Analysing the ability to retain sidechain hydrogen-bonds in mutant proteins

Motivation: Hydrogen bonds are one of the most important inter-atomic interactions in biology. Previous experimental, theoretical and bioinformatics analyses have shown that the hydrogen bonding potential of amino acids is generally satisfied and that buried unsatisfied hydrogen-bond-capable residues are destabilizing. When studying mutant proteins, or introducing mutations to residues involved in hydrogen bonding, one needs to know whether a hydrogen bond can be maintained. Our aim, therefore, was to develop a rapid method to evaluate whether a sidechain can form a hydrogen-bond. Results: A novel knowledge-based approach was developed in which the conformations accessible to the residues involved are taken into account. Residues involved in hydrogen bonds in a set of high resolution crystal structures were analyzed and this analysis is then applied to a given protein. The program was applied to assess mutations in the tumour-suppressor protein, p53. This raised the number of distinct mutations identified as disrupting sidechain-sidechain hydrogen bonding from 181 in our previous analysis to 202 in this analysis.

Protein-disulfide isomerase-mediated reduction of two disulfide bonds of HIV envelope glycoprotein 120 occurs post-CXCR4 binding and is required for fusion

The human immunodeficiency virus (HIV) envelope (Env) glycoprotein (gp) 120 is a highly disulfide-bonded molecule that attaches HIV to the lymphocyte surface receptors CD4 and CXCR4. Conformation changes within gp120 result from binding and trigger HIV/cell fusion. Inhibition of lymphocyte surface-associated protein-disulfide isomerase (PDI) blocks HIV/cell fusion, suggesting that redox changes within Env are required. Using a sensitive assay based on a thiol reagent, we show that (i) the thiol content of gp120, either secreted by mammalian cells or bound to a lymphocyte surface enabling CD4 but not CXCR4 binding, was 0.5-1 pmol SH/pmol gp120 (SH/gp120), whereas that of gp120 after its interaction with a surface enabling both CD4 and CXCR4 binding was raised to 4 SH/gp120; (ii) PDI inhibitors prevented this change; and (iii) gp120 displaying 2 SH/gp120 exhibited CD4 but not CXCR4 binding capacity. In addition, PDI inhibition did not impair gp120 binding to receptors. We conclude that on average two of the nine disulfides of gp120 are reduced during interaction with the lymphocyte surface after CXCR4 binding prior to fusion and that cell surface PDI catalyzes this process. Disulfide bond restructuring within Env may constitute the molecular basis of the post-receptor binding conformational changes that induce fusion competence.

Stabilisation of two Cu(I)-amino N bonds in presence of imino N's

Two structurally characterised examples of air stable Cu-1 (amino N)(2)(imino N)(2) chromophores having a Cu(II/I) potential of 0.01-0.19 V vs SCE in CH2Cl2 are provided using two tetradentate N-donor ligands.

Heterogeneously catalyzed asymmetric hydrogenation of C = C bonds directed by surface-tethered chiral modifiers

Asymmetric hydrogenation of C=C bonds is of the highest importance in organic synthesis, and such reactions are currently carried out with organometallic homogeneous catalysts. Achieving heterogeneous metal-catalyzed hydrogenation, a highly desirable goal, necessitates forcing the crucial enantiodifferentiating step to take place at the metal surface. By synthesis and application of six chiral sulfide ligands that anchor robustly to Pd nanoparticles and resist displacement, we have for the first time accomplished heterogeneous enantioselective catalytic hydrogenation of isophorone. High resolution XPS data established that ligand adsorption from solution occurred exclusively on the Pd nanoparticles and not on the carbon support. All ligands contained a pyrrolidine nitrogen to enable their interaction with the isophorone substrate while the sulfide functionality provided the required interaction with the Pd surface. Enantioselective turnover numbers of up to similar to 100 product molecules per ligand molecule were found with a very large variation in asymmetric induction between ligands: observed enantiomeric excesses increased with increasing size of the alkyl group in the sulfide. This likely reflects varying degrees of ligand dispersion on the surface: bulky substituent groups hinder close approach of ligand molecules to each other, inhibiting close-packed island formation, favoring dispersion as separate molecules, and leading to effective asymmetric induction. Conversely, small substituents favor island formation leading to very low asymmetric induction. Enantioselective reaction most likely involves initial formation of an enamine or iminium species, confirmed by use of an analogous tertiary amine, which leads to racemic product. Ligand rigidity and resistance to self-assembled monolayer formation are important attributes that should be designed into improved chiral modifiers.

