Stereochemical studies on cyclic peptides. XIII. Energy minimization studies on cyclic hexapeptides having hydrogen bonds

The basic cyclic hexapeptide conformations which accommodate hydrogen bonded β and γ turns in the backbone have been worked out using stereochemical criteria and energy minimization procedures. It was found that cyclic hexapeptides can be made up of all possible combinations of 4 ± 1 hydrogen bonded types I, I', II and II' β turns, giving rise to symmetric conformations having twofold and inversion symmetries as well as nonsymmetric structures. Conformations having exclusive features of 3 ± 1 hydrogen bonded γ turns were found to be possible in threefold and S6 symmetric cyclic hexapeptides. The results show that the cyclic hexapeptides formed by the linking of two β turn tripeptide fragments differ mainly in (a) the hydrogen bonding scheme present in the β turn tripeptides and (b) the conformation at the α-carbon atoms where the two tripeptide fragments link. The different hydrogen bonding schemes found in the component β turns are: 1) a β turn with only a 4 ± 1 hydrogen bond, 2) a type I or I' β turn with 4 ± 1 and 3 ± 1 hydrogen bonds occurring in a bifurcated form and 3) a type II or II' β turn having both the 4 ± 1 and the 3 ± 1 hydrogen bonds with the same acceptor oxygen atom. The conformation at the linking α-carbon atoms was found to lie either in the extended region or in the 3 ± 1 hydrogen bonded γ turn or inverse γ turn regions. Further, the threefold and the S6 symmetric conformations have three γ turns interleaved by three extended regions or three inverse γ turns, respectively. The feasibility of accommodating alanyl residues of both isomeric forms in the CHP minima has been explored. Finally, the available experimental data are reviewed in the light of the present results.

Crystal structure from packing studies: application to the triclinic structure of the cyclic hexapeptide cyclo-(gly-tyr-gly)2

The paper describes a novel method of finding the position and orientation of a relatively rigid molecule in the unit cell from criteria concerning allowed contact distances between atoms. On application to the crystal structure of a hexapeptide, C25H31N6O8.2H2O, it was possible to solve the structure from this starting point, by a series of SFLS refinements with an increasingly larger number of reflexions at successive stages. The packing analysis succeeded, even though the water molecules were not included to start with.

Sterochemical studies on cyclic peptides-VIII. Conformational analysis of hydrogen bonded cyclohexaglycyl molecule with a centre of inversion symmetry

A study on the conformational aspects of cyclo-hexaglycyl having inversion symmetry has been made. The cyclic backbone has been assumed to have two internal 4→1 types of NH... O hydrogen bonds. This molecule has been found to take up two types of conformations designated asA* andB* having nearly the same energy values. The theoretical conformations have been compared with the conformations of cyclohexaglycyl hemihydrate observed in the crystal structure. Two molecules with an approximate inversion symmetry are close to the conformation of the typeB* and two other molecules with exact inversino symmetry correspond nearly to the typesB* andA*. comparison with the theoretically possible conformations of cyclohexaglycyl molecule with 2-fold symmetry has been made. The preference of inversion symmetry and preferred ranges ofψ for glycyl molecules is discussed.

Conformational studies on cyclic dipeptides

An analysis of 11 crystal structures of cyclic dipeptides so far reported in the literature is made, with main reference to the internal parameters of these molecules. Preferred conformations of the side chains of cyclic dipeptides with different α-amino acid residues have been studied by classical energy calculations. The possible conformations of the DKP ring are also studied. The significance of the non-bonded interaction in deciding the pathway for conformational change has also been investigated. The agreement between theoretical results and experimental observations is quite good, both with respect to the conformation of these molecules as well as the enthalpy difference as estimated from n.m.r. studies between different conformers.

NMR and X-ray crystallographic studies on cyclic tetrapeptide, cyclo (D-Phe-Pro-Sar-Gly)

The conformation of the synthetic cyclic tetrapeptide cyclo(D-Phe-Pro-Sar-Gly) has been determined in solution using the nuclear magnetic resonance technique and in the crystal state by X-ray crystallography. Results showed that the peptide exhibited two different conformations in solution, conformer 1 having cis-trans-cis-trans peptide bonds and conformer 2 having trans-cis-trans-cis peptide bonds. No intramolecular hydrogen bonds were observed in the structures. The X-ray diffraction studies showed the crystals to be orthorhombic with space group P2(1)2(1)2(1) with unit-cell dimensions, a = 5.790, b = 10.344, c = 31.446 A, Z = 4, R = 0.104 for 2301 observed reflections. The crystal structure showed only one type of conformer having cis-trans-cis-trans peptide bonds similar to the conformer 1 in solution.

