Structural mobility and transformations in globular proteins

Although globular proteins are endowed with well defined three-dimensional structures, they exhibit substantial mobility within the framework of the given threedimensional structure. The different types of mobility found in proteins by and large correspond to the different levels of organisational hierarchy in protein architecture. They are of considerable structural and functional significance, and can be broadly classified into(a) thermal and conformational fluctuations, (b) segmental mobility, (c) interdomain mobility and (d) intersubunit mobility. Protein crystallographic studies has provided a wealth of information on all of them. The temperature factors derived from X-ray diffraction studies provide a measure of atomic displacements caused by thermal and conformational fluctuations. The variation of displacement along the polypeptide chain have provided functionally significant information on the flexibility of different regions of the molecule in proteins such as myoglobin, lysozyme and prealbumin. Segmental mobility often involves the movement of a region or a segment of a molecule with respect to the rest, as in the transition between the apo and the holo structures of lactate dehydrogenase. It may also involve rigidification of a disordered region of the molecule as in the activation of the zymogens of serine proteases. Transitions between the apo and the holo structures of alcohol dehydrogenase,and between the free and the sugar bound forms of hexokinase, are good examples of interdomain mobility caused by hinge-bending. The capability of different domains to move semi-independently contributes greatly to the versatility of immunoglobulin molecules. Interdomain mobility in citrate synthase appears to be more complex and its study has led to an alternative description of domain closure. The classical and the most thoroughly studied case of intersubunit mobility is that in haemoglobin. The stereochemical mechanism of the action of this allosteric protein clearly brings out the functional subtilities that could be achieved through intersubunit movements. In addition to ligand binding and activation,environmental changes also often cause structural transformations. The reversible transformation between 2 Zn insulin and 4 Zn insulin is caused by changes in the ionic strength of the medium. Adenylate Kinase provides a good example for functionally significant reversible conformational transitions induced by variation in pH. Available evidences indicate that reversible structural transformations in proteins could also be caused by changes in the aqueous environment, including those in the amount of water surrounding protein molecules.

Structural Transformations in Protein Crystals caused by controlled Dehydration

Recent experiments in this laboratory on structural transformations caused by controlled dehydration of protein crystals have been reviewed. X-ray diffraction patterns of the following crystals have been examined under varying conditions of environmental humidity in the relative humidity range of 100-75%: a new crystal form of bovine pancreatic ribonuclease A grown from acetone solution in tris buffer (I), the well-known monoclinic form of the protein grown from aqueous ethanol (II), the same form grown from a solution of 2-methyl pentan-2,4-diol in phosphate buffer (III), tetragonal (IV), orthorhombic (V), monoclinic (VI) and triclinic (VII) hen egg white lysozyme, porcine 2 Zn insulin (VIII), porcine 4 Zn insulin (IX) and the crystals of concanavalin A(X). I, II, IV, V and VI undergo one or more transformations as evidenced by discontinuous changes in the unit cell dimensions, the diffraction pattern and the solvent content. Such water-mediated transformations do not appear to occur in the remaining crystals in the relative humidity range explored. The relative humidity at which the transformation occurs is reduced when 2-methyl pentan-2,4-diol is present in the mother liquor. The transformations are affected by the crystal structure but not by the amount of solvent in the crystals. The X-ray investigations reviewed here and other related investigations emphasize the probable importance of water-mediated transformations in exploring hydration of proteins and conformational transitions in them.

Structural studies of analgesics and their interactions .10. A hydrated 1-1 complex between niflumic acid and ethanolamine, c13h8f3n2o-2.c2h8no+.h2o.