Three-centre hydrogen bonds in triphenylphosphine oxide-hydroquinone (1/1)

The title cocrystal, C18H15OP center dot C6H6O2, belongs to a series of molecular systems based on triphenylphosphine P-oxide. The O atom of the oxide group acts as an acceptor for hydrogen bonds from OH groups of two hydroquinone molecules which lie on inversion centres [O center dot center dot center dot O = 2.7451 (17) and 2.681 (2) A S]. The crystal structure is stabilized by weak C-H center dot center dot center dot O hydrogen bonds, forming a C-2(1)(8) chain which runs parallel to the [100] direction.

Redox-active polymers based on nonbridged metal−metal bonds. Electrochemical formation of [Os(bpy)(CO)(L)]n(bpy = 2,2‘-bipyridine; L = CO, MeCN) and of their reduced forms: a spectroelectrochemical study

IR, UV-vis, and EPR spectroelectrochemistry at variable temperatures and in different solvents were applied to investigate in situ the formation of electroactive molecular chains with a nonbridged Os-Os backbone, in particular, the polymer [Os-0(bpy)(CO)(2)](n), (bpy = 2,2'-bipyridine), from a mononuclear Os(II) carbonyl precursor, [Os-II(bpy)(CO)(2)Cl-2]. The one-electron-reduced form, [Os-II(bpy(.-))(CO)(2)Cl-2](-), has been characterized spectroscopically at low temperatures. This radical anion is the key intermediate in the electrochemical propagation process responsible for the metal-metal bond formation. Unambiguous spectroscopic evidence has been gained also for the formation of [{Os-0(bpy(.-))(CO)(2)}(-)](n), the electron-rich electrocatalyst of CO2 reduction. The polymer species are fairly well soluble in butyronitrile, which is important for their potential utilization in nanoscience, for example, as conducting molecular wires. We have also shown that complete solubility is accomplished for the monocarbonyl-acetonitrile derivative of the polymer, [Os-0(bpy)(CO)(MeCN)(2)Cl](n).

Synthesis, structure and solution chemistry of dioxidovanadium(V) complexes with a family of hydrazone ligands. Evidence of formation of centrosymmetric dimers via H-bonds in the solid state

[(VO)-O-IV(acac) 2] reacts with the methanol solution of tridentate ONO donor hydrazone ligands (H2L1-4, general abbreviation H2L; are derived from the condensation of benzoyl hydrazine with 2-hydroxyacetophenone and its 5-substituted derivatives) in presence of neutral monodentate alkyl amine bases having stronger basicity than pyridine e. g., ethylamine, diethylamine, triethylamine and piperidine (general abbreviation B) to produce BH+[VO2L] (1-16) complexes. Five of these sixteen complexes are structurally characterized revealing that the vanadium is present in the anionic part of the molecule, [VO2L] in a distorted square pyramidal environment. The complexes 5, 6, 15 and 16 containing two H-atoms associated with the amine-N atom in their cationic part (e. g., diethylammonium and piperidinium ion) are involved in H-bonding with a neighboring molecule resulting in the formation of centrosymmetric dimers while the complex 12 (containing only one hydrogen atom in the cationic part) exhibits normal H-bonding. The nature of the H-bonds in each of the four centrosymmetric dimeric complexes is different. These complexes have potential catalytic activity in the aerial oxidation of L-ascorbic acid and are converted into the [VO(L)(hq)] complexes containing VO3+ motif on reaction with equimolar amount of 8-hydroxyquinoline (Hhq) in methanol.

Multiple hydrogen bonds induce formation of nanoparticles with internal microemulsion structure by an amphiphilic copolymer

A particulate microemulsion is generated in a simple two-component system comprising an amphiphilic copolymer (Pluronic P123) in mixtures with tannic acid. This is correlated to complexation between the poly(ethylene oxide) in the Pluronic copolymer and the multiple hydrogen bonding units in tannic acid which leads to the breakup of the ordered structure formed in gels of Pluronic copolymers, and the formation of dispersed nanospheres containing a bicontinuous internal structure. These novel nanoparticles termed ‘‘emulsomes’’ are self-stabilized by a coating layer of Pluronic copolymer. The microemulsion exhibits a pearlescent appearance due to selective light scattering from the emulsion droplets. This simple formulation based on a commercial copolymer and a biofunctional and biodegradable additive is expected to find applications in the fast moving consumer goods sector.

Credit risk in covered bonds

Covered bonds are a promising alternative for prime mortgage securitization. In this paper, we explore risk premia in the covered bond market and particularly investigate whether and how credit risk is priced. In extant literature, yield spreads between high-quality covered bonds and government bonds are often interpreted as pure liquidity premia. In contrast, we show that although liquidity is important, it is not the exclusive risk factor. Using a hand-collected data set of cover pool information, we find that the credit quality of the cover assets is an important determinant of covered bond yield spreads. This effect is particularly strong in times of financial turmoil and has a significant influence on the issuer's refinancing cost.

