Steric Specificity Research Articles

Highlighting Aglycone-dependent Glycosylation Aspects in Caryophyllaceae Saponins by a Simplex Simulation Approach.

Saponin metabolism shows high structural variability due to the diversity of aglycones and glycosylations (Gly). Although they represent a potential source of drug design, their metabolism remains misunderstood yet due to insufficient investments in analytical methods. Bibliographic structural data offer a wide field for extensive statistical analysis, highlighting mechanistic orders governing metabolic diversity. This work presents an original simulation method based on simplex rule for highlighting regulatory mechanisms of metabolism from categorical structural data. Simulation was applied on a set of 231 saponins of the Caryophyllaceae plant family initially affiliated to four aglycone types: gypsogenin (Gyp), quillaic acid (QA), gypsogenic acid (GA), and 16-OH-gypsogenic acid (16-OH-GA). Molecules were initially characterized by relative glycosylation levels of different carbons. Simplex approach was applied by combining saponins of the four aglycone groups using a complete set of N gradual weightings between structural groups. In silico combinations were applied by randomly sampling representative saponins from the four groups conforming to their weights given by mixture design. Gly profiles of sampled saponins were averaged to calculate a barycentric molecular profile for each mixture. With N mixtures, N barycentric molecules were iteratively calculated by bootstrap, leading to smoothed data from which Gly trends between carbons were highlighted. Sequential, competing and cooperative Gly trends were highlighted according to the types of aglycones, attached saccharides and positions of substituted carbons. Such various conditional Gly trends seemed to be linked to multiple factors, including steric effects, regio-selectivity, enzymatic specificity and enzymatic promiscuity. These simulated results could be helpfully useful in chemical synthesis and drug design. These simulated results could usefully help for chemical syntheses and drug design.

Formation of odorant haloanisoles and variation of microorganisms during microbial O-methylation in annular reactors equipped with different coupon materials

Taste and odor (T & O) issues in drinking water have become serious problems which cannot be ignored by customers. Several studies have confirmed that microbes in water can biotransform halophenols (HPs) to haloanisoles (HAs) with earthy and musty flavors via microbial O-methylation. In this paper, the formation of 2-chloroanisole (2-CA), 2,4-dichloroanisole (2,4-DCA), 2,4,6-trichloroanisole (2,4,6-TCA), 2,3,6-trichloroanisole (2,3,6-TCA) and 2,4,6-tribromoanisole (2,4,6-TBA), and the microbial variation during the microbial O-methylation were investigated in annular reactors (ARs) with three coupon materials. For precursors, 42.5% of 2-CP and 68.9% of 2,4-DCP decayed during the reaction. Among the five HAs, the formation rate constant followed an order of 2,4,6-TCA > 2-CA > 2,4,6-TBA > 2,4-DCA ~ 2,3,6-TCA, while [HA]max followed a totally opposite one. The simulated flow velocity had no significant effect (p > 0.05) on HA formation. Ductile iron (DI) AR could produce more HAs than stainless steel (SS) and polyvinyl chloride (PVC) ARs. The final HA molar concentration followed an order of 2,3,6-TCA > 2,4-DCA > 2,4,6-TBA ~ 2,4,6-TCA > 2-CA, which might be explained by multiple factors including HP's dissociation degree, halogen atom's steric hindrance and specificity of HP O-methyltransferases. During the reaction, the microbial biomass dramatically increased 6.8–9.0 times in bulk water but dropped significantly on coupon biofilms. The effect of HPs significantly changed the bacterial communities on coupon in terms of composition and diversity, and declined the relative abundance of HA-producing bacteria, while fungi and their HA-producing genus showed better resistance ability towards HPs. By using Pearson correlation analysis, a significant correlation (p = 0.0003) was found between [HA]max and initial coupon biofilm biomass. Finally, a linear relationship was established between initial total biomass and HA formation potential.

The predicted role of steric specificity in crowding-mediated effects on reversible biomolecular association

A fundamental question in biology is whether the presence of non-reacting macromolecules in the cytoplasm affects the rates and extents of reversible association reactions, a phenomenon often referred to as ‘macromolecular crowding.’ Under certain conditions, crowding has been proposed to dramatically alter the kinetics and thermodynamics of chemical reactions, making it difficult to quantitatively relate rates and extents of reactions measured in vitro to those occurring in vivo. In this work, we use Brownian dynamics simulation and Monte Carlo methods to (1) quantify the overall thermodynamic and kinetic effects of crowding by independently investigating each step of reversible bimolecular association (i.e. translational diffusion, steric specific binding, and dissociation), and (2) provide an explicit, quantitative investigation of how the degree of steric specificity of protein dimerization influences crowding-mediated effects on association and dissociation. We find that kon decreases by ∼2-fold for non-steric specific reactions, and increases by ∼3-fold for highly steric specific reactions. In addition, koff decreases by only ∼30%–60% in the presence of crowders, depending on the strength of the bond between the reactant pair, so that the equilibrium constant is increased by ∼4-fold, at most. These results suggest that crowding-mediated effects on globular protein dimerization reactions in the cytoplasm are modulated by the steric specificity of the reactants, and that reversible protein–protein association is relatively insensitive to the physical presence of crowders (i.e. steric repulsion effects in the cytoplasm) for crowders of similar size and shape to reactants over a range of volume fractions (0–0.3).