Stereochemical studies on cyclic peptides: Detailed energy minimization studies on hydrogen bonded all-trans cyclic pentapeptide backbones

Conformational studies have been carried out on hydrogenbonded all-trans cyclic pentapeptide backbone. Application of a combination of grid search and energy minimization on this system has resulted in obtaining 23 minimum energy conformations, which are characterized by unique patterns of hydrogen bonding comprising of β- and γ-turns. A study of the minimum energy conformationsvis-a-vis non-planar deviation of the peptide units reveals that non-planarity is an inherent feature in many cases. A study on conformational clustering of minimum energy conformations shows that the minimum energy conformations fall into 6 distinct conformational families. Preliminary comparison with available X-ray structures of cyclic pentapeptide indicates that only some of the minimum energy conformations have formed crystal structures. The set of minimum energy conformations worked out in the present study can form a consolidated database of prototypes for hydrogen bonded backbone and be useful for modelling cyclic pentapeptides both synthetic and bioactive in nature.

Stereochemical studies on cyclic peptides. Part XI. Conformation of cyclic pentapeptides having intramolecular 3 leads to 1 hydrogen bonds.

Conformational analysis of cyclic pentapeptides having two intra-ring 3 leads to 1 hydrogen bonds has been carried out. It is found that the structure can easily be formed with trans planar peptide units without causing significant angular strain at the alpha-carbon atoms. Four different types of conformations designated Types I--IV are possible for the backbone structure. Details of these four types of conformations and also the accommodating possibility of these types for allglycyl and all-alanyl residues are presented. Three of the four types have relatively low energies for glycyl residues whereas the other one has a slightly higher energy. When alanyl residues are introduced at the five alpha-carbon atoms, the types that are energetically favourable depend upon the sequence of isomers. Energy calculations have also been carried out for the combinations of glycyl, L- and D-alanyl residues. The theoretical results are compared with available experimental observations both from solution and solid state studies.

Topology of wolfgram proteins and 2?, 3?-cyclic nucleotide 3?-phosphodiesterase in CNS myelin: Studies with proteases

The topological disposition of Wolfgram proteins (WP) and their relationship with 2', 3'-cyclic nucleotide 3'-phosphodiesterase (CNPase) in human, rat, sheep, bovine, guinea pig and chicken CNS myelin was investigated. Controlled digestion of myelin with trypsin gave a 35KDa protein band (WP-t) when electrophoresed on dodecyl sulfate-polyacrylamide gel in all species. Western blot analysis showed that the WP-t was derived from WP. WP-t was also formed when rat myelin was treated with other proteases such as kallikrein, thermolysin and leucine aminopeptidase. Staining for CNPase activity on nitrocellulose blots showed that WP-t is enzymatically active. Much of the CNPase activity remained with the membrane fraction even after treatment with high concentrations of trypsin when WP were completely hydrolysed and no protein bands with M.W > 14KDa were detected on the gels. Therefore protein fragments of WP with M.W < 14KDa may contain CNPase activity. From these results, it is suggested that the topological disposition of all the various WP is such that a 35KDa fragment is embedded in the lipid bilayer and the remaining fragment exposed at the intraperiod line in the myelin structure which may play a role in the initiation of myelinogenesis.

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.

Role of elasto-plastic analysis under cyclic loading in fatigue crack growth studies

Linear Elastic Fracture Mechanics (LEFM) has been widely used in the past for fatigue crack growth studies, but this is acceptable only in situations which are within small scale yielding (SSY). In many practical structural components, conditions of SSY could be violated and one has to look for fracture criteria based on elasto-plastic analysis. Crack closure phenomenon, one of the most striking discoveries based on inelastic deformations during crack growth, has significant effect on fatigue crack growth rate. Numerical simulation of this phenomenon is computationally intensive and involved but has been successfully implemented. Stress intensity factors and strain energy release rates lose their meaning, J-integral (or its incremental) values are applicable only in specific situations, whereas alternate path independent integrals have been proposed in the literature for use with elasto-plastic fracture mechanics (EPFM) based criteria. This paper presents certain salient features of two independent finite element (numerical) studies of relevance to fatigue crack growth, where elasto-plastic analysis becomes significant. These problems can only be handled in the current day computational environment, and would have been only a dream just a few years ago.

