Effects of post-translational modifications catalysed by pollen transglutaminase on the functional properties of microtubules and actin filaments

TGases (transglutaminases) are a class of calcium-dependent enzymes that catalyse the interactions between acyl acceptor glutamyl residues and amine donors, potentially making crosslinks between proteins. To assess the activity of apple (Malus domestica) pollen TGase on the functional properties of actin and tubulin, TGase was prepared from apple pollen by hydrophobic interaction chromatography and assayed on actin and tubulin purified from the same cell type. The enzyme catalysed the incorporation of putrescine in the cytoskeleton monomers. When tested on actin filaments, pollen TGase induced the formation of high-molecular-mass aggregates of actin. Use of fluorescein– cadaverine showed that the labelled polyamine was incorporated into actin by pollen TGase, similar to with guinea pig liver TGase. The pollen TGase also reduced the enzyme activity and the binding of myosin to TGase-treated actin filaments. Polymerization of tubulin in the presence of pollen TGase also yielded the formation of high molecular mass aggregates. Furthermore, the pollen TGase also affected the binding of kinesin to microtubules and reduced the motility of microtubules along kinesincoated slides. These results indicate that the pollen tube TGase can control different properties of the pollen tube cytoskeleton (including the ability of actin and tubulin to assemble and their interaction with motor proteins) and consequently regulate the development of pollen tubes

Empathes: A general code for nudged elastic band transition states search

An easy and flexible interface, Empathes (Extensible Minimum PATH EStimator), that allows to perform Nudged Elastic Band calculation for the determination of transition states is presented. The code is designed to be easily modified, in order to be associated with the user's preferred calculation software, even with those which implement composite approaches. In particular, the interfaces to Gaussian and Siesta programs are discussed in details, being the former only used for testing purpose, while the latter can be productively employed for transition states search with that commonly used density functional theory software for periodic calculations. Program summary: Program Title: Empathes CPC Library link to program files: https://doi.org/10.17632/v525mwf3cc.1 Developer's repository link: https://github.com/marberti/empathes Code Ocean capsule: https://codeocean.com/capsule/2394233 Licensing provisions: GPLv3 Programming language: Fortran 08 Nature of problem: The search for the structure of transition states through computational methods, essentially based on Density Functional Theory, is of overwhelming importance for the determination of the elementary steps forming a reaction mechanism. Allowing to develop basic knowledge, these investigations can be used to direct experimentalists towards a more efficient realization of chemical compounds synthetic processes. In cases where it is necessary to describe the reactive system through periodic calculations, which is very common in heterogeneous catalysis, this research must be done through the use of non-analytical methods. Solution method: In case of lacking of analytical procedures, the search for the transition states associated with the elementary stages that make up chemical reactions must take place through numerical methods. The Nudged Elastic Band (NEB) approach is, together with its variants, one of the most used for this purpose. In accordance with the NEB algorithm, a chain of geometric structures, generated by interpolating between the reactant and product geometries and joined by fictitious springs, is relaxed on the minimum energy path, allowing the association of the transition state to the maximum along this path. The NEB method involves the determination of molecular energies and forces acting on the nuclei of the system, which is generally carried out through a program for electronic structure calculation. The present code is a useful general interface

Kinematical Limits on Higgs Boson Production via Gluon Fusion in Association with Jets

In this paper, we analyze the high-energy limits for Higgs boson plus two jet production. We consider two high-energy limits, corresponding to two different kinematic regions: a) the Higgs boson is centrally located in rapidity between the two jets, and very far from either jet; b) the Higgs boson is close to one jet in rapidity, and both of these are very far from the other jet. In both cases the amplitudes factorize into impact factors or coefficient functions connected by gluons exchanged in the t channel. Accordingly, we compute the coefficient function for the production of a Higgs boson from two off-shell gluons, and the impact factors for the production of a Higgs boson in association with a gluon or a quark jet. We include the full top quark mass dependence and compare this with the result obtained in the large top-mass limit.Comment: 35 pages, 6 figure

Coherent States in Null-Plane Q.E.D

Light front field theories are known to have the usual infra-red divergences of the equal time theories, as wellas new `spurious' infra-red divergences. The formar kind of IR divergences are usually treated by giving a small mass to the gauge particle. An alternative method to deal with these divergences is to calculate the transition matrix elements in a coherent state basis. In this paper we present, as a model calculation the lowest order correction to the three point vertex in QED using a coherent state basis in the light cone formalism. The relevant transition matrix element is shown to be free of the true IR divergences up to $O(e^2)$.Comment: 20 pages and two figures, REVTEX, ITP-SB-93-7

DFT insights into competing mechanisms of guaiacol hydrodeoxygenation on a platinum cluster

