Thermodynamic and structural consequences of changing a sulfur atom to a methylene group in the M13Nle mutation in ribonuclease-S

Two fragments of pancreatic ribonuclease A, a truncated version of S-peptide (residues 1-15) and S-protein (residues 21-124), combine to give a catalytically active complex. We have substituted the wild-type residue at position 13, methionine (Met), with norleucine (Nle), where the only covalent change is the replacement of the sulfur atom with a methylene group. The thermodynamic parameters associated with the binding of this variant to S-protein, determined by titration calorimetry in the temperature range 10-40 degrees C, are reported and compared to values previously reported [Varadarajan, R., Connelly, P. R., Sturtevant, J. M., & Richards, F. M. (1992) Biochemistry 31, 1421-1426] for other position 13 analogs. The differences in the free energy and enthalpy of binding between the Met and Nle peptides are 0.6 and 7.9 kcal/mol at 25 degrees C, respectively. These differences are slightly larger than, but comparable to, the differences in the values for the Met/Ile and Met/Leu pairs. The structure of the mutant complex was determined to 1.85 Angstrom resolution and refined to an R-factor of 17.4% The structures of mutant and wild-type complexes are practically identical although the Nle side chain has a significantly higher average B-factor than the corresponding Met side chain. In contrast, the B-factors of the atoms of the cage of residues surrounding position 13 are all somewhat lower in the Nle variant than in the Met wild-type. Thus, the large differences in the binding enthalpy appear to reside entirely in the difference in chemical properties or dynamic behavior of the -S- and -CH2- groups and not in differences in the geometry of the side chains or the internal cavity surface. In addition, a novel method of obtaining protein stability data by means of isothermal titration calorimetry is introduced.

Social selection and the evolution of cooperative groups: The example of the cellular slime moulds

In social selection the phenotype of an individual depends on its own genotype as well as on the phenotypes, and so genotypes, of other individuals. This makes it impossible to associate an invariant phenotype with a genotype: the social context is crucial. Descriptions of metazoan development, which often is viewed as the acme of cooperative social behaviour, ignore or downplay this fact. The implicit justification for doing so is based on a group-selectionist point of view. Namely, embryos are clones, therefore all cells have the same evolutionary interest, and the visible differences between cells result from a common strategy. The reasoning is flawed, because phenotypic heterogeneity within groups can result from contingent choices made by cells from a flexible repertoire as in multicellular development. What makes that possible is phenotypic plasticity, namely the ability of a genotype to exhibit different phenotypes. However, co-operative social behaviour with division of labour requires that different phenotypes interact appropriately, not that they belong to the same genotype, or have overlapping genetic interests. We sketch a possible route to the evolution of social groups that involves many steps: (a) individuals that happen to be in spatial proximity benefit simply by virtue of their number; (b) traits that are already present act as preadaptations and improve the efficiency of the group; and (c) new adaptations evolve under selection in the social context-that is, via interactions between individuals-and further strengthen group behaviour. The Dictyostelid or cellular slime mould amoebae (CSMs) become multicellular in an unusual way, by the aggregation of free-living cells. In nature the resulting group can be genetically homogeneous (clonal) or heterogeneous (polyclonal); in either case its development, which displays strong cooperation between cells (to the extent of so-called altruism) is not affected. This makes the CSMs exemplars for the study of social behaviour.

Structure of N-tert-butyloxycarbonyl-[alpha]-aminoisobutyryl-DL-pipecolyl-[alpha]-aminoisobutyric acid methyl ester

C20H35N3O6 (Boc-Aib-DL-Pip-Aib-OMe, Boc = tert-butyloxycarbonyl, Aib = alpha-aminoisobutyric acid, Pip = pipecolic acid, OMe = methoxy), M(r) = 413.5, monoclinic, P2(1)/c, a = 18.055 (3), b = 15.048 (3), c = 17.173 (3) angstrom, beta = 91.7 (1)-degrees, V = 4663.8 (9) angstrom3, Z = 8, D(m) = 1.16, D(x) = 1.178 Mg m-3, lambda(Mo Kalpha) = 0.71069 angstrom, mu = 0.081 mm-1, F(000) = 1792, T = 297 K. The final R value for 4925 [I greater-than-or-equal-to 3sigma(I)] reflections is 0.065 (wR = 0.067). The peptide backbone of the two independent molecules in the asymmetric unit is folded at the -Aib-Pip- sequence to form a type-I (I') beta-bend stabilized by a 1 <-- 4 intramolecular N-H...O=C hydrogen bond between the Aib(3) peptide N-H and Boc urethane C=O groups.

