Crystal state conformation of three model monomer units for the beta-bend ribbon structure

The molecular and crystal structures of three compounds, representing the repeating units of the -bend ribbon (an approximate 310-helix, with an intramolecular hydrogen-bonding donor every two residues), have been determined by x-ray diffraction. They are Boc-Aib-Hib-NHBzl, Z-Aib-Hib-NHBzl, and Z-L-Hyp-Aib-NHMe (Aib, -aminoisobutyric acid; Bzl, benzyl; Boc, t-butyloxycarbonyl; Hyp, hydroxyproline Hib, -hydroxyisobutyric acid; Z, benzyloxycarbonyl). The two former compounds are folded in a -bend conformation: type III (III) for Boc-Aib-Hib-NHBzl, while type II (II) for the Z analogue. Conversely, the structure of Z-L-Hyp-Aib-NHMe, although not far from a type II -bend, is partially open.

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.

Conformational studies on beta-bend containing a cis peptide unit

Conformational studies have been carried out on the X-cis-Pro tripeptide system (a system of three linked peptide units, in the trans-cis-trans configuration) using energy minimization techniques. For X, residues Gly, L-Ala, D-Ala and L-Pro have been used. The energy minima have been classified into different groups based upon the conformational similarity. There are 15, 20, 18 and 6 minima that are possible for the four cases respectively and these fall into 11 different groups. A study of these minima shows that, (i) some minima contain hydrogen bonds - either 4-->1 or 1-->2 type, (ii) the low energy minima qualify themselves as bend conformations, (iii) cis' and trans' conformations are possible for the prolyl residue as also the C(gamma)-endo and C(gamma)-exo puckerings, and (iv) for Pro-cis-Pro, cis' at the first prolyl residue is ruled out, due to the high energy. The available crystal structure data on proteins and peptides, containing cis-Pro segment have been examined with a view to find the minima that occur in solid state. The data from protein show that they fall under two groups. The conformation at X in X-cis-Pro is near extended when it is a non-glycyl residue. In both peptides and proteins there exists a preference for trans' conformation at prolyl residue over cis' when X is a non-glycyl residue. The minima obtained can be useful in modelling studies.

Dynamic analysis of three point bend specimens under impact

A simple one dimensional inertial model is presented for transient response analysis of notched beams under impact, and extracting dynamic initiation toughness values. The model includes the effects of striker mass interactions, and contact deformations of the beam. Displacement time history of the striker mass is applied to the model as forcing function. The model is validated by comparison with the experimental investigation on ductile aluminium 6061 alloy and brittle polymer, PMMA.

Influence of anvil supports and overhangs in dynamic analysis of three point bend testing

Optimum design of dynamic fracture test rigs demands a thorough appreciation of beam vibration under impact. Analyses invariably presume rigid anvils, and neglect overhang effects. The beam response predicted analytically and numerically in this paper highlights the significant role of anvil rigidity and beam overhangs on the impact dynamics of three point bend (3PB) specimens.

A new method for fracture toughness determination of graded (Pt,Ni)Al bond coats by microbeam bend tests

A novel method is proposed for fracture toughness determination of graded microstructurally complex (Pt,Ni)Al bond coats using edge-notched doubly clamped beams subjected to bending. Micron-scale beams are machined using the focused ion beam and loaded in bending under a nanoindenter. Failure loads gathered from the pop-ins in the load-displacement curves combined with XFEM analysis are used to calculate K-c at individual zones, free from substrate effects. The testing technique and sources of errors in measurement are described and possible micromechanisms of fracture in such heterogeneous coatings discussed.

Design of S bend waveguides for delay line applications in integrated optics

A novel scheme for generation of phase using optical delay lines is proposed. The design of the optical components in the circuit which includes the S bend waveguides and straight waveguide couplers are very important for integrated optics. Beam propagation Method and MatLab is employed for the design.

