Crystal structures, dynamics and functional implications of molybdenum-cofactor biosynthesis protein MogA from two thermophilic organisms

Molybdenum-cofactor (Moco) biosynthesis is an evolutionarily conserved pathway in almost all kingdoms of life, including humans. Two proteins, MogA and MoeA, catalyze the last step of this pathway in bacteria, whereas a single two-domain protein carries out catalysis in eukaryotes. Here, three crystal structures of the Moco-biosynthesis protein MogA from the two thermophilic organisms Thermus thermophilus (TtMogA; 1.64 angstrom resolution, space group P2(1)) and Aquifex aeolicus (AaMogA; 1.70 angstrom resolution, space group P2(1) and 1.90 angstrom resolution, space group P1) have been determined. The functional roles and the residues involved in oligomerization of the protein molecules have been identified based on a comparative analysis of these structures with those of homologous proteins. Furthermore, functional roles have been proposed for the N- and C-terminal residues. In addition, a possible protein-protein complex of MogA and MoeA has been proposed and the residues involved in protein-protein interactions are discussed. Several invariant water molecules and those present at the subunit interfaces have been identified and their possible structural and/or functional roles are described in brief. In addition, molecular-dynamics and docking studies with several small molecules (including the substrate and the product) have been carried out in order to estimate their binding affinities towards AaMogA and TtMogA. The results obtained are further compared with those obtained for homologous eukaryotic proteins.

Critical earthquake input power spectral density function models for engineering structures

The problem of determining optimal power spectral density models for earthquake excitation which satisfy constraints on total average power, zero crossing rate and which produce the highest response variance in a given linear system is considered. The solution to this problem is obtained using linear programming methods. The resulting solutions are shown to display a highly deterministic structure and, therefore, fail to capture the stochastic nature of the input. A modification to the definition of critical excitation is proposed which takes into account the entropy rate as a measure of uncertainty in the earthquake loads. The resulting problem is solved using calculus of variations and also within linear programming framework. Illustrative examples on specifying seismic inputs for a nuclear power plant and a tall earth dam are considered and the resulting solutions are shown to be realistic.

Thermomechanical generalization of partial contact in pin joints

Mechanical fasteners introduce structural weakness, still they are an essential constituent of most structures as they permit interchangeability of parts and flexible construction programs; Variable temperature operations of Aerospace and Nuclear structures make it imperative to investigate the thermoelastic behaviour of joints. This paper explores analytically similar mechanical and thermal parameters to generalise the thermomechanical behaviour of a pin joint in an isotropic Sheet for a class of configurations. This generalization enables virtually direct application of existing information regarding joints under pure mechanical loading to joints subjected to combined thermomechanical loading, thus reducing the efforts of both the analyst and the designer by an order of magnitude. Copyright (C) 1996 Published by Elsevier Science Ltd.

Stability of laminated composite plates with cut-outs

Critical buckling loads of laminated fibre-reinforced plastic square panels have been obtained using the finite element method. Various boundary conditions, lay-up details, fibre orientations, cut-out sizes are considered. A 36 degrees of freedom triangular element, based on the classical lamination theory (CLT) has been used for the analysis. The performance of this element is validated by comparing results with some of those available in literature. New results have been given for several cases of boundary conditions for [0°/ ± 45°/90°]s laminates. The effect of fibre-orientation in the ply on the buckling loads has been investigated by considering [±?]6s laminates.

Stiffened composite cylindrical panels�Optimum lay-up for buckling by ranking

Buckling of discretely stiffened composite cylindrical panels made of repeated sublaminate construction is studied using a finite element method. In repeated sublaminate construction, a full laminate is obtained by repeating a basic sublaminate, which has a smaller number of plies. This paper deals with the determination of the optimum lay-up for buckling by ranking of such stiffened (longitudinal and hoop) composite cylindrical panels. For this purpose we use the particularized form of a four-noded, 48 degrees of freedom doubly curved quadrilateral thin shell finite element together with a fully compatible two-noded, 16 degrees of freedom composite stiffener element. The computer program developed has been used, after extensive checking for correctness, to obtain an optimum orientation scheme of the plies in the sublaminate so as to achieve maximum buckling load for a specified thickness of typical stiffened composite cylindrical panels.