Molecular dynamics studies on nucleoside 2',3'-cyclic phosphates

2',3'-cyclic nucleotides are intermediates and substrates of Ribonuclease (RNase)-catalysed reactions. The characterization of the equilibrium conformation as well as the flexibility inherent in these molecules helps in understanding the enzymatic action of RNases. The present study explores parameters like phase angle, glycosydic torsion angle and hydrogen bond to find possible interrelationship between them through Molecular Dynamics (MD) simulations on 3'-GMP, 3'-UMP, A>p, G>p, U>p, C>p, GpA>p and UpA>p. Interesting results of the effect of cyclisation and other constraints such as hydrogen bond between certain groups on the equilibrium ribose conformation have emerged from this study.

Low-temperature structure of two copper-based precursors for MOCVD: Aquabis(tert-butyl acetoacetato)copper(II) and Bis(dipivaloylmethanido)copper(II)

The Cu atoms in aquabis(tert-butyl acetoacetato)copper(II),[Cu(C8H13O3)(2)(H2O)], and bis(dipivaloylmethanido)copper(II), [Cu(C11H19O2)(2)], adopt square-pyramidal and planar conformations, respectively, with average Cu--O distances of 1.933 Angstrom in the former (not including the water ligand) and 1.892 Angstrom in the latter. It is interesting to note that the lability of the tert-butyl and methyl groups in both structures, which renders even the location of the terminal C atoms difficult, is reduced at T = 130 K, enabling location of all the protons in the difference Fourier map.

Microscopic origin of the chirality driven morphologies of the amphiphilic monolayers and bilayers

It is widely known that the compressed monolayers and bilayers of chiral lipids or fatty acids form helical morphologies, while the corresponding racemic modification gives only flat platelets without twist. No molecular explanation of this phenomenon is yet available, although subtle interactions at the chiral centers have often been proposed as the driving force behind the morphology of the aggregate to form a particular shape. In the present study, the morphologies of the chiral amphiphilic assemblies have been predicted on the basis of an effective pair potential between the molecules, which depends on the relative sizes of the groups attached to the chiral centers, the orientation of the amphiphilic molecules and also on the distance between them. It is shown that fur a pair of same kind of enantiomers, the minimum energy conformation favours a twist angle between them. This twist between the neighbouring molecules gives rise to the helicity of the aggregate. The present theory also shows from the molecular considerations that for a pair of mirror-image isomers (i.e. the racemic modification) the minimum energy conformation corresponds to the zero angle between the molecules, thus giving rise to flat platelets as observed in experiments. Another fascinating aspect of such chirality driven helical structures is that the sense (or the handedness) of the helix is highly specific about the chirality of the monomer concerned. The molecular theory shows, for the first time, that the sense of the helical structures in many cases is determined by the sizes of the groups attached to the chiral centers and the effective potential between them. The predicted senses of the helical structures are in complete agreement with the experimental results.

Modulating effect of gelonin gp330 conjugate on Heymann's nephritis induced in rats - A pathomorphological evaluation

Heymann's nephritis (HN) in rats induced by injecting renal proximal tubule brush border protein gp330, is an animal model replicating human autoimmune membranous glomerulonephritis(1). Endogenous IgG gets deposited between the foot processes in the epithelial side of the glomerulus and causes complement-mediated membrane injury, leading to proteinuria and basement membrane thickening. We investigated the effect of a toxin, gelonin conjugated to gp330 and targetted against antigp330-producing cells in ameliorating immune injury and nephrotic state in rats. The groups of animals injected with purified gp330 revealed by immunofluorescence, characteristic granular deposits of IgG along the basement membrane. The rats intravenously injected with gelonin gp330 conjugate, four days after the antigenic challenge with gp330 in two doses, showed amelioration of the nephrotic state and appreciable reduction in glomerular IgG deposits against immune injury. This substantiates our earlier biochemical results and corroborates the possibility of using toxins conjugated to specific antigen in treating antibody-mediated autoimmune diseases.

