Differential stability of beta-sheets and alpha-helices in beta-lactamase: a high temperature molecular dynamics study of unfolding intermediates

Beta-Lactamase, which catalyzes beta-lactam antibiotics, is prototypical of large alpha/beta proteins with a scaffolding formed by strong noncovalent interactions. Experimentally, the enzyme is well characterized, and intermediates that are slightly less compact and having nearly the same content of secondary structure have been identified in the folding pathway. In the present study, high temperature molecular dynamics simulations have been carried out on the native enzyme in solution. Analysis of these results in terms of root mean square fluctuations in cartesian and [phi, psi] space, backbone dihedral angles and secondary structural hydrogen bonds forms the basis for an investigation of the topology of partially unfolded states of beta-lactamase. A differential stability has been observed for alpha-helices and beta-sheets upon thermal denaturation to putative unfolding intermediates. These observations contribute to an understanding of the folding/unfolding processes of beta-lactamases in particular, and other alpha/beta proteins in general.

Analysis of Hydrogen Bonding and Stability of Protein Secondary Structures in Molecular Dynamics Simulation

Molecular Dynamics (MD) simulations provide an atomic level account of the molecular motions and have proven to be immensely useful in the investigation of the dynamical structure of proteins. Once an MD trajectory is obtained, specific interactions at the molecular level can be directly studied by setting up appropriate combinations of distance and angle monitors. However, if a study of the dynamical behavior of secondary structures in proteins becomes important, this approach can become unwieldy. We present herein a method to study the dynamical stability of secondary structures in proteins, based on a relatively simple analysis of backbone hydrogen bonds. The method was developed for studying the thermal unfolding of beta-lactamases, but can be extended to other systems and adapted to study relevant properties.

Edge-sharing bioctahedral diruthenium(III) complexes containing methoxy and carboxylate bridges:x-ray structures, redox behavior, and core stability

Edge-sharing bioctahedral (ESBO) complexes [Ru-2(OMe)(O2CC6H4-p-X)3(1-MeIm)(4)](ClO4)2 (X = OMe (1a), Me (1b)) and [Ru-2(O2CC6H4-P-X)(4)(1-MeIm)(4)](ClO4)(2) (X = OMe (2a), Me (2b)) are prepared by reacting Ru2Cl(O(2)CR)(4) with 1-methylimidazole (1-MeIm) in methanol followed by treatment with NaClO4. Complex 2a and the PF6- salt (1a') of 1a have been structurally characterized. Crystal data for 1a.1.5MeCN. 0.5Et(2)O: triclinic, P (1) over bar, a = 13.125(2) Angstrom, b = 15.529(3) Angstrom, c 17.314(5) Angstrom, a; 67.03(2)degrees, beta 68.05(2)degrees, gamma = 81.38(1)degrees, V 3014(1) Angstrom(3), Z = 2. Crystal data for 2a: triclinic, P (1) over bar, a 8.950(1) Angstrom, b = 12.089(3) Angstrom, c = 13.735(3) Angstrom, alpha 81.09(2)degrees, beta = 72.27(1)degrees, gamma = 83.15(2)degrees, V = 1394(1) Angstrom(3), Z = 1. The complexes consist of a diruthenium(III) unit held by two monoatomic and two three-atom bridging ligands. The 1-MeIm ligands are at the terminal sites of the [Ru-2(mu-L)(eta(1):mu-O(2)CR)(eta(1):eta(1):mu-O(2)CR)(2)](2+) core having a Ru-Ru single bond (L = OMe or eta(1)-O(2)CR). The Ru-Ru distance and the Ru-O-Ru angle in the core of 1a' and 2a are 2.49 Angstrom and similar to 76 degrees. The complexes undergo one-electron oxidation and reduction processes in MeCN-0.1 M TBAP to form mixed-valence diruthenium species with Ru-Ru bonds of orders 1.5 and 0.5, respectively.