Mr= 361.3, triclinic, P1, a = 6-239 (2), b=11.280(2), c=12-451(2)A, a=101.2 (1), B= 92.3 (1), 7=99.9(1)°, V=844.123 A3, Z=2, Dx= 1.42, D m = 1.42 (1) Mg m -3, n(Cu Ka) = 1.5418 ,A., g = 1-102 mm -1, F(000) = 376, T= 293 K. Final R = 0.064 for 2150 observed reflections. The niflumic acid anions consist essentially of three planar groupings, namely, two six-membered rings and a carboxylate group attached to one of them. The invariant common structural features observed in the crystal structures of fenamates, namely, the coplanarity of the carboxyl group and the six-membered ring bearing it, and the internal hydrogen bond between the carboxyl group and the imino N atom that bridges the two sixmembered rings, are retained in the complex. The amino N atom is gauche with respect to the terminal hydroxyl group in the ethanolamine cation. The complexation between the two molecules is achieved through ionic and hydrogen-bonded interactions involving the carboxylate group in niflumic acid.

Structural basis for the function of anti-idiotypic antibody in immune memory

We had earlier proposed a hypothesis to explain the mechanism of perpetuation of immunological memory based on the operation of idiotypic network in the complete absence of antigen. Experimental evidences were provided for memory maintenance through anti-idiotypic antibody (Ab(2)) carrying the internal image of the antigen. In the present work, we describe a structural basis for such memory perpetuation by molecular modeling and structural analysis studies. A three-dimensional model of Ab(2) was generated and the structure of the antigenic site on the hemagglutinin protein H of Rinderpest virus was modeled using the structural template of hemagglutinin protein of Measles virus. Our results show that a large portion of heavy chain containing the CDR regions of Ab(2) resembles the domain of the hemagglutinin housing the epitope regions. The similarity demonstrates that an internal image of the H antigen is formed in Ab(2), which provides a structural basis for functional mimicry demonstrated earlier. This work brings out the importance of the structural similarity between a domain of hemagglutinin protein to that of its corresponding Ab(2). It provides evidence that Ab(2) is indeed capable of functioning as surrogate antigen and provides support to earlier proposed relay hypothesis which has provided a mechanism for the maintenance of immunological memory.

Phase relations and dielectric properties of BaTi03 ceramics heavily substituted with neodymium

Investigations on the phase relations and dielectric properties of (1 -x)BaTiO3 + xNd2/3TiO 3 (BNT) ceramics sintered in air below 1650 K have been carried out. X-ray powder diffraction studies indicate apparent phase singularity for compositions with x < 0.3. Nd2Ti207 is detected at higher neodymium concentrations. The unit cell parameter changes continuously with neodymium content, and BaTiO3 is completely cubic at room temperature with x -- 0.0525, whereas electron diffraction studies indicate that the air-sintered BNT ceramics with x > 0.08 contain additional phases that are partly amorphous even to an electron beam. SEM observations reveal that BaTiO3 grains are mostly covered by a molten intergranular phase, and show the presence of randomly distributed Nd2Ti207 grains. Energy dispersive X-ray analysis shows the Ba-Nd-Ti ternary composition of the intergranular phase. Differential thermal analysis studies support the formation of a partial melt involving dissolution-precipitation of boundary layers of BaTiO3 grains. These complex phase relations are accounted for in terms of the phase instability of BaTiO3 with large cation-vacancy concentration as a result of heavy Nd 3+ substitution. The absence of structural intergrowth in (1 - x)BaTiO3 + xNd2/3TiO3 under oxidative conditions leads to a separation of phases wherein the new phases undergo melting and remain X-ray amorphous. BNT ceramics with 0.1 < x < 0.3 have ~eff >~ 104 with tan 6 < 0.1 and nearly flat temperature capacitance characteristics. The grain-size dependence of ee,, variations of ~eff and tan 6 with the measuring frequency, the non-ohmic resistivities, and the non-linear leakage currents at higher field-strengths which are accompanied by the decrease in eeff and rise in tan 3, are explained on the basis of an intergranular (internal boundary layer) dielectric characteristic of these ceramics.

