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.

A Mycobacterial Cyclic AMP Phosphodiesterase That Moonlights as a Modifier of Cell Wall Permeability

Mycobacterium tuberculosis utilizes many mechanisms to establish itself within the macrophage, and bacterially derived cAMP is important in modulating the host cellular response. Although the genome of M. tuberculosis is endowed with a number of mammalian-like adenylyl cyclases, only a single cAMP phosphodiesterase has been identified that can decrease levels of cAMP produced by the bacterium. We present the crystal structure of the full-length and sole cAMP phosphodiesterase, Rv0805, found in M. tuberculosis, whose orthologs are present only in /the genomes of slow growing and pathogenic mycobacteria. The dimeric core catalytic domain of Rv0805 adopts a metallophosphoesterase fold, and the C-terminal region builds the active site and contributes to multiple substrate utilization.Localization of Rv0805 to the cell wall is dependent on its C terminus, and expression of either wild type or mutationally inactivated Rv0805 in M. smegmatis alters cell permeability to hydrophobic cytotoxic compounds. Rv0805 may therefore play a key role in the pathogenicity of mycobacteria, not only by hydrolyzing bacterial cAMP, but also by moonlighting as a protein that can alter cell wall functioning.

[B4O9H2] Cyclic Borate Units as the Building Unit in a Family of Zinc Borate Structures

A solvothermal reaction of ZnO, boric acid (B(OH)(3)), and aliphatic airlines in a water-pyridine mixture gave four zinc borate phases of different dimensionalities: [Zn(B4O8H2)(C3H10N2)], I (one-dimensional); [Zn(B4O8H2)(C3H10N2)] H2O, II (two-dimensional); [Zn(B5O10H3)(C10H24N4)]center dot H2O, III (two-dimensional): and [Zn-2(B8O15H2)(C3H10N2)(2)], IV (three-dimensional). The structures are formed by the connectivity involving polyborate chains and layers with Zn2+ species. In all the compounds, the amine molecules act its file ligand binding either the same or different zn centers. The formation of two different structures, II and IV, from the same amine by varying the reaction time is noteworthy. Transformation studies on II indicate that the formation of IV. from II, is facile and has been investigated for the first time. Two of file compounds, I and III, exhibit activity for second-order nonlinear optical behavior. The UV exposure of the sample indicates the absorption of all the UV radiation suggesting that the zinc borate compounds could be exploited for UV-blocking applications. The compounds have been characterized by powder X-ray diffraction, infrared spectroscopy, thermogravimetric analysis, UV-vis, photoluminescence, and NMR studies.

Cyclic-oxidation behavior of Ti3SiC2-base material at 1100°c

The cyclic-oxidation behavior of Ti3SiC2-base material was studied at 1100°C in air. Scale spallation and weight loss were not observed in the present tests and the weight gain would just continue if the experiments were not interrupted. The present results demonstrated that the scale growth on Ti3SiC2-base material obeyed a parabolic rate law up to 20 cycles. It then changed to a linear rate with further increasing cycles. The scales formed on the Ti3SiC2base material were composed of an inward-growing, fine-grain mixture of Ti022 + SiO2 and an outward-growing, coarse-grain TiO2. Theoretical calculations show that the mismatch in thermal expansion coefficients between the inner scale and Ti3SiC2-base matrix is small. The outer TiO2 layer was under very low compressive stress, while the inner TiO2 + SiO2 layer was under tensile stress during cooling. Scale spaliation is, therefore, not expected and the scale formed on Ti3SiC2-base material is adherent and resistant to cyclic oxidation.

Improving the selectivity of engineered protease inhibitors: Optimizing the P2 prime residue using a versatile cyclic peptide library

Standard mechanism inhibitors are attractive design templates for engineering reversible serine protease inhibitors. When optimizing interactions between the inhibitor and target protease, many studies focus on the nonprimed segment of the inhibitor's binding loop (encompassing the contact β-strand). However, there are currently few methods for screening residues on the primed segment. Here, we designed a synthetic inhibitor library (based on sunflower trypsin inhibitor-1) for characterizing the P2′ specificity of various serine proteases. Screening the library against 13 different proteases revealed unique P2′ preferences for trypsin, chymotrypsin, matriptase, plasmin, thrombin, four kallikrein-related peptidases, and several clotting factors. Using this information to modify existing engineered inhibitors yielded new variants that showed considerably improved selectivity, reaching up to 7000-fold selectivity over certain off-target proteases. Our study demonstrates the importance of the P2′ residue in standard mechanism inhibition and unveils a new approach for screening P2′ substitutions that will benefit future inhibitor engineering studies.