Engineering complementary hydrophobic interactions to control β-hairpin peptide self-assembly, network branching, and hydrogel properties.

The MAX1 β-hairpin peptide (VKVKVKVK-V(D)PPT-KVKVKVKV-NH2) has been shown to form nanofibrils having a cross-section of two folded peptides forming a hydrophobic, valine-rich core, and the polymerized fibril exhibits primarily β-sheet hydrogen bonding.1-7 These nanofibrils form hydrogel networks through fibril entanglements as well as fibril branching.8 Fibrillar branching in MAX1 hydrogel networks provide the ability to flow under applied shear stress and immediately reform a hydrogel solid on cessation of shear. New β-hairpins were designed to limit branching during nanofibril growth because of steric specificity in the assembled fibril hydrophobic core. The nonturn valines of MAX1 were substituted by 2-naphthylalanine (Nal) and alanine (A) residues, with much larger and smaller side chain volumes, respectively, to obtain LNK1 (Nal)K(Nal)KAKAK-V(D)PPT-KAKAK(Nal)K(Nal)-NH2. LNK1 was targeted to self-associate with a specific "lock and key" complementary packing in the hydrophobic core in order to accommodate the Nal and Ala residue side chains. The experimentally observable manifestation of reduced fibrillar branching in the LNK1 peptide is the lack of solid hydrogel formation after shear in stark contrast to the MAX1 branched fibril system. Molecular dynamics simulations provide a molecular picture of interpeptide interactions within the assembly that is consistent with the branching propensity of MAX1 vs LNK1 and in agreement with experimental observations.

The solvatochromic effects of side chain substitution on the binding interaction of novel tricarbocyanine dyes with human serum albumin

The effects of solvatochromism on protein-ligand interactions have been studied by absorbance and near-infrared laser induced fluorescence (NIR-LIF) spectroscopy. The utility of three novel classes of cyanine dyes designed for this purpose illustrates that the affinity interactions of ligands at the hydrophobic binding pockets of Human Serum Albumin (HSA) are not only dependent on the overall hydrophobic characteristics of the molecules but are highly influenced by the size of the ligands as well. Whereas changes to the chromophore moiety exhibited slight to moderate changes to the hydrophobic nature of these molecules, substitution at the alkyl indolium side chain has enabled us to vary the binding affinity towards serum albumin. Substitution at the indolium side chain among an ethyl to butyl group results in improved binding characteristics and an almost three-fold increase in affinity constant. In addition, replacement of the ethyl side chain with a phenylpropyl group also yielded unique solvotachromic patterns such as increased hydrophobicity and subsequent biocompatibility with the HSA binding regions. Ligand interaction was however inhibited by steric hindrance associated with the bulky phenyl ring system thus affecting the increased binding that could be realized from the improved hydrophobic nature of the molecules. This characteristic change in binding affinity is of potential interest to developing a methodology which reveals information on the hydrophobic character and steric specificity of the binding cavities.

Evolutionary Diversification of the Sm Family of RNA-Associated Proteins

The Sm family of proteins is closely associated with RNA metabolism throughout all life. These proteins form homomorphic and heteromorphic rings consisting of six or seven subunits with a characteristic central pore, the presence of which is critical for binding U-rich regions of single-stranded RNA. Eubacteria and Archaea typically carry one or two forms of Sm proteins and assemble one homomorphic ring per Sm protein. Eukaryotes typically carry 16 or more Sm proteins that assemble to form heteromorphic rings which lie at the center of a number of critical RNA-associated small nuclear ribonucleoproteins (snRNPs). High Sm protein diversity and heteromorphic Sm rings are features stretching back to the origin of eukaryotes; very deep phylogenetic divisions among existing Sm proteins indicate simultaneous evolution across essentially all existing eukaryotic life. Two basic forms of heteromorphic Sm rings are found in eukaryotes. Fixed Sm rings are highly stable and static and are assembled around an RNA cofactor. Flexible Sm rings also stabilize and chaperone RNA but assemble in the absence of an RNA substrate and, more significantly, associate with and dissociate from RNA substrates more freely than fixed rings. This suggests that the conformation of flexible Sm rings might be modified in some specific manner to facilitate association and dissociation with RNA. Diversification of eukaryotic Sm proteins may have been initiated by gene transfers and/or genome clashes that accompanied the origin of the eukaryotic cell itself, with further diversification driven by a greater need for steric specificity within increasingly complex snRNPs.

