Conformational properties of hybrid peptides containing alpha and omega-amino acids

This review briefly surveys the conformational properties of guest omega-amino acid residues when incorporated into host alpha-peptide sequences. The results presented focus primarily on the use of beta- and gamma-residues in alphaomega sequences. The insertion of additional methylene groups into peptide backbones enhances the range of accessible conformations, introducing additional torsional variables. A nomenclature system, which permits ready comparisons between alpha-peptides and hybrid sequences, is defined. Crystal structure determination of hybrid peptides, which adopt helical and beta-hairpin conformations permits the characterization of backbone conformational parameters for beta- and gamma-residues inserted into regular alpha-polypeptide structures. Substituted beta- and gamma-residues are more limited in the range of accessible conformation than their unsubstituted counterparts. The achiral beta,beta-disubstituted gamma-amino acid, gabapentin, is an example of a stereochemically constrained residue in which the torsion angles about the C-beta-C-gamma (theta(1)) and C-alpha-C-beta (theta(2)) bonds are restricted to the gauche conformation. Hybrid sequences permit the design of novel hydrogen bonded rings in peptide structures.

Solution structure of Am2766: A highly hydrophobic d-conotoxin from Conus amadis that inhibits inactivation of brain voltage gated sodium channels

The three-dimensional (3D) NMR solution structure (MeOH) of the highly hydrophobic δ-conotoxin δ-Am2766 from the molluscivorous snail Conus amadis has been determined. Fifteen converged structures were obtained on the basis of 262 distance constraints, 25 torsion-angle constraints, and ten constraints based on disulfide linkages and H-bonds. The root-mean-square deviations (rmsd) about the averaged coordinates of the backbone (N, Cα, C) and (all) heavy atoms were 0.62±0.20 and 1.12±0.23 Å, respectively. The structures determined are of good stereochemical quality, as evidenced by the high percentage (100%) of backbone dihedral angles that occupy favorable and additionally allowed regions of the Ramachandran map. The structure of δ-Am2766 consists of a triple-stranded antiparallel β-sheet, and of four turns. The three disulfides form the classical ‘inhibitory cysteine knot’ motif. So far, only one tertiary structure of a δ-conotoxin has been reported; thus, the tertiary structure of δ-Am2766 is the second such example.Another Conus peptide, Am2735 from C. amadis, has also been purified and sequenced. Am2735 shares 96% sequence identity with δ-Am2766. Unlike δ-Am2766, Am2735 does not inhibit the fast inactivation of Na+ currents in rat brain Nav1.2 Na+ channels at concentrations up to 200 nM.

Visualisation of a 2′-5′ parallel stranded double helix at atomic resolution: crystal structure of cytidylyl-2′,5′-adenosine

X-ray crystallographlc studies on 3′–5′ ollgomers have provided a great deal of information on the stereochemistry and conformational flexibility of nucleic acids and polynucleotides. In contrast, there is very little Information available on 2′–5′ polynucleotides. We have now obtained the crystal structure of Cytidylyl-2′,5′-Adenoslne (C2′p5′A) at atomic resolution to establish the conformational differences between these two classes of polymers. The dlnucleoside phosphate crystallises in the monocllnlc space group C2, with a = 33.912(4)Å, b =16.824(4)Å, c = 12.898(2)Å and 0 = 112.35(1) with two molecules in the asymmetric unit. Spectacularly, the two independent C2′p5′A molecules in the asymmetric unit form right handed miniature parallel stranded double helices with their respective crystallographic two fold (b axis) symmetry mates. Remarkably, the two mini duplexes are almost indistinguishable. The cytosines and adenines form self-pairs with three and two hydrogen bonds respectively. The conformation of the C and A residues about the glycosyl bond is anti same as in the 3′–5′ analog but contrasts the anti and syn geometry of C and A residues in A2′p5′C. The furanose ring conformation is C3′endo, C2′endo mixed puckering as in the C3′p5′A-proflavine complex. A comparison of the backbone torsion angles with other 2′–5′ dinucleoside structures reveals that the major deviations occur in the torsion angles about the C3′–C2′ and C4′-C3′ bonds. A right-handed 2′–5′ parallel stranded double helix having eight base pairs per turn and 45° turn angle between them has been constructed using this dinucleoside phosphate as repeat unit. A discussion on 2′–5′ parallel stranded double helix and its relevance to biological systems is presented.

