Structural analysis of dihydrofolate reductases enables rationalization of antifolate binding affinities and suggests repurposing possibilities

Antifolates are competitive inhibitors of dihydrofolate reductase ( DHFR), a conserved enzyme that is central to metabolism and widely targeted in pathogenic diseases, cancer and autoimmune disorders. Although most clinically used antifolates are known to be target specific, some display a fair degree of cross-reactivity with DHFRs from other species. A method that enables identification of determinants of affinity and specificity in target DHFRs from different species and provides guidelines for the design of antifolates is currently lacking. To address this, we first captured the potential druggable space of a DHFR in a substructure called the `supersite' and classified supersites of DHFRs from 56 species into 16 `site-types' based on pairwise structural similarity. Analysis of supersites across these site-types revealed that DHFRs exhibit varying extents of dissimilarity at structurally equivalent positions in and around the binding site. We were able to explain the pattern of affinities towards chemically diverse antifolates exhibited by DHFRs of different site-types based on these structural differences. We then generated an antifolate-DHFR network by mapping known high-affinity antifolates to their respective supersites and used this to identify antifolates that can be repurposed based on similarity between supersites or antifolates. Thus, we identified 177 human-specific and 458 pathogen-specific antifolates, a large number of which are supported by available experimental data. Thus, in the light of the clinical importance of DHFR, we present a novel approach to identifying differences in the druggable space of DHFRs that can be utilized for rational design of antifolates.

A unified construction of space-time codes with optimal rate-diversity tradeoff

The problem of constructing space-time (ST) block codes over a fixed, desired signal constellation is considered. In this situation, there is a tradeoff between the transmission rate as measured in constellation symbols per channel use and the transmit diversity gain achieved by the code. The transmit diversity is a measure of the rate of polynomial decay of pairwise error probability of the code with increase in the signal-to-noise ratio (SNR). In the setting of a quasi-static channel model, let n(t) denote the number of transmit antennas and T the block interval. For any n(t) <= T, a unified construction of (n(t) x T) ST codes is provided here, for a class of signal constellations that includes the familiar pulse-amplitude (PAM), quadrature-amplitude (QAM), and 2(K)-ary phase-shift-keying (PSK) modulations as special cases. The construction is optimal as measured by the rate-diversity tradeoff and can achieve any given integer point on the rate-diversity tradeoff curve. An estimate of the coding gain realized is given. Other results presented here include i) an extension of the optimal unified construction to the multiple fading block case, ii) a version of the optimal unified construction in which the underlying binary block codes are replaced by trellis codes, iii) the providing of a linear dispersion form for the underlying binary block codes, iv) a Gray-mapped version of the unified construction, and v) a generalization of construction of the S-ary case corresponding to constellations of size S-K. Items ii) and iii) are aimed at simplifying the decoding of this class of ST codes.

A general construction of space-time trellis codes for PSK signal sets

The diversity order and coding gain are crucial for the performance of a multiple antenna communication system. It is known that space-time trellis codes (STTC) can be used to achieve these objectives. In particular, we can use STTCs to obtain large coding gains. Many attempts have been made to construct STTCs which achieve full-diversity and good coding gains, though a general method of construction does not exist. Delay diversity code (rate-1) is known to achieve full-diversity, for any number of transmit antennas and any signal set, but does not give a good coding gain. A product distance code based delay diversity scheme (Tarokh, V. et al., IEEE Trans. Inform. Theory, vol.44, p.744-65, 1998) enables one to improve the coding gain and construct STTCs for any given number of states using coding in conjunction with delay diversity; it was stated as an open problem. We achieve such a construction. We assume a shift register based model to construct an STTC for any state complexity. We derive a sufficient condition for this STTC to achieve full-diversity, based on the delay diversity scheme. This condition provides a framework to do coding in conjunction with delay diversity for any signal constellation. Using this condition, we provide a formal rate-1 STTC construction scheme for PSK signal sets, for any number of transmit antennas and any given number of states, which achieves full-diversity and gives a good coding gain.