Reaction of diisopropoxytitanium(III) tetrahydroborate with selected organic compounds containing representative functional groups

Diisopropoxytitanium(III) tetrahydroborate, ((PrO)-Pr-1)(2)TiBH4), generated in situ in dichloromethane from diisopropoxytitanium dichloride and benzyltriethylammonium borohydride in a 1:2 ratio selectively reduces aldehydes, ketones, acid chlorides, carboxylic acids, and N-Boc-protected amino acids to the corresponding alcohols in excellent yield under very mild reaction conditions (-78 to 25 degrees C).

Substitution of chromium for univalent copper in superconducting Pb2Sr2(Ca,Y)Cu3O8+delta

Following considerations of geometry and the similarity between chromate and carbonate groups in terms of size and charge, we have investigated the possibility of replacing the two-coordinate Cu-I in superconducting lead cuprates of the general formula Pb2Sr2(Ca, Y)CU3O8 by Cr. A high-resolution electron microscopy study coupled with energy dispersive X-ray analysis on small crystals of the title phases suggests that between 10 and 15% of the Cu-I can be replaced by Cr. While from the present structural study using HRTEM and Rietveld refinement of X-ray powder data we are unable to precisely obtain the oxidation state and oxygen coordination of Cr, we suggest in analogy with Cr substitution in other similar cuprates that in the title phases (CuO2)-O-I rods are partially replaced by tetrahedral CrO42- groups. Infrared spectroscopy supports the presence of CrO42- groups. The phases Pb1.75Sr2Ca0.2Y0.8O8+delta and Pb1.75Sr2Ca0.2Y0.8CCu2.85Cr0.15O8+delta are superconducting as-prepared, but the substitution of Cr for Cu-I results in a decrease of the Te as well as the superconducting volume fraction. (C) 1996 Academic Press, lnc.

Application of selective F-1 decoupled H-1 NMR for enantiomer resolution and accurate measurement of enantiomeric excess at low chiral substrate/auxiliary concentration

The higher substrate and chiral auxiliary concentration is a pre-requisite to obtain efficient separation of H-1 NMR signals of enantiomers. The higher concentration of chiral lanthanide shift reagents provides broadened spectral lines resulting in a severe loss of resolution between the enantiomer resonances. In order to circumvent such difficulties, herein we present the application and the usefulness of a selective F-1 decoupled correlation (COSY) experiment which yields proton decoupled proton spectra in the indirect dimension. The potentiality of the experiment is demonstrated on several chiral compounds possessing different functional groups, employing either a lanthanide shift reagent or a solvating reagent as chiral auxiliaries. (C) 2011 Elsevier B.V. All rights reserved.

The structures of bacteriorhodopsin with different retinal-Schiff base orientations--computer modeling and energy minimization studies

Bacteriorhodopsin has been the subject of intense study in order to understand its photochemical function. The recent atomic model proposed by Henderson and coworkers based on electron cryo-microscopic studies has helped in understanding many of the structural and functional aspects of bacteriorhodopsin. However, the accuracy of the positions of the side chains is not very high since the model is based on low-resolution data. In this study, we have minimized the energy of this structure of bacteriorhodopsin and analyzed various types of interactions such as - intrahelical and interhelical hydrogen bonds and retinal environment. In order to understand the photochemical action, it is necessary to obtain information on the structures adopted at the intermediate states. In this direction, we have generated some intermediate structures taking into account certain experimental data, by computer modeling studies. Various isomers of retinal with 13-cis and/or 15-cis conformations and all possible staggered orientations of Lys-216 side chain were generated. The resultant structures were examined for the distance between Lys-216-schiff base nitrogen and the carboxylate oxygen atoms of Asp-96 - a residue which is known to reprotonate the schiff base at later stages of photocycle. Some of the structures were selected on the basis of suitable retinal orientation and the stability of these structures were tested by energy minimization studies. Further, the minimized structures are analyzed for the hydrogen bond interactions and retinal environment and the results are compared with those of the minimized rest state structure. The importance of functional groups in stabilizing the structure of bacteriorhodopsin and in participating dynamically during the photocycle have been discussed.