In a scenario of declining fossil resources and increasing demand for renewable and sustainable alternatives, biomass is the only source able to offer an easy and gradual transition in the use of current energy technologies based on the exploitation of carbon derivatives. Its conversion to liquid fuels has oriented our study towards the computational mechanistic analysis of the guaiacol catalytic hydrodeoxygenation, which is currently considered one of the most challenging routes for upgrading biomass-derived bio-oils. For this purpose, a subnanometric Pt10 platinum cluster was chosen as the catalyst model, with Pt as a computational reference element for catalytic hydrogenation, and guaiacol as a model compound of bio-oils. DFT calculations revealed that the energy barriers related to the cleavage of C(sp2)-O bonds in the direct deoxygenation mechanism are significantly lower (by an average of 60 kJ mol−1) than those in the deoxygenation-through-hydrogenation mechanism in which C(sp3)-O bond breaking from a saturated ring occurs. Even if the ring hydrogenation is easier in the oxygenated compound, the analysis reveals that the direct deoxygenation mechanism is favoured at all temperatures. Furthermore, the results obtained highlight that, from a thermodynamic perspective, the removal of oxygen groups preferentially occurs by the elimination of the -OCH3 fragment as methanol and then of the -OH fragment as a water molecule

DFT Study of Pt Particle Growth inside β-Zeolite Cages

The preferred location and the corresponding energetics of zeolite-embedded single metal atoms and small metal particles are hot topics within active site optimization and catalyst tuning, even as part of bifunctional materials design. In this context, periodic density functional theory was used to provide insights on the interactions of a platinum atom with the microporous cages of a purely silicious β-zeolite (BEA) framework. Cluster growth was subsequently addressed, up to Pt3@BEA systems, following a one-by-one platinum atom addition; platinum migration between cages was taken into account as well. An unbiased approach was employed, which allowed a wide panorama of structures being considered in addition to a thorough analysis in terms of energetics, cluster geometries, and cavity distortions. Calculations revealed that the optimal interaction geometry for a single platinum atom is realized where two strong Pt-O bonds in almost linear arrangement can form, regardless of the cavity involved. This can cause distortions or even breaking of the zeolite structure, a factor which however is not decisive in determining the energetics of systems with two and three platinum atoms. Platinum migration is associated with energy barriers ranging from 100 to 200 kJ mol-1, depending on the cages. Up to the dimensions considered here, preference for clustering is observed, being the embedded Pt3 systems in almost all cases energetically favored with respect to isolated atoms within the BEA framework

DFT study on zeolites’ intrinsic Brønsted acidity: The case of BEA

Since Brønsted acidity is a crucial aspect for the applications of zeolitic materials in heterogeneous catalysis, great effort was devolved to characterize the number, strength and location of the potentially active acidic sites. Quantum chemical calculations can turn out essential in estimating the intrinsic acidity by computing deprotonation energy (DPE) values, although each method comes with its own difficulties. In this context, three approaches within density functional theory were employed to study the intrinsic acidity of 30 topologically distinct Brønsted sites in the β-zeolite framework. Advantages and disadvantages of the three methods were outlined and the acidity order between the sites was assessed, being the DPE range 59 kJ mol−1 wide, with the proposed best approach. By dividing the range into three portions, the sites were classified as having high, medium and low acidity. Hydrogen bonds formation was found to be a contributing factor in determining a low Brønsted acidity

Higgs boson production with one bottom quark jet at hadron colliders

We present total rates and kinematic distributions for the associated production of a single bottom quark and a Higgs boson at the Tevatron and the LHC. We include next-to-leading order QCD corrections and compare the results obtained in the four and five flavor number schemes for parton distribution functions.Comment: 4 pages, 8 figures, RevTeX

Hopf algebras, coproducts and symbols: an application to Higgs boson amplitudes

We show how the Hopf algebra structure of multiple polylogarithms can be used to simplify complicated expressions for multi-loop amplitudes in perturbative quantum field theory and we argue that, unlike the recently popularized symbol-based approach, the coproduct incorporates information about the zeta values. We illustrate our approach by rewriting the two-loop helicity amplitudes for a Higgs boson plus three gluons in a simplified and compact form involving only classical polylogarithms.Comment: 46 page

The role of gene elongation in the evolution of histidine biosynthetic genes

Gene elongation is a molecular mechanism consisting of an in-tandem duplication of a gene and divergence and fusion of the two copies, resulting in a gene constituted by two divergent paralogous modules. The aim of this work was to evaluate the importance of gene elongation in the evolution of histidine biosynthetic genes and to propose a possible evolutionary model for some of them. Concerning the genes hisA and hisF, which code for two homologous (β/α)8-barrels, it has been proposed that the two extant genes could be the result of a cascade of gene elongation/domain shuffling events starting from an ancestor gene coding for just one (β/α) module. A gene elongation event has also been proposed for the evolution of hisB and hisD; structural analyses revealed the possibility of an early elongation event, resulting in the repetition of modules. Furthermore, it is quite possible that the gene elongations responsible for the evolution of the four proteins occurred before the earliest phylogenetic divergence. In conclusion, gene elongation events seem to have played a crucial role in the evolution of the histidine biosynthetic pathway, and they may have shaped the structures of many genes during the first steps of their evolution