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.

Rationalizing the effects of amino acid side chain, pyridine, and imidazole on the assembly and reversible disassembly of a octanuclear Cu(III) complex

This paper reports the observation of a reversible disassembly process for a previously reported octanuclear Cu(II) complex with imidazole. To identify the factors responsible for the process, five Cu(II) complexes of different nuclearity with different amino acid-derived tetradentate ligands were structurally characterized. The results show that the coordination geometry preference of Cu(II), the tendency of imidazole to act as in-plane ligand, and H-bonding played important role in the formation and disassembly of the octanuclear complex. A general scheme describing the effect of different amino acid side arms, solvents, and exogenous ligands on the nuclearity of the Cu(II) complexes has been presented. The crystals of the complexes also showed formation of multifaceted networks in the resulting complexes.

A Comparative Assessment of Hand Preference in Captive Red Howler Monkeys, Alouatta seniculus and Yellow-Breasted Capuchin Monkeys, Sapajus xanthosternos

There are two major theories that attempt to explain hand preference in non-human primates-the `task complexity' theory and the `postural origins' theory. In the present study, we proposed a third hypothesis to explain the evolutionary origin of hand preference in non-human primates, stating that it could have evolved owing to structural and functional adaptations to feeding, which we refer to as the `niche structure' hypothesis. We attempted to explore this hypothesis by comparing hand preference across species that differ in the feeding ecology and niche structure: red howler monkeys, Alouatta seniculus and yellow-breasted capuchin monkeys, Sapajus xanthosternos. The red howler monkeys used the mouth to obtain food more frequently than the yellow-breasted capuchin monkeys. The red howler monkeys almost never reached for food presented on the opposite side of a wire mesh or inside a portable container, whereas the yellow-breasted capuchin monkeys reached for food presented in all four spatial arrangements (scattered, on the opposite side of a wire mesh, inside a suspended container, and inside a portable container). In contrast to the red howler monkeys that almost never acquired bipedal and clinging posture, the yellow-breasted capuchin monkeys acquired all five body postures (sitting, bipedal, tripedal, clinging, and hanging). Although there was no difference between the proportion of the red howler monkeys and the yellow-breasted capuchin monkeys that preferentially used one hand, the yellow-breasted capuchin monkeys exhibited an overall weaker hand preference than the red howler monkeys. Differences in hand preference diminished with the increasing complexity of the reaching-for-food tasks, i.e., the relatively more complex tasks were perceived as equally complex by both the red howler monkeys and the yellow-breasted capuchin monkeys. These findings suggest that species-specific differences in feeding ecology and niche structure can influence the perception of the complexity of the task and, consequently, hand preference.

A New Class Of Photo-Cross-Linkable Side-Chain Liquid Crystalline Polymers Containing Bis(Benzylidene)Cyclohexanone Units

This paper reports a new class of photo-cross-linkable side chain liquid crystalline polymers (PSCLCPs) based on the bis(benzylidene)cyclohexanone unit, which functions as both a mesogen and a photoactive center. Polymers with the bis(benzylidene)cyclohexanone unit and varying spacer length have been synthesized. Copolymers of bis(benzylidene)cyclohexanone containing monomer and cholesterol benzoate containing monomer with different compositions have also been prepared. All these polymers have been structurally characterized by spectroscopic techniques. Thermal transitions were studied by DSC, and mesophases were identified by polarized light optical microscopy (POM). The intermediate compounds OH-x, the monomers SCLCM-x, and the corresponding polymers PSCLCP-x, which are essentially based on bis(benzylidene)cyclohexanone, all show a nematic mesophase. Transition temperatures were observed to decrease with increasing spacer length. The copolymers with varying compositions exhibit a cholesteric mesophase, and the transition temperatures increase with the cholesteric benzoate units in the copolymer. Photolysis of the low molecular weight liquid crystalline bis(benzylidene)-cyclohexanone compound reveals that there are two kinds of photoreactions in these systems: the EZ photoisomerization and 2 pi + 2 pi addition. The EZ photoisomerization in the LC phase disrupts the parallel stacking of the mesogens, resulting in the transition from the LC phase to the isotropic phase. The photoreaction involving the 2 pi + 2 pi addition of the bis(benzylidene)cyclohexanone units in the polymer results in the cross-linking of the chains. The liquid crystalline induced circular dichroism (LCICD) studies of the cholesterol benzoate copolymers revealed that the cholesteric supramolecular order remains even after the photo-cross-linking.