Structural Response of Partially Fibrous Concrete Beams

The inclusion of fibers into a matrix over only a partial thickness of the beam is regarded as partially fiber reinforcing a beam. This concept is fully invoked in the present investigation. A tensile strain enhancement factor, t, as determined by a direct tension test, forms a convenient engineering parameter that takes care of the influence of the aspect ratio and volume fraction of the given type of fiber. The appropriate thickness of the beam section to be reinforced with fibers is computed using the above parameter. Necessary analytical expressions were developed to compute the moment enhancement factor associated with different values of the parameter, t. The validity of the approach was experimentally demonstrated. Practically similar deflection patterns for fully and partially fibrous sections were observed. The applicability of the method developed in practical situations, such as the design of airfield and highway pavements with fiber conretes, is cited.

Unusual Structural Isomerization Of Monopropiophenone Thiocarbonohydrazone

Monopropiophenone thiocarbonohydrazone has been isolated in both linear and cyclic isomeric forms. Each form has been shown to isomerize and exist in equilibrium with the other in DMSO-d6 solution by 1H and 13C NMR spectroscopy. The kinetics of this transformation show attainment of equilibrium in approximately 6 h, with a linear to cyclic configuration ratio of 40:60.

Structural Basis of Drug Resistance by Genetic Variants of HIV Type 1 Clade C Protease from India

Using computer modeling of three-dimensional structures and structural information available on the crystal structures of HIV-1 protease, we investigated the structural effects of mutations, in treatment-naive and treatment-exposed individuals from India and postulated mechanisms of resistance in clade C variants. A large number of models (14) have been generated by computational mutation of the available crystal structures of drug bound proteases. Localized energy minimization was carried out in and around the sites of mutation in order to optimize the geometry of interactions present. Most of the mutations result in structural differences at the flap that favors the semiopen state of the enzyme. Some of the mutations were also found to confer resistance by affecting the geometry of the active site. The E35D mutation affects the flap structure in clade B strains and E35N and E35K mutation, seen in our modeled strains, have a more profound effect. Common polymorphisms at positions 36 and 63 in clade C also affected flap structure. Apart from a few other residues Gln-58, Asn-83, Asn-88, and Gln-92 and their interactions are important for the transition from the closed to the open state. Development of protease inhibitors by structure-based design requires investigation of mechanisms operative for clade C to improve the efficacy of therapy.

Calorimetric, infrared and ESR studies of the plastically crystalline state of organic compounds

Enthalpy changes of the crystal-plastic and plastic-liquid transitions are related to the temperature range of stability of the plastic phase. Thermodynamics of the plastic state of binary mixtures have been examined. Infrared correlation times, τc, and activation energies have been measured for a few molecules in the plastic state. Molecular tumbling times, τt, have also been measured employing ESR spectra of a spin-probe. Plots of log τc(τt) 1/T are continuous through the plastic-liquid transition. Activation energies for molecular motion seem to vary in the same direction as the ΔH of the plastic-crystal transition. Infrared correlation times of solute molecules in binary solutions in the plastic and the liquid states show interesting variations with solute concentration.

Electrical, structural and magnetic properties of polyaniline/pTSA-TiO2 nanocomposites

Polyaniline (PANI)/para-toluene sulfonic acid (pTSA) and PANI/pTSA-TiO2 composites were prepared using chemical method and characterized by infrared spectroscopy (IR), powder X-ray diffraction (XRD), scanning electron microscopy (SEM). The electrical conductivity and magnetic properties were also measured. In corroboration with XRD, the micrographs of SEM indicated the homogeneous dispersion of TiO nanoparticles in bulk PANI/pTSA matrix. Conductivity of the PANI/pTSA-TiO2 was higher than the PAN[/pTSA, and the maximum conductivity obtained was 9.48 (S/cm) at 5 wt% of TiO2. Using SQUID magnetometer, it was found that PANI/pTSA was either paramagnetic or weakly ferromagnetic from 300 K down to 5 K with H-C approximate to 30 Oe and M-r approximate to 0.015 emu/g. On the other hand,PANI/pTSA-TiO2 was diamagnetic from 300 K down to about 50 K and below which it was weakly ferromagnetic. Furthermore, a nearly temperature-independent magnetization was observed in both the cases down to 50 K and below which the magnetization increased rapidly (a Curie like susceptibility was observed). The Pauli susceptibility (chi(pauli)) was calculated to be about 4.8 X 10(-5) and 1.6 x 10(-5)emug(-1) Oe(-1) K for PANI/pTSA and PANI/pTSA-TiO2, respectively.

