Thermodynamic and structural consequences of changing a sulfur atom to a methylene group in the M13Nle mutation in ribonuclease-S

Two fragments of pancreatic ribonuclease A, a truncated version of S-peptide (residues 1-15) and S-protein (residues 21-124), combine to give a catalytically active complex. We have substituted the wild-type residue at position 13, methionine (Met), with norleucine (Nle), where the only covalent change is the replacement of the sulfur atom with a methylene group. The thermodynamic parameters associated with the binding of this variant to S-protein, determined by titration calorimetry in the temperature range 10-40 degrees C, are reported and compared to values previously reported [Varadarajan, R., Connelly, P. R., Sturtevant, J. M., & Richards, F. M. (1992) Biochemistry 31, 1421-1426] for other position 13 analogs. The differences in the free energy and enthalpy of binding between the Met and Nle peptides are 0.6 and 7.9 kcal/mol at 25 degrees C, respectively. These differences are slightly larger than, but comparable to, the differences in the values for the Met/Ile and Met/Leu pairs. The structure of the mutant complex was determined to 1.85 Angstrom resolution and refined to an R-factor of 17.4% The structures of mutant and wild-type complexes are practically identical although the Nle side chain has a significantly higher average B-factor than the corresponding Met side chain. In contrast, the B-factors of the atoms of the cage of residues surrounding position 13 are all somewhat lower in the Nle variant than in the Met wild-type. Thus, the large differences in the binding enthalpy appear to reside entirely in the difference in chemical properties or dynamic behavior of the -S- and -CH2- groups and not in differences in the geometry of the side chains or the internal cavity surface. In addition, a novel method of obtaining protein stability data by means of isothermal titration calorimetry is introduced.

Density-matrix renormalization-group studies of the spin-1/2 Heisenberg system with dimerization and frustration

Using the density-matrix renormalization-group technique, we study the ground-state phase diagram and other low-energy properties of an isotropic antiferromagnetic spin-1/2 chain with both dimerization and frustration, i.e., an alternation delta of the nearest-neighbor exchanges and a next-nearest-neighbor exchange J(2). For delta = 0, the system is gapless for J(2) < J(2c) and has a gap for J(2) > J(2c) where J(2c) is about 0.241. For J(2) = J(2c) the gap above the ground state grows as delta to the power 0.667 +/- 0.001. In the J(2)-delta plane, there is a disorder line 2J(2) + delta = 1. To the left of this line, the peak in the static structure factor S(q) is at q(max) = pi (Neel phase), while to the right of the line, q(max) decreases from pi to pi/2 as J(2) is increased to large values (spiral phase). For delta = 1, the system is equivalent to two coupled chains as on a ladder and it is gapped for all values of the interchain coupling.

Synthesis and biological evaluation of novel 2-aralkyl-5-substituted-6-(4 `-fluorophenyl)-imidazo2,1-b]1,3,4]thiadiazole derivatives as potent anticancer agents

Levamisole, the imidazo2,1-b]thiazole derivative has been reported as a potential antitumor agent. In the present study, we synthesized, characterized and evaluated biological activity of its novel analogues with substitution in the aralkyl group and on imidazothiadiazole molecules with same chemical backbone but different side chains namely 2-aralkyl-6-(4'-fluorophenyl)-imidazo2,1-b]1,3,4]thiadiazoles (SCR1), 2-aralkyl-5-bromo-6-(4'-fluorophenyl)-imidazo2,1-b]1,3,4]-thiadiaz oles (SCR2), 2-aralkyl-5-formyl-6-(4'-fluorophenyl)-imidazo2,1-b]1,3,4]-thiadia zoles (SCR3) and 2-aralkyl-5-thiocyanato-6-(4'-fluorophenyl)-imidazo2,1-b]1,3,4]-th iadiazoles (SCR4) on leukemia cells. The cytotoxic studies showed that 3a, 4a, and 4c exhibited strong cytotoxicity while others had moderate cytotoxicity. Among these we chose 4a (IC50, 8 mu M) for understanding its mechanism of cytotoxicity. FACS analysis in conjunction with mitochondrial membrane potential and DNA fragmentation studies indicated that 4a induced apoptosis without cell cycle arrest suggesting that it could be used as a potential chemotherapeutic agent. (C) 2011 Elsevier Masson SAS. All rights reserved.