A comparative study of side-band Fresnel holograms recorded with self-imaging and general objects

This paper deals with new results obtained in regard to the reconstruction properties of side-band Fresnel holograms (SBFH) of self-imaging type objects (for example, gratings) as compared with those of general objects. The major finding is that a distribution I2, which appears on the real-image plane along with the conventional real-image I1, remains a 2Z distribution (where 2Z is the axial distance between the object and its self-imaging plane) under a variety of situations, while its nature and focusing properties differ from one situation to another. It is demonstrated that the two distributions I1 and I2 can be used in the development of a novel technique for image subtraction.

Side Chain Structure Determines Unique Physiologic and Therapeutic Properties of norUrsodeoxycholic Acid in Mdr2(-/-) Mice

24-norursodeoxycholic acid (norUDCA), a side chain-modified ursodeoxycholic acid derivative, has dramatic therapeutic effects in experimental cholestasis and may be a promising agent for the treatment of cholestatic liver diseases. We aimed to better understand the physiologic and therapeutic properties of norUDCA and to test if they are related to its side chain length and/or relative resistance to amidation. For this purpose, Mdr2-/- mice, a model for sclerosing cholangitis, received either a standard diet or a norUDCA-, tauro norursodeoxycholic acid (tauro- norUDCA)-, or di norursodeoxycholic acid (di norUDCA)-enriched diet. Bile composition, serum biochemistry, liver histology, fibrosis, and expression of key detoxification and transport systems were investigated. Direct choleretic effects were addressed in isolated bile duct units. The role of Cftr for norUDCA-induced choleresis was explored in Cftr-/- mice. norUDCA had pharmacologic features that were not shared by its derivatives, including the increase in hepatic and serum bile acid levels and a strong stimulation of biliary HCO3- -output. norUDCA directly stimulated fluid secretion in isolated bile duct units in a HCO3- -dependent fashion to a higher extent than the other bile acids. Notably, the norUDCA significantly stimulated HCO 3- -output also in Cftr-/- mice. In Mdr2-/- mice, cholangitis and fibrosis strongly improved with norUDCA, remained unchanged with tauro- norUDCA, and worsened with di norUDCA. Expression of Mrp4, Cyp2b10, and Sult2a1 was increased by norUDCA and di norUDCA, but was unaffected by tauro- norUDCA. Conclusion:The relative resistance of norUDCA to amidation may explain its unique physiologic and pharmacologic properties. These include the ability to undergo cholehepatic shunting and to directly stimulate cholangiocyte secretion, both resulting in a HCO3- -rich hypercholeresis that protects the liver from cholestatic injury.

Side-band intensities in the deuterium magnetic resonance spectra of oriented molecules spinning near the magic angle

The appearance of spinning side bands in the 2H NMR spectra of oriented molecules is investigated. A theoretical interpretation of the side-band intensities is carried out. Information derived on the director orientation and distribution as a function of spinning speedis reported.

Preferred conformations and flexibility of aminoacyl side chain of penicillins

Possible conformations of penicillin G; d and l isomers of ampicillin; α-amino-α-methyl-benzyl penicillins and 3- pyridyl methyl penicillin have been studied by an energy minimization procedure using empirical potential functions. The preferred conformations of these antibiotics have been correlated with their biological activity. The conformational requirement of the antibiotic to be active against Gram-positive and Gram-negative (β-lactamase-negative) bacterial strains seems to be the same. The reduced activity of penicillin G against Gram-negative bacteria has been attributed to its lower ability to permeate the outer membrane. The flexibility of the sidechains of these antibiotics is also shown to be important for the desired biological activity.

Precise Values of the "C Component Vicinal Coupling Constants for Calculating Side-Chain Conformations in Amino Acids

From consideration of 'H-lH vicinal coupling constants and '"G'H long-range coupling constants in a series of amino acid derivatives, the precise values of uC component vicinal coupling constants have been calculated for the three minimum energy staggered rotamers for the C(or)H-C(P)H, side-chains of amino acids.