Template directed asymmetric synthesis of the 1,1?-binaphthol unit

An oxidative binaphthol coupling with 65% yield and 65% selectivity has been accomplished using 7-deoxycholic acid as a chiral template.

Prediction of the senses of helical amphiphilic assemblies from effective intermolecular pair potential: Studies on chiral monolayers and bilayers

It is well-known that the senses (or the handedness) of the helical assemblies formed from compressed monolayers and bilayers of chiral amphiphiles are highly specific about the chirality of the monomers concerned. We present here a molecular approach that can successfully predict the senses of such helical morphologies. The present approach is based on a reduced tractable description in terms of an effective pair potential (EPP) which depends on the distance of separation and the relative orientations of the two amphiphiles. This approach explicitly considers the pairwise intermolecular interactions between the groups attached to the chiral centers of the two neighboring amphiphiles. It is found that for a pair of the same kind of enantiomers the minimum energy configuration favors a twist angle between molecules and that this twist from neighbor to neighbor gives rise to the helicity of the aggregate. From the known twist angles at the minimum energy configuration the successive arrangement of an array of molecules can be predicted. Therefore, the sense of the helicity can be predicted from the molecular interactions. The predicted senses of the helical structures are in complete agreement with all known experimental results.

Anomalous Behavior of Linear Hydrocarbon Chains in Water-DMSO Binary Mixture at Low DMSO Concentration

We find that at a mole fraction 0.05 of DMSO (x(DMSO) = 0.05) in aqueous solution, a linear hydrocarbon chain of intermediate length (n = 30-40) adopts the most stable collapsed conformation. In pure water, the same chain exhibits an intermittent oscillation between the collapsed and the extended coiled conformations. Even when the mole fraction of DMSO in the bulk is 0.05, the concentration of the same in the first hydration layer around the hydrocarbon of chain length 30 (n = 30) is as large as 17%. Formation of such hydrophobic environment around the hydrocarbon chain may be viewed as the reason for the collapsed conformation gaining additional stability. We find a second anomalous behavior to emerge near x(DMSO) = 0.15, due to a chain-like aggregation of the methyl groups of DMSO in water that lowers the relative concentration of the DMSO molecules in the hydration layer. We further find that as the concentration of DMSO is gradually increased, it progressively attains the extended coiled structure as the stable conformation. Although Flory-Huggins theory (for binary mixture solvent) fails to predict the anomaly at x(DMSO) = 0.05, it seems to capture the essence of the anomaly at 0.15.

``Clickable'', Trifunctional Magnetite Nanoparticles and Their Chemoselective Biofunctionalization

A multifunctional iron oxide based nanoformulation for combined cancer-targeted therapy and multimodal imaging has been meticulously designed and synthesized using a chemoselective ligation approach. Novel superparamagnetic magnetite nanoparticles simultaneously functionalized with amine, carboxyl, and azide groups were fabricated through a sequence of stoichiometrically controllable partial succinylation and Cu (II) catalyzed diazo transfer on the reactive amine termini of 2-aminoethylphosphonate grafted magnetite nanoparticles (MNPs). Functional moieties associated with MNP surface were chemoselectively conjugated with rhodamine B isothiocyanate (RITC), propargyl folate (FA), and paclitaxel (PTX) via tandem nucleophic addition of amine to isothithiocyanates, Cu (I) catalyzed azide-alkyne click chemistry and carbodiimide-promoted esterification. An extensive in vitro study established that the bioactives chemoselectively appended to the magnetite core bequeathed multifunctionality to the nanoparticles without any loss of activity of the functional molecules. Multifunctional nanoparticles, developed in the course of the study, could selectively target and induce apoptosis to folate-receptor (FR) overexpressing cancer cells with enhanced efficacy as compared to the free drug. In addition, the dual optical and magnetic properties of the synthesized nanoparticles aided in the real-time tracking of their intracellular pathways also as apoptotic events through dual fluorescence and MR-based imaging.