Thermal Stability of Spherical Nanoporous Aggregates and Formation of Hollow Structures by Sintering-A Phase-Field Study

Nanoporous structures are widely used for many applications and hence it Is important to investigate their thermal stability. We study the stability of spherical nanoporous aggregates using phase-field simulations that explore systematically the effect of grain boundary diffusion, surface diffusion, and grain boundary mobility on the pathways for microstructural evolution. Our simulations for different combinations of surface and GB diffusivity and GB mobility show four distinct microstructural pathways en route to 100% density: multiple dosed pores, hollow shells, hollow shells with a core, and multiple interconnected pores. The microstructures from our simulations are consistent with experimental observations in several different systems. Our results have important implications for rational synthesis of hollow nanostructures or aggregates with open pores, and for controlling the stability of nanoporous aggregates that are widely used for many applications.

Estimation of low-velocity impact damage in laminated composite circular plates using nonlinear finite element analysis

Nonlinear finite element analysis is used for the estimation of damage due to low-velocity impact loading of laminated composite circular plates. The impact loading is treated as an equivalent static loading by assuming the impactor to be spherical and the contact to obey Hertzian law. The stresses in the laminate are calculated using a 48 d.o.f. laminated composite sector element. Subsequently, the Tsai-Wu criterion is used to detect the zones of failure and the maximum stress criterion is used to identify the mode of failure. Then the material properties of the laminate are degraded in the failed regions. The stress analysis is performed again using the degraded properties of the plies. The iterative process is repeated until no more failure is detected in the laminate. The problem of a typical T300/N5208 composite [45 degrees/0 degrees/-45 degrees/90 degrees](s) circular plate being impacted by a spherical impactor is solved and the results are compared with experimental and analytical results available in the literature. The method proposed and the computer code developed can handle symmetric, as well as unsymmetric, laminates. It can be easily extended to cover the impact of composite rectangular plates, shell panels and shells.

Synthesis, properties and crystal structures of diastereomeric areneruthenium(II) chiral Schiff-base complexes

Diastereomers (SRu,Sc)-1a and (RRu,Sc)-1b, in a ratio of 85: 15 and formulated as [Ru(η-MeC6H4Pri-p)Cl(L*)], have been prepared by treating [{Ru(η-MeC6H4Pri-p)Cl2}2] with the sodium salt of (S)-α-methylbenzylsalicylaldimine (HL*) in tetrahydrofuran at –70 °C. The reaction of 1(1a+1b) with AgClO4 in acetone followed by an addition of PPh3 or 4-methylpyridine (4Me-py) leads to the formation of adducts [Ru(η-MeC6H4Pri-p)(PPh3)(L*)]ClO42[(SRu,Sc)2a, (FRu,Sc)2b] and [Ru(η-MeC6H4Pri-p)(4Me-py)(L*)]ClO43[(SRu,Sc)3a, (RRu,Sc)3b] in the diastereomeric ratios (SRu,Sc) : (RRu,Sc) of 2 : 98 and 76 : 24, respectively. Complex 1 crystallises with equal numbers of 1a and 1b molecules in an asymmetric unit of monoclinic space group P21 with a= 10.854(1), b= 17.090(1), c= 12.808(4)Å, β= 110.51(1)°, and Z= 4. The structure was refined to R= 0.0552 and R′= 0.0530 with 2893 reflections having I[gt-or-equal] 1.5σ(I). The absolute configurations of the chiral centres in the optically pure single crystal of the PPh3 adduct have been obtained from an X-ray study. Crystals of formulation [Ru(η-MeC6H4Pri-p)-(PPh3)(L*)]2[ClO4][PF6]·1.5 CHCl3, obtained in presence of both ClO4 and PF6 anions, belong to the non-centric triclinic space group P1 with a= 10.852(2), b= 14.028(1), c= 15.950(2)Å, α= 91.51(1), β= 105.97(1), γ= 106.11(1)°, and Z= 2. The final residuals were R= 0.0713, R′= 0.0752 with 7283 reflections having I[gt-or-equal] 2.5σ(I). The crystal structures of 1a,1b, and the PPh3 adduct (2b,2b′) consist of a ruthenium(II) centre bonded to a η-p-cymene, a bidentate chelating Schiff base, and a unidentate ligand (Cl or PPh3). The chirooptical properties of the complexes have been studied using 1H NMR and CD spectral data. The presence of a low-energy barrier for the intermediate involved in these reactions, showing both retention as well as inversion of the metal configuration, is discussed.

