The 310 Helical Conformation of the Amino Terminal Decapeptide of Suzukacillin. 270 MHz 'H NMR Evidence for Eight Intramolecular Hydrogen Bonds

The amino terminal suzukacillin decapeptide fragment, Boc-Aib-Pro-Val-Aib-Val-Ala-Aib-Ala-Aib-Aitbh-eO Me, two pentapeptides Boc-AibPrc-Val-AibVal-OMe and Boc-Ala-AibAla-AibAibOMe, and the tripeptide Boc-Ala-AibAibOMe have been studied by 270-MHz 'H NMR spectroscopy. By use of solvent dependence of chemical shifts in a CDC13-(CD3),S0 system and temperature dependence of amide NH chemical shifts in (CD3),S0, the intramolecularly hydrogen bonded NH groups in these peptides have been identified. The tripeptide possesses one hydrogen bond, both pentapeptides show evidence for three intramolecular hydrogen bonds, and the decapeptide has eight NH groups participating in hydrogen bonding. An Ala( 1)-Aib(2) @ turn is proposed for the tripeptide. Both pentapeptides favor 310 helical conformations composed of three consecutive B turns. The decapeptide adopts a 310 helical conformation with some flexibility at the Va1(5)-Ala(6) segment. The proposed conformations are consistent with the known stereochemical preferences of Aib residues.

Characterization of Mycobacterium leprae RecA intein, a LAGLIDADG homing endonuclease, reveals a unique mode of DNA-binding, helical distortion and cleavage, compared to a canonical LAGLIDADG homing endonuclease

Mycobacterium leprae, which has undergone reductive evolution leaving behind a minimal set of essential genes, has retained intervening sequences in four of its genes implicating a vital role for them in the survival of the leprosy bacillus. A single in-frame intervening sequence has been found embedded within its recA gene. Comparison of M. leprae recA intervening sequence with the known intervening sequences indicated that it has the consensus amino acid sequence necessary for being a LAGLIDADG-type homing endonuclease. In light of massive gene decay and function loss in the leprosy bacillus, we sought to investigate whether its recA intervening sequence encodes a catalytically active homing endonuclease. Here we show that the purified M. leprae RecA intein (PI-MleI) binds to cognate DNA and displays endonuclease activity in the presence of alternative divalent cations, Mg2+ or Mn2+. A combination of approaches including four complementary footprinting assays such as DNase I, Cu/phenanthroline, methylation protection and KMnO4, enhancement of 2-aminopurine fluorescence and mapping of the cleavage site revealed that PI-MleI binds to cognate DNA flanking its insertion site, induces helical distortion at the cleavage site and generates two staggered double-strand breaks. Taken together, these results implicate that PI-MleI possess a modular structure with separate domains for DNA target recognition and cleavage, each with distinct sequence preferences. From a biological standpoint, it is tempting to speculate that our findings have implications for understanding the evolution of LAGLIDADG family of homing endonucleases

The crystal and molecular structure of the amino terminal tetrapeptide of alamethicin. A novel 310 helical conformation

The molecular structure of N-benzyloxycarbonyl-α-aminoisobutyryl-prolyl-α-aminoisobutyryl-alanyl methyl ester (Z-Aib-Pro-Aib-Ala-OMe), the amino terminal tetrapeptide of alamethicin is reported. The molecule contains two consecutive β-turns with Aib-Pro and Pro-Aib at the corners, forming an incipient 310 helix. This constitutes the first example of an X2-Pro3 β-turn in the crystal structure of a small peptide.

Fourier transform of the collagen triple-helical structure and its significance

The Fourier transforms of the collagen molecular structure have been calculated taking into consideration various side chain atoms, as well as the presence of bound water molecules. There is no significant change in the calculated intensity distribution on including the side chain atoms of non-imino-acid residues. Taking into account the presence of about two bound water molecules per tripeptide unit, the agreement with the observed x-ray pattern is slightly improved. Fourier transforms have also been calculated for the detailed molecular geometries proposed from other laboratories. It is found that there are no major differences between them, as compared to our structure, either in the positions of peak intensity or in the intensity distribution. Hence it is not possible to judge the relative merits of the various molecular geometries for the collagen triple helix from a comparison of the calculated transforms with the meagre data available from its x-ray fibre pattern. It is also concluded that the collagen molecular structure should be regarded as a somewhat flexible chain structure, capable of adapting itself to the requirements of the different side groups which occur in each local region.

