Protein sequence design on the basis of topology optimization techniques -Using continuous modeling of discrete amino acid types

The notion of optimization is inherent in protein design. A long linear chain of twenty types of amino acid residues are known to fold to a 3-D conformation that minimizes the combined inter-residue energy interactions. There are two distinct protein design problems, viz. predicting the folded structure from a given sequence of amino acid monomers (folding problem) and determining a sequence for a given folded structure (inverse folding problem). These two problems have much similarity to engineering structural analysis and structural optimization problems respectively. In the folding problem, a protein chain with a given sequence folds to a conformation, called a native state, which has a unique global minimum energy value when compared to all other unfolded conformations. This involves a search in the conformation space. This is somewhat akin to the principle of minimum potential energy that determines the deformed static equilibrium configuration of an elastic structure of given topology, shape, and size that is subjected to certain boundary conditions. In the inverse-folding problem, one has to design a sequence with some objectives (having a specific feature of the folded structure, docking with another protein, etc.) and constraints (sequence being fixed in some portion, a particular composition of amino acid types, etc.) while obtaining a sequence that would fold to the desired conformation satisfying the criteria of folding. This requires a search in the sequence space. This is similar to structural optimization in the design-variable space wherein a certain feature of structural response is optimized subject to some constraints while satisfying the governing static or dynamic equilibrium equations. Based on this similarity, in this work we apply the topology optimization methods to protein design, discuss modeling issues and present some initial results.

Structural studies of model peptides containing beta-, gamma- and delta-amino acids

The crystal structures of five model peptides Piv-Pro-Gly-NHMe (1), Piv-Pro-beta Gly-NHMe (2), Piv-Pro-beta Gly-OMe (3), Piv-Pro-delta Ava-OMe (4) and Boc-Pro-gamma Abu-OH (5) are described (Piv:pivaloyl; NHMe: N-methylamide; beta Gly:beta-glycine; OMe:O-methyl ester; delta Ava:delta-aminovaleric acid; gamma Abu:gamma-aminobutyric acid). A comparison of the structures of peptides 1 and 2 illustrates the dramatic consequences upon backbone homologation in short sequences. 1 adopts a type II beta-turn conformation in the solid state, while in 2, the molecule adopts an open conformation with the beta-residue being fully extended. Piv-Pro-beta Gly-OMe (3), which differs from 2 by replacement of the C-terminal NH group by an O-atom, adopts an almost identical molecular conformation and packing arrangement in the solid state. In peptide 4, the observed conformation resembles that determined for 2 and 3, with the delta Ava residue being fully extended. In peptide 5, the molecule undergoes a chain reversal, revealing a beta-turn mimetic structure stabilized by a C-H center dot center dot center dot O hydrogen bond.

Effect of calcium deficiency on the mechanical properties of hydroxyapatite crystals

The deterioration of the mechanical properties of bone with age is related to several factors including the structure, organization and chemistry of the constituent phases; however, the relative contribution of each of these factors is not well understood. In this study, we have investigated the effect of chemistry (calcium deficiency) on the mechanical properties of single crystals of hydroxyapatite. Single crystals of stoichiometric crystals grown by the flux method and calcium-deficient platelet crystals grown using wet chemical methods were used as model systems. Using nanoindentation, we show that calcium deficiency leads to an 80% reduction in the hardness and elastic modulus and at least a 75% reduction in toughness in plate-shaped hydroxyapatite crystals. Measurement of local mechanical properties using nanoindentation and nanoscale chemistry through elemental mapping in a transmission electron microscope points to a direct correlation between the observed spatial variation in composition and the large scatter in the measured hardness and modulus values. (C) 2010 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Redistribution of subcellular calcium in rat liver on administration of vanadate

Mitochondria isolated from the livers of rats administered with sodium meta-, ortho-, or polyvanadate, but not vanadyl sulphate, exhibited enhanced Ca2+ — stimulated respiration and uptake of calcium. These effects were shown also by mitochondria isolated from livers perfused with polyvanadate. The concentration of acid-soluble calcium decreased significantly in the mitochondrial fraction on vanadate treatment, while that in the cytosol showed a corresponding increase. Phenoxybenzamine, an antagonist to a-adrenergic receptors, effectively inhibited vanadate-induced Ca2+ mobilization, but surgical sympathectomy was without effect. This is the first demonstration of vanadate mimicking agr-adrenergic agonists in vivo.

Novel organic porous solids with channel and layered structures from 1,3,5-triazine-2,4,6-triaminehexaacetic acid and its calcium salt

Single crystals of a symmetrically substituted molecule, 1,3,5-triazine-2,4,6-triaminehexaacetic acid, (TTHA) and its Ca2+ salt have been synthesized, the analysis of which reveals the existence of novel channel type cavities and helical packing organizations in the crystals.