High-temperature stability of Ca2ZrSi4O12

The standard Gibbs free energy of formation of orthorhombic Ca2ZrSi4O12 from component oxides ZrO2 (monoclinic), CaO (rock salt), and SiO2 (quartz) has been determined in the temperature range 973 to 1273 K using a solid-state cell incorporating single-crystal CaF2 as the electrolyte: Delta G(f) degrees = -219930 + 11.77T (+/- 1500) J.mol(-1) This is the only quantitative information now available on the stability of Ca2ZrSi4O12.

Interactions of L-serine at the active site of serine hydroxymethyltransferases: induction of thermal stability

Serine hydroxymethyltransferase (SHMT), EC 2.1.2.1, exhibits broad substrate and reaction specificity. In addition to cleaving many 3-hydroxyamino acids to glycine and an aldehyde, the enzyme also catalyzed the decarboxylation, transamination and racemization of several substrate analogues of amino acids. To elucidate the mechanism of interaction of substrates, especially L-serine with the enzyme, a comparative study of interaction of L-serine with the enzyme from sheep liver and Escherichia coli, was carried out. The heat stability of both the enzymes was enhanced in the presence of serine, although to different extents. Thermal denaturation monitored by spectral changes indicated an alteration in the apparent T, of sheep liver and E. coli SHMTs from 55 +/- 1 degrees C to 72 +/- 3 degrees C at 40 mM serine and from 67 +/- 1 degrees C to 72 +/- 1 degrees C at 20 mM serine, respectively. Using stopped flow spectrophotometry k values of (49 +/- 5)(.)10(-3) s(-1) and (69 +/- 7).10(-3) s(-1) for sheep liver and E. coli enzymes were determined at 50 mM serine. The binding of serine monitored by intrinsic fluorescence and sedimentation velocity measurements indicated that there was no generalized change in the structure of both proteins. However, visible CD measurements indicated a change in the asymmetric environment of pyridoxal 5'-phosphate at the active site upon binding of serine to both the enzymes. The formation of an external aldimine was accompanied by a change in the secondary structure of the enzymes monitored by far UV-CD spectra. Titration microcalorimetric studies in the presence of serine (8 mM) also demonstrated a single class of binding and the conformational changes accompanying the binding of serine to the enzyme resulted in a more compact structure leading to increased thermal stability of the enzyme.

Phase relations in the system Cu─Ho─O and stability of Cu2Ho2O5

The phase relations in the system Cu-Ho-O have been determined at 1300 K using X-ray diffraction, optical microscopy, and electron microprobe analysis of samples equilibrated in evacuated quartz ampules and in pure oxygen. Only one ternary compound, Cu2Ho2O5, was found to be stable. The Gibbs free energy of formation of this compound has been measured using the solid-state cell Pt,Cu2O + Cu2Ho2O5 + Ho2O3/(Y2O3)ZrO2/CuO + Cu2O,Pt in the temperature range of 973 to 1350 K. For the formation of Cu2Ho2O5 from its binary component oxides, 2CuO(s) + Ho2O3(S) --> Cu2Ho2O5(s) DELTAG-degrees = 11190 - 13.8T(+/- 120) J-mol-1 Since the formation is endothermic, CU2Ho2O5 becomes thermodynamically unstable with respect to CuO and Ho2O3 below 810 K. When the oxygen partial pressure over Cu2Ho2O5 is lowered, it decomposes according to the reaction 2Cu2Ho2O5(s) --> 2Ho2O3(s) + 2Cu2O(S) + O2(g) for which the equilibrium oxygen potential is given by DELTAmu(O2) = - 238510 + 160.2T(+/- 450) J.mol-1 The decomposition temperature at an oxygen partial pressure of 1.52 x 10(4) Pa was measured using a combined DTA-TGA apparatus. Based on these results, an oxygen potential diagram for the system Cu-Ho-O at 1300 K is presented.

