Family resemblances? Ligand binding and activation of family A and B G-protein-coupled receptors

In April 2007, the Biochemical Society held a meeting to compare and contrast ligand binding and activation of Family A and B GPCRs (G-protein-coupled receptors). Being the largest class, Family A GPCRs usually receive the most attention, although a previous Biochemical Society meeting has focused on Family B GPCRs. The aim of the present meeting was to bring researchers of both families together in order to identify commonalities between the two. The present article introduces the proceedings of the meeting, briefly commenting on the focus of each of the following articles. ©The Authors.

A key role for transmembrane prolines in calcitonin receptor-like receptor agonist binding and signalling:implications for family B G-protein-coupled receptors

Calcitonin receptor like-receptor is a family B G-protein coupled receptor (GPCR). It requires receptor activity modifying protein (RAMP) 1 to give a calcitonin gene-related peptide (CGRP) receptor. Little is known of how members of this receptor family function. Proline residues often form important kinks in alpha-helices. Therefore, all proline residues within the transmembrane helices of the receptor (Pro241, Pro244 in helix 4, Pro275 in helix 5, Pro321 and Pro331 in helix 6) were mutated to alanine. Pro241 Pro275, and Pro321 are highly conserved throughout all family B GPCRs. The binding of CGRP and its ability to stimulate cAMP production were investigated in mutant and wild-type receptors after transient transfection into COS-7 cells with RAMP1. The P321A mutation significantly decreased the pEC(50) for CGRP and reduced its affinity but did not change cell-surface expression. Antagonist binding [CGRP(8-37) and 1-piperidinecarboxamide N-[2-[[5amino-1-[[4-(4-pyridinyl)-1-piperazinyl]carbonyl]pentyl]amino]-1-[(3 5-dibromo-4-hydroxyphenyl)methyl]-2-oxoethyl]-4-(1,4-dihydro-2-oxo-3(2H)-quina zolinyl) (BIBN4096BS)] was little altered by the mutation. Adrenomedullin-mediated signaling was disrupted when P321A was coexpressed with RAMP1, RAMP2, or RAMP3. The P331A mutant produced a moderate reduction in CGRP binding and receptor activation. Mutation of the other residues had no effect on receptor function. Thus, Pro321 and Pro331 are required for agonist binding and receptor activation. Modeling suggested that Pro321 induces a bend in helix 6, bringing its C terminus near that of helix 3, as seen in many family A GPCRs. This is abolished in P321A. P321A-I325P predicted to restore this conformation, showed wild-type activation. Modeling can also rationalize the effects of transmembrane proline mutants previously reported for another family B GPCR, the VPAC(1) receptor.

Quantitative risk assessment of groundwater quality utilizing GIS technology and coupled groundwater models

The thesis presents a two-dimensional Risk Assessment Method (RAM) where the assessment of risk to the groundwater resources incorporates both the quantification of the probability of the occurrence of contaminant source terms, as well as the assessment of the resultant impacts. The approach emphasizes the need for a greater dependency on the potential pollution sources, rather than the traditional approach where assessment is based mainly on the intrinsic geo-hydrologic parameters. The risk is calculated using Monte Carlo simulation methods whereby random pollution events were generated to the same distribution as historically occurring events or a priori potential probability distribution. Integrated mathematical models then simulate contaminant concentrations at the predefined monitoring points within the aquifer. The spatial and temporal distributions of the concentrations were calculated from repeated realisations, and the number of times when a user defined concentration magnitude was exceeded is quantified as a risk. The method was setup by integrating MODFLOW-2000, MT3DMS and a FORTRAN coded risk model, and automated, using a DOS batch processing file. GIS software was employed in producing the input files and for the presentation of the results. The functionalities of the method, as well as its sensitivities to the model grid sizes, contaminant loading rates, length of stress periods, and the historical frequencies of occurrence of pollution events were evaluated using hypothetical scenarios and a case study. Chloride-related pollution sources were compiled and used as indicative potential contaminant sources for the case study. At any active model cell, if a random generated number is less than the probability of pollution occurrence, then the risk model will generate synthetic contaminant source term as an input into the transport model. The results of the applications of the method are presented in the form of tables, graphs and spatial maps. Varying the model grid sizes indicates no significant effects on the simulated groundwater head. The simulated frequency of daily occurrence of pollution incidents is also independent of the model dimensions. However, the simulated total contaminant mass generated within the aquifer, and the associated volumetric numerical error appear to increase with the increasing grid sizes. Also, the migration of contaminant plume advances faster with the coarse grid sizes as compared to the finer grid sizes. The number of daily contaminant source terms generated and consequently the total mass of contaminant within the aquifer increases in a non linear proportion to the increasing frequency of occurrence of pollution events. The risk of pollution from a number of sources all occurring by chance together was evaluated, and quantitatively presented as risk maps. This capability to combine the risk to a groundwater feature from numerous potential sources of pollution proved to be a great asset to the method, and a large benefit over the contemporary risk and vulnerability methods.