Parallel and antiparallel aggregation of alpha-helices. Crystal structures of two apolar decapeptides X-Trp-Ile-Ala-Aib-Ile-Val-Aib-Leu-Aib-Pro-OMe (X = Boc, Ac)

An apolar helical decapeptide with different end groups, Boc- or Ac-, crystallizes in a completely parallel fashion for the Boc-analog and in an antiparallel fashion for the Ac-analog. In both crystals, the packing motif consists of rows of parallel molecules. In the Boc-crystals, adjacent rows assemble with the helix axes pointed in the same direction. In the Ac-crystals, adjacent rows assemble with the helix axes pointed in opposite directions. The conformations of the molecules in both crystals are quite similar, predominantly alpha-helical, except for the tryptophanyl side chain where chi 1 congruent to 60 degrees in the Boc- analog and congruent to 180 degrees in the Ac-analog. As a result, there is one lateral hydrogen bond between helices, N(1 epsilon)...O(7), in the Ac-analog. The structures do not provide a ready rationalization of packing preference in terms of side-chain interactions and do not support a major role for helix dipole interactions in determining helix orientation in crystals. The crystal parameters are as follow. Boc-analog: C60H97N11O13.C3H7OH, space group Pl with a = 10.250(3) A, b = 12.451(4) A, c = 15.077(6) A, alpha = 96.55(3) degrees, beta = 92.31(3) degrees, gamma = 106.37(3) degrees, Z = 1, R = 5.5% for 5581 data ([F] greater than 3.0 sigma(F)), resolution 0.89 A. Ac-analog: C57H91N11O12, space group P2(1) with a = 9.965(1) A, b = 19.707(3) A, c = 16.648(3) A, beta = 94.08(1), Z = 2, R = 7.2% for 2530 data ([F] greater than 3.0 sigma(F)), resolution 1.00 A.

Synthesis Based On Cyclohexadienes .6. A New Total Synthesis Of (+/-)-Methyl Acorate And (+/-)-Methyl Epi-Acorate

A new method of construction of carbon-carbon bond is described. Thus the dianions generated from the metal-ammonia reduction of substituted benzoic acids readily undergo Michael addition with methyl crotonate resulting in synthetically useful products having a quaternary carbon. Based on this strategy, new syntheses of (+/-)-methyl acorate (14b) and (+/-)-methyl epi-corate (15) are reported.

Photobehavior of crystalline 4-styrylcoumarin dimorphs: structure-reactivity correlations

4-Styrylcoumarin crystallizes from chloroform and hexane mixture in two morphologically different modifications. The monoclinic form (needles, P2(1)/c) undergoes stereospecific photodimerization producing anti head-to-tail dimer across pyrone double bond, whereas the triclinic modification (prisms, P ($) over bar 1) dimerizes yielding photodimer of the same configuration, but across styrenic double bond. Single crystal X-ray analyses of the dimorphs reveal the packing differences permitting rationalization of the regio- and stereochemistry of the photoproducts. The significantly low dimer yield from the prismatic crystals is rationalized.

Rheometry of dense granular materials: the crucial effects of gravity and confining walls

We describe here the rheological response of dense, slowly deforming granular materials to shear in a cylindrical Couette cell. All components of the stress on the outer cylinder are measured pointwise as a function of the depth, for different methods of construction of the bed that presumably lead to distinct fabrics. The static stress profiles for the different construction protocols are different, but a stress profile that is independent of construction history emerges when the granular column is sheared for sufficient time, in accord with the predictions of plasticity theories. However the qualitative features of the the stress profile under shear differs radically from the predictions of plasticity theories and data reported in earlier studies. We discuss a hypothesis for the anomalous stress profiles that was proposed recently by us, and the ways in which further experiments may to conducted to verify it.

Paraxial-wave optics and relativistic front description .1. The scalar theory

With the extension of the work of the preceding paper, the relativistic front form for Maxwell's equations for electromagnetism is developed and shown to be particularly suited to the description of paraxial waves. The generators of the Poincaré group in a form applicable directly to the electric and magnetic field vectors are derived. It is shown that the effect of a thin lens on a paraxial electromagnetic wave is given by a six-dimensional transformation matrix, constructed out of certain special generators of the Poincaré group. The method of construction guarantees that the free propagation of such waves as well as their transmission through ideal optical systems can be described in terms of the metaplectic group, exactly as found for scalar waves by Bacry and Cadilhac. An alternative formulation in terms of a vector potential is also constructed. It is chosen in a gauge suggested by the front form and by the requirement that the lens transformation matrix act locally in space. Pencils of light with accompanying polarization are defined for statistical states in terms of the two-point correlation function of the vector potential. Their propagation and transmission through lenses are briefly considered in the paraxial limit. This paper extends Fourier optics and completes it by formulating it for the Maxwell field. We stress that the derivations depend explicitly on the "henochromatic" idealization as well as the identification of the ideal lens with a quadratic phase shift and are heuristic to this extent.

