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.

Boson-fermion duality in SU(m vertical bar n) supersymmetric Haldane-Shastry spin chain

By using the Y(gl(m|n)) super Yangian symmetry of the SU(m|n) supersymmetric Haldane-Shastry spin chain, we show that the partition function of this model satisfies a duality relation under the exchange of bosonic and fermionic spin degrees of freedom. As a byproduct of this study of the duality relation, we find a novel combinatorial formula for the super Schur polynomials associated with some irreducible representations of the Y(gl(m|n)) Yangian algebra. Finally, we reveal an intimate connection between the global SU(m|n) symmetry of a spin chain and the boson-fermion duality relation. (C) 2007 Elsevier B.V. All rights reserved.

Low energy properties of the SU(m|n) supersymmetric Haldane–Shastry spin chain

The ground state and low energy excitations of the SU(m|n) supersymmetric Haldane–Shastry spin chain are analyzed. In the thermodynamic limit, it is found that the ground state degeneracy is finite only for the SU(m|0) and SU(m|1) spin chains, while the dispersion relation for the low energy and low momentum excitations is linear for all values of m and n. We show that the low energy excitations of the SU(m|1) spin chain are described by a conformal field theory of m non-interacting Dirac fermions which have only positive energies; the central charge of this theory is m/2. Finally, for ngreater-or-equal, slanted1, the partition functions of the SU(m|n) Haldane–Shastry spin chain and the SU(m|n) Polychronakos spin chain are shown to be related in a simple way in the thermodynamic limit at low temperatures.

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.

Mixed saturated-unsaturated alkyl-chain assemblies: Solid solutions of zinc stearate and zinc oleate

The linear saturated stearic acid and the bent mono-unsaturated oleic acid do not mix and form solid solutions. However, the zinc salts of these acids can. From X-ray diffraction and DSC measurements we show that the layered zinc stearate and zinc oleate salts form a homogeneous solid solution at all composition ratios. The solid solutions exhibit a single melting endotherm, with the melting temperature varying linearly with composition but with the enthalpy change showing a minimum. By monitoring features in the infrared spectra that are characteristic of the global conformation of the hydrocarbon chain, and hence can distinguish between stearate and oleate chains, it is shown that solid solution formation is realized by the introduction of gauche defects in a fraction of the stearate chains that are then no longer linear. This fraction increases with oleate concentration. It has also been possible from the spectroscopic measurements to establish a quantitative relation between molecular conformational order and the thermodynamic enthalpy of melting of the solid solutions.

Modified density matrix renormalization group algorithm for the zigzag spin-1/2 chain with frustrated antiferromagnetic exchange: Comparison with field theory at large J(2)/J(1)

A modified density matrix renormalization group (DMRG) algorithm is applied to the zigzag spin-1/2 chain with frustrated antiferromagnetic exchange J(1) and J(2) between first and second neighbors. The modified algorithm yields accurate results up to J(2)/J(1) approximate to 4 for the magnetic gap Delta to the lowest triplet state, the amplitude B of the bond order wave phase, the wavelength lambda of the spiral phase, and the spin correlation length xi. The J(2)/J(1) dependences of Delta, B, lambda, and xi provide multiple comparisons to field theories of the zigzag chain. The twist angle of the spiral phase and the spin structure factor yield additional comparisons between DMRG and field theory. Attention is given to the numerical accuracy required to obtain exponentially small gaps or exponentially long correlations near a quantum phase transition.

Effect of Chain Length of Alcohol on the Lipase-Catalyzed Esterification of Propionic Acid in Supercritical Carbon Dioxide

The esterification of propionic acid was investigated using three different alcohols, namely, isopropyl alcohol, isobutyl alcohol, and isoamyl alcohol. The variation of conversion with time for the synthesis of isoamyl propionate was investigated in the presence of five enzymes. Novozym 435 showed the highest activity, and this was used as the enzyme for investigating the various parameters that influence the esterification reaction. The Ping-Pong Bi-Bi model with inhibition by both acid and alcohol was used to model the experimental data and determine the kinetics of the esterification reaction.

