Experimental adiabatic vortex ratchet effect in Nb films with asymmetric pinning trap

Nb films grown on top of an array of asymmetric pinning centers show a vortex ratchet effect. A net flow of vortices is induced when the vortex lattice is driven by fluctuating forces on an array of pinning centers without reflection symmetry. This effect occurs in the adiabatic regime and it could be mimiced only by reversible DC driven forces.     

Minimal surfaces: a geometric three dimensional segmentation approach

Summary. A novel geometric approach for three dimensional object segmentation is presented. The scheme is based on geometric deformable surfaces moving towards the objects to be detected. We show that this model is related to the computation of surfaces of minimal area (local minimal surfaces). The space where these surfaces are computed is induced from the three dimensional image in which the objects are to be detected. The general approach also shows the relation between classical deformable surfaces obtained via energy minimization and geometric ones derived from curvature flows in the surface evolution framework. The scheme is stable, robust, and automatically handles changes in the surface topology during the deformation. Results related to existence, uniqueness, stability, and correctness of the solution to this geometric deformable model are presented as well. Based on an efficient numerical algorithm for surface evolution, we present a number of examples of object detection in real and synthetic images. Received January 4, 1996 / Revised version received August 2, 1996     

New coordination cyano-bridged polymers based on tetranuclear rhenium chalcocyanide clusters and copper(ii) ammonia complexes

The reactions of aqueous solutions of the tetranuclear chalcocyanide cluster anions [Re₄Q₄(CN)₁₂]^4–, where Q = S, Se, or Te, with an ammonia solution of copper(ii) chloride at room temperature afforded a series of polymeric cyano-bridged compounds [{Cu(NH₃)₃}₂{Re₄Q₄(CN)₁₂}]·nH₂O (Q = S (1), Se (2)) and [{Cu(NH₃)₃}_1.7{Cu(NH₃)₄}_0.3Re₄Te₄(CN)₁₂] (3) having chain structures. The structures of the compounds were established by X-ray diffraction analysis. Compounds 1 and 2 are isostructural and have ordered structures. In structurally similar compound 3, the copper atoms are disordered over two positions in such a way that the structure contains the bridging {Cu(NH₃)₃} fragments along with the terminal {Cu(NH₃)₄} fragments.     

Carbohydrate recognition at the minor-groove of the self-complementary duplex d(CGCGAATTCGCG)2 by a synthetic glyco-oligoamide

The structure of a neutral glyco-conjugate β-Gal-Py-γ-Py-Ind (1), designed as a probe for analyzing sugar-DNA interactions, when bound to a self-complementary oligonucleotide duplex d(CGCG AATT CGCG)(2) has been deduced by employing (1)H NMR techniques. Analysis of the formed 1:1 complex demonstrated that the glycol ligand is bound in a hairpin-like conformation in which both pyrrole amino acid moieties are stacked, whereas the indole and the sugar residues are spatially close. The binding site is defined by the minor groove formed by the -AATT- stretch. In particular, the -Py-γ-Py- region of the ligand is sited near the A5-A6 oligonucleotide residues, whereas the indole and the sugar rings are next to the T7-T8 base pairs. More relevant, the existence of a variety of intermolecular NOE correlations permitted the close proximity of the sugar to the minor groove to be assessed, thus showing that the binding of the glycoconjugate at the minor groove is the origin of the specificity of the glycoconjugate-DNA interaction. The experimental NMR data have been combined with restrained and unrestrained molecular dynamics calculations, to provide the 3D structure of the complex.     

Volume Growth,Number of Ends,and the Topology of a Complete Submanifold

Given a complete isometric immersion φ:P ^m ?N ⁿ in an ambient Riemannian manifold N ⁿ with a pole and with radial sectional curvatures bounded from above by the corresponding radial sectional curvatures of a radially symmetric space  \(M^{n}_{w}\) , we determine a set of conditions on the extrinsic curvatures of P that guarantee that the immersion is proper and that P has finite topology in line with the results reported in Bessa et al. (Commun. Anal. Geom. 15(4):725–732, 2007) and Bessa and Costa (Glasg. Math. J. 51:669–680, 2009). When the ambient manifold is a radially symmetric space, an inequality is shown between the (extrinsic) volume growth of a complete and minimal submanifold and its number of ends, which generalizes the classical inequality stated in Anderson (Preprint IHES, 1984) for complete and minimal submanifolds in ? ⁿ . As a corollary we obtain the corresponding inequality between the (extrinsic) volume growth and the number of ends of a complete and minimal submanifold in hyperbolic space, together with Bernstein-type results for such submanifolds in Euclidean and hyperbolic spaces, in the manner of the work Kasue and Sugahara (Osaka J. Math. 24:679–704, 1987).