Prediction of the antigenic sites of the cystic fibrosis transmembrane conductance regulator protein by molecular modelling

Antibodies are powerful tools for studying the in situ localizationand physiology of proteins. The prediction of epitopes by molecularmodelling has been used successfully for the papilloma virus,and valuable antibodies have been raised [Muller et aL (1990)J. Gen. Virol, 71, 2709–2717]. We have improved the modellingapproach to allow us to predict epitopes from the primary sequencesof the cystic fibrosis transmembrane conductance regulator.The procedure involves searching for fragments of primary sequenceslikely to make amphipathic secondary structures, which are hydrophilicenough to be at the surface of the folded protein and thus accessibleto antibodies. Amphipathic helices were predicted using themethods of Berzofsky, Eisenberg and Jahnig. Their hydrophobichydrophilicinterface was calculated and drawn, and used to predict theorientation of the helices at the surface of the native protein.Amino acids involved in turns were selected using the algorithmof Eisenberg. Tertiary structures were calculated using ‘FOLDING’,a software developed by R.Brasseur for the prediction of smallprotein structures [Brasseur (1995) J. MoL Graphics, in press].We selected sequences that folded as turns with at least fiveprotruding polar residues. One important property of antibodiesis selectivity. To optimize the selectivity of the raised antibodies,each sequence was screened for similarity (FASTA) to the proteinsequences from several databanks. Ubiquitous sequences werediscarded. This approach led to the identification of 13 potentialepitopes in the cystic fibrosis transmembrane conductance regulator:seven helices and six loops.     

Different strategies to recover the activity of monomeric triosephosphate isomerase by directed evolution

A monomeric version of triosephosphate isomerase from Trypanosomabrucei, MonoTIM, has very low activity, and the same is truefor all of the additional monomeric variants so far constructed.Here, we subjected MonoTIM to directed evolution schemes toachieve an activity improvement. The construction of a suitablestrain for genetic selection provided an effective way to obtainactive catalysts from a diverse population of protein variants.We used this tool to identify active mutants from two differentstrategies of mutagenesis: random mutagenesis of the whole geneand randomization of loop 2. Both strategies converged in theisolation of mutations Ala43 to Pro and Thr44 to either Alaor Ser, when randomizing the entire gene or to Arg in the caseof randomization of loop 2. The kinetic characterization ofthe two more active mutants showed an increase of 11-fold ink_cat and a reduction of 4-fold in K_m for both of them, demonstratingthe sensitivity of the selection method. A small differencein growth rate is observed when both mutant genes are compared,which seems to be attributable to a difference in solubilityof the expressed proteins.     

Effects of nematic coupling on the phase behaviour of nematogen mixtures

The phase behaviour of binary nematogen mixtures of side‐chain liquid crystal crosslinked polymers and low molecular weight liquid crystals is investigated with particular emphasis on the effects of nematic coupling. The cross nematic quadrupole parameter ν₁₂ is assumed to be proportional to the geometric average of ν₁₁ and ν₂₂ characteristic of single nematogens. In the weak coupling limit, the proportionality constant is lower than 1, and the phase diagram exhibits a reduced miscibility of the nematogens. In the case of strong coupling, the proportionality constant exceeds 1 resulting in higher miscibility. This is characterized by a nematic order that extends to temperatures above the upper nematic–isotropic transition temperature. A wide region of miscibility emerges showing a single nematic phase. Nematogens having similar nematic–isotropic transition temperatures exhibit different phase properties from systems with widely separated transition temperatures. Effects of the polymer volume fraction at crosslinking, rubber elasticity parameters of the network, and the Flory–Huggins interaction parameter on the equilibrium phase diagram of these systems are discussed. © 2001 Society of Chemical Industry     

Subroutines for some plasma surface interaction processes: physical sputtering, chemical erosion, radiation enhanced sublimation, backscattering and thermal evaporation

A suite of FORTRAN subroutines/functions to generate data using empirical formulas for physical sputtering of mono-atomic targets for any elemental incident ion (atom), chemical erosion of graphite, Radiation Enhanced Sublimation (RES) of graphite, the number and energy backscattering coefficients for any elemental incident ion (atom) on a compound target and thermal evaporation of graphite is presented. Since chemical erosion, RES and thermal evaporation depend on the surface temperature of graphite, a subroutine implementing the 1-D heat diffusion equation to determine the temperature of any plasma-facing graphite surface is implemented. As an example to illustrate the use of these subroutines/functions, a simple model for the erosion of a plasma-facing surface, consisting of a simple collisionless sheath model, a 1-dimensional steady state heat diffusion model and 0-dimensional steady state particle balance at the target is developed and a sample listing of the program is presented.