RAMPs and the modulation of G-protein coupled receptors

Receptor activity modifying proteins (RAMPs) are a family of three proteins that can interact with G-protein coupled receptors (GPCRs) to create new receptors and also alter the signalling and trafficing of existing receptors. There are frequently changes in RAMP expression in cardiovascular disease RAMPs represent important drug targets.

Surface:plasma interactions in GaAs subjected to capacitively coupled RF plasmas

Surface compositional changes in GaAs due to RF plasmas of different gases have been investigated by XPS and etch rates were measured using AFM. Angular Resolved XPS (ARXPS) was also employed for depth analysis of the composition of the surface layers. An important role in this study was determination of oxide thickness using XPS data. The study of surface - plasma interaction was undertaken by correlating results of surface analysis with plasma diagnosis. Different experiments were designed to accurately measure the BEs associated with the Ga 3d, Ga 2P3/2 and LMM peaks using XPS analysis and propose identification in terms of the oxides of GaAs. Along with GaAs wafers, some reference compounds such as metallic Ga and Ga2O3 powder were used. A separate study aiming the identification of the GaAs surface oxides formed on the GaAs surface during and after plasma processing was undertaken. Surface compositional changes after plasma treatment, prior to surface analysis are considered, with particular reference to the oxides formed in the air on the activated surface. Samples exposed to ambient air for different periods of time and also to pure oxygen were analysed. Models of surface processes were proposed for explanation of the stoichiometry changes observed with the inert and reactive plasmas used. In order to help with the understanding of the mechanisms responsible for surface effects during plasma treatment, computer simulation using SRIM code was also undertaken. Based on simulation and experimental results, models of surface phenomena are proposed. Discussion of the experimental and simulated results is made in accordance with current theories and published results of different authors. The experimental errors introduced by impurities and also by data acquisition and processing are also evaluated.

Gain switching of an external cavity grating-coupled surface emitting laser with wide tunability

The gain-switched, single frequency operation of an external cavity grating-coupled surface emitting laser with a wavelength tuning range of 100 nm was presented. The light in the grating section was coupled out of the laser at a specific angle to the surface of the device. Analysis showed that within the driving current range, lasing in the device only occurred when the external cavity was properly aligned.

Multiphase modelling of the characteristics of close coupled gas atomization

Not withstanding the high demand of metal powder for automotive and High Tech applications, there are still many unclear aspects of the production process. Only recentlyhas supercomputer performance made possible numerical investigation of such phenomena. This thesis focuses on the modelling aspects of primary and secondary atomization. Initially two-dimensional analysis is carried out to investigate the influence of flow parameters (reservoir pressure and gas temperature principally) and nozzle geometry on final powder yielding. Among the different types, close coupled atomizers have the best performance in terms of cost and narrow size distribution. An isentropic contoured nozzle is introduced to minimize the gas flow losses through shock cells: the results demonstrate that it outperformed the standard converging-diverging slit nozzle. Furthermore the utilization of hot gas gave a promising outcome: the powder size distribution is narrowed and the gas consumption reduced. In the second part of the thesis, the interaction of liquid metal and high speed gas near the feeding tube exit was studied. Both axisymmetric andnon-axisymmetric geometries were simulated using a 3D approach. The filming mechanism was detected only for very small metal flow rates (typically obtained in laboratory scale atomizers). When the melt flow increased, the liquid core overtook the adverse gas flow and entered in the high speed wake directly: in this case the disruption isdriven by sinusoidal surface waves. The process is characterized by fluctuating values of liquid volumes entering the domain that are monitored only as a time average rate: it is far from industrial robustness and capability concept. The non-axisymmetric geometry promoted the splitting of the initial stream into four cores, smaller in diameter and easier to atomize. Finally a new atomization design based on the lesson learned from previous cases simulation is presented.