Fast-Group-Decodable STBCs via Codes over GF(4)

In this paper we construct low decoding complexity STBCs by using the Pauli matrices as linear dispersion matrices. In this case the Hurwitz-Radon orthogonality condition is shown to be easily checked by transferring the problem to $\mathbb{F}_4$ domain. The problem of constructing low decoding complexity STBCs is shown to be equivalent to finding certain codes over $\mathbb{F}_4$. It is shown that almost all known low complexity STBCs can be obtained by this approach. New codes are given that have the least known decoding complexity in particular ranges of rate.

Density-matrix renormalization-group study of low-lying excitations of polyacene within a Pariser-Parr-Pople model

We have carried out symmetrized density-matrix renormalization-group calculations to study the nature of excited states of long polyacene oligomers within a Pariser-Parr-Pople Hamiltonian. We have used the C-2 symmetry, the electron-hole symmetry, and the spin parity of the system in our calculations. We find that there is a crossover in the lowest dipole forbidden two-photon state and the lowest dipole allowed excited state with size of the oligomer. In the long system limit, the two-photon state lies below the lowest dipole allowed excited state. The triplet state lies well below the two-photon state and energetically does not correspond to its description as being made up of two triplets. These results are in agreement with the general trends in linear conjugated polymers. However, unlike in linear polyenes wherein the two-photon state is a localized excitation, we find that in polyacenes, the two-photon excitation is spread out over the system. We have doped the systems with a hole and an electron and have calculated the charge excitation gap. Using the charge gap and the optical gap, we estimate the binding energy of the 1(1)B(-) exciton to be 2.09 eV. We have also studied doubly doped polyacenes and find that the bipolaron in these systems, to be composed of two separated polarons, as indicated by the calculated charge-density profile and charge-charge correlation function. We have studied bond orders in various states in order to get an idea of the excited state geometry of the system. We find that the ground state, the triplet state, the dipole allowed state, and the polaron excitations correspond to lengthening of the rung bonds in the interior of the oligomer while the two-photon excitation corresponds to the rung bond lengths having two maxima in the system.

On four-group ML decodable distributed space time codes for cooperative communication

A construction of a new family of distributed space time codes (DSTCs) having full diversity and low Maximum Likelihood (ML) decoding complexity is provided for the two phase based cooperative diversity protocols of Jing-Hassibi and the recently proposed Generalized Non-orthogonal Amplify and Forward (GNAF) protocol of Rajan et al. The salient feature of the proposed DSTCs is that they satisfy the extra constraints imposed by the protocols and are also four-group ML decodable which leads to significant reduction in ML decoding complexity compared to all existing DSTC constructions. Moreover these codes have uniform distribution of power among the relays as well as in time. Also, simulations results indicate that these codes perform better in comparison with the only known DSTC with the same rate and decoding complexity, namely the Coordinate Interleaved Orthogonal Design (CIOD). Furthermore, they perform very close to DSTCs from field extensions which have same rate but higher decoding complexity.

Control of Molecular Weight and Polydispersity of Hyperbranched Polymers Using a Reactive B(3) Core: A Single-Step Route to Orthogonally Functionalizable Hyperbranched Polymers

Molecular weight and polydispersity are two structural features of hyperbranched polymers that are difficult to control because of the statistical nature of the step-growth polycondensation of AB(2) type monomers; the statistical growth also causes the polydispersity index to increase with percent conversion (or molecular weight). We demonstrate that using controlled amounts of a specifically designed B(3) core, containing B-type functionality that are more reactive than those present in the AB(2) monomer, both the molecular weight and the polydispersity can be readily controlled; the PDI was shown to improve with increasing mole-fraction of the B(3) core while the polymer molecular weight showed an expected decrease. Incorporation of a ``clickable'' propargyl group in the B(3) core unit permitted the generation of a core-functionalizable hyperbranched polymer. Importantly, this clickable core, in combination with a recently developed AB(2) monomer, wherein the B-type groups are allyl ethers and A is an hydroxyl group, led to the generation of a hyperbranched polymer carrying orthogonally functionalizable core and peripheral groups, via a single-step melt polycondensation. Selective functionalization of the core and periphery using two different types of chromophores was achieved, and the occurrence of fluorescence resonance energy transfer (FRET) between the donor and acceptor chromophores was demonstrated.