Epoxy resin chamber for high voltage breakdown studies in high vacuum

As the study of electrical breakdown phenomena in vacuum systems, gains more importance, a thorough understanding of the breakdown mechanism at high voltages necessitates a chamber for experimental studies. An epoxy-resin chamber has been constructed by casting ring sections which were joined together. The advantages of such a chamber over the conventional metal or glass chamber are given especially as regards the electric field configuration, high voltage lead-in, and the ease of construction. Special facilities can be incorporated while constructing the chamber which makes it more versatile; for example, in pre-breakdown current measurements, electron beam focusing studies, etc.

Quantum spin models with exact dimer ground states

Inspired by the exact solution of the Majumdar-Ghosh model, a family of one-dimensional, translationally invariant spin Hamiltonians is constructed. The exchange coupling in these models is antiferromagnetic, and decreases linearly with the separation between the spins. The coupling becomes identically zero beyond a certain distance. It is rigorously proved that the dimer configuration is an exact, superstable ground-state configuration of all the members of the family on a periodic chain. The ground state is twofold degenerate, and there exists an energy gap above the ground state. The Majumdar-Ghosh Hamiltonian with a twofold degenerate dimer ground state is just the first member of the family. The scheme of construction is generalized to two and three dimensions, and illustrated with the help of some concrete examples. The first member in two dimensions is the Shastry-Sutherland model. Many of these models have exponentially degenerate, exact dimer ground states.

C-13-H-1 dipolar couplings for probing rod-like hydrogen bonded mesogens

Hydrogen bonding is the most important non-covalent interaction utilised in building supramolecular assemblies and is preferred often as a means of construction of molecular, oligomeric as well as polymeric materials that show liquid crystalline properties. In this work, a pyridine based nematogenic acceptor has been synthesized and mixed with non-mesogenic 4-methoxy benzoic acid to get a hydrogen bonded mesogen. The existence of hydrogen bonding between the pyridyl unit and the carboxylic acid was established using FT-IR spectroscopy from the observation of characteristic stretching vibrations of unionized type at 2425 and 1927 cm(-1). The mesogenic acceptor and the complex have been investigated using C-13 NMR in solution, solid and liquid crystalline states. Together with the 2D separated local field NMR experiments, the studies confirm the molecular structure in the mesophase and yield the local orientational order parameters. It is observed that the insertion of 4-methoxy benzoic acid not only enhances the mesophase stability but also induces a smectic phase due to an increase in the core length of the hydrogen bonded mesogen.

A multi-level multi-scale approach to study essential genes in Mycobacterium tuberculosis

Background: The set of indispensable genes that are required by an organism to grow and sustain life are termed as essential genes. There is a strong interest in identification of the set of essential genes, particularly in pathogens, not only for a better understanding of the pathogen biology, but also for identifying drug targets and the minimal gene set for the organism. Essentiality is inherently a systems property and requires consideration of the system as a whole for their identification. The available experimental approaches capture some aspects but each method comes with its own limitations. Moreover, they do not explain the basis for essentiality in most cases. A powerful prediction method to recognize this gene pool including rationalization of the known essential genes in a given organism would be very useful. Here we describe a multi-level multi-scale approach to identify the essential gene pool in a deadly pathogen, Mycobacterium tuberculosis. Results: The multi-level workflow analyses the bacterial cell by studying (a) genome-wide gene expression profiles to identify the set of genes which show consistent and significant levels of expression in multiple samples of the same condition, (b) indispensability for growth by using gene expression integrated flux balance analysis of a genome-scale metabolic model, (c) importance for maintaining the integrity and flow in a protein-protein interaction network and (d) evolutionary conservation in a set of genomes of the same ecological niche. In the gene pool identified, the functional basis for essentiality has been addressed by studying residue level conservation and the sub-structure at the ligand binding pockets, from which essential amino acid residues in that pocket have also been identified. 283 genes were identified as essential genes with high-confidence. An agreement of about 73.5% is observed with that obtained from the experimental transposon mutagenesis technique. A large proportion of the identified genes belong to the class of intermediary metabolism and respiration. Conclusions: The multi-scale, multi-level approach described can be generally applied to other pathogens as well. The essential gene pool identified form a basis for designing experiments to probe their finer functional roles and also serve as a ready shortlist for identifying drug targets.