The poly dA helix: a new structural motif for high performance DNA-based molecular switches

We report a pH-dependent conformational transition in short, defined homopolymeric deoxyadenosines (dA(15)) from a single helical structure with stacked nucleobases at neutral pH to a double-helical, parallel-stranded duplex held together by AH-HA base pairs at acidic pH. Using native PAGE, 2D NMR, circular dichroism (CD) and fluorescence spectroscopy, we have characterized the two different pH dependent forms of dA(15). The pH-triggered transition between the two defined helical forms of dA(15) is characterized by CD and fluorescence. The kinetics of this conformational switch is found to occur on a millisecond time scale. This robust, highly reversible, pH-induced transition between the two well-defined structured states of dA(15)represents a new molecular building block for the construction of quick-response, pH-switchable architectures in structural DNA nanotechnology.

On the structural features of doped amorphous chalcogenide semiconductors

A study of Bi-doped amorphous (Ge42S58)100−xBix and Ge20S80−xBix has been carried out by differential thermal analysis (DTA) and X-ray diffraction methods so as to elucidate the impurity-induced modifications in the semiconductors. Thermal analysis reveals the presence of complex structural units in the modified material. An interesting feature of this study is the existence of a double glass transition in Ge20S80−xBix, which is reported for the first time in this system.

Structural Analysis by X-Ray Diffraction of a Polar Mesogen 4-Cyanobiphenyl-4'-heptylbiphenyl Carboxylate

Crystal and molecular structure of a compound 4-cyanobiphenyl-4'-heptylbiphenyl carboxylate (7CBB), which exhibit both monolayer smectic A and nematic phases, have been determined by direct methods using single crystal X-ray diffraction data. The structure is monoclinic with the space group P21/c and Z = 4. The unit cell parameters are a = 16.9550(5) Aring, b = 5.5912(18) Aring, c = 27.5390(9) Aring, agr = 90.000°, β = 93.986(6)°, and γ = 90.000°. Packing of the molecules is found to be precursor to SmC phase, although SmA1 phase is observed on melting. Several strong van der Waals interactions are observed in the core part of the neighboring molecular pairs. Crystal to mesophase transition is probably of reconstitutive nature. Geometry, packing, and nature of crystal-mesophase transition are compared to those in 6CBB.

Structural Polymorphism of the Nucleosomal DNA and Implications for Protein Binding

A nucleosome forms a basic unit of the chromosome structure. A biologically relevant question is how much of the nucleosomal conformational space is accessible to protein-free DNA, and what proportion of the nucleosomal conformations are induced by bound histones. To investigate this, we have analysed high resolution xray crystal structure datasets of DNA in protein-free as well as protein-bound forms, and compared the dinucleotide step parameters for the two datasets with those for high resolution nucleosome structures. Our analysis shows that most of the dinucleotide step parameter values for the nucleosome structures lie within the range accessible to protein-free DNA, indirectly indicating that the histone core plays more of a stabilizing role. The nucleosome structures are observed to assume smooth and nearly planar curvature, implying that ‘normal’ B-DNA like parameters can give rise to a curved geometry at the gross structural level. Different nucleosome

A computerized methodology for structural synthesis of kinematic chains: Part 1- Formulation

In an effort to develop a fully computerized approach for structural synthesis of kinematic chains the steps involved in the method of structural synthesis based on transformation of binary chains [38] have been recast in a format suitable for implementation on a digital computer. The methodology thus evolved has been combined with the algebraic procedures for structural analysis [44] to develop a unified computer program for structural synthesis and analysis of simple jointed kinematic chains with a degree of freedom 0. Applications of this program are presented in the succeeding parts of the paper.