Cyclic AMP in Mycobacteria: Characterization and Functional Role of the Rv1647 Ortholog in Mycobacterium smegmatis{triangledown}

Mycobacterial genomes are endowed with many eukaryote-like nucleotide cyclase genes encoding proteins that can synthesize 3',5'-cyclic AMP (cAMP). However, the roles of cAMP and the need for such redundancy in terms of adenylyl cyclase genes remain unknown. We measured cAMP levels in Mycobacterium smegmatis during growth and under various stress conditions and report the first biochemical and functional characterization of the MSMEG_3780 adenylyl cyclase, whose orthologs in Mycobacterium tuberculosis (Rv1647) and Mycobacterium leprae (ML1399) have been recently characterized in vitro. MSMEG_3780 was important for producing cAMP levels in the logarithmic phase of growth, since the {Delta}MSMEG_3780 strain showed lower intracellular cAMP levels at this stage of growth. cAMP levels decreased in wild-type M. smegmatis under conditions of acid stress but not in the {Delta}MSMEG_3780 strain. This was correlated with a reduction in MSMEG_3780 promoter activity, indicating that the effect of the reduction in cAMP levels on acid stress was caused by a decrease in the transcription of MSMEG_3780. Complementation of the {Delta}MSMEG_3780 strain with the genomic integration of MSMEG_3780 or the Rv1647 gene could restore cAMP levels during logarithmic growth. The Rv1647 promoter was also acid sensitive, emphasizing the biochemical and functional similarities in these two adenylyl cyclases. This study therefore represents the first detailed biochemical and functional analysis of an adenylyl cyclase that is important for maintaining cAMP levels in mycobacteria and underscores the subtle roles that these genes may play in the physiology of the organism.

Cyclic porphyrin dimers as hosts for coordinating ligands

Bicovalently linked tetraphenylporphyrins bearing dioxypentane groups at the opposite (transoid, H4A) and adjacent (cisoid, H4B) aryl groups have been synthesised. Protonation of the free-base porphyrins leads to fully protonated species H8A4+/H8A4+ accompanied by expansion of cavity size of the bisporphyrins. The electrochemical redox studies of these porphyrins and their Zinc(II) derivatives revealed that the first ring oxidation proceeds through a two-electron process while the second ring oxidation occurs at two distinct one-electron steps indicating unsymmetrical charge distribution in the oxidized intermediate. The axial ligation properties of the Zinc(Il) derivatives of H4A/H4B with DABCO and PMDA investigated by spectroscopic and single crystal X-ray diffraction studies showed predominant existence of 1: I complex. The Zn2A.DABCO complex assumes an interesting eclipsed structure wherein DABCO is located inside the cavity between the two porphyrin planes with Zn-N distances at 2.08 and 2.22 Å. The Zn atoms are pulled into the cavity due to coordination towards nitrogen atoms of DABCO and deviate from the mean porphyrin plane by 0.35 Å. The electrochemical redox potentials of the axially ligated metal derivatives are found to be sensitive function of the relative coordinating ability of the ligands and the conformation of the hosts.

Structure and Bonding in Cyclic Isomers of B2AlHnm (n = 3−6, m = −2 to +1): A Comparative Study with B3Hnm, BAl2Hnm and Al3Hnm†

The structure, bonding and energetics of B2AlHnm (n = 3−6, m = −2 to +1) are compared with corresponding homocyclic boron, aluminum analogues and BAl2Hnm using density functional theory (DFT). Divalent to hexacoordinated boron and aluminum atoms are found in these species. The geometrical and bonding pattern in B2AlH4− is similar to that for B2SiH4. Species with lone pairs on the divalent boron and aluminum atoms are found to be minima on the potential energy surface of B2AlH32−. A dramatic structural diversity is observed in going from B3Hnm to B2AlHnm, BAl2Hnm and Al3Hnm and this is attributable to the preference of lower coordination on aluminum, higher coordination on boron and the higher multicenter bonding capability of boron. The most stable structures of B3H6+, B2AlH5 and BAl2H4− and the trihydrogen bridged structure of Al3H32− show an isostructural relationship, indicating the isolobal analogy between trivalent boron and divalent aluminum anion.

Characterisation of head-hardened rail steel in terms of cyclic plasticity response and microstructure for improved material modelling

Stress- and strain-controlled tests of heat treated high-strength rail steel (Australian Standard AS1085.1) have been performed in order to improve the characterisation of the said material׳s ratcheting and fatigue wear behaviour. The hardness of the rail head material has also been studied and it has been found that hardness reduces considerably below four-millimetres from the rail top surface. Historically, researchers have used test coupons with circular cross-sections to conduct cyclic load tests. Such test coupons, typically five-millimetres in gauge diameter and ten‐millimetres in grip diameter, are usually taken from the rail head sample. When there is considerable variation of material properties over the cross-section it becomes likely that localised properties of the rail material will be missed. In another case from the literature, disks 47 mm in diameter for a twin-disk rolling contact test machine were obtained directly from the rail sample and used to validate ratcheting and rolling contact fatigue wear models. The question arises: How accurate are such tests, especially when large material property gradients exist? In this research paper, the effects of rail sampling location on the ratcheting behaviour of AS1085.1 rail steel were investigated using rectangular-shaped specimens obtained at four different depths to observe their respective cyclic plasticity behaviour. The microstructural features of the test coupons were also analysed, especially the pearlite inter-lamellar spacing which showed strong correlation with both hardness and cyclic plasticity behaviour of the material. This work ultimately provides new data and testing methodology to aid the selection of valid parameters for material constitutive models to better understand rail surface ratcheting and wear.

