Importance of tyrosine residues of Bacillus stearothermophilus serine hydroxymethyltransferase in cofactor binding and l-allo-Thr cleavage

Serine hydroxymethyltransferase (SHMT) from Bacillus stearothermophilus (bsSHMT) is a pyridoxal 5'-phosphate-dependent enzyme that catalyses the conversion of l-serine and tetrahydrofolate to glycine and 5,10-methylene tetrahydrofolate. In addition, the enzyme catalyses the tetrahydrofolate-independent cleavage of 3-hydroxy amino acids and transamination. In this article, we have examined the mechanism of the tetrahydrofolate-independent cleavage of 3-hydroxy amino acids by SHMT. The three-dimensional structure and biochemical properties of Y51F and Y61A bsSHMTs and their complexes with substrates, especially l-allo-Thr, show that the cleavage of 3-hydroxy amino acids could proceed via Cα proton abstraction rather than hydroxyl proton removal. Both mutations result in a complete loss of tetrahydrofolate-dependent and tetrahydrofolate-independent activities. The mutation of Y51 to F strongly affects the binding of pyridoxal 5'-phosphate, possibly as a consequence of a change in the orientation of the phenyl ring in Y51F bsSHMT. The mutant enzyme could be completely reconstituted with pyridoxal 5'-phosphate. However, there was an alteration in the λmax value of the internal aldimine (396 nm), a decrease in the rate of reduction with NaCNBH3 and a loss of the intermediate in the interaction with methoxyamine (MA). The mutation of Y61 to A results in the loss of interaction with Cα and Cβ of the substrates. X-Ray structure and visible CD studies show that the mutant is capable of forming an external aldimine. However, the formation of the quinonoid intermediate is hindered. It is suggested that Y61 is involved in the abstraction of the Cα proton from 3-hydroxy amino acids. A new mechanism for the cleavage of 3-hydroxy amino acids via Cα proton abstraction by SHMT is proposed.

Hybrid learning scheme for data mining applications

Classification of large datasets is a challenging task in Data Mining. In the current work, we propose a novel method that compresses the data and classifies the test data directly in its compressed form. The work forms a hybrid learning approach integrating the activities of data abstraction, frequent item generation, compression, classification and use of rough sets.

Hybrid learning scheme for data mining applications

Classification of large datasets is a challenging task in Data Mining. In the current work, we propose a novel method that compresses the data and classifies the test data directly in its compressed form. The work forms a hybrid learning approach integrating the activities of data abstraction, frequent item generation, compression, classification and use of rough sets.

Characterization of Alkali Induced Formation of Lanthionine, Trisulfides, and Tetrasulfides from Peptide Disulfides using Negative Ion Mass Spectrometry

Peptide disulfides are unstable under alkaline conditions, resulting in the formation of products containing lanthionine and polysulfied linkages. Electrospray ionization mass spectrometry has been used to characterize major species obtained when cyclic and acyclic peptide disulfides are exposed to alkaline media. Studies on a model cyclic peptide disulfide (Boc - Cys - Pro - Leu - Cys - NHMe) and an acyclic peptide, oxidized glutathione, bis ((gamma)Glu Cys - Gly - COOH), are described. Disulfide cleavage reactions are initiated by the abstraction of (CH)-H-alpha or (CH)-H-beta protons of Cys residues, with Subsequent elimination of H2S or H2S2. The buildup of reactive thiol species which act on intermediates containing dehydroalanine residues, rationalizes the formation of lanthionine and polysulfide products. In the case of the cyclic peptide disulfide, the formation of cyclic products is facilitated by the intramolecular nature of the Michael addition reaction of thiols to the dehydroalanine residue. Mass spectral evidence for the intermediate species is presented by using alkylation of thiol groups as a trapping method. Mass spectral fragmentation in the negative ion mode of the peptides derived from trisulfides and tetrasulfides results in elimination of S-2. (J Am Soc Mass Spectrom 2009, 20, 783-791) (C) 2009 American Society for Mass Spectrometry.