Electrocatalytic efficiency of polyaniline by cyclic voltammetry and electrochemical impedance spectroscopy studies

Electrochemical redox reactions of ferrous/ferric (Fe2+/Fe3+) and hydroquinone/quinone (H(2)Q/Q) were studied on Pt and polyaniline (PANI)-deposited Pt electrodes in 0.5 M H2SO4-supporting electrolyte by cyclic voltammetry and ac impedance spectroscopy. A comparison of the experimental data obtained with the Pt and PANI/Pt electrodes suggested that the reactions were catalyzed by the PANI. Based on a relative increase in peak currents of cyclic voltammograms, catalytic efficiency (gamma(cv)) of the PANI was defined. There was an increase in gamma(cv) with an increase of scan rate and a decrease of concentration of Fe2+/Fe3+ or H(2)Q. The complex plane impedance spectrum of the electrode consisted of a semicircle in high frequency range and a linear spike in low frequency range. The exchange current density (i(0)) calculated using the semicircle part of the impedance showed Butler-Volmer kinetics with respect to concentration dependence. From a relative increase of i(0) on the PANI/Pt electrode, catalytic efficiency (gamma(eis)) was evaluated. (C) 2002 Elsevier Science B.V. All rights reserved.

The influence of mesoporous silica in low T-g cyclic olefin copolymer nanocomposite films: Mechanical and moisture barrier studies

In this study, mesoporous silica-cyclic olefin copolymer nanocomposite films were fabricated by solution casting. With an increase in silica loading, the stiffness of the matrix increased. The nanocomposite film shows increased strain to failure with moisture after aging by matrix plasticization. The storage modulus and loss factor for samples with silica content show better results compared with pristine polymer, as indicated by dynamic mechanical analysis. The interaction between filler-polymer chain exhibit hydrophobicity compared to the neat polymer. Water absorption studies at room temperature and near the T-g of the polymer (similar to 64 degrees C) were carried out. The nanocomposites up to 4 wt% filler reduces the water diffusion by forming hydrogen and chemical bonding. The result by calcium degradation test method for moisture permeability and Schottky structured organic device encapsulation under weathering condition confirms the effective reinforcement effect of silica particles in the matrix. (C) 2014 Elsevier Ltd. All rights reserved.

Conformation-activity correlations for chemotactic tripeptide analogs incorporating dialkyl residues with linear and cyclic alkyl sidechains at position 2

Five stereochemically constrained analogs of the chemotactic tripeptide incorporating 1-aminocycloalkane-1-carboxylic acid (Ac(n)c) and alpha,alpha-dialkylglycines (Deg, diethylglycine; Dpg, n,n-dipropylglycine and Dbg, n,n-dibutylglycine) at position 2 have been synthesized. NMR studies of peptides For-Met-Xxx-Phe-OMe (Xxx = Ac(7)c, I; Ac(8)c, II; Deg, III; Dpg, IV and Dbg, V; For, formyl) establish that peptides with cycloalkyl residues, I and II, adopt folded beta-turn conformations in CDCl3 and (CD3)(2)SO. In contrast, analogs with linear alkyl sidechains, III-V, favour fully extended (C-5) conformations in solution. Peptides I-V exhibit high activity in inducing beta-glucosaminidase release from rabbit neutrophils, with ED(50) values ranging from 1.4-8.0 x 10(-11)M. In human neutrophils the Dxg peptides III-V have ED(50) values ranging from 2.3 x 10(-8) to 5.9 x 10(-10) M, with the activity order being V > IV > III. While peptides I-IV are less active than the parent. For-Met-Leu-Phe-OH, in stimulating histamine release from human basophils, the Dbg peptide V is appreciably more potent, suggesting its potential utility as a probe for formyl peptide receptors.

Titration calorimetric studies to elucidate the specificity of the interactions of polymyxin B with lipopolysaccharides and lipid A

Lipopolysaccharide (LPS), the major cell wall constituent of Gram-negative bacteria, evokes a multitude of biological effects in mammals including pyrogenicity and toxic shock syndrome. Polymyxin B (PmB), a polycationic cyclic peptide, is known to neutralize most of its activities. The nature of the interaction of PmB with LPS and lipid A was investigated by isothermal titration calorimetry. PmB binds to LPS as well as lipid A stoichiometrically and non-co-operatively with micromolar affinity. These interactions are driven primarily by a favourable change in entropy (delta S) and are endothermic in nature. These positive changes in enthalpies decrease with increasing temperature, yielding a heat capacity change, delta Cp, of -2385 J.mol-1.degree-1 for PmB-LPS interactions while the binding of PmB to lipid A displays a delta Cp of -2259 J.mol-1.degree-1. The negative heat capacity changes provide strong evidence for the role of hydrophobic interactions as the driving force for the association of PmB with LPS and lipid A. A correlation of the energetics of these interactions with analyses of the molecular models of PmB suggests that a cluster of solvent-exposed non-polar amino acid side-chains that line one surface of the molecule, together with a ring of positively charged residues on its other surface, are responsible for its strong and stoichiometric binding to LPS.