241 research outputs found

    Reliable in silico ranking of engineered therapeutic TCR binding affinities with MMPB/GBSA

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    Accurate and efficient in silico ranking of proteinprotein binding affinities is useful for protein design with applications in biological therapeutics. One popular approach to rank binding affinities is to apply the molecular mechanics Poisson-Boltzmann/generalized Born surface area (MMPB/ GBSA) method to molecular dynamics (MD) trajectories. Here, we identify protocols that enable the reliable evaluation of T-cell receptor (TCR) variants binding to their target, peptide-human leukocyte antigens (pHLAs). We suggest different protocols for variant sets with a few (<= 4) or many mutations, with entropy corrections important for the latter. We demonstrate how potential outliers could be identified in advance and that just 5-10 replicas of short (4 ns) MD simulations may be sufficient for the reproducible and accurate ranking of TCR variants. The protocols developed here can be applied toward in silico screening during the optimization of therapeutic TCRs, potentially reducing both the cost and time taken for biologic development

    Peptide cargo tunes a network of correlated motions in human leukocyte antigens

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    Most biomolecular interactions are typically thought to increase the (local) rigidity of a complex, for example, in drug‐target binding. However, detailed analysis of specific biomolecular complexes can reveal a more subtle interplay between binding and rigidity. Here, we focussed on