Characterization of Alkali Induced Formation of Lanthionine, Trisulfides, and Tetrasulfides from Peptide Disulfides using Negative Ion Mass Spectrometry

Peptide disulfides are unstable under alkaline conditions, resulting in the formation of products containing lanthionine and polysulfied linkages. Electrospray ionization mass spectrometry has been used to characterize major species obtained when cyclic and acyclic peptide disulfides are exposed to alkaline media. Studies on a model cyclic peptide disulfide (Boc - Cys - Pro - Leu - Cys - NHMe) and an acyclic peptide, oxidized glutathione, bis ((gamma)Glu Cys - Gly - COOH), are described. Disulfide cleavage reactions are initiated by the abstraction of (CH)-H-alpha or (CH)-H-beta protons of Cys residues, with Subsequent elimination of H2S or H2S2. The buildup of reactive thiol species which act on intermediates containing dehydroalanine residues, rationalizes the formation of lanthionine and polysulfide products. In the case of the cyclic peptide disulfide, the formation of cyclic products is facilitated by the intramolecular nature of the Michael addition reaction of thiols to the dehydroalanine residue. Mass spectral evidence for the intermediate species is presented by using alkylation of thiol groups as a trapping method. Mass spectral fragmentation in the negative ion mode of the peptides derived from trisulfides and tetrasulfides results in elimination of S-2. (J Am Soc Mass Spectrom 2009, 20, 783-791) (C) 2009 American Society for Mass Spectrometry.

Investigating novelty-outcome relationships in engineering design

Design creativity involves developing novel and useful solutions to design problems The research in this article is an attempt to understand how novelty of a design resulting from a design process is related to the kind of outcomes. described here as constructs, involved in the design process A model of causality, the SAPPhIRE model, is used as the basis of the analysis The analysis is based on previous research that shows that designing involves development and exploration of the seven basic constructs of the SAPPhIRE model that constitute the causal connection between the various levels of abstraction at which a design can be described The constructs am state change, action, parts. phenomenon. input. organs. and effect The following two questions are asked. Is there a relationship between novelty and the constructs? If them is a relationship, what is the degree of this relationship? A hypothesis is developed to answer the questions an increase in the number and variety of ideas explored while designing should enhance the variety of concept space. leading to an increase in the novelty of the concept space Eight existing observational studies of designing sessions are used to empirically validate the hypothesis Each designing session involves an individual designer. experienced or novice. solving a design problem by producing concepts and following a think-aloud protocol. The results indicate dependence of novelty of concept space on variety of concept space and dependence of variety of concept space on variety of idea space. thereby validating the hypothesis The Jesuits also reveal a strong correlation between novelty and the constructs, correlation value decreases as the abstraction level of the constructs reduces. signifying the importance of using constructs at higher abstraction levels for enhancing novelty

Adsorption of oxygen and reactivity with HCl on a barium-doped lead surface

X.p.s. studies on the adsorption of oxygen on a barium-covered Pb surface have shown the presence of two distinct types of oxygen species: oxidic, O2–, and the peroxo-like O2–2(ads), and the surface has been identified as a composite of PbO and BaPbO3. On a barium pre-covered surface, the sticking probability of oxygen on Pb is increased. The O2–(ads) species preferentially reacts with HCl forming PbCl2(ads)via proton abstraction, whereas O2–2(ads) is not reactive with HCl vapour. On the Pb surface, the PbCl2 overlayer reacts with excess HCl, forming a volatile compound believed to be Pb(ClHCl)2, while in the presence of coadsorbed barium, the stability of PbCl2 is increased and the activation energy for the reaction: PbCl2(ads)+ 2HCl(g) Pb(ClHCl)2(g) is increased. Stronger intermetallic interaction is suggested to be the reason for higher PbCl2 stability.

Distributed nonlinear optimization algorithms for general network problems

There are a number of large networks which occur in many problems dealing with the flow of power, communication signals, water, gas, transportable goods, etc. Both design and planning of these networks involve optimization problems. The first part of this paper introduces the common characteristics of a nonlinear network (the network may be linear, the objective function may be non linear, or both may be nonlinear). The second part develops a mathematical model trying to put together some important constraints based on the abstraction for a general network. The third part deals with solution procedures; it converts the network to a matrix based system of equations, gives the characteristics of the matrix and suggests two solution procedures, one of them being a new one. The fourth part handles spatially distributed networks and evolves a number of decomposition techniques so that we can solve the problem with the help of a distributed computer system. Algorithms for parallel processors and spatially distributed systems have been described.There are a number of common features that pertain to networks. A network consists of a set of nodes and arcs. In addition at every node, there is a possibility of an input (like power, water, message, goods etc) or an output or none. Normally, the network equations describe the flows amoungst nodes through the arcs. These network equations couple variables associated with nodes. Invariably, variables pertaining to arcs are constants; the result required will be flows through the arcs. To solve the normal base problem, we are given input flows at nodes, output flows at nodes and certain physical constraints on other variables at nodes and we should find out the flows through the network (variables at nodes will be referred to as across variables).The optimization problem involves in selecting inputs at nodes so as to optimise an objective function; the objective may be a cost function based on the inputs to be minimised or a loss function or an efficiency function. The above mathematical model can be solved using Lagrange Multiplier technique since the equalities are strong compared to inequalities. The Lagrange multiplier technique divides the solution procedure into two stages per iteration. Stage one calculates the problem variables % and stage two the multipliers lambda. It is shown that the Jacobian matrix used in stage one (for solving a nonlinear system of necessary conditions) occurs in the stage two also.A second solution procedure has also been imbedded into the first one. This is called total residue approach. It changes the equality constraints so that we can get faster convergence of the iterations.Both solution procedures are found to coverge in 3 to 7 iterations for a sample network.The availability of distributed computer systems — both LAN and WAN — suggest the need for algorithms to solve the optimization problems. Two types of algorithms have been proposed — one based on the physics of the network and the other on the property of the Jacobian matrix. Three algorithms have been deviced, one of them for the local area case. These algorithms are called as regional distributed algorithm, hierarchical regional distributed algorithm (both using the physics properties of the network), and locally distributed algorithm (a multiprocessor based approach with a local area network configuration). The approach used was to define an algorithm that is faster and uses minimum communications. These algorithms are found to converge at the same rate as the non distributed (unitary) case.