Control of Molecular Weight and Polydispersity of Hyperbranched Polymers Using a Reactive B(3) Core: A Single-Step Route to Orthogonally Functionalizable Hyperbranched Polymers

Molecular weight and polydispersity are two structural features of hyperbranched polymers that are difficult to control because of the statistical nature of the step-growth polycondensation of AB(2) type monomers; the statistical growth also causes the polydispersity index to increase with percent conversion (or molecular weight). We demonstrate that using controlled amounts of a specifically designed B(3) core, containing B-type functionality that are more reactive than those present in the AB(2) monomer, both the molecular weight and the polydispersity can be readily controlled; the PDI was shown to improve with increasing mole-fraction of the B(3) core while the polymer molecular weight showed an expected decrease. Incorporation of a ``clickable'' propargyl group in the B(3) core unit permitted the generation of a core-functionalizable hyperbranched polymer. Importantly, this clickable core, in combination with a recently developed AB(2) monomer, wherein the B-type groups are allyl ethers and A is an hydroxyl group, led to the generation of a hyperbranched polymer carrying orthogonally functionalizable core and peripheral groups, via a single-step melt polycondensation. Selective functionalization of the core and periphery using two different types of chromophores was achieved, and the occurrence of fluorescence resonance energy transfer (FRET) between the donor and acceptor chromophores was demonstrated.

Low ML Decoding Complexity STBCs via Codes Over the Klein Group

In this paper, we give a new framework for constructing low ML decoding complexity space-time block codes (STBCs) using codes over the Klein group K. Almost all known low ML decoding complexity STBCs can be obtained via this approach. New full- diversity STBCs with low ML decoding complexity and cubic shaping property are constructed, via codes over K, for number of transmit antennas N = 2(m), m >= 1, and rates R > 1 complex symbols per channel use. When R = N, the new STBCs are information- lossless as well. The new class of STBCs have the least knownML decoding complexity among all the codes available in the literature for a large set of (N, R) pairs.

Effect of dimerization on dynamics of spin-charge separation in Pariser-Parr-Pople model: A time-dependent density matrix renormalization group study

We investigate the effect of static electron-phonon coupling on real-time dynamics of spin and charge transport in pi-conjugated polyene chains. The polyene chain is modeled by the Pariser-Parr-Pople Hamiltonian with dimerized nearest-neighbor parameter t(0)(1 + delta) for short bonds and t(0)(1 - delta) for long bonds, and long-range electron-electron interactions. We follow the time evolution of the spin and charge using time-dependent density matrix renormalization group technique when a hole is injected at one end of the chain in its ground state. We find that spin and charge dynamics followed through spin and charge velocities depend both on chain length and extent of dimerization delta. Analysis of the results requires focusing on physical quantities such as average spin and charge polarizations, particularly in the large dimerization limit. In the dimerization range 0.0 <= delta <= 0.15, spin-charge dynamics is found to have a well-defined behavior, with spin-charge separation (measured as the ratio of charge velocity to spin velocity) as well as the total amount of charge and spin transported in a given time along the chain decreasing as dimerization increases. However, in the range 0.3 <= delta <= 0.5, it is observed that the dynamics of spin and charge transport becomes complicated. It is observed that, for large delta values, spin-charge separation is suppressed and the injected hole fails to travel the entire length of the chain.

Real-time density matrix renormalization group dynamics of spin and charge transport in push-pull polyenes and related systems

In this paper we investigate the effect of terminal substituents on the dynamics of spin and charge transport in donor-acceptor substituted polyenes [D-(CH)(x)-A] chains, also known as push-pull polyenes. We employ a long-range correlated model Hamiltonian for the D-(CH)(x)-A system, and time-dependent density matrix renormalization group technique for time propagating the wave packet obtained by injecting a hole at a terminal site, in the ground state of the system. Our studies reveal that the end groups do not affect spin and charge velocities in any significant way, but change the amount of charge transported. We have compared these push-pull systems with donor-acceptor substituted polymethine imine (PMI), D-(CHN)(x)-A, systems in which besides electron affinities, the nature of p(z) orbitals in conjugation also alternate from site to site. We note that spin and charge dynamics in the PMIs are very different from that observed in the case of push-pull polyenes, and within the time scale of our studies, transport of spin and charge leads to the formation of a ``quasi-static'' state.