Epoch extraction from linear prediction residual for identification of closed glottis interval

In voiced speech analysis epochal information is useful in accurate estimation of pitch periods and the frequency response of the vocal tract system. Ideally, linear prediction (LP) residual should give impulses at epochs. However, there are often ambiguities in the direct use of LP residual since samples of either polarity occur around epochs. Further, since the digital inverse filter does not compensate the phase response of the vocal tract system exactly, there is an uncertainty in the estimated epoch position. In this paper we present an interpretation of LP residual by considering the effect of the following factors: 1) the shape of glottal pulses, 2) inaccurate estimation of formants and bandwidths, 3) phase angles of formants at the instants of excitation, and 4) zeros in the vocal tract system. A method for the unambiguous identification of epochs from LP residual is then presented. The accuracy of the method is tested by comparing the results with the epochs obtained from the estimated glottal pulse shapes for several vowel segments. The method is used to identify the closed glottis interval for the estimation of the true frequency response of the vocal tract system.

Analysis of side-chain conformation in proteins

The crystal structures of a number of globular proteins are currently available. An analysis of the distribution of side-chains among different allowed conformations in these proteins has been carried out. The observed conformations of individual residues are discussed on the basis of well-known stereochemical criteria. The population distribution of side-chains in different allowed regions in conformational space can be explained largely on the basis of simple steric considerations. In addition to examining the conformational behaviour of individual residues, some population distributions of conformational angles of general interest involving groups of residues have also been analyzed.

Structural features of B-DNA dodecamer crystal structures: Influence of crystal packing versus base sequence

We have analyzed the set of inter and intra base pair parameters for each dinucleotide step in single crystal structures of dodecamers, solved at high and medium resolution and all crystallized in P2(1)2(1)2(1) space group. The objective was to identify whether all the structures which have either the Drew-Dickerson (DD) sequence d[CGCGAATTCGCG] with some base modification or related sequence (non-DD), would display the same sequence dependent structural variability about its palindromic sequence, despite the molecule being bent at one end because of similar crystal lattice packing effect. Most of the local doublet parameters for base pairs steps G2-C3 and G10-C11 positions, symmetrically situated about the lateral twofold, were significantly correlated between themselves. In non-DD sequences, significant correlations between these positional parameters were absent. The different range of local step parameter values at each sequence position contributed to the gross feature of smooth helix axis bending in all structures. The base pair parameters in some of the positions, for medium resolution DD sequence, were quite unlike the high-resolution set and encompassed a higher range of values. Twist and slide are the two main parameters that show wider conformational range for the middle region of non-DD sequence structures in comparison to DD sequence structures. On the contrary, the minor and major groove features bear good resemblance between DD and non-DD sequence crystal structure datasets. The sugar-phosphate backbone torsion angles are similar in all structures, in sharp contrast to base pair parameter variation for high and low resolution DD and non-DD sequence structures, consisting of unusual (epsilon =g(-), xi =t) B-II conformation at the 10(th) position of the dodecamer sequence. Thus examining DD and non-DD sequence structures packed in the same crystal lattice arrangement, we infer that inter and intra base pair parameters are as symmetrically equivalent in its value as the symmetry related step for the palindromic DD sequence about lateral two-fold axis. This feature would lead us to agree with the conclusion that DNA conformation is not substantially affected by end-to-end or lateral inter-molecular interaction due to crystal lattice packing effect. Non-DD sequence structures acquire step parameter values which reflect the altered sequence at each of the dodecamer sequence position in the orthorhombic lattice while showing similar gross features of DD sequence structures