Present perspectives on the automated classification of the G-protein coupled receptors (GPCRs) at the protein sequence level

The G-protein coupled receptors--or GPCRs--comprise simultaneously one of the largest and one of the most multi-functional protein families known to modern-day molecular bioscience. From a drug discovery and pharmaceutical industry perspective, the GPCRs constitute one of the most commercially and economically important groups of proteins known. The GPCRs undertake numerous vital metabolic functions and interact with a hugely diverse range of small and large ligands. Many different methodologies have been developed to efficiently and accurately classify the GPCRs. These range from motif-based techniques to machine learning as well as a variety of alignment-free techniques based on the physiochemical properties of sequences. We review here the available methodologies for the classification of GPCRs. Part of this work focuses on how we have tried to build the intrinsically hierarchical nature of sequence relations, implicit within the family, into an adaptive approach to classification. Importantly, we also allude to some of the key innate problems in developing an effective approach to classifying the GPCRs: the lack of sequence similarity between the six classes that comprise the GPCR family and the low sequence similarity to other family members evinced by many newly revealed members of the family.

Collective behaviour in a square lattice of driven Duffing resonators coupled to van der Pol oscillators

The global and local synchronisation of a square lattice composed of alternating Duffing resonators and van der Pol oscillators coupled through displacement is studied. The lattice acts as a sensing device in which the input signal is characterised by an external driving force that is injected into the system through a subset of the Duffing resonators. The parameters of the system are taken from MEMS devices. The effects of the system parameters, the lattice architecture and size are discussed.

Nonlinear dynamics of a periodically driven Duffing resonator coupled to a Van der Pol oscillator

We explore the dynamics of a periodically driven Duffing resonator coupled elastically to a van der Pol oscillator in the case of 1?:?1 internal resonance in the cases of weak and strong coupling. Whilst strong coupling leads to dominating synchronization, the weak coupling case leads to a multitude of complex behaviours. A two-time scales method is used to obtain the frequency-amplitude modulation. The internal resonance leads to an antiresonance response of the Duffing resonator and a stagnant response (a small shoulder in the curve) of the van der Pol oscillator. The stability of the dynamic motions is also analyzed. The coupled system shows a hysteretic response pattern and symmetry-breaking facets. Chaotic behaviour of the coupled system is also observed and the dependence of the system dynamics on the parameters are also studied using bifurcation analysis.

The design of fault tolerant software for loosely coupled distributed systems

Requirements for systems to continue to operate satisfactorily in the presence of faults has led to the development of techniques for the construction of fault tolerant software. This thesis addresses the problem of error detection and recovery in distributed systems which consist of a set of communicating sequential processes. A method is presented for the `a priori' design of conversations for this class of distributed system. Petri nets are used to represent the state and to solve state reachability problems for concurrent systems. The dynamic behaviour of the system can be characterised by a state-change table derived from the state reachability tree. Systematic conversation generation is possible by defining a closed boundary on any branch of the state-change table. By relating the state-change table to process attributes it ensures all necessary processes are included in the conversation. The method also ensures properly nested conversations. An implementation of the conversation scheme using the concurrent language occam is proposed. The structure of the conversation is defined using the special features of occam. The proposed implementation gives a structure which is independent of the application and is independent of the number of processes involved. Finally, the integrity of inter-process communications is investigated. The basic communication primitives used in message passing systems are seen to have deficiencies when applied to systems with safety implications. Using a Petri net model a boundary for a time-out mechanism is proposed which will increase the integrity of a system which involves inter-process communications.

The relative performance of scalable load balancing algorithms in loosely-coupled distributed systems. Available in 2 volumes.

The computer systems of today are characterised by data and program control that are distributed functionally and geographically across a network. A major issue of concern in this environment is the operating system activity of resource management for different processors in the network. To ensure equity in load distribution and improved system performance, load balancing is often undertaken. The research conducted in this field so far, has been primarily concerned with a small set of algorithms operating on tightly-coupled distributed systems. More recent studies have investigated the performance of such algorithms in loosely-coupled architectures but using a small set of processors. This thesis describes a simulation model developed to study the behaviour and general performance characteristics of a range of dynamic load balancing algorithms. Further, the scalability of these algorithms are discussed and a range of regionalised load balancing algorithms developed. In particular, we examine the impact of network diameter and delay on the performance of such algorithms across a range of system workloads. The results produced seem to suggest that the performance of simple dynamic policies are scalable but lack the load stability of more complex global average algorithms.