Conformation of polypeptide-chains containing both l-residues and D-residues .2. Double-helical structures of poly-ld-peptides

Polypeptides with alternating L- and D-amino acid residues can take up stereochemically satisfactory coaxial double-helical structures, both antiparallel and parallel, which are stabilized by systematic interchain NH O hydrogen bonds. Semiempirical energy calculations over allowed regions of conformational space have yielded the characteristics of these double-helices. There are four possible types of antiparallel double-helices - A3, A4, A5 and A6, with n, the number of LD peptide units per turn, around 2.8, 3.6, 4.5 and 5.5 respectively, while for the parallel double-helices there are two types, P3 and P4, having similar helical parameters as in A3 and A4. The hydrogen-bonding scheme restricts the pitch in all the models to the narrow range of 10.0 to 11.5 Å. All these helices have large central cores whose radii increase proportionately with n. In this respect, A3 and A4 are suitable models for the structure of gramicidin A. In terms of their relative energies, antiparallel double-helices are marginally more stable than those with parallel strands. Our results indicate that the energy differences amongst the members in the antiparallel family are not significant and thus provide an explanation for the polymorphism reported for poly(γ-benzyl-LD-glutamate).

The 310 helical conformation of a pentapeptide containing a-aminoisobutyric acid (Aib): X-ray crystal structure of Tos-(Aib)5 OMe

The pentapeptide Tos-(Aib)5-OMe adopts a 310 helical conformation in the solid state, with three consecutive Type III B-turns stabilized by intramolecular hydrogen bonds.

X-Pro peptides: Synthesis and solution conformation of benzyloxycarbonyl-(Aib-Pro)4methyl ester. Evidence for a novel helical structure

The synthesis of the octapeptide, benzyloxycarbonyl-(-aminoisobutyryl-L-prolyl)4-methyl ester [Z-(Aib-Pro)4-OMe] and an analysis of its solution conformation is reported. The octapeptide is shown to possess three strong intramolecular hydrogen bonds on the basis of studies of the solvent and temperature dependence of NH chemical shifts and rates of hydrogen-deuterium exchange. 13C studies are consistent with a structure involving only trans Aib-Pro bonds, while ir experiments support a hydrogen-bonded conformation. The Aib 3, 5, and 7 NH groups are shown to participate in hydrogen bonding. A 310 helical conformation compatible with the spectroscopic data is suggested. The proposed conformation consists of three type III -turns with Aib and Pro at the corners and stabilized by 4 1 intramolecular hydrogen bonds.

Aggregation of apolar peptides in organic solvents. Concentration dependence of 1H-nmr parameters for peptide NH groups in 310 helical decapeptide fragment of suzukacillin

Peptide NH chemical shifts and their temperature dependences have been monitored as a function of concentration for the decapeptide, Boc-Aib-Pro-Val-Aib-Val-Ala-Aib-Ala-Aib-Aib-OMe in CDCl3 (0.001-0.06M) and (CD3)2SO (0.001-0.03M). The chemical shifts and temperature coefficients for all nine NH groups show no significant concentration dependence in (CD3)2SO. Seven NH groups yield low values of temperature coefficients over the entire range, while one yields an intermediate value. In CDCl3, the Aib(1) NH group shows a large concentration dependence of both chemical shift and temperature coefficient, in contrast to the other eight NH groups. The data suggest that in (CD3)2SO, the peptide adopts a 310 helical conformation and is monomeric over the entire concentration range. In CDCl3, the 310 helical peptide associates at a concentration of 0.01M, with the Aib(1) NH involved in an intermolecular hydrogen bond. Association does not disrupt the intramolecular hydrogen-bonding pattern in the decapeptide.

Expanding the Peptide beta-Turn in alpha gamma Hybrid Sequences: 12 Atom Hydrogen Bonded Helical and Hairpin Turns

Hybrid peptide segments containing contiguous alpha and gamma amino acid residues can form C-12 hydrogen bonded turns which may be considered as backbone expanded analogues of C-10 beta-turns) found in alpha alpha segments. Exploration of the regular hydrogen bonded conformations accessible for hybrid alpha gamma sequences is facilitated by the use of a stereochemically constrained gamma amino acid residue gabapentin (1-aminomethylcyclohexaneacetic acid, Gpn), in which the two torsion angles about C-gamma-C-beta (theta(1)) and C-beta-C-alpha (theta(2)) are predominantly restricted to gauche conformations. The crystal structures of the octapeptides Boc-Gpn-Aib-Gpn-Aib-Gpn-Aib-Gpn-Aib-OMe (1) and Boc-Leu-Phe-Val-Aib-Gpn-Leu-Phe-Val-OMe (2) reveal two distinct conformations for the Aib-Gpn segment. Peptide 1 forms a continuous helix over the Aib(2)-Aib(6) segment, while the peptide 2 forms beta-hairpin structure stabilized by four cross-strand hydrogen bonds with the Aib-Gpn segment forming a nonhelical C-12 turn. The robustness of the helix in peptide 1 in solution is demonstrated by NMR methods. Peptide 2 is conformationally fragile in solution with evidence of beta-hairpin conformations being obtained in methanol. Theoretical calculations permit delineation of the various C-12 hydrogen bonded structures which are energetically feasible in alpha gamma and gamma alpha sequences.

