Studies on the conformation of amino acids XII. Energy calculations on prolyl residue

The favoured conformations of the prolyl residue have been obtained by calculating their potential energies arising from bond-angle strain, torsion-angle strain, non-bonded and electrostatic interatomic energies. In addition to the five membered ring, the peptide unit at the amino end (with ω = 180°) and the C′ atom at the carboxyl end have been taken into account. It is found that there are two local minima in the configurational space of the parameters defining the conformation, as is actually observed-one (denoted by B) with Cγ displaced on the same side as C′, which is lower in energy than the other (denoted by A) with Cγ displaced on the opposite side of C′. The other four atoms Cδ, N, Cα, Cβ are nearly in a plane. The conformations of minimum energy (for both A and B) have bond angles very close to the mean observed values while the torsion angles are well within the range observed in various structures for each type. Taking into account the fact that the influence of neighbouring molecules in a crystal structure may make the conformation of a molecule different from the minimal one, the ranges of the conformational parameters for which the energy is within 0.6 kcal/mole above the minimum value (called the "most probable range") and within 1.2 kcal/mole (called the "probable range") have been determined. The ranges thus obtained, agree well with observation, and most of the observed data lie within the most probable ranges, although differing appreciably from the conformation of minimum energy. The study has been extended, in a limited way, to the conformation of the ring in the amino acid proline. Since the nitrogen is tetrahedral in this (as contrasted with being planar in the prolyl residue), it is found that any one of the five atoms can be out of plane (either way), with the other four lying nearly in a plane. These correspond to low energy conformations (up to 1.2 kcal/mole above the minimum). One such example, in which the Cα atom is out of plane is known for dl-proline · HCl. It is also shown that in these calculations energies due to bond length distortions can be neglected to a good degree of approximation, provided the 'best' values of the bond lengths for the particular compound are used in the theoretical calculations.

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.

Computing a matrix symmetrizer exactly using modified multiple modulus residue arithmetic

A symmetric solution X satisfying the matrix equation XA = AtX is called a symmetrizer of the matrix A. A general algorithm to compute a matrix symmetrizer is obtained. A new multiple-modulus residue arithmetic called floating-point modular arithmetic is described and implemented on the algorithm to compute an error-free matrix symmetrizer.

Conformations of dehydrophenylalanine containing peptides. NMR studies on three tripeptides with a central dehydrophenylalanyl residue.

Three tripeptides containing a central Z-dehydrophenylalanine residue (Δz-Phe), Boc-L-Phe-Δz-Phe-X-OMe (X = L-Val 1, L-Leu 2 and X = L-Ala 3) have been synthesized and their solution conformations investigated by 270 MHz 1H NMR spectroscopy. In all three peptides, conformations involving the X residue NH in an intramolecular hydrogen bond were favoured in CDCl3 solutions. Studies of the nuclear Overhauser effect (NOE) provided support for a Type II β turn conformation in these peptides with Phe and Δz-Phe occupying the i + 1 and i + 2 positions, respectively. Significantly different conformations lacking any intramolecular hydrogen bonds were observed for peptide 1 in (CD3)2SO. NOE results were consistent with a significant population of molecules having semi-extended conformations (ø > 100°) at the Δz-Phe residue.

Conformation of a 16-residue zervamicin IIA analog peptide containing three different structural features: 310-helix, alpha helix and ß-bend ribbon

