Hierarchical Modeling of Activation Mechanisms in the ABL and EGFR Kinase Domains: Thermodynamic and Mechanistic Catalysts of Kinase Activation by Cancer Mutations

Structural and functional studies of the ABL and EGFR kinase domains have recently suggested a common mechanism of activation by cancer-causing mutations. However, dynamics and mechanistic aspects of kinase activation by cancer mutations that stimulate conformational transitions and thermodynamic stabilization of the constitutively active kinase form remain elusive. We present a large-scale computational investigation of activation mechanisms in the ABL and EGFR kinase domains by a panel of clinically important cancer mutants ABL-T315I, ABL-L387M, EGFR-T790M, and EGFR-L858R. We have also simulated the activating effect of the gatekeeper mutation on conformational dynamics and allosteric interactions in functional states of the ABL-SH2-SH3 regulatory complexes. A comprehensive analysis was conducted using a hierarchy of computational approaches that included homology modeling, molecular dynamics simulations, protein stability analysis, targeted molecular dynamics, and molecular docking. Collectively, the results of this study have revealed thermodynamic and mechanistic catalysts of kinase activation by major cancer-causing mutations in the ABL and EGFR kinase domains. By using multiple crystallographic states of ABL and EGFR, computer simulations have allowed one to map dynamics of conformational fluctuations and transitions in the normal (wild-type) and oncogenic kinase forms. A proposed multi-stage mechanistic model of activation involves a series of cooperative transitions between different conformational states, including assembly of the hydrophobic spine, the formation of the Src-like intermediate structure, and a cooperative breakage and formation of characteristic salt bridges, which signify transition to the active kinase form. We suggest that molecular mechanisms of activation by cancer mutations could mimic the activation process of the normal kinase, yet exploiting conserved structural catalysts to accelerate a conformational transition and the enhanced stabilization of the active kinase form. The results of this study reconcile current experimental data with insights from theoretical approaches, pointing to general mechanistic aspects of activating transitions in protein kinases

Reliable Software Development for Machine Protection Systems

The Controls software for the Large Hadron Collider (LHC) at CERN, with more than 150 millions lines of code, resides amongst the largest known code bases in the world1. Industry has been applying Agile software engineering techniques for more than two decades now, and the advantages of these techniques can no longer be ignored to manage the code base for large projects within the accelerator community. Furthermore, CERN is a particular environment due to the high personnel turnover and manpower limitations, where applying Agile processes can improve both, the codebase management as well as its quality. This paper presents the successful application of the Agile software development process Scrum for machine protection systems at CERN, the quality standards and infrastructure introduced together with the Agile process as well as the challenges encountered to adapt it to the CERN environment

Testing Quality and Metrics for the LHC Magnet Powering System throughout Past and Future Commissioning

The LHC magnet powering system is composed of thousands of individual components to assure a safe operation when operating with stored energies as high as 10GJ in the superconducting LHC magnets. Each of these components has to be thoroughly commissioned following interventions and machine shutdown periods to assure their protection function in case of powering failures. As well as having dependable tracking of test executions it is vital that the executed commissioning steps and applied analysis criteria adequately represent the operational state of each component. The Accelerator Testing (AccTesting) framework in combination with a domain specific analysis language provides the means to quantify and improve the quality of analysis for future campaigns. Dedicated tools were developed to analyse in detail the reasons for failures and success of commissioning steps in past campaigns and to compare the results with newly developed quality metrics. Observed shortcomings and discrepancies are used to propose additional verification and mitigation for future campaigns in an effort to improve the testing quality and hence assure the overall dependability of subsequent operational periods

Supervision Software for the Integration of the Beam Interlock System with the CERN Accelerator Complex

The Accelerator complex at the European Organisation for Nuclear Research (CERN) is composed of many systems which are required to function in a valid state to ensure safe beam operation. One key component of machine protection, the Beam Interlock System (BIS), was designed to interface critical systems around the accelerator chain, provide fast and reliable transmission of beam dump requests and trigger beam extraction in case of malfunctioning of equipment systems or beam losses. Numerous upgrades of accelerator and controls components during the Long Shutdown 1 (LS1) are followed by subsequent software updates that need to be thoroughly validated before the restart of beam operation in 2015. In parallel, the ongoing deployments of the BIS hardware in the PS booster (PSB) and the future LINAC4 give rise to new requirements for the related controls and monitoring software due to their fast cycle times. This paper describes the current status and ongoing work as well as the long-term vision for the integration of the Beam Interlock System software into the operational environment