Control aspects in proportionality Markov manpower systems

In this paper, the control aspects of a hierarchical organization under the influence of "proportionality" policies are analyzed. Proportionality policies are those that restrict the recruitment to every level of the hierarchy (except the bottom most level or base level) to be in strict proportion to the promotions into that level. Both long term and short term control analysis have been discussed. In long term control the specific roles of the parameters of the system with regard to control of the shape and size of the system have been analyzed and yield suitable control strategies. In short term control, the attainability of a target or goal structure within a specific time from a given initial structure has been analyzed and yields the required recruitment strategies. The theoretical analyses have been illustrated with computational examples and also with real world data.

Chain structures in alkali metal borophosphates: synthesis and characterization of K3[BP3O9(OH)3] and Rb3[B2P3O11(OH)2]

Two new alkali metal borophosphates, K-3[BP(3)o(9)(OH)(3)] and Rb-3[B2P3O11(OH)(2)], were synthesized by applying solvothermal techniques using ethanol as solvent. The crystal structures were solved by means of single-crystal X-ray diffraction (K-3[BP3O9(OH)(3)], monoclinic, C2/c (No. 15), a = 2454.6(8) pm, b = 736.3(2) pm, c = 1406.2(4) pm, beta = 118.35(2)degrees, Z = 8; Rb-3[B2P3O11(OH)(2)], monoclinic, P2(1)/c (No. 14), a = 781.6(2) pm, b:= 667.3(2) pm, c = 2424.8(5) pm, beta = 92.88(1)degrees, Z = 4). Both crystal structures comprise borophosphate chain anions. While for the rubidium compound a loop-branched chain motif is found as common for most of the chain anions in alkali metal borophosphates, the crystal structure of the potassium phase comprises the first open-branched chain with the highest phosphate content found so far in this group of compounds. Both chain anions are Closely related to known anhydrous or hydrated phases, and the structural relations are discussed in terms of how the presence of OH groups and hydrogen bonds as well as number, charge, and size of charge balancing cations influence the 3D structural arrangement. The anionic entities are classified in terms of general principles of structural systematics for borophosphates.

Control aspects in proportionality Markov manpower systems

In this paper, the control aspects of a hierarchical organization under the influence of "proportionality" policies are analyzed. Proportionality policies are those that restrict the recruitment to every level of the hierarchy (except the bottom most level or base level) to be in strict proportion to the promotions into that level. Both long term and short term control analysis have been discussed. In long term control the specific roles of the parameters of the system with regard to control of the shape and size of the system have been analyzed and yield suitable control strategies. In short term control, the attainability of a target or goal structure within a specific time from a given initial structure has been analyzed and yields the required recruitment strategies. The theoretical analyses have been illustrated with computational examples and also with real world data. The control of such proportionality systems is then compared with that of the general systems (which do not follow such policies) with some significant conclusions. The control relations of such proportionality systems are found to be simpler and more practically feasible than those of general Markov systems, which do not have such restrictions. Such proportionality systems thus not only retain and match the flexibility of general Markov systems but also have the added advantage of simpler and more practically feasible controls. The proportionality policies hence act as an alternative and more practicably feasible means of control. (C) 2004 Elsevier Inc. All rights reserved.

Chain of excitation spot generation by aperture engineering

An optical technique is proposed for obtaining multiple excitation spots. Phase-matched counter propagating extended depth-of-focus fields were superimposed along the optical axis for generating multiple localized excitation spots. Moreover, the filtering effect due to the optical mask increases the lateral resolution. Proposed technique introduces the concept of simultaneous multiplane excitation and improves three-dimensional resolution. (C) 2010 American Institute of Physics.

