Structure determination and biochemical studies on Bacillus stearothermophilus E53Q serine hydroxymethyltransferase and its complexes provide insights on function and enzyme memory

Serine hydroxymethyltransferase (SHMT) belongs to the alpha-family of pyridoxal 5'-phosphate-dependent enzymes and catalyzes the reversible conversion of L-Ser and etrahydrofolate to Gly and 5,10-methylene tetrahydrofolate. 5,10-Methylene tetrahydrofolate serves as a source of one-carbon fragment in many biological processes. SHMT also catalyzes the tetrahydrofolate-independent conversion of L-allo-Thr to Gly and acetaldehyde. The crystal structure of Bacillus stearothermophilus SHMT (bsSHMT) suggested that E53 interacts with the substrate, L-Ser and etrahydrofolate. To elucidate the role of E53, it was mutated to Q and structural and biochemical studies were carried out with the mutant enzyme. The internal aldimine structure of E53QbsSHMT was similar to that of the except for significant changes at Q53, Y60 and Y61. The wild-type enzyme, carboxyl of Gly and side chain of L-Ser were in two conformations in the respective external aldimine structures. The mutant enzyme was completely inactive for tetrahydrofolate-depen dent cleavage of L-Ser, whereas there was a 1.5-fold increase in the rate of tetrahydrofolate-independent reaction with L-allo-Thr. The results obtained from these studies suggest that E53 plays an essential role in tetrahydrofolate/5-formyl tetrahydrofolate binding and in the proper positioning of C beta of L-Ser for direct attack by N5 of tetrahydrofolate. Most interestingly, the structure of the complex obtained by cocrystallization of E53QbsSHMT with Gly and 5-formyl tetrahydrofolate revealed the gem-diamine form of pyridoxal 5'-phosphate bound to Gly and active site Lys. However, density for 5-formyl tetrahydrofolate was not observed. Gly carboxylate was in a single conformation, whereas pyridoxal 5'-phosphate had two distinct conformations. The differences between the structures of this complex and Gly external aldimine suggest that the changes induced by initial binding of 5-formyl tetrahydrofolate are retained even though 5-formyl tetrahydrofolate is absent in the final structure. Spectral studies carried out with this mutant enzyme also suggest that 5-formyl tetrahydrofolate binds to the E53QbsSHMT-Gly complex forming a quinonoid intermediate and falls off within 4 h of dialysis, leaving behind the mutant enzyme in the gemdiamine form. This is the first report to provide direct evidence for enzyme memory based on the crystal structure of enzyme complexes.

Microcalorimetric indications for ligand binding as a function of the protein for galactoside-specific plant and avian lectins

The process cascade leading to the final accommodation of the carbohydrate ligand in the lectin’s binding site comprises enthalpic and entropic contributions of the binding partners and solvent molecules. With emphasis on lactose, N-acetyllactosamine, and thiodigalactoside as potent inhibitors of binding of galactoside-specific lectins, the question was addressed to what extent these parameters are affected as a function of the protein. The microcalorimetric study of carbohydrate association to the galectin from chicken liver (CG-16) and the agglutinin from Viscum album (VAA) revealed enthalpy–entropy compensation with evident protein type-dependent changes for N-acetyllactosamine. Reduction of the entropic penalty by differential flexibility of loops or side chains and/or solvation properties of the protein will have to be reckoned with to assign a molecular cause to protein type-dependent changes in thermodynamic parameters for lectins sharing the same monosaccharide specificity.

On the effect of matrix cracks in composite helicopter rotor blade

This paper investigates the feasibility of an on-line damage detection capability for helicopter main rotor blades made of composite material. Damage modeled in the composite is matrix cracking. A box-beam with stiffness properties similar to a hingeless rotor blade is designed using genetic algorithm for the typical [+/-theta(m)/90(n)](s) family of composites. The effect of matrix cracks is included in an analytical model of composite box-beam. An aeroelastic analysis of the helicopter rotor based on finite elements in space and time is used to study the effects of matrix cracking in the rotor blade in forward flight. For global fault detection, rotating frequencies, tip bending and torsion response, and blade root loads are studied. It is observed that the effect of matrix cracking on lag bending and elastic twist deflection at the blade tip and blade root yawing moment is significant and these parameters can be monitored for online health monitoring. For implementation of local fault detection technique, the effect on axial and shear strain, for matrix cracks in the whole blade as well as matrix cracks occurring locally is studied. It is observed that using strain measurement along the blade it is possible to locate the matrix cracks as well as to predict density of matrix cracks. (C) 2004 Elsevier Ltd. All rights reserved.

Approximate methods for step function response of undamped non-linear spring mass systems with arbitrary hardening type spring characteristic

The possibility of applying two approximate methods for determining the salient features of response of undamped non-linear spring mass systems subjected to a step input, is examined. The results obtained on the basis of these approximate methods are compared with the exact results that are available for some particular types of spring characteristics. The extension of the approximate methods for non-linear systems with general polynomial restoring force characteristics is indicated.