Realistic protein-protein association rates from a simple diffusional model neglecting long-range interactions, free energy barriers, and landscape ruggedness.

We develop a simple but rigorous model of protein-protein association kinetics based on diffusional association on free energy landscapes obtained by sampling configurations within and surrounding the native complex binding funnels. Guided by results obtained on exactly solvable model problems, we transform the problem of diffusion in a potential into free diffusion in the presence of an absorbing zone spanning the entrance to the binding funnel. The free diffusion problem is solved using a recently derived analytic expression for the rate of association of asymmetrically oriented molecules. Despite the required high steric specificity and the absence of long-range attractive interactions, the computed rates are typically on the order of 10(4)-10(6) M(-1) sec(-1), several orders of magnitude higher than rates obtained using a purely probabilistic model in which the association rate for free diffusion of uniformly reactive molecules is multiplied by the probability of a correct alignment of the two partners in a random collision. As the association rates of many protein-protein complexes are also in the 10(5)-10(6) M(-1) sec(-1) range, our results suggest that free energy barriers arising from desolvation and/or side-chain freezing during complex formation or increased ruggedness within the binding funnel, which are completely neglected in our simple diffusional model, do not contribute significantly to the dynamics of protein-protein association. The transparent physical interpretation of our approach that computes association rates directly from the size and geometry of protein-protein binding funnels makes it a useful complement to Brownian dynamics simulations.

Interaction of benzene thiol and thiolate with small gold clusters.

We studied the interaction between benzene thiol and thiolate molecules, and gold clusters made of 1 to 3 atoms, by means of ab initio density functional theory in the local density approximation. We find that the thiolate is energetically more stable than the thiol, however the process of detachment of H from the thiol appears to be possibly mediated by the intermediate step of H chemisorption on Au. Cleavage of the S-H bond is accompanied by a 90 degrees rotation of the molecule around the S-Au bond, showing a strong steric specificity. Such a rotation is induced by the relative energy shift of the S atom p orbitals with respect to the benzene pi ring and the Au d orbitals. By analyzing the correlation of the bond energy, bond lengths, and HOMO-LUMO gap with the number of S-Au bonds, we find that the thiolate S atom appears to prefer a low-coordination condition on Au clusters.

A General Expression for Bimolecular Association Rates with Orientational Constraints

We present a general expression for the association rate for partially diffusion-controlled reactions between spherical molecules with an asymmetric reactive patch on each surface. Reaction can occur only if the two patches are in contact and properly aligned to within specified angular tolerances. This extends and generalizes previous approaches that considered only axially symmetric patches; the earlier solutions are shown to be limiting cases of our general expression. Previous numerical results on the rate of protein -protein association with high steric specificity are in very good agreement with the value computed from our analytic expression. Using the new expression, we investigate the influence of orientational constraints on the rate constant. We find that for angular constraints of 5°-15°, a typical range for example in the case of protein-protein interactions, the reaction rate is about 2 to 3 orders of magnitude higher than expected from a naive geometric model.

Dibenzylic structures on macromolecular chain: IX. The interaction of urethane-isocyanate groups in polyurethane formation

The interaction of isocyanate-urethane and isocyanate-amide groups in urethane group formation is studied. Bibenzil-2,2′-di-yl diisocyanate (2,2′ BBDI) presents specific behaviour due to the steric specificity of its structure. Rotation of the two aromatic nuclei around ethylenic bridges favours strong intramolecular anchimeric assistance in the second step of the 2,2′ BBDI with n-butanol (BuOH) reaction. This assistance also enhances secondary reactions leading to unexpected cyclic allophanate structure. Mechanisms for these reactions are proposed in concordance with kinetic measurements.

Characterization of adrenal cytochrome P450c21 from the blacktip shark (Carcharhinus limbatus)

AbstractThe characteristics of cytochrome P450c21 (21 hydroxylase; E.C. 1.14.99.10) were determined in interrenal tissue from blacktip shark (Carcharhinus limbatus). Consistent with other vertebrates, 21‐hydroxylase activity was enriched in the microsomal fraction of the interrenal and was dependent upon a source of reducing equivalents. The reduced form of nicotinamide adenine dinucleotide phosphate supported the highest level of activity. Specific activity increased with increasing temperature (Q10 = 2.5) with a maximum at 35°C. At 30°C, maximal 21‐hydroxylase activity reached a plateau around pH 7.5. Elasmobranchs maintain high concentrations of intracellular nitrogenous compounds known to disturb protein function. While urea (400 mM) had no apparent effect upon 21‐hydroxylase activity, trimethylamine oxide (200 mM) inhibited conversion of progesterone to 11‐deoxycorticosterone by 23%. This inhibition was not reversed by urea. Potassium chloride (150 mM) inhibited 21‐hydroxylase activity by 33%. Kinetic parameters of shark 21‐hydroxylase were determined for [3H]progesterone (Km = 80 nM; Vmax = 2.94 nmol/min/mg protein) and [3H]17α‐hydroxyprogesterone (Km = 90 nM; Vmax = 0.89 nmol/min/mg protein). Substituted progestins were used to determine the steric specificity of this enzyme. Of thirteen steroid substrates studied, nine were metabolized, indicating a relatively broad specificity. The addition of trimethylamine oxide did not alter the substrate specificity. Although the blacktip shark homolog of cytochrome P450c21 is similar in some respects to other vertebrate forms, its temperature dependence, preferential use of progesterone and broad substrate specificity are unusual characteristics. © 1995 Wiley‐Liss, Inc.