Stability of copper tolerance in Thiobacillus ferrooxidans

A strain of Thiobacillus ferrooxidans MAL-4-1 was adapted to grow at higher concentrations of copper by repeated subculturing in the presence of increasing levels of added cupric ions in 9K medium. The strains adapted to copper were found to be more efficient in bioleaching of copper from concentrates. When copper tolerant strains were back cultured repeatedly in 9K medium without cupric ions, the initially developed metal tolerance was observed to be lost. This indicates that the copper tolerance developed is stress-dependent and not a permanent trait of the adapted strain.

Structure and stability of human telomeric sequence

Telomeric DNA of a variety of vertebrates including humans contains the tandem repeat d(TTAGGG)(n). We have investigated the structural properties of the human telomeric repeat oligonucleotide models d(T(2)AG(3))(4), d(G(3)T(2)A)(3)G(3), and d(G(3)T(2)AG(3)) using CD, gel electrophoresis, and chemical probing techniques. The sequences d(G(3)T(2)A)(3)G(3) and d(T(2)AG(3))(4) assume an antiparallel G quartet structure by intramolecular folding, while the sequence d(G(3)T(2)AG(3)) also adopts an antiparallel G quartet structure but by dimerization of hairpins. In all the above cases, adenines are in the loop. The TTA loops are oriented at the same end of the G tetrad stem in the case of hairpin dimer. Further, the oligonucleotide D(G(3)T(2)AG(3)) forms a higher order structure by the association of two hairpin dimers via stacking of G tetrad planes. Here we show that N-7 of adenine in the hairpin dimer is Hoogsteen hydrogen-bonded. The partial reactivity of loop adenines with DEPC in d(T(2)AG(3))(4) suggests that the intramolecular G quartet structure is highly polymorphic and structures with different loop orientations and topologies are formed in solution. Intra- and interloop hydrogen bonding schemes for the TTA loops are proposed to account for the observed diethyl pyrocarbonate reactivities of adenines. Sodium-induced G quartet structures differ from their potassium-induced counterparts not only in stability but also in loop conformation and interactions. Thus, the overall structure and stability of telomeric sequences are modulated by the cation present, loop sequence, and the number of G tracts, which might be important for the telomere function.

Use of L matrix to obtain reliable ab initio force constants of polyatomic molecules: ethylene as a test system

Direct use of experimental eigenvalues of the vibrational secular equation on to the ab initio predicted eigenvector space is suggested as a means of obtaining a reliable set of intramolecular force constants. This method which we have termed RECOVES (recovery in the eigenvector space) is computationally simple and free from arbitrariness. The RECOVES force constants, by definition, reproduce the experimental vibrational frequencies of the parent molecule exactly. The ab initio calculations were carried out for ethylene as a test molecule and the force constants obtained by the present procedure also correctly predict the vibrational frequencies of the deuterated species. The RECOVES force constants for ethylene are compared with those obtained by using the SQM procedure.

Flap-lag-torsion stability in hover and forward flight with three-dimensional wake

The contributions of full-wake dynamics in trim analysis are demonstrated for finding the control inputs and periodic responses simultaneously, as well as in Floquet eigenanalysis for finding the damping levels. The equations of flap bending, lag bending, and torsion are coupled with a three-dimensional, finite state wake, and low-frequency (<1/rev) to high frequency (>1/rev) multiblade modes are considered. Full blade-wake dynamics is used in trim analysis and Floquet eigenanalysis. A uniform cantilever blade in trimmed flight is investigated over a range of thrust levels, advance ratios, number of blades, and blade torsional frequencies. The investigation includes the convergence characteristics of control inputs, periodic responses, and damping levels with respect to the number of spatial azimuthal harmonics and radial shape functions in the wake representation. It also includes correlation with the measured lag damping of a three-bladed untrimmed rotor. The parametric study shows the dominant influence of wake dynamics on control inputs, periodic responses, and damping levels, and wake theory generally improves the correlation.

