Histidine hydrogen bonding in MHC at pH 5 and pH 7 modeled by molecular docking and molecular dynamics simulations

Hydrogen bonds play important roles in maintaining the structure of proteins and in the formation of most biomolecular protein-ligand complexes. All amino acids can act as hydrogen bond donors and acceptors. Among amino acids, Histidine is unique, as it can exist in neutral or positively charged forms within the physiological pH range of 5.0 to 7.0. Histidine can thus interact with other aromatic residues as well as forming hydrogen bonds with polar and charged residues. The ability of His to exchange a proton lies at the heart of many important functional biomolecular interactions, including immunological ones. By using molecular docking and molecular dynamics simulation, we examine the influence of His protonation/deprotonation on peptide binding affinity to MHC class II proteins from locus HLA-DP. Peptide-MHC interaction underlies the adaptive cellular immune response, upon which the next generation of commercially-important vaccines will depend. Consistent with experiment, we find that peptides containing protonated His residues bind better to HLA-DP proteins than those with unprotonated His. Enhanced binding at pH 5.0 is due, in part, to additional hydrogen bonds formed between peptide His+ and DP proteins. In acidic endosomes, protein His79β is predominantly protonated. As a result, the peptide binding cleft narrows in the vicinity of His79β, which stabilizes the peptide - HLA-DP protein complex. © 2014 Bentham Science Publishers.

Computer control of chemical process plants with special reference to distillation

A sieve plate distillation column has been constructed and interfaced to a minicomputer with the necessary instrumentation for dynamic, estimation and control studies with special bearing on low-cost and noise-free instrumentation. A dynamic simulation of the column with a binary liquid system has been compiled using deterministic models that include fluid dynamics via Brambilla's equation for tray liquid holdup calculations. The simulation predictions have been tested experimentally under steady-state and transient conditions. The simulator's predictions of the tray temperatures have shown reasonably close agreement with the measured values under steady-state conditions and in the face of a step change in the feed rate. A method of extending linear filtering theory to highly nonlinear systems with very nonlinear measurement functional relationships has been proposed and tested by simulation on binary distillation. The simulation results have proved that the proposed methodology can overcome the typical instability problems associated with the Kalman filters. Three extended Kalman filters have been formulated and tested by simulation. The filters have been used to refine a much simplified model sequentially and to estimate parameters such as the unmeasured feed composition using information from the column simulation. It is first assumed that corrupted tray composition measurements are made available to the filter and then corrupted tray temperature measurements are accessed instead. The simulation results have demonstrated the powerful capability of the Kalman filters to overcome the typical hardware problems associated with the operation of on-line analyzers in relation to distillation dynamics and control by, in effect, replacirig them. A method of implementing estimator-aided feedforward (EAFF) control schemes has been proposed and tested by simulation on binary distillation. The results have shown that the EAFF scheme provides much better control and energy conservation than the conventional feedback temperature control in the face of a sustained step change in the feed rate or multiple changes in the feed rate, composition and temperature. Further extensions of this work are recommended as regards simulation, estimation and EAFF control.

A systematic approach to establish fundamental principles of computer applications packages design

This work attempts to create a systemic design framework for man-machine interfaces which is self consistent, compatible with other concepts, and applicable to real situations. This is tackled by examining the current architecture of computer applications packages. The treatment in the main is philosophical and theoretical and analyses the origins, assumptions and current practice of the design of applications packages. It proposes that the present form of packages is fundamentally contradictory to the notion of packaging itself. This is because as an indivisible ready-to-implement solution, current package architecture displays the following major disadvantages. First, it creates problems as a result of user-package interactions, in which the designer tries to mould all potential individual users, no matter how diverse they are, into one model. This is worsened by the minute provision, if any, of important properties such as flexibility, independence and impartiality. Second, it displays rigid structure that reduces the variety and/or multi-use of the component parts of such a package. Third, it dictates specific hardware and software configurations which probably results in reducing the number of degrees of freedom of its user. Fourth, it increases the dependence of its user upon its supplier through inadequate documentation and understanding of the package. Fifth, it tends to cause a degeneration of the expertise of design of the data processing practitioners. In view of this understanding an alternative methodological design framework which is both consistent with systems approach and the role of a package in its likely context is proposed. The proposition is based upon an extension of the identified concept of the hierarchy of holons* which facilitates the examination of the complex relationships of a package with its two principal environments. First, the user characteristics and his decision making practice and procedures; implying an examination of the user's M.I.S. network. Second, the software environment and its influence upon a package regarding support, control and operation of the package. The framework is built gradually as discussion advances around the central theme of a compatible M.I.S., software and model design. This leads to the formation of the alternative package architecture that is based upon the design of a number of independent, self-contained small parts. Such is believed to constitute the nucleus around which not only packages can be more effectively designed, but is also applicable to many man-machine systems design.

Niederdeutsch im Internet. Möglichkeiten und Grenzen computervermittelter Kommunikation für den Spracherhalt:possibilities and limitations of computer-mediated communication for language preservation

Der vorliegende Beitrag untersucht die Frage, in welchem Maße sich Institutionen, die niederdeutsche Kulturszene und individuelle Sprecher des Niederdeutschen moderne Kommunikationstechnologien wie das Internet zunutze machen und ob computervermittelte Kommunikation helfen kann, dem Rückgang des Niederdeutschen Einhalt zu gebieten. Die grundsätzliche Herangehensweise ist eine soziolinguistische, die das Internet als sozialen Handlungsraum versteht, in dem Individuen und Institutionen kommunizieren. Für eine derartige Perspektive stehen weniger das Medium oder das Genre im Mittelpunkt des Interesses als vielmehr das kommunizierende Individuum und die Sprachgemeinschaft, in diesem Fall die virtuelle Sprachgemeinschaft. Based on studies that analyse the potential of computer-mediated communication (cmc) to help fight language shift in lesser-used languages, this paper discusses the situation of Low German in Northern Germany. Over the last three decades, Low German has lost more than half of its active speakers. The article raises the question of whether and, if so, how Low German speakers make use of cmc to stem this tide. Following a sociolinguistic approach focussed on the individual speakers who use the Internet as a space for social interaction, it gives an overview of the discursive field of Low German on the internet and analyses in detail the most popular Low German discussion board. It shows that one of the main obstacles to a more successful use of cmc can be found in speakers' complex attitude toward written Low German. © Franz Steiner Verlag Stuttgart.