Ion Transport in a Polymer-Plastic Solid Soft Matter Electrolyte in the Light of Solvent Dynamics and Ion Association

Ion transport in a recently demonstrated promising soft matter solid plastic-polymer electrolyte is discussed here in the context of solvent dynamics and ion association. The plastic-polymer composite electrolytes display liquid-like ionic conductivity in the solid state,compliable mechanical strength (similar to 1 MPa), and wide electrochemical voltage stability (>= 5 V). Polyacrylonitrile (PAN) dispersed in lithium perchlorate (LiClO4)-succinonitrile (SN) was chosen as the model system for the study (abbreviated LiClO4-SN:PAN). Systematic observation of various mid-infrared isomer and ion association bands as a function of temperature and polyme concentration shows an effective increase in trans conformer concentration along with free Li+ ion concentration. This strongly supports the view that enhancement in LiClO4-SN:PAN ionic conductivity over the neat plastic electrolyte (LiClO4-SN) is due to both increase in charge mobility and concentration. The ionic conductivity and infrared spectroscopy studies are supported by Brillouin light scattering. For the LiClO4-SN:PAN composites, a peak at 17 GHz was observed in addition to the normal trans-gauche isomerism (as in neat SN) at 12 GHz. The fast process is attributed to increased dynamics of those SN molecules whose energy barrier of transition from gauche to trans has reduced under influences induced by the changes in temperature and polymer concentration. The observations from ionic conductivity, spectroscopy, and light scattering studies were further supplemented by temperature dependent nuclear magnetic resonance H-1 and Li-7 line width measurements.

Ring loading of a long, thin, circular cylindrical shell enclosing a soft, solid core: A recalculation by the love function method of elasticity.

The problem is solved using the Love function and Flügge shell theory. Numerical work has been done with a computer for various values of shell geometry parameters and elastic constants.

Step function response of non-linear spring mass systems in the presence of Coulomb damping

The transient response of non-linear spring mass systems with Coulomb damping, when subjected to a step function is investigated. For a restricted class of non-linear spring characteristics, exact expressions are developed for (i) the first peak of the response curves, and (ii) the time taken to reach it. A simple, yet accurate linearization procedure is developed for obtaining the approximate time required to reach the first peak, when the spring characteristic is a general function of the displacement. The results are presented graphically in non-dimensional form.

Urey-Bradley potential function for the in-plane vibrations of boric acid

The Urey-Bradley force constants for the in-plane vibrations of the boric acid molecule are calculated using the Wilson's F-G matrix method. They are as follows: KO-H=5·23, KB-O=4·94, HBOH=0·36, {Mathematical expression}, F00=0·68 and FBH=0·98 in units of 105 dynes/cm. Using the force constants, the frequencies are recalculated and the calculated values agree with the observed values satisfactorily. The in-plane vibrational frequencies of deuterated boric acid are also calculated and again satisfactory agreement with the observed values is found.

Potential functions for hydrogen bond interactions - III. Empirical Potential Function for the Peptide N-H...O=C Hydrogen Bond

A careful comparison of the distribution in the (R, θ)-plane of all NH ... O hydrogen bonds with that for bonds between neutral NH and neutral C=O groups indicated that the latter has a larger mean R and a wider range of θ and that the distribution was also broader than for the average case. Therefore, the potential function developed earlier for an average NH ... O hydrogen bond was modified to suit the peptide case. A three-parameter expression of the form {Mathematical expression}, with △ = R - Rmin, was found to be satisfactory. By comparing the theoretically expected distribution in R and θ with observed data (although limited), the best values were found to be p1 = 25, p3 = - 2 and q1 = 1 × 10-3, with Rmin = 2·95 Å and Vmin = - 4·5 kcal/mole. The procedure for obtaining a smooth transition from Vhb to the non-bonded potential Vnb for large R and θ is described, along with a flow chart useful for programming the formulae. Calculated values of ΔH, the enthalpy of formation of the hydrogen bond, using this function are in reasonable agreement with observation. When the atoms involved in the hydrogen bond occur in a five-membered ring as in the sequence[Figure not available: see fulltext.] a different formula for the potential function is needed, which is of the form Vhb = Vmin +p1△2 +q1x2 where x = θ - 50° for θ ≥ 50°, with p1 = 15, q1 = 0·002, Rmin = 2· Å and Vmin = - 2·5 kcal/mole. © 1971 Indian Academy of Sciences.

Effect of matrix cracking and material uncertainty on composite plates

A laminated composite plate model based on first order shear deformation theory is implemented using the finite element method.Matrix cracks are introduced into the finite element model by considering changes in the A, B and D matrices of composites. The effects of different boundary conditions, laminate types and ply angles on the behavior of composite plates with matrix cracks are studied.Finally, the effect of material property uncertainty, which is important for composite material on the composite plate, is investigated using Monte Carlo simulations. Probabilistic estimates of damage detection reliability in composite plates are made for static and dynamic measurements. It is found that the effect of uncertainty must be considered for accurate damage detection in composite structures. The estimates of variance obtained for observable system properties due to uncertainty can be used for developing more robust damage detection algorithms. (C) 2010 Elsevier Ltd. All rights reserved.

Note: Dynamic point spread function for single and multiphoton fluorescence microscopy

We propose and demonstrate a dynamic point spread function (PSF) for single and multiphoton fluorescence microscopy. The goal is to generate a PSF whose shape and size can be maneuvered from highly localized to elongated one, thereby allowing shallow-to-depth excitation capability during active imaging. The PSF is obtained by utilizing specially designed spatial filter and dynamically altering the filter parameters. We predict potential applications in nanobioimaging and fluorescence microscopy.

Note: Dynamic point spread function for single and multiphoton fluorescence microscopy

We propose and demonstrate a dynamic point spread function (PSF) for single and multiphoton fluorescence microscopy. The goal is to generate a PSF whose shape and size can be maneuvered from highly localized to elongated one, thereby allowing shallow-to-depth excitation capability during active imaging. The PSF is obtained by utilizing specially designed spatial filter and dynamically altering the filter parameters. We predict potential applications in nanobioimaging and fluorescence microscopy.