Structure-Reactivity Correlations of Benzoin Alkyl Ethers. Structures of 2-Methoxy-1,2-diphenylethanone (I) and 2-Isopropoxy-1,2-diphenylethanone (II)

(I): C15H1402, Mr---226.27, triclinic, Pi,a=8.441 (2), b= 10.276 (1), c= 15.342 (2)A, a=91.02 (2), ~ t= 79.26 (2), y= 105.88 (2) °, V=1256.8 (4)A 3, Z=4, D,,= 1.209 (flotation in KI),D x - 1.195 g cm -3, #(Mo, 2 = 0.7107/~) = 0.44 cm -~,F(000) = 480, T= 293 K, R -- 0.060 for 1793 significant reflections. (II): C~THlsO2, Mr= 254.83, orthorhombic, Pca21, a=8.476 (1); b= 16.098 (3), c=10.802(3)A, V=1473.9 (5) A s, Z=4, Dm=1.161 (flotation in KI), Dx= 1.148gem -3, /~(Mo, 2=0.7107 A) =0.41 cm -~, F(000) = 544, T= 293 K, R = 0.071 for 867 significant reflections. Both (I) and (II) crystallize in a cisoid conformation for the carbonyl group and alkoxy groups. Compounds (I) and (II) are photostable on irradiation in the solid state in spite of the favourable conformation of the functional groups for intramolecular H abstraction. Absence of photoreaction of (I)and (II) in the solid state is rationalized in the light of unfavourable intramolecular geometry.

Reactivity studies of highly electrophilic ruthenium complexes

The 16-electron, coordinatively unsaturated, dicationic ruthenium complex Ru(P(OH)(2)(OMe))(dppe)(2)]OTf](2) (1a) brings about the heterolysis of the C-H bond in phenylacetylene to afford the phenylacetylide complex trans-Ru(C CPh)(P(OH)(2)(OMe))(dppe)(2)]OTf] (2). The phenylacetylide complex undergoes hydrogenation to give a ruthenium hydride complex trans-Ru(H)(P(OH)(2)(OMe))(dppe)(2)]OTf] (3) and phenylacetylene via the addition of H-2 across the Ru-C bond. The 16-electron complex also reacts with HSiCl3 quite vigorously to yield a chloride complex trans-Ru(Cl)(P(OH)(2)(OMe))(dppe)(2)]OTf] (4). On the other hand, the other coordinatively unsaturated ruthenium complex Ru(P(OH)(3))(dppe)(2)]OTf](2) (1b) reacts with a base N-benzylideneaniline to afford a phosphonate complex Ru(P(O)(OH)(2))(dppe)(2)]OTf] (5) via the abstraction of one of the protons of the P(OH)(3) ligand by the base. The phenylacetylide, chloride, and the phosphonate complexes have been structurally characterized. The phosphonate complex reacts with H-2 to afford the corresponding dihydrogen complex trans-Ru(eta(2)-H-2)(P(O)(OH)(2))(dppe)(2)]OTf] (5-H2). The intact nature of the H-H bond in this species was established using variable temperature H-1 spin-lattice relaxation time measurements and the observation of a significant J(H,D) coupling in the HD isotopomer trans-Ru(eta(2)-HD)(P(O)(OH)(2))(dppe)(2)]OTf] (5-HD). (C) 2010 Elsevier B. V. All rights reserved.