Vertical uplift capacity of a group of two coaxial anchors in a general c-phi soil

The vertical uplift resistance of a group of two horizontal coaxial strip anchors, embedded in a general c-phi soil (where c is the unit cohesion and phi is the soil friction angle), has been determined by using the lower bound finite element limit analysis. The variation of uplift factors F-c and F-gamma, due to the components of soil cohesion and unit weight, respectively, with changes in depth (H)/width (B) has been established for different values of vertical spacing (S)/B. As compared to a single isolated anchor, the group of two anchors provides a significantly greater magnitude of F-c for phi <= 20 degrees and with H/B >= 3. The magnitude of F-c becomes almost maximum when S/B is kept closer to 0.5H/B. On the other hand, with the same H/B, as compared to a single anchor, hardly any increase in F-gamma occurs for a group of two anchors.

Density matrix renormalization group algorithm for Bethe lattices of spin-1/2 or spin-1 sites with Heisenberg antiferromagnetic exchange

A density matrix renormalization group (DMRG) algorithm is presented for the Bethe lattice with connectivity Z = 3 and antiferromagnetic exchange between nearest-neighbor spins s = 1/2 or 1 sites in successive generations g. The algorithm is accurate for s = 1 sites. The ground states are magnetic with spin S(g) = 2(g)s, staggered magnetization that persists for large g > 20, and short-range spin correlation functions that decrease exponentially. A finite energy gap to S > S(g) leads to a magnetization plateau in the extended lattice. Closely similar DMRG results for s = 1/2 and 1 are interpreted in terms of an analytical three-site model.

Genetic analysis of an Indian family with members affected with Waardenburg syndrome and Duchenne muscular dystrophy

Purpose: Waardenburg syndrome (WS) is characterized by sensorineural hearing loss and pigmentation defects of the eye, skin, and hair. It is caused by mutations in one of the following genes: PAX3 (paired box 3), MITF (microphthalmia-associated transcription factor), EDNRB (endothelin receptor type B), EDN3 (endothelin 3), SNAI2 (snail homolog 2, Drosophila) and SOX10 (SRY-box containing gene 10). Duchenne muscular dystrophy (DMD) is an X-linked recessive disorder caused by mutations in the DMD gene. The purpose of this study was to identify the genetic causes of WS and DMD in an Indian family with two patients: one affected with WS and DMD, and another one affected with only WS. Methods: Blood samples were collected from individuals for genomic DNA isolation. To determine the linkage of this family to the eight known WS loci, microsatellite markers were selected from the candidate regions and used to genotype the family. Exon-specific intronic primers for EDN3 were used to amplify and sequence DNA samples from affected individuals to detect mutations. A mutation in DMD was identified by multiplex PCR and multiplex ligation-dependent probe amplification method using exon-specific probes. Results: Pedigree analysis suggested segregation of WS as an autosomal recessive trait in the family. Haplotype analysis suggested linkage of the family to the WS4B (EDN3) locus. DNA sequencing identified a novel missense mutation p.T98M in EDN3. A deletion mutation was identified in DMD. Conclusions: This study reports a novel missense mutation in EDN3 and a deletion mutation in DMD in the same Indian family. The present study will be helpful in genetic diagnosis of this family and increases the mutation spectrum of EDN3.

Perturbative expansion of the QCD Adler function improved by renormalization-group summation and analytic continuation in the Borel plane

We examine the large-order behavior of a recently proposed renormalization-group-improved expansion of the Adler function in perturbative QCD, which sums in an analytically closed form the leading logarithms accessible from renormalization-group invariance. The expansion is first written as an effective series in powers of the one-loop coupling, and its leading singularities in the Borel plane are shown to be identical to those of the standard ``contour-improved'' expansion. Applying the technique of conformal mappings for the analytic continuation in the Borel plane, we define a class of improved expansions, which implement both the renormalization-group invariance and the knowledge about the large-order behavior of the series. Detailed numerical studies of specific models for the Adler function indicate that the new expansions have remarkable convergence properties up to high orders. Using these expansions for the determination of the strong coupling from the hadronic width of the tau lepton we obtain, with a conservative estimate of the uncertainty due to the nonperturbative corrections, alpha(s)(M-tau(2)) = 0.3189(-0.0151)(+0.0173), which translates to alpha(s)(M-Z(2)) = 0.1184(-0.0018)(+0.0021). DOI: 10.1103/PhysRevD.87.014008