A comparative study of failure features in aerospace grade unidirectional and bidirectional woven CFRP composite laminates under four-point bend fatigue loads

Damage mechanisms in unidirectional (UD) and bi-directional (BD) woven carbon fiber reinforced polymer (CFRP) laminates subjected to four point flexure, both in static and fatigue loadings, were studied. The damage progression in composites was monitored by observing the slopes of the load vs. deflection data that represent the stiffness of the given specimen geometry over a number of cycles. It was observed that the unidirectional composites exhibit gradual loss in stiffness whereas the bidirectional woven composites show a relatively quicker loss during stage II of fatigue damage progression. Both, the static and the fatigue failures in unidirectional carbon fiber reinforced polymer composites originates due to generation of cracks on compression face while in bidirectional woven composites the damage ensues from both the compression and the tensile faces. These observations are supported by a detailed fractographic analysis.

Conformational flexibility of DNA: polymorphism and handedness

It is shown that left-handed duplexes are possible for A, B, and D forms of DNA. These duplexes are stereochemically satisfactory and are consistent with the observed x-ray intensity data. On scrutiny the refined right-handed models of B and D DNA by Arnott and coworkers are found to be stereochemically unacceptable. It was possible to formulate a stereochemical guideline for molecular model building based on theory and analysis of single-crystal structure data of dinucleoside monophosphate and higher oligomers. This led to both right- and left-handed DNA duplexes. The right-handed B and D DNA duplexes so obtained are stereochemically superior to earlier models and agree well with the observed x-ray intensity data. The observation that DNA can exist in either handedness for all the polymorphous forms of DNA at once explained A in equilibrium B and B in equilibrium D transitions. Hence it is confirmed that polymorphism of DNA is a reflection on the conformational flexibility inherent in DNA, the same cause that ultimately allows DNA in either handedness. The possibility of various types of right- and left-handed duplexes generated by using dinucleoside monophosphate and trinucleoside diphosphate as repeating units resulted in a variety of models, called RL models. All these models have alternating right and left helical segments and inverted stacking at the bend region as suggested by us earlier. It turns out that the B-Z DNA model of Wang et al. is only an example of RL models.

The possible influence of curvature and rotation on ocean currents

Recent laboratory investigations have shown that rotation and (streamwise) curvature can have spectacular effects on momentum transport in turbulent shear flows. A simple model that takes account of these effects (based on an analogy with buoyant flows) utilises counterparts of the Richardson number Rg and the Monin-Oboukhov length. Estimates of Rg for meanders in ocean currents like the Gulf Stream show it to be of order 1 or more, while laboratory investigations reveal strong effects even at |Rg|∼0·1. These considerations lead to the conclusion that at a cyclonic bend in the Gulf Stream, a highly unstable flow in the outer half of the jet rides over a highly stable flow in the inner half. It is conjectured that the discrepancies noticed between observation and the various theories of Gulf Stream meanders, and such phenomena as the observed detachment of eddies from the Gulf Stream, may be due to the effects of curvature and rotation on turbulent transport.

Observation of kink shear bands in an aluminium single crystal fracture specimen

The near-tip deformation field in a high-constraint three-point bend specimen of pure aluminium single crystal is studied using in situ electron back-scattered diffraction and optical metallography. The orientation considered has the notch lying on the (0 1 0) plane and the notch front along direction. Results clearly show the occurrence of a kink shear sector boundary at 90° to the notch line on the specimen free surface as predicted by the analytical model of Rice [J.R. Rice, Mech. Mater. 6 (1987) 317].

The Crystal Structure of Pivaloyl- D- prolyl-L- prolyl- L-alanyl-N- methylamide

Pivaloyl-D-prolyl-L-prolyl-L-analyl-N-methylam~de (I), C1UH32N40c4r,y stallizes in the orthorhombic space group P21212,w ith four molecules in a unit cell of dimensions a = 9.982 (l),b = 10.183 (3), c = 20.746 (2)A . The structure has been refined to R 0.048 for 1 745 observed reflections. All the peptide bonds in the molecule are trans and both the prolyl residues are in the CY-exo-conformation. The molecule assumes a highly folded conformation in which a Type II' DL bend is followed by a Type I LL bend, both stabilised by intramolecular 4 + 1 hydrogen bonds. This conformation, which has been observed for the first time, is of interest in relation to the structure of gramicidin S.