Disulfide Bond Assignments by Mass Spectrometry of Native Natural Peptides: Cysteine Pairing in Disulfide Bonded Conotoxins

The critical, and often most difficult, step in structure elucidation of diverse classes of natural peptides is the determination of correct disulfide pairing between multiple cysteine residues. Here, we present a direct mass spectrometric analytical methodology for the determination of disulfide pairing. Protonated peptides, having multiple disulfide bonds, fragmented under collision induced dissociation (CID) conditions and preferentially cleave along the peptide backbone, with occasional disulfide fragmentation either by C-beta-S bond cleavage through H-alpha abstraction to yield dehydroalanine and cysteinepersulfide, or by S-S bond cleavage through H-beta abstraction to yield the thioaldehyde and cysteine. Further fragmentation of the initial set of product ions (MSn) yields third and fourth generation fragment ions, permitting a distinction between the various possible disulfide bonded structures. This approach is illustrated by establishing cysteine pairing patterns in five conotoxins containing two disulfide bonds. The methodology is extended to the Conus araneosus peptides An 446 and Ar1430, two 14 residue sequences containing 3 disulfide bonds. A distinction between 15 possible disulfide pairing schemes becomes possible using direct mass spectral fragmentation of the native peptides together with fragmentation of enzymatically nicked peptides.

Structure and thermal stability relationships in ring-substituted arylammonium nitrates

The thermal stability of ring-substituted arylammonium nitrates has been investigated using thermal methods of analysis. The decomposition temperature of meta- and para-substituted derivatives is found to be linearly related to the Hammett substituent constant σ. The activation energy for decomposition determined by isothermal gravimetry increases with the increasing basicity of the corresponding amine. The results suggest that the primary step in the decomposition process of these salts is proton abstraction by the anion from the arylammonium ion.

A methodology for supporting ``transfer'' in biomimetic design

Biomimetics involves transfer from one or more biological examples to a technical system. This study addresses four questions. What are the essential steps in a biomimetic process? What is transferred? How can the transferred knowledge be structured in a way useful for biologists and engineers? Which guidelines can be given to support transfer in biomimetic design processes? In order to identify the essential steps involved in carrying out biomimetics, several procedures found in the literature were summarized, and four essential steps that are common across these procedures were identified. For identification of mechanisms for transfer, 20 biomimetic examples were collected and modeled according to a model. of causality called the SAPPhIRE model. These examples were then analyzed for identifying the underlying similarity between each biological and corresponding analogue technical system. Based on the SAPPhIRE model, four levels of abstraction at which transfer takes place were identified. Taking into account similarity, the biomimetic examples were assigned to the appropriate levels of abstraction of transfer. Based on the essential steps and the levels of transfer, guidelines for supporting transfer in biomimetic design were proposed and evaluated using design experiments. The 20 biological and analogue technical systems that were analyzed were similar in the physical effects used and at the most abstract levels of description of their functionality, but they were the least similar at the lowest levels of abstraction: the parts involved. Transfer most often was carried out at the physical effect level of abstraction. Compared to a generic set of guidelines based on the literature, the proposed guidelines improved design performance by about 60%. Further, the SAPPhIRE model turned out to be a useful representation for modeling complex biological systems and their functionality. Databases of biological systems, which are structured using the SAPPhIRE model, have the potential to aid biomimetic concept generation.

Photochromism of alkylisophthalaldehydes in the solid state: structure–reactivity correlations

The crystal and molecular structures of the photochromic compounds 2,5-dimethylisophthalaldehyde (I) and 5-isopropyl-2-methylisophthalaldehyde (II) have been determined by single crystal X-ray analyses. The intramolecular gamma-hydrogen abstraction process involved in the photoenolisation of I and II in the solid state has been rationalised in the light of relevant geometrical parameters.

Kinetics of sono-photooxidative degradation of poly(alkyl methacrylate)s

The mechano-chemical degradation of poly(methyl methacrylate) (PMMA), poly(ethyl methacrylate) (PEMA) and poly(n-butyl methacrylate) (PBMA) using ultrasound (US), ultraviolet (UV) radiation and a photoinitiator (benzoin) has been investigated. The degradation of the polymers was monitored using the reduction in number average molecular weight (M-n) and polydispersity (PDI). A degradation mechanism that included the decomposition of the initiator, generation of polymer radicals by the hydrogen abstraction of initiator radicals, reversible chain transfer between stable polymer and polymer radicals was proposed. The mechanism assumed mid-point chain scission due to US and random scission due to UV radiation. A series of experiments with different initial M-n of the polymers were performed and the results indicated that, irrespective of the initial PDI, the PDI during the sono-photooxidative degradation evolved to a steady state value of 1.6 +/- 0.05 for all the polymers. This steady state evolution of PDI was successfully predicted by the continuous distribution kinetics model. The rate coefficients of polymer scission due to US and UV exhibited a linear increase and decrease with the size of the alkyl group of the poly(alkyl methacrylate)s, respectively. (C) 2010 Elsevier B.V. All rights reserved.