Cystine peptides Antiparallel β-sheet conformation of the cyclic biscystine peptide [Boc-Cys-Ala-Cys-NHCH3]2

The crystal structure analysis of the cyclic biscystine peptide [Boc-Cys1-Ala2-Cys3-NHCH3]2 with two disulfide bridges confirms the antiparallel ?-sheet conformation for the molecule as proposed for the conformation in solution. The molecule has exact twofold rotation symmetry. The 22-membered ring contains two transannular NH ? OC hydrogen bonds and two additional NH ? OC bonds are formed at both ends of the molecule between the terminal (CH3)3COCO and NHCH3 groups. The antiparallel peptide strands are distorted from a regularly pleated sheet, caused mainly by the L-Ala residue in which ?=� 155° and ?= 162°. In the disulfide bridge C? (1)-C? (1)-S(1)-(3')-C?(3')-C?(3'), S�S = 2.030 Å, angles C? SS = 107° and 105°, and the torsional angles are �49, �104, +99, �81, �61°, respectively. The biscystine peptide crystallizes in space group C2 with a = 14.555(2) Ã…, b = 10.854(2) Ã…, c = 16.512(2)Ã…, and ?= 101.34(1) with one-half formula unit of C30H52N8O10S4· 2(CH3)2SO per asymmetric unit. Least-squares refinement of 1375 reflections observed with |F| > 3?(F) yielded an R factor of 7.2%.

Stimulation by adenosine 3′,5′-cyclic monophosphate of protein synthesis by adenohypophyseal polyribosomes

Addition of dibutyryl 3′,5′-cyclic AMP to slices of bovine pituitary stimulated incorporation of [3H]leucine into protein, whether or not actinomycin D was present; therefore the influence of 3′,5′-cyclic AMP on protein synthesis by bovine pituitary polysomes was studied. If the cyclic nucleotide was added to the complete protein-synthesizing system (including pH 5.0 enzyme), stimulation of [3H]leucine incorporation occurred only with pH 5.0 enzyme from rat liver; there was no stimulation when homologous enzyme, i.e., from bovine pituitary, was used. Addition of 3′,5′-cyclic AMP to the polysomes, before addition of pH 5.0 enzyme, resulted in stimulation of protein synthesis with either source of enzyme, but stimulation was facilitated to a greater degree, over the range 0.5-2 mM 3′,5′-cyclic AMP, when rat liver was the source. The stimulation of protein synthesis was prevented by the addition of cycloheximide. With rat liver pH 5.0 enzyme the product of hydrolysis of 3′,5′-cyclic AMP was mainly 5′-AMP whereas with pituitary pH 5.0 enzyme there was also dephosphorylation and deamination resulting in production of hypoxanthine and other bases. However, using either source of pH 5.0 enzyme and the complete protein-synthesizing system (i.e., including an ATP-regenerating mechanism) most of the 3H from hydrolysis of [3H]3′,5′-cyclic AMP was incorporated into ATP. The data are seen as compatible with a stimulation by 3′,5′-cyclic AMP of translation by pituitary polysomes; the significance of the importance of the source of pH 5.0 enzyme used in the system is obscure.

Reaction of benzisoxazolium cations with cyclic β-diketones

Reaction of 2-ethylbenzisoxazolium fluoborate (III) with dimedone, dihydroresorcinol, 2-methyldihydroresorcinol and 2-methylcyclopentane-1,3-dione in the presence of base leads to the formation of amides VIII, XI, X and XIII respectively, via the benzoketoketenimine intermediate (IX) and an intramolecular migration. The 7-hydroxy-2-ethylbenzisoxazolium salt (IV) gives the amide (XIV) by double migration. Amides VIII, XI, X and XIII undergo intramolecular Michael reaction to furnish the benzoxazinones (XVI, XVIII, XVII and XXVI). Stereochemistry of this addition is discussed and the conformation in which the CN bond at C-1′ is attached equatorially to the cyclohexanone ring is assigned to the Spirans (XX, XXX and XXVIII). Effect of acids and bases on the amide (VIII) and the spiran (XVI) is described.

Behaviour of autonomous mobile agents using linear cyclic pursuit laws

In this paper, the behaviour of a group of autonomous mobile agents under cyclic pursuit is studied. Cyclic pursuit is a simple distributed control law, in which the agent i pursues agent i + 1 modulo n.. The equations of motion are linear, with no kinematic constraints on motion. Behaviourally, the agents are identical, but may have different controller gains. We generalize existing results in the literature and show that by selecting these gains, the behavior of the agents can be controlled. They can be made to converge at a point or be directed to move in a straight line. The invariance of the point of convergence with the sequence of pursuit is also shown.