Effect of vitamin A deprivation on the cholesterol side-chain cleavage enzyme activity of testes and ovaries of rats (Short Communication)

The cholesterol side-chain cleavage enzyme activity is decreased considerably at the mild stage of vitamin A deficiency in rat testes and ovaries and the decrease in activity becomes more pronounced with progress of deficiency. Supplementation of the deficient rats with retinyl acetate, but not retinoic acid, restores the enzyme activity to normal values. The cholesterol side-chain cleavage enzyme of adrenals is not affected by any of the above treatments.

Conformational studies of the triphenylphosphazenyl side chain in cyclophosphazenes. II. Crystal and molecular structure of 2,4,4,6,6,8,8-heptachloro-2-triphenylphosphazenylcyclotetra(phosphazene), N4P4Cl7(NPPh3)

Abstract is not available.

A playful side to twelfth-century mathematics

As editors of the book Lilavati's Daughters: The Women Scientists of India, reviewed by Asha Gopinathan (Nature 460, 1082; 2009), we would like to elaborate on the background to its title. Lilavati was a mathematical treatise of the twelfth century, composed by the mathematician and astronomer Bhaskaracharya (1114–85) — also known as Bhaskara II — who was a teacher of repute and author of several other texts. The name Lilavati, which literally means 'playful', is a surprising title for an early scientific book. Some of the mathematical problems posed in the book are in verse form, and are addressed to a girl, the eponymous Lilavati. However, there is little real evidence concerning Lilavati's historicity. Tradition holds that she was Bhaskaracharya's daughter and that he wrote the treatise to console her after an accident that left her unable to marry. But this could be a later interpolation, as the idea was first mentioned in a Persian commentary. An alternative view has it that Lilavati was married at an inauspicious time and was widowed shortly afterwards. Other sources have implied that Lilavati was Bhaskaracharya's wife, or even one of his students — raising the possibility that women in parts of the Indian subcontinent could have participated in higher education as early as eight centuries ago. However, given that Bhaskara was a poet and pedagogue, it is also possible that he chose to address his mathematical problems to a doe-eyed girl simply as a whimsical and charming literary device.

Distributed joint source channel coding on a multiple access channel with side information

We consider the problem of transmission of several discrete sources over a multiple access channel (MAC) with side information at the sources and the decoder. Source-channel separation does not hold for this channel. Sufficient conditions are provided for transmission of sources with a given distortion. The channel could have continuous alphabets (Gaussian MAC is a special case). Various previous results are obtained as special cases.

Propargyloxycarbonyl as a protecting group for the side chains of serine, threonine and tyrosine

Propargyloxycarbonyl group is used as a protecting group for the hydroxyl groups of serine, threonine and tyrosine. The propargyloxycarbonyl derivatives of these hydroxy amino acids are stable to acidic and basic reagents commonly employed in peptide synthesis. The deprotection of the O-Poc derivatives using tetrathiomolybdate does not affect commonly used protecting groups such as N-Boc, N-Cbz, N-Fmoc, methyl and benzyl esters. The di-and tripeptides synthesized using O-Poc derivatives of serine, threonine and tyrosine are stable, isolable compounds and give the hydroxy peptides in good yields when treated with tetrathiomolybdate.

Structure and bonding of MCB5H7 and its sandwiched dimer CB5H6M–MCB5H6 (M = Si, Ge, Sn): Isomer stability and preference for slip distorted structure

We find sandwiched metal dimers CB5H6M–MCB5H6 (M = Si, Ge, Sn) which are minima in the potential energy surface with a characteristic M–M single bond. The NBO analysis and the M–M distances (Å) (2.3, 2.44 and 2.81 for M = Si, Ge, Sn) indicate substantial M–M bonding. Formal generation of CB5H6M–MCB5H6 has been studied theoretically. Consecutive substitution of two boron atoms in B7H−27 by M (Si, Ge, Sn) and carbon, respectively followed by dehydrogenation may lead to our desired CB5H6M–MCB5H6. We find that the slip distorted geometry is preferred for MCB5H7 and its dehydrogenated dimer CB5H6M–MCB5H6. The slip-distortion of M–M bond in CB5H6M–MCB5H6 is more than the slip distortion of M–H bond in MCB5H7. Molecular orbital analysis has been done to understand the slip distortion. Larger M–M bending (CB5H6M–MCB5H6) in comparison with M–H bending (MCB5H7) is suspected to be encouraged by stabilization of one of the M–M π bonding MO’s. Preference of M to occupy the apex of pentagonal skeleton of MCB5H7 over its icosahedral analogue MCB10H11 has been observed.