Effect of high pressure on the steric specificity of the helferich glycosylation

Effect of high pressure on the steric specificity of the helferich glycosylation

Steric specificity of the direct13C-1H spin-spin coupling constants in the vinyl group in N-vinylpyrroles

The direct13C-1H spin-spin coupling constants of the vinyl group β-carbon in N-vinyl-pyrroles display steric specificity and change depending on the dihedral angle between the planes of the vinyl group and the heterocycle.

The reaction of nitronium fluorosulfate with fluoroolefins

1. Nitronium fluorosulfate added to fluoroolefins and bis(trifluoromethyl)ketene to form β-nitropolyfluoroalkyl fluorosulfates and α-nitrohexafluoroisobutyroyl fluorosulfate, respectively. High steric specificity was demonstrated for the addition of nitronium fluorosulfate to hexafluoro-l,3-butadiene. 2. The combined nitrofluorination of trifluoroethylene and 2-hydropentafluoro-1-propene by nitronium fluorosulfate in anhydrous hydrogen fluoride provides evidence for an electrophilic mechanism for the reaction of nitronium fluorosulfate with fluoroolefins.

Epoxidation of 4?-chloro-3(10)carene

1. The epoxidation of 4β-chloro-3(10)-carene proceeds without steric specificity to give two stereoisomeric epoxides with predominance of the trans isomer. 2. 4β-Chloro-3(10)-carene and its isomeric epoxides have half-chair conformation with equatorial C-Cl bonds.

Synthesis of optically active o-methyl-o-aryl phenylthiophosphonates and their properties

Optically active isomers of (O-methy1-O-2,3-dichlorophenyl) phenylthiophosphonate were obtained. Steric specificity of the insecticide activity and toxicity of the organophosphorus compounds obtained relative to mice was observed.

ChemInform Abstract: CATALYTIC AND HYDRIDE REDUCTION OF HEXAFLUOROPROPYLENE DIMERS

AbstractDie Redu‐ktion der Verbindungen (I) und (III) wird unter den im Formelschema angegebenen Bedingungen untersucht.

Catalytic and hydride reduction of hexafluoropropylene dimers

1. Higher internal perfluoroolefins are readily reduced by catalytic hydrogenation and treatment with complex metal hydrides. 2. The hydrogenation of fluoroolefins on palladium catalysts proceeds with rigorous steric specificity.

A Glycolipid Antigen Associated with Burkitt Lymphoma Defined by a Monoclonal Antibody

The antigen defined by a rat monoclonal antibody directed to a Burkitt lymphoma cell line was identified as globotriaosylceramide [Gal alpha (1 leads to 4)-Gal beta (1 leads to 4)-Glc beta (1 leads to 1)-ceramide]. The antibody demonstrated a strict steric specificity since it did not react with globoisotriaosylceramide [Gal alpha (1 leads to 3)-Gal beta (1 leads to 4)-Glc beta (1 leads to 1)-ceramide], the positional isomer of the antigen associated with the Burkitt lymphoma. Chemical analysis of various Burkitt lymphoma cell lines revealed that the Burkitt lymphoma cells contained more than 100 times as much of the glycolipid antigen as was found in other human lymphoma and leukemia cell lines.

Cysteine as a system-specific substrate for transport system [formula omitted] in rat hepatocytes

The rapid transport of L -cysteine into isolated rat hepatocytes escapes detectable inhibition by 2-(methylamino)-isobutyric acid at levels up to 50 mM. The system transporting cysteine instead is convincingly similar to the ASC system described for the Ehrlich cell in structural and steric specificity and in pH sensitivity. The Na +-dependent uptake of 2-aminoisobutyric acid is almost evenly divided between Systems A and ASC , showing better accommodation of its two α-methyl groups by ASC than in the Ehrlich cell. The hepatocyte ASC system tolerates Li +-for-Na + substitution better than does System A , although the tolerance depends on amino acid structure. Adaptive regulation and insulin and glucagon stimulation were not seen under conditions producing these effects for System A .