HELANAL: A program to characterise helix geometry in proteins,

A detailed analysis of structural and position dependent characteristic features of helices will give a better understanding of the secondary structure formation in globular proteins. Here we describe an algorithm that quantifies the geometry of helices in proteins on the basis of their C-alpha atoms alone. The Fortran program HELANAL can extract the helices from the PDB files and then characterises the overall geometry of each helix as being linear, curved or kinked, in terms of its local structural features, viz. local helical twist and rise, virtual torsion angle, local helix origins and bending angles between successive local helix axes. Even helices with large radius of curvature are unambiguously identified as being linear or curved. The program can also be used to differentiate a kinked helix and other motifs, such as helix-loop-helix or a helix-turn-helix (with a single residue linker) with the help of local bending angles. In addition to these, the program can also be used to characterise the helix start and end as well as other types of secondary structures.

Local variability and base sequence effects in DNA crystal structures.

The importance and usefulness of local doublet parameters in understanding sequence dependent effects has been described for A- and B-DNA oligonucleotide crystal structures. Each of the two sets of local parameters described by us in the NUPARM algorithm, namely the local doublet parameters, calculated with reference to the mean z-axis, and the local helical parameters, calculated with reference to the local helix axis, is sufficient to describe the oligonucleotide structures, with the local helical parameters giving a slightly magnified picture of the variations in the structures. The values of local doublet parameters calculated by NUPARM algorithm are similar to those calculated by NEWHELIX90 program, only if the oligonucleotide fragment is not too distorted. The mean values obtained using all the available data for B-DNA crystals are not significantly different from those obtained when a limited data set is used, consisting only of structures with a data resolution of better than 2.4 A and without any bound drug molecule. Thus the variation observed in the oligonucleotide crystals appears to be independent of the quality of their crystallinity. No strong correlation is seen between any pair of local doublet parameters but the local helical parameters are interrelated by geometric relationships. An interesting feature that emerges from this analysis is that the local rise along the z-axis is highly correlated with the difference in the buckle values of the two basepairs in the doublet, as suggested earlier for the dodecamer structures (Bansal and Bhattacharyya, in Structure & Methods: DNA & RNA, Vol. 3 (Eds., R.H. Sarma and M.H. Sarma), pp. 139-153 (1990)). In fact the local rise values become almost constant for both A- and B-forms, if a correction is applied for the buckling of the basepairs. In B-DNA the AA, AT, TA and GA basepair sequences generally have a smaller local rise (3.25 A) compared to the other sequences (3.4 A) and this seems to be an intrinsic feature of basepair stacking interaction and not related to any other local doublet parameter. The roll angles in B-DNA oligonucleotides have small values (less than +/- 8 degrees), while mean local twist varies from 24 degrees to 45 degrees. The CA/TG doublet sequences show two types of preferred geometries, one with positive roll, small positive slide and reduced twist and another with negative roll, large positive slide and increased twist.(ABSTRACT TRUNCATED AT 400 WORDS)

Analysis of sequence dependent variations in secondary and tertiary structure of tRNA molecules

The double helical regions of the five tRNA(Phe) and two tRNA(Asp) crystal structures have been analyzed using the local basepair step parameters. The sequence dependent effects in the mini double helices of tRNA are very similar to those observed in the crystal structures of oligonucleotides in the A-form, the purine-pyrimidine and purine-purine steps have small roll angles when compared to the fiber models of A-DNA as well as A-RNA, while the pyrimidine-purine doublet steps have large roll angles. The orientation of the basepairs in the D-stem is unusual and invariant i.e. they are different from the other three stems but are very similar in all the five tRNA(Phe) crystal structures, presumably due to tertiary interaction of the Watson-Crick basepairs with other bases, with all bases being highly conserved. The origin of the differences between the tertiary structures of tRNA(Phe) and tRNA(Asp) from yeast has also been investigated. It is found that even though the angle between the acceptor arm and the D-stem is very similar in the two structures, the angle subtended by the acceptor arm and the anticodon arm is smaller in the tRNA(Phe) structure (by more than 10 degrees). This is due to differences in the orientation of the two mini helices constituting the anticodon arm, which are inclined to each other by approximately 25 degrees in tRNA(Phe) and 16 degrees in tRNA(Asp). In addition, the acceptor arm, the D-stem and the anticodon stem are nearly coplanar in tRNA(Phe), while in tRNA(Asp) the anticodon stem projects out of the plane defined by the acceptor arm and the anticodon stem. These two features together lead to a larger separation between the acceptor and anticodon ends in tRNA(Asp) and indicate that the junction between the D-stem and the anticodon stem is quite variable, with features characteristic of a ball-and-socket type joint and determined for each tRNA molecule by the base sequence at the junction.