Synthesis and Antileukemic Activity of 1-((S)-2-Amino-4,5,6,7-tetrahydrobenzo[d]thiazol-6-yl)-3-(substituted phenyl)urea Derivatives

Heterocyclic urea derivatives play an important role as anticancer agents because of their good inhibitory activity against receptor tyrosine kinases (RTKs), raf kinases, protein tyrosine kinases (PTKs), and NADH oxidase, which play critical roles in many aspects of tumorigenesis. Benzothiazole moiety constitutes an important scaffold of drugs, possessing several pharmacological functions, mainly the anticancer activity. Based on these interesting properties of benzothiazoles and urea moiety to obtain new biologically active agents, we synthesized a series of novel 1-((S)-2-amino-4,5,6.7-tetrahydrobenzo[d]thiazol-6-yl)-3-(substituted phenyl)urea derivatives and evaluated for their efficacy as antileukemic agents against two human leukemic cell lines (K562 and Reh). These compounds showed good and moderate cytotoxic effect to cancer cell lines tested. Compounds with electron-withdrawing chloro and fluoro substituents on phenyl ring showed good activity and compounds with electron-donating methoxy group showed moderate activity. Compound with electron-withdrawing dichloro substitution on phenyl ring of aryl urea showed good activity. Further, lactate dehydrogenase (LDH) assay, flow cytometric analysis of annexin V-FITC/propidium iodide (PI) double staining and DNA fragmentation studies showed that compound with dichloro substitution on phenyl ring of aryl urea can induce apoptosis.

Bicyclic Phosphazenes Derived from (Amino) Cyclotetraphosphazenes

Amination reactions of 2,6-bis(primary amino)cyclotetraphosphazenes yield not only the expected (amino)cyclotetraphosphazenes but also novel trans-annular bridged bicyclic phosphazenes by an intramolecular substitution pathway. In addition, resins are formed in some reactions by an intermolecular condensation. The effect of substituents attached to the phosphazene ring, the attacking nucleophile and solvent on the formation of the trans-annular P-N-P bridge is considered in detail in relation to plausible reaction mechanisms. Analytical separation of bicyclic phosphazenes by high performance liquid chromatography (HPLC) on a reverse phase silica column is demonstrated. Structural features of bicyclic phosphazenes and salient aspects of their NVR spectroscopic data are discussed.

ESR studies of X-irradiated strontium mixed calcium tartrate crystals

The electron spin resonance spectra of X-ray irradiated single crystals of strontium doped calcium tartrate tetrahydrate (CST) with molecular formula Ca0.88Sr0.12C4H4O6.4H(2)O grown in gels has been investigated. Only one species of free radical but with two magnetically unequivalent sites was observed at room temperature. The free radical was found to be the result of the splitting of a C-II bond adjacent to both the hydroxyl and carboxyl groups. The a factor was found to be slightly anisotropic. Couplings with two H nuclei, believed to be the proton of the OH group attached directly to the unsaturated asymmetric carbon atom and the proton attached directly to the: other asymmetric carbon atom of the molecule were observed. The principal g-values were found to be 2.0030, 2.0017, 2.0027. The principal elements of the nuclear coupling are 7.45, 6.59, 4.28 and 8.56, 7.22, 18.71 G, respectively. The radical was found to be very stable. (C) 2000 Elsevier Science Ltd. All rights reserved.

Adsorption behaviour of an oxidised starch onto haematite in the presence of calcium

The adsorption behaviour of an oxidised starch AP as well as that of calcium onto haematite have been studied both individually and together. While the adsorption density of starch AP onto haematite is enhanced in the presence of calcium, the adsorption of calcium onto haematite is not promoted by starch AP. Flocculation tests on haematite ore fines in the presence of starch AP and calcium chloride reveal that the sequence in which calcium and starch are added governs the settling rates and turbidity values. Zeta potential, viscosity and conductivity measurements, and calcium ion binding studies with starch AP indicate calcium-starch interactions. Possible mechanisms involved in such interactions with respect to haematite flocculation have been discussed.

Aggregation of calcium ionophore (A23187) in phospholipid vesicles

The circular dichroism studies on calcium ionophore, A23187, incorporated in Dipalmitoyl phosphatidyl choline (DPPC) vesicle showed interesting time dependent changes in the CD spectra. Analysis of the data indicated the possible aggregation of the observed dimeric structure of this molecule in non-polar solvents into a stacked dimeric pore in the phospholipid vesicle.

Low-temperature polymer precursor-based synthesis of nanocrystalline particles of lanthanum calcium manganese oxide (La0.67Ca0.33MnO3) with enhanced ferromagnetic transition temperature

We report a simple modified polymeric precursor route for the synthesis of highly crystalline and homogenous nanoparticles of lanthanum calcium manganese oxide (LCMO). The LCMO phase formation was studied by thermal analysis, x-ray powder diffraction, and infrared spectroscopy at different stages of heating. These nanocrystallites (average particle size of 30 nm) possess ferromagnetic-paramagnetic transition temperature (T-c) of 300 K, nearly 50 K higher than that of a single crystal. The Rietveld analysis of the powder x-ray diffraction data of the nanopowders reveals significant lattice contraction and reduction in unit cell anisotropy-these structural changes are correlated to the enhancement in T-c.