AE energy release during the fracture of HSC beams

An attempt has been made experimentally to investigate the acoustic emission (AE) energy release in high-strength concrete (HSC) beams subjected to monotonically increasing load. Acoustic emission energy release during the fracture process of the HSC beams is measured. Stress waves released during the fracture process in materials cause acoustic emissions. AE energy released during the fracture of a notched three-point bend plain concrete beam specimens having 28-day compressive strengths of 50.0 MPa, 69.0 MPa and 78.0 MPa and mortar (cement: sand (1: 4) by weight) specimens are studied. Mortar consists of one part cement and four parts sand by weight. The specimens were tested by a material testing system of 1200 kN capacity employing crack mouth opening displacement control at the rate of 0.0004 mm/s. The fracture energy and the AE energy released during the fracture process of all the tested TPB and mortar specimens are compared and discussed. The observations made in the present experimental study have some applications for monitoring the integrity of structures.

Conformation of the LL and LD hairpin bends with internal hydrogen bonds in proteins and peptides

The conformation of three linked peptide units having an internal 4 → 1 type of hydrogen bond has been studied in detail, and the low energy conformations are listed. These conformations all lead to the reversal of the chain direction, and may therefore be called as “hairpin bends” or “U-bends”. Since this bend can occur at the end of two chains hydrogen-bonded in the antiparallel β-conformation, it is also known as the “β-bend”. Two types of conformation are possible when the residues at the second and third Cα atoms are both of type L (the LL bend), while only one type is possible for the LD and the DL bend. The LL bend can also accommodate the sequences LG, GL, GG (G = glycine), while the LD bend can accommodate the sequences LG, GD and GG. The conformations for the sequences DD and DL are exact inverses (or mirror images) of those for the sequences LL and LD, respectively, and have dihedral angles (phi2, ψ2), (phi3, ψ3) of the same magnitudes, but of opposite signs as those for the former types, which are listed, along with the characteristics (length, angle and energy) of the hydrogen bonds. A comparison of the theoretical predictions with experimental data (from X-ray diffraction and NMR studies) on proteins and peptides, show reasonably good agreement. However, a systematic trend is observable in the experimental data, slightly deviating from theory, which indicates that some deformations occur in the shapes of the peptide units forming the bend, differing from that of the standard planar peptide unit.

Pi-turns in proteins and peptides: Classification, conformation, occurrence, hydration and sequence.

The i + 5-->i hydrogen bonded turn conformation (pi-turn) with the fifth residue adopting alpha L conformation is frequently found at the C-terminus of helices in proteins and hence is speculated to be a "helix termination signal." An analysis of the occurrence of i + 5-->i hydrogen bonded turn conformation at any general position in proteins (not specifically at the helix C-terminus), using coordinates of 228 protein crystal structures determined by X-ray crystallography to better than 2.5 A resolution is reported in this paper. Of 486 detected pi-turn conformations, 367 have the (i + 4)th residue in alpha L conformation, generally occurring at the C-terminus of alpha-helices, consistent with previous observations. However, a significant number (111) of pi-turn conformations occur with (i + 4)th residue in alpha R conformation also, generally occurring in alpha-helices as distortions either at the terminii or at the middle, a novel finding. These two sets of pi-turn conformations are referred to by the names pi alpha L and pi alpha R-turns, respectively, depending upon whether the (i + 4)th residue adopts alpha L or alpha R conformations. Four pi-turns, named pi alpha L'-turns, were noticed to be mirror images of pi alpha L-turns, and four more pi-turns, which have the (i + 4)th residue in beta conformation and denoted as pi beta-turns, occur as a part of hairpin bend connecting twisted beta-strands. Consecutive pi-turns occur, but only with pi alpha R-turns. The preference for amino acid residues is different in pi alpha L and pi alpha R-turns. However, both show a preference for Pro after the C-termini. Hydrophilic residues are preferred at positions i + 1, i + 2, and i + 3 of pi alpha L-turns, whereas positions i and i + 5 prefer hydrophobic residues. Residue i + 4 in pi alpha L-turns is mainly Gly and less often Asn. Although pi alpha R-turns generally occur as distortions in helices, their amino acid preference is different from that of helices. Poor helix formers, such as His, Tyr, and Asn, also were found to be preferred for pi alpha R-turns, whereas good helix former Ala is not preferred. pi-Turns in peptides provide a picture of the pi-turn at atomic resolution. Only nine peptide-based pi-turns are reported so far, and all of them belong to pi alpha L-turn type with an achiral residue in position i + 4. The results are of importance for structure prediction, modeling, and de novo design of proteins.