Phase stability and dielectric properties of ceramics in the Pb(Zn1/3Nb2/3)O3-Pb(Ni1/3Nb2/3)O3-PbTio3 relaxor ferroelectric system

The perovskite structure in Pb(Zn1/3Nb2/3)O3 can be stabilized by the addition of Pb(Ni1/3Nb2/3)O3 and PbTiO3.Pb(Ni1/3Nb2/3)O3 assists in lowering the sintering temperature and shifting the Curie temperature of ceramics while PbTiO3 helps to optimize the dielectric properties. The phase stability and dielectric properties of several compositions in the Pb(Zn1/3Nb2/3)O3-Pb(Ni1/3Nb2/3)O3-PbTiO3 ternary relaxor ferroelectric system were investigated for possible capacitor applications. The effect of calcining and sintering temperature on the stability of perovskite phase in PZN rich compositions was studied extensively as a function of composition. The boundary line separating perovskite and mixed phases was determined for compositions near PZN. Several compositions can be sintered below 1050°C. The dielectric properties of compositions near the mixed phase boundary showed strong dependence on the percentage of pyrochlore phase. Compositions with a dielectric constant of 12.500 at room temperature have been identified which meet Z5T and Y5U specifications for dielectric constant and tan δ.

Parallel computing concepts and methods for floquet analysis of helicopter trim and stability

Floquet analysis is widely used for small-order systems (say, order M < 100) to find trim results of control inputs and periodic responses, and stability results of damping levels and frequencies, Presently, however, it is practical neither for design applications nor for comprehensive analysis models that lead to large systems (M > 100); the run time on a sequential computer is simply prohibitive, Accordingly, a massively parallel Floquet analysis is developed with emphasis on large systems, and it is implemented on two SIMD or single-instruction, multiple-data computers with 4096 and 8192 processors, The focus of this development is a parallel shooting method with damped Newton iteration to generate trim results; the Floquet transition matrix (FTM) comes out as a byproduct, The eigenvalues and eigenvectors of the FTM are computed by a parallel QR method, and thereby stability results are generated, For illustration, flap and flap-lag stability of isolated rotors are treated by the parallel analysis and by a corresponding sequential analysis with the conventional shooting and QR methods; linear quasisteady airfoil aerodynamics and a finite-state three-dimensional wake model are used, Computational reliability is quantified by the condition numbers of the Jacobian matrices in Newton iteration, the condition numbers of the eigenvalues and the residual errors of the eigenpairs, and reliability figures are comparable in both the parallel and sequential analyses, Compared to the sequential analysis, the parallel analysis reduces the run time of large systems dramatically, and the reduction increases with increasing system order; this finding offers considerable promise for design and comprehensive-analysis applications.

Pillaring of smectites using an aluminium oligomer: A study of pillar density and thermal stability

Two smectite samples having different layer charges were pillared using hydroxy aluminium oligomers at a OH/Al ratio of 2.5 and at pH 4.3 to 4.6. Pillaring was carried out at different conditions such as ageing, temperature and base addition time of the pillaring solution, and also in the presence of nonionic surfactant polyoxyethylene sorbitanmonooleate (Tween-80). The primary objective of preparing at different conditions was to introduce varied quantities of aluminium oligomer between the layers and to study its effect on the properties of the pillared products. A simple method has been followed to estimate the amount of interlayer aluminium. A quantity called pillar density number (PDN) based on the ratio of interlayer Al adsorbed to CEC of the parent clay has been effectively used to evaluate the nature of the resulting pillared product. PDN, for a given clay, was found to correlate well with the sharpness of the d(001) peaks for the air dried samples. The calculated number of pillars, varied from 3.00 x 10(18) to 5.32 x 10(18) per meq charge. The present study shows that a higher value of PDN is indicative of better thermal stability. Pillar density number may be conveniently used as a measure of the thermal stability of pillared samples.

Response, loads and stability of rotors with interconnected blades

An isolated rotor with blades interconnected through viscoelastic elements is analyzed for response, loads and stability in moment trim under forward flight conditions. A conceptual model of a multibladed rotor with rigid flap and lag motions is considered, Although the interconnecting elements are placed in the In-plane direction, considerable coupling between the flap-lag motions of the blades can occur in certain ranges of interblade element stiffness. Interblade coupling can yield significant changes in the response, loads and stability which are dependent on the interblade element and rotor parameters.