Program summary

Title of program: Plasma Surface Interaction Codes (PSIC)Catalog identifier: ADTRProgram summary URL:http://cpc.cs.qub.ac.uk/summaries/ADTRProgram obtainable from: CPC Program Library, Queen's University of Belfast, N. IrelandComputers for which the program has been designed for and others on which it has been tested: Program is designed for any computer with a FORTRAN-77 compiler. It has been tested on a Linux PC with g77, Absoft f77, f90, f95, Fujitsu f95, Lahey f95Operating systems under which the program has been tested: Linux, UNIXProgramming language used: FORTRAN-77Memory required to execute with typical data: Negligible (executable is 178 861 bytes; add to it the memory used by the Fortran library linked to)No. of bits in a word: 16No. of processors used: 1Has the code been vectorized or parallelized?: NoNo. of bytes in distributed program, including test data, etc.: 11 619No. of lines in distributed program, including test data, etc.: 1015Distribution format: tar gzip fileNature of physical problems: 0-D plasma surface interaction model used to demonstrate calls to subroutines for physical sputtering yield, chemical erosion yield of graphite, RES of graphite, backscattering coefficients, thermal evaporation of graphite and 1-D heat diffusion in graphite.Method of solution: Semi-empirical formulas are used for the PSIs and analytical formulas are used for thermal evaporation and 1-D heat diffusion in graphite.Restrictions on the complexity of the problem: All the PSIs (except for the backscattering coefficients) are valid only for a monoatomic target. The heat diffusion solution is not valid for non-uniform plasmas and for targets for which the heat diffusion is not isotropic.Typical running time: Example program takes much less than 0.01 secondUniversal features of the program: None     

Competing topological phases in few-layer graphene

We investigate the effect of spin-orbit coupling on the band structure of graphene-based two-dimensional Dirac fermion gases in the quantum Hall regime. Taking monolayer graphene as our first candidate, we show that a quantum phase transition between two distinct topological states—the quantum Hall and the quantum spin Hall phases—can be driven by simply tuning the Fermi level with a gate voltage. This transition is characterized by the existence of a chiral spin-polarized edge state propagating along the interface separating the two topological phases. We then apply our analysis to the more difficult case of bilayer graphene. Unlike in monolayer graphene, spin-orbit coupling by itself has indeed been predicted to be unsuccessful in driving bilayer graphene into a topological phase, due to the existence of an even number of pairs of spin-polarized edge states. While we show that this remains the case in the quantum Hall regime, we point out that by additionally breaking the layer inversion symmetry, a non-trivial quantum spin Hall phase can re-emerge in bilayer graphene at low energy. We consider two different symmetry-breaking mechanisms: inducing spin-orbit coupling only in the upper layer, and applying a perpendicular electric field. In both cases, the presence at low energy of an odd number of pairs of edge states can be driven by an exchange field. The related situation in trilayer graphene is also discussed.     

Disruption of Vector Host Preference with Plant Volatiles May Reduce Spread of Insect-Transmitted Plant Pathogens

Plant pathogens can manipulate the odor of their host; the odor of an infected plant is often attractive to the plant pathogen vector. It has been suggested that this odor-mediated manipulation attracts vectors and may contribute to spread of disease; however, this requires further broad demonstration among vector-pathogen systems. In addition, disruption of this indirect chemical communication between the pathogen and the vector has not been attempted. We present a model that demonstrates how a phytophathogen (Candidatus Liberibacter asiaticus) can increase its spread by indirectly manipulating the behavior of its vector (Asian citrus psyllid, Diaphorina citri Kuwayama). The model indicates that when vectors are attracted to pathogen-infected hosts, the proportion of infected vectors increases, as well as, the proportion of infected hosts. Additionally, the peak of infected host populations occurs earlier as compared with controls. These changes in disease dynamics were more important during scenarios with higher vector mortality. Subsequently, we conducted a series of experiments to disrupt the behavior of the Asian citrus psyllid. To do so, we exposed the vector to methyl salicylate, the major compound released following host infection with the pathogen. We observed that during exposure or after pre-exposure to methyl salicylate, the host preference can be altered; indeed, the Asian citrus psyllids were unable to select infected hosts over uninfected counterparts. We suggest mechanisms to explain these interactions and potential applications of disrupting herbivore host preference with plant volatiles for sustainable management of insect vectors.     

Heck–Matsuda Arylation of Olefins Through a Bicatalytic Approach: Improved Procedures and Rationalization

The scope of the palladium‐catalyzed Heck–Matsuda reaction, proceeding through the catalytic activation of anilines into the corresponding diazonium salts, has been considerably extended and is now working with deactivated electrophiles. Two different procedures, using catalytic amounts of both palladium and acid, have been optimized allowing the concept of bicatalysis to cover the complete electronic range of anilines. These environmentally friendly procedures proceed under very mild conditions, at room temperature in methanol, and only generate tert‐butyl alcohol, water and nitrogen as by‐products. Rationalization of reaction outcomes encountered in this work has been discussed with the support of computational studies.