Boc-Trp-Ile-Ala-Aib-Ile-Val-Aib-Leu-Aib- Pro-Ala-Aib-Pro-Aib-Pro-Phe-OM(we here Boc is t-butoxycarbonyla nd Aib is a-aminoisobutyriac cid), a synthetica polar analog of the membrane-activefu ngal peptide antibioticz ervamtycinII A, crystallizesi n spaceg roupP 1 withZ =1 and cell parameters a = 9.086 ?0.002 A, b = 10.410 ?+ 0.002 A, c = 28.188 ? 0.004 A, a = 86.13 ? 0.01?, 13 = 87.90 ? 0.01?, and y = 89.27 ? 0.01?;o veralla greementf actorR = 7.3% for 7180 data (Fo > 3cr) and 0.91-A resolution. The peptide backbone makes a continuous spiral that begins as a 310-helix at the N-terminus, changes to an a-helix for two turns, and ends in a spiral of three fl-bends in a ribbon. Each of the fl-bends contains a proline residue at one of the corners. The torsion angles 4i range from -51? to -91? (average value -64o), and the torsion angles ai range from -1? to -46? (average value -31?). There are 10 intramolecularN H...OCh ydrogenb onds in the helix and two directh ead-to-taihl ydrogenb ondsb etween successive molecules. Two H20 and two CH30H solvent molecules fill additional space with appropriate hydrogen bonding in the head-to-tail region, and two additional H20 molecules form hydrogen bonds with carbonyl oxygens near the curve in the helix at Pro-10. Since there is only one peptide molecule per cell in space group P1, the molecules repeat only by translation, and consequently the helices pack parallel to each other.

Crystallographic characterization of the conformation of the 1-aminocyclohexane-1-carboxylic acid residue in simple derivatives and peptides

The crystal structures of 1-aminocyclohexane-1-carboxylic acid (H-Acc6-OH) and six derivatives (including dipeptides) have been determined. The derivatives are Boc-Acc6-OH, Boc-(Acc6)2-OH, Boc-L-Met-Acc6-OMe, ClCH2CO-Acc6-OH, p-BrC6H4CO-Acc6-OH oxazolone, and the symmetrical anhydride from Z-Acc6-OH, [(Z-Acc6)2O]. The cyclohexane rings in all the structures adopt an almost perfect chair conformation. The amino group occupies the axial position in six structures; the free amino acid is the only example where the carbonyl group occupies an axial position. The values determined for the torsion angles about the N–Cα(φ) and Cα–CO (ψ) bonds correspond to folded, potentially helical conformations for the Acc6 residue.

A nonhelical, multiple β-turn conformation in a glycine-rich heptapeptide fragment of trichogin A IV containing a single central α-aminoisobutyric acid residue

The conformational properties of the protected seven-residue C-terminal fragment the lipopeptaibol antibiotic Trichogin A IV (Boc-Gly-Gly-Leu-Aib-Gly-Ile-Leu-OMe) has been examined in CDCl3 and (CD3)2SO by 1H-nmr. Evidence for a multiple β-turn conformation [type I′ at Gly(1)-Gly(2), type II at Leu(3)-Aib(4), and a type I′ at Aib(4)-Gly(5)] suggests that Leu(3) has preferred an extended or semiextended conformation over a helical conformation in CDCl3. This structure is thus in contrast to earlier observations of seven-residue peptides containing a single central Aib preferring helical conformations in both solution and crystalline slates. A structural transition to a frayed right-handed helix is absented in (CD3)2SO. These results suggest that nonhelical conformations may be important in Gly-rich peptides containing Aib. Further, the presence of amino acids with contradictory influences on backbone conformational freedom can lead to well-defined conformational transitions even in small peptides

Flocculation, filtration and selective flocculation studies on haematite ore fines using starch

The flocculation and filtration characteristics of typical Indian iron ore fines have been studied using starch as flocculant in the presence of an inorganic electrolyte, namely calcium chloride. The effect of various parameters such as pH, starch and calcium chloride concentrations and pulp density on the settling and filtration rates, turbidity of the supernatant and on residual starch and calcium ion concentrates has been investigated through a statistical design and analysis approach and subsequently optimised on a laboratory scale. The adsorption mechanisms of starch onto haematite have been elucidated through adsorption density measurements, infrared and X-ray photoelectron spectroscopic techniques. The rheological property of the polymer solutions of relevance to flocculations has also been investigated. Further, the role of metal ion-starch interactions in the bulk solution, has been studied. In order to understand the nature of polymer adsorption at the double-layer, electrokinetic studies have been carried out with the iron ore mineral samples using starch and calcium chloride. Based on the above findings, selective floculaation tests on artificial mixtures of iron ore minerals have been carried out to determine the separation efficiencies from the view point of alumina and silica removal from haematite as well as the control of alumina: silica ratio in Indian iron ores.