A new model for coalescence efficiency of drops in stirred dispersions

A model for coalescence efficiency of two drops embedded in an eddy has been developed. Unlike the other models which consider only head-on collisions, the model considers the droplets to approach at an arbitrary angle. The drop pair is permitted to undergo rotation while they approach each other. For coalescence to occur, the drops are assumed to approach each other under a squeezing force acting over the life time of eddy but which can vary with time depending upon the angle of approach. The model accounts for the deformation of tip regions of the approaching drops and, describes the rupture of the intervening film, based on stability considerations while film drainage is continuing under the combined influence of the hydrodynamic and van der Waals forces. The coalescence efficiency is defined as the ratio of the range of angles resulting in coalescence to the total range of all possible approach angles. The model not only reconciles the contradictory predictions made by the earlier models based on similar framework but also brings out the important role of dispersed-phase viscosity. It further predicts that the dispersions involving pure phases can be stabilized at high rps values. Apart from explaining the hitherto unexplained experimental data of Konno et al. qualitatively, the model also offers an alternate explanation for the interesting observations of Shinnar.

Crystal structures, spectral and magnetic properties of (µ-hydroxo)(µ-acetato)dicopper(II) complexes containing chelating amines

The reaction of [Cu2(O2CMe)4(H2O)2] with N, N, N′, N′-tetramethylethane- 1,2-diamine (tmen) in ethanol yielded the dicopper(II) complex [Cu2(OH)(O2CMe)(tmen)2][ClO4]21. A similar reaction with N, N- dimethylethane- 1,2-diamine (dmen) afforded a crystalline product 2 in which two dicopper(II) complexes, [Cu2(OH)(O2CMe)(dmen)2][ClO4]22a and [Cu2(OH)(O2CMe)(H2O)2(dmen)2][ClO4]22b, are cocrystallized in a 1 : 1 molar ratio along with 2NaClO4. The crystal structures of 1 and 2 have been determined. The complexes have an asymmetrically dibridged [Cu2(µ-OH)(µ-O2CMe)]2+ core. The co-ordination geometry of the metal is square planar (CuO2N2). The copper atoms in 2b have a square-pyramidal CuO3N2 co-ordination sphere. The Cu Cu distances and Cu–O–Cu angles in 1, 2a and 2b are 3.339(2), 3.368(3), 3.395(7)Å, 120.1(2), 116.4(1) and 123.6(2)°, respectively. Complex 1 exhibits an axial ESR spectrum in a methanol glass giving g∥= 2.26 (A∥= 164 × 10–4 cm–1) and g⊥= 2.04. The ESR spectra obtained from the bulk material of the dmen product are indicative of the presence of two dimers, viz. complex 2a(g∥= 2.25, A∥= 165 × 10–4 cm–1; g⊥= 2.03) and 2b(g∥= 2.19, A∥= 184 × 10–4 cm–1; g⊥= 2.0). Variable-temperature magnetic susceptibility measurements on these complexes show an intramolecular antiferromagnetic coupling in the dimeric core. The fitting parameters are J=–27.8 cm–1, g= 2.1 for complex 1 and J=–10.1 cm–1, g= 2.0 for 2. The magnetostructural properties of the complexes are discussed. There is a linear correlation of the –2J values with the Cu Cu distances among dibridged complexes having square-planar copper(II) centres.