The influence of pH on the corrosion of medium strength aerospace alloys 8090, 2091 and 2014

The influence of pH on the corrosion behaviour of two aluminium-lithium-copper-magnesium-zirconium (8090 and 2091) alloys was studied and compared with a standard aircraft alloy, 2014 (Al-4.4% Cu) and 99.9% pure Al. In constant exposure and potentiodynamic polarization studies conducted in 3.5% NaCl solution having different pH values, all the alloys exhibited high corrosion rates in acidic and alkaline environments, with a minimum in less hostile environments close to neutral pH. The pitting potentials for aluminium-lithium alloys were slightly lower than those for 2014 and pure Al. The effect of pH on the passive current density was also less for aluminium-lithium alloys.

Link Conditions for Simplifying Meshes with Embedded Structures

Interactive visualization applications benefit from simplification techniques that generate good-quality coarse meshes from high-resolution meshes that represent the domain. These meshes often contain interesting substructures, called embedded structures, and it is desirable to preserve the topology of the embedded structures during simplification, in addition to preserving the topology of the domain. This paper describes a proof that link conditions, proposed earlier, are sufficient to ensure that edge contractions preserve the topology of the embedded structures and the domain. Excluding two specific configurations, the link conditions are also shown to be necessary for topology preservation. Repeated application of edge contraction on an extended complex produces a coarser representation of the domain and the embedded structures. An extension of the quadric error metric is used to schedule edge contractions, resulting in a good-quality coarse mesh that closely approximates the input domain and the embedded structures.

Network approach for capturing ligand-induced subtle global changes in protein structures

Ligand-induced conformational changes in proteins are of immense functional relevance. It is a major challenge to elucidate the network of amino acids that are responsible for the percolation of ligand-induced conformational changes to distal regions in the protein from a global perspective. Functionally important subtle conformational changes (at the level of side-chain noncovalent interactions) upon ligand binding or as a result of environmental variations are also elusive in conventional studies such as those using root-mean-square deviations (r.m.s.d.s). In this article, the network representation of protein structures and their analyses provides an efficient tool to capture these variations (both drastic and subtle) in atomistic detail in a global milieu. A generalized graph theoretical metric, using network parameters such as cliques and/or communities, is used to determine similarities or differences between structures in a rigorous manner. The ligand-induced global rewiring in the protein structures is also quantified in terms of network parameters. Thus, a judicious use of graph theory in the context of protein structures can provide meaningful insights into global structural reorganizations upon perturbation and can also be helpful for rigorous structural comparison. Data sets for the present study include high-resolution crystal structures of serine proteases from the S1A family and are probed to quantify the ligand-induced subtle structural variations.

The structures of bacteriorhodopsin with different retinal-Schiff base orientations--computer modeling and energy minimization studies

Bacteriorhodopsin has been the subject of intense study in order to understand its photochemical function. The recent atomic model proposed by Henderson and coworkers based on electron cryo-microscopic studies has helped in understanding many of the structural and functional aspects of bacteriorhodopsin. However, the accuracy of the positions of the side chains is not very high since the model is based on low-resolution data. In this study, we have minimized the energy of this structure of bacteriorhodopsin and analyzed various types of interactions such as - intrahelical and interhelical hydrogen bonds and retinal environment. In order to understand the photochemical action, it is necessary to obtain information on the structures adopted at the intermediate states. In this direction, we have generated some intermediate structures taking into account certain experimental data, by computer modeling studies. Various isomers of retinal with 13-cis and/or 15-cis conformations and all possible staggered orientations of Lys-216 side chain were generated. The resultant structures were examined for the distance between Lys-216-schiff base nitrogen and the carboxylate oxygen atoms of Asp-96 - a residue which is known to reprotonate the schiff base at later stages of photocycle. Some of the structures were selected on the basis of suitable retinal orientation and the stability of these structures were tested by energy minimization studies. Further, the minimized structures are analyzed for the hydrogen bond interactions and retinal environment and the results are compared with those of the minimized rest state structure. The importance of functional groups in stabilizing the structure of bacteriorhodopsin and in participating dynamically during the photocycle have been discussed.

Structures, Stabilities and Strain in C60 and C70 Derivatives Fullerenes, Nanotubes and Carbon Nanostructures

The stabilities of a number of small adducts as well as larger hydrides of C-60 and C-70 are reported using semiempirical MO methods. The data are shown to be consistent with the nature of bond alternation in the parent fullerenes and strain effects in the cage systems.