C-H…O hydrogen bond mediated chain reversal in a peptide containing g-amino acid residue, determined directly from powder X-ray diffraction data

The finding that peptides containing -amino acid residues give rise to folding patterns hitherto unobserved in -amino acid peptides[1] has stimulated considerable interest in the conformational properties of peptides built from , and residues,[2] as the introduction of additional methylene (CH2) units into peptide chains provides further degrees of conformational freedom.

Influence of Starch Polysaccharide on the Remolded Properties of 2 Indian clay Samples

The reported presence in marine clays and the recognized role of polysaccharide as a bonding agent provided the motivation to examine the role of starch polysaccharide in the remoulded properties of nonswelling (kaolinite) and swelling (bentonite) groups of clays. The starch polysaccharide belongs to a group of naturally occurring, large-sized organic molecules (termed polymers) and is built up by extensive repetition of simple chemical units called repeat units. The results of the study indicate that the impact of the starch polysaccharide on the remoulded properties of clays is dependent on the mineralogy of the clays. On addition to bentonite clay, the immensely large number of segments (repeat units) of the starch polysaccharide create several polymer segment - clay surface bonds that cause extensive aggregation of the bentonite units layers. The aggregation of the bentonite unit layers greatly curtails the available surface area of the clay mineral for diffuse ion layer formation. The reduction in diffuse ion layer thickness markedly lowers the consistency limits and vane shear strength of the bentonite clay. On addition to kaolinite, the numerous polymer segment - clay surface bonds enhance the tendency of the kaolinite particles to flocculate. The enhanced particle flocculation is responsible apparently for a small to moderate increase in the liquid limit and remoulded undrained strength of the nonswelling clay.

Hybrid Polypeptides: Gabapentin as a Stereochemically Constrained gamma-Amino Acid Residue

The design of folded structures in peptides containing the higher homologues of alpha-amino acid residues requires the restriction of the range of local conformational choices In alpha-amino acids stereochemically constrained residues like alpha,alpha-dialkylated residue, aminoisobutyric acid (Aib), and D-Proline ((D)Pro) have proved extremely useful in the design of helices and hairpins in short peptides Extending this approach, backbone substitution and cyclization are anticipated to bc useful in generating conformationally constrained beta- and gamma-residues This brief review provides a survey of work on hybrid peptide sequences concerning the conformationally constrained gamma-amino acid residue 1-aminomethyl cyclohexane acetic acid, gabapentin (Gpn) This achiral, beta,beta-disubstituted, gamma-residue strongly favors gauche-gauche conformations about the C-alpha-C-beta (0(2)) and C-alpha-C-gamma (0(1)) bonds, facilitating local folding The Gpn residue can adopt both C-7 (NH1 -> CO1) and C-9 (CO1 (I)<- NH1+I) hydrogen bonds which are analogous to the C-5 and C7 (gamma-turn) conformations at alpha-residues In conjunction with adjacent residues, Gpn may be used in ay and gamma alpha segments to generate C-12 hydrogen bonded conformations which may be considered as expanded analogs of conventional beta-turns The structural characterization of C-12 helices, C-12/C-10 helices with mixed hydrogen bond directionalities and beta-hairpins incorporating Gpn residues at the turn segment is illustrated (C) 2010 Wiley Periodicals, Inc Biopolymers (Pept Sci) 94 733-741 2010

The effect of a starch envelope on fly ash particles on the impact properties of filled epoxy composites

The impact behaviour of epoxy specimens containing 20% by volume of fly ash particles without (coded, FA20) and with surface enveloped by starch in dry (FAS20) and water-ingresses (FASM20) conditions is studied. The resulting behavioural patterns are documented and compared to the composites containing as received fly ash particles. The data on unreinforced (i.e. neat) epoxy system (designated, NE) are also included. Samples with starch covering for the fillers whether tested in dry or wet conditions (i.e. FAS20 & FASM20) showed greater absorption of energy and maximum load compared to the ones derived on composites having as received fillers tested in unexposed (dry) condition (FA20). Ductility Index, D.I. on the other hand, showed a reversal in trends; the energy absorbed was highest for NE and lowest FA20 samples. Scanning microscopic examination of the fracture features was undertaken to correlate the microstructure to impact response.