Differential stability of beta-sheets and alpha-helices in beta-lactamase: a high temperature molecular dynamics study of unfolding intermediates

Beta-Lactamase, which catalyzes beta-lactam antibiotics, is prototypical of large alpha/beta proteins with a scaffolding formed by strong noncovalent interactions. Experimentally, the enzyme is well characterized, and intermediates that are slightly less compact and having nearly the same content of secondary structure have been identified in the folding pathway. In the present study, high temperature molecular dynamics simulations have been carried out on the native enzyme in solution. Analysis of these results in terms of root mean square fluctuations in cartesian and [phi, psi] space, backbone dihedral angles and secondary structural hydrogen bonds forms the basis for an investigation of the topology of partially unfolded states of beta-lactamase. A differential stability has been observed for alpha-helices and beta-sheets upon thermal denaturation to putative unfolding intermediates. These observations contribute to an understanding of the folding/unfolding processes of beta-lactamases in particular, and other alpha/beta proteins in general.

Effect of constraints by threonine on proline containing αa-helix—A molecular dynamics approach

Proline plays an important role in the secondary structure of proteins. In the pursuit of understanding its structural role, Proline containing helices with constraints have been studied by employing molecular dynamics (MD) technique. In the present study, the constraint introduced is a threonine residue, whose sidechain has intramolecular hydrogen bond interaction with the backbone oxygen atom. The three systems that have been chosen for characterization are: (1) Ace-(Ala)12−Thr-Pro-(Ala)10−NHMe, (2) Ace-(Ala)13-Pro-Ala-Thr- (Ala)8-NHMe and (3) Ace-(Ala)13-Pro-(Ala)3-Thr-(Ala)6-NHMe. The equilibrium structures and structural transitions have been identified by monitoring the backbone dihedral angles, bend related parameters and the hydrogen bond interactions. The MD averages and root mean square (r.m.s.) fluctuations are compared and discussed. Energy minimization has been carried out on selected MD simulated points in order to analyze the characteristics of different conformations.

Kinetic approach to dislocation bending in low-mobility films

A kinetic model has been developed for dislocation bending at the growth surface in compressively stressed low-mobility films such as III-V nitrides. It is based on a reduction in the number of atoms at the growth surface. Stress and nonstress sources of driving force for such a reduction are discussed. A comparison between the derived equations and experimentally measured stress evolution data yields good agreement between the predicted and observed angles through which dislocations bend.

The scratch hardness and friction of a soft rigid-plastic solid

The paper describes an experimental and analytical study of the normal and scratch hardnesses of a model soft rigid-plastic solid. The material known as ‘Plasticine’, a mixture of dry particles and a mineral oil, has been deformed with a range of rigid conical indentors with included angles of between 30° and 170°. The sliding velocity dependence of the computed scratch hardness and friction has been examined in the velocity range 0.19 mm/s to 7.3 m/s. Data are also described for the time dependence of the normal hardness and also the estimated rate dependence of the intrinsic flow stress. The latter values were estimated from data obtained during the upsetting of right cylinders. Three major conclusions are drawn from these data and the associated analysis. (1) A first-order account of the scratching force may be provided by adopting a model which sums the computed plastic deformation and interfacial sliding contributions to the total sliding work. This is tantamount to the adoption of the two-term non-interacting model of friction. (2) For this system during sliding, at high sliding velocities at least, the interface shear stress which defines the boundary condition is not directly related to the bulk shear stress. The interface rheological characteristics indicate an appreciable dependence on the imposed strain or strain rate. In particular, the relative contributions of the slip and stick boundary conditions appear to be a function of the imposed sliding velocity. (3) The computed normal and scratch hardness values are not simply interrelated primarily because of the evolving boundary conditions which appear to exist in the scratching experiments.