Main chain and segmental dynamics of semi interpenetrating based on polyisoprene and poly(methyl methacrylate)

Main chain and segmental dynamics of polyisoprene (PI) and poly(methyl methacrylate)(PMMA) chains in semi IPNs were systematically studied over a wide range of temperatures (above and below T-g of both polymers) as a function of composition, crosslink density, and molecular weight. The immiscible polymers retained most of its characteristic molecular motion; however, the semi IPN synthesis resulted in dramatic changes in the motional behavior of both polymers due to the molecular level interpenetration between two polymer chains. ESR spin probe method was found to be sensitive to the concentration changes of PMMA in semi IPNs. Low temperature spectra showed the characteristics of rigid limit spectra, and in the range of 293-373 K.complex spectra were obtained with the slow component mostly arisingout of the PMMA rich regions and fast component from the PI phase. We found that the rigid PMMA chains closely interpenetrated into thehighly mobile PI network imparts motional restriction in nearby PI chains, and the highly mobile PI chains induce some degree of flexibility in highly rigid PMMA chains. Molecular level interchain mixing was found to be more efficient at a PMMA concentration of 35 wt.%. Moreover, the strong interphase formed in the above mentionedsemi IPN contributed to the large slow component in the ESR spectra at higher temperature. The shape of the spectra along with the data obtained from the simulations of spectra was correlated to the morphology of the semi IPNs. The correlation time measurement detected the motional region associated with the glass transition of PI and PMMA, and these regions were found to follow the same pattern of shifts in a-relaxation of PI and PMMA observed in DMA analysis. Activation energies associated with the T-g regions were also calculated. T-50G was found to correlate with the T-g of PMMA, and the volume of polymer segments undergoing glass transitional motion was calculated to be 1.7 nm(3).C-13 T-1 rho measurements of PMMA carbons indicate that the molecular level interactions were strong in semi IPN irrespective of the immiscible nature of polymers. The motional characteristics of H atoms attached to carbon atoms in both polymers were analyzed using 2D WISE NMR. Main relaxations of both components shifted inward, and both SEM and TEM analysis showed the development of a nanometer sized morphology in the case of highly crosslinked semi IPN. (C) 2010 Elsevier Ltd. All rights reserved.

Studies in the Sandalwood Oil Series. III. Chain Effect on Terpene Transformations

The carboxyl chain of some molecules has been found to be responsible for causing rearrangements and controlling their course. This chain effect, which operates during reactions involving carbonium ions, is illustrated with examples from Sandalwood oil chemistry.

Enhanced Ion Anisotropy by Nonconventional Coordination Geometry: Single-Chain Magnet Behavior for a [{(FeL)-L-II}(2){Nb-IV(CN)(8)}] Helical Chain Compound Designed with Heptacoordinate Fe-II

Nonconventional heptacoordination in combination with efficient magnetic exchange coupling is shown to yield a 1-D heteronuclear {(FeNbIV)-Nb-II} compound with remarkable magnetic features when compared to other Fe(II)-based single chain magnets (SCM). Cyano-bridged heterometallic {3d-4d} and {3d-5d} chains are formed upon assembling Fe(II) bearing a pentadentate macrocycle as the blocking ligand with octacyano metallates, [M(CN)(8)](4-) (M = Nb-IV, Mo-IV, W-IV.) X-ray diffraction (single-crystal and powder) measurements reveal that the [{(H2O)Fe(L-1)}{M(CN)(8)}{Fe(L-1)}](infinity) architectures consist of isomorphous 1-D polymeric structures based on the alternation of {Fe(L-1)}(2+) and {M(CN)(8)}(4-) units (L-1 stands for the pentadentate macrocycle). Analysis of the magnetic susceptibility behavior revealed cyano-bridged {Fe-Nb} exchange interaction to be antiferromagnetic with J = -20 cm(-1) deduced from fitting an Ising model taking into account the noncollinear spin arrangement. For this ferrimagnetic chain a slow relaxation of its magnetization is observed at low temperature revealing a SCM behavior with Delta/k(B) = 74 K and tau(0) = 4.6 x 10(-11) s. The M versus H behavior exhibits a hysteresis loop with a coercive field of 4 kOe at 1 K and reveals at 380 mK magnetic avalanche processes, i.e., abrupt reversals in magnetization as H is varied. The origin of these characteristics is attributed to the combination of efficient {Fe-Nb} exchange interaction and significant anisotropy of the {Fe(L-1)) unit. High field EPR and magnetization experiments have revealed for the parent compound [Fe(L-1)(H2O)(2)]Cl-2 a negative zero field splitting parameter of D approximate to -17 cm(-1). The crystal structure, magnetic behavior, and Mossbauer data for [Fe(L-1)(H2O)(2)]Cl-2 are also reported.