Inter-helical Interactions in Membrane Proteins: Analysis Based on the Local Backbone Geometry and the Side Chain Interactions

The availability of a significant number of the Structures of helical membrane proteins has prompted us to investigate the mode of helix-helix packing. In the present study, we have considered a dataset of alpha-helical membrane proteins representing Structures solved from all the known superfamilies. We have described the geometry of all the helical residues in terms of local coordinate axis at the backbone level. Significant inter-helical interactions have been considered as contacts by weighing the number of atom-atom contacts, including all the side-chain atoms. Such a definition of local axis and the contact criterion has allowed us to investigate the inter-helical interaction in a systematic and quantitative manner. We show that a single parameter (designated as alpha), which is derived from the parameters representing the Mutual orientation of local axes, is able to accurately Capture the details of helix-helix interaction. The analysis has been carried Out by dividing the dataset into parallel, anti-parallel, and perpendicular orientation of helices. The study indicates that a specific range of alpha value is preferred for interactions among the anti-parallel helices. Such a preference is also seen among interacting residues of parallel helices, however to a lesser extent. No such preference is seen in the case of perpendicular helices, the contacts that arise mainly due to the interaction Of Surface helices with the end of the trans-membrane helices. The Study Supports the prevailing view that the anti-parallel helices are well packed. However, the interactions between helices of parallel orientation are non-trivial. The packing in alpha-helical membrane proteins, which is systematically and rigorously investigated in this study, may prove to be useful in modeling of helical membrane proteins.

Conformation of di-n-propylglycine residues (Dpg) in peptides: crystal structures of a type I-turn forming tetrapeptide and an -helical tetradecapeptide

The crystal structures of two oligopeptides containing di-n-propylglycine (Dpg) residues, Boc-Gly-Dpg-Gly-Leu-OMe (1) and Boc-Val-Ala-Leu-Dpg-Val-Ala-Leu-Val-Ala-Leu-Dpg-Val-Ala-Leu-OMe (2) are presented. Peptide 1 adopts a type I-turn conformation with Dpg(2)-Gly(3) at the corner positions. The 14-residue peptide 2 crystallizes with two molecules in the asymmetric unit, both of which adopt -helical conformations stabilized by 11 successive 5 1 hydrogen bonds. In addition, a single 4 1 hydrogen bond is also observed at the N-terminus. All five Dpg residues adopt backbone torsion angles (, ) in the helical region of conformational space. Evaluation of the available structural data on Dpg peptides confirm the correlation between backbone bond angle NCC() and the observed backbone , values. For > 106° , helices are observed, while fully extended structures are characterized by < 106° . The mean values for extended and folded conformations for the Dpg residue are 103.6° ± 1.7° and 109.9° ± 2.6° , respectively.

Dual-frequency characteristics of Minkowski-square ring antennas

Fractal Minkowski curves to design a compact dual-frequency microstrip ring antenna are proposed. Sides of a square ring have been selectively replaced with first and second iterations of the generalised fractal geometry to design a smaller antenna with dual-frequency operation. This behaviour has been explained based on current distributions on the antenna structure. Measured results compare well with electromagnetic simulations.

A design procedure for micromachined antennas on semiconductor substrates

Micromachined antennas are recieving great interest as carrier frequencies move higher into the frequency spectrum due to their superior performance and amenability for integration with active devices. However their design is cumbersome owing to the complexity of the structure. To overcome this, in this paper, an iterative procedure is suggested to facilitate fast design of micromachined patch antennas based on a simulation study. A microstrip line on a micromachined Silicon substrate is simulated in a full wave simulator by solving for the ports only. From the obtained propagation constant, the effective dilectric constant for the micromachined substrate is estimated. The process is repeated for a number of values of the width of the microstrip and a plot is made for the variation of the effective dielectric constant with the microstrip width. Then an iterative method in combination with the extrapolated permittivity which includes the effect of cavity extensions in all the directions, is used to obtain the width and the corresponding effective dielectric constant. This method has been verified to be quite accurate by comparison with full wave simulations and hence it can function as a good starting point for designers to design micromachined antennas.

Aggregation studies in crystals of apolar helical peptides: Boc-Aib-Val-Ala-Leu-Aib-Val-Ala-Leu-Aib-OMe

In the crystal, the backbone of Boc-(Aib-Val-Ala-Leu)2-Aib-OMe adopts a helical form with four alpha-type hydrogen bonds in the middle, flanked by 3(10)-type hydrogen bonds at either end. The helical molecules stack in columns with head-to-tail hydrogen bonds, either directly between NH and CO, or bridged by solvent molecules. The packing of the helices is parallel, even in space group P2(1). Cell parameters are a = 9.837(2) A, b = 15.565(3) A, c = 20.087(5) A, beta = 96.42(2) degrees, dcalc = 1.091 g/cm3 for C46H83N9O12.1.5H2O.0.67CH3OH. There appears to be some hydration of the backbone in this apolar helix.