Phosphorescence quantum yield enhanced by intermolecular hydrogen bonds in Cu4I4 clusters in the solid state

Organo-copper(I) halide complexes with a Cu4I4 cubane core and cyclic amines as ligands have been synthesized and their crystal structures have been defined. Their solid state photophysical properties have been measured and correlated with the crystal structure and packing. A unique and remarkably high luminescence quantum yield (76%) has been measured for one of the complexes having the cubane clusters arranged in a columnar structure and held together by N–HI hydrogen bonds. This high luminescence quantum yield is correlated with a slow radiationless deactivation rate of the excited state and suggests a rather strong enhancement of the cubane core rigidity bestowed by the hydrogen bond pattern. Some preliminary thin film deposition experiments show that these compounds could be considered to be good candidates for applications in electroluminescent devices because of their bright luminescence, low cost and relatively easy synthesis processes

OX133, a monoclonal antibody recognizing protein-bound N-ethylmaleimide for the identification of reduced disulfide bonds in proteins

In vivo, enzymatic reduction of some protein disulfide bonds, allosteric disulfide bonds, provides an important level of structural and functional regulation. The free cysteine residues generated can be labeled by maleimide reagents, including biotin derivatives, allowing the reduced protein to be detected or purified. During the screening of monoclonal antibodies for those specific for the reduced forms of proteins, we isolated OX133, a unique antibody that recognizes polypeptide resident, N-ethylmaleimide (NEM)-modified cysteine residues in a sequence-independent manner. OX133 offers an alternative to biotin-maleimide reagents for labeling reduced/alkylated antigens and capturing reduced/alkylated proteins with the advantage that NEM-modified proteins are more easily detected in mass spectrometry, and may be more easily recovered than is the case following capture with biotin based reagents.

Role of Halogen Bonds in Thyroid Hormone Receptor Selectivity: Pharmacophore-Based 3D-QSSR Studies

Most physiological effects of thyroid hormones are mediated by the two thyroid hormone receptor subtypes, TR alpha and TR beta. Several pharmacological effects mediated by TR beta might be beneficial in important medical conditions such as obesity, hypercholesterolemia and diabetes, and selective TR beta activation may elicit these effects while maintaining an acceptable safety profile, To understand the molecular determinants of affinity and subtype selectivity of TR ligands, we have successfully employed a ligand- and structure-guided pharmacophore-based approach to obtain the molecular alignment of a large series of thyromimetics. Statistically reliable three-dimensional quantitative structure-activity relationship (3D-QSAR) and three-dimensional quantitative structure-selectivity relationship (3D-QSSR) models were obtained using the comparative molecular field analysis (CoMFA) method, and the visual analyses of the contour maps drew attention to a number of possible opportunities for the development of analogs with improved affinity and selectivity. Furthermore, the 3D-QSSR analysis allowed the identification of a novel and previously unmentioned halogen bond, bringing new insights to the mechanism of activity and selectivity of thyromimetics.

Structural effects and hydrogen bonds on N,N `-di(methoxycarbonylsulfenyl)urea, [CH(3)OC(O)SNH](2)CO, studied by experimental and theoretical methods

Pure N,N`-di(methoxycarbonylsulfenyl)urea, [CH(3)OC(O)SNH](2)CO, is quantitatively prepared by the hydrolysis reaction of CH(3)OC(O)SNCO and characterized by (1)H NMR, GC-MS and FTIR spectroscopy techniques. Structural and conformational properties are analyzed using a combined approach with data obtained from X-ray diffraction, vibrational spectra and theoretical calculation methods. The IR and Raman spectra for normal and deuterated species are reported. The crystal structure of [CH(3)OC(O)SNH](2)CO was determined by X-ray diffraction methods. The substance crystallizes in the orthorhombic P2(1)2(1)2 space group with a = 9.524(2), b = 12.003(1), c = 4.481 (1) angstrom, and Z = 2 moieties in the unit cell. The molecule is sited on a twofold crystallographic axis (C(2)) parallel to c and shows the anti-anti conformation (S-N single bonds antiperiplanar with respect to the opposite C-N single bonds in sulfenyl-urea-sic group). Neighboring molecules are arranged in a chain motif that extends along the C(2)-axis and is held by bifurcated NH center dot center dot center dot O center dot center dot center dot HN intermolecular bonds. A local planar symmetry is observed in the crystal for the central -SN(H)C(O)N(H)S- skeleton. Experimental and calculated data allow to trace this structural feature to the occurrence of N-H center dot center dot center dot O=C hydrogen bonding interactions. Calculated vibrational and structural properties are in good agreement with the experimentally determined features. (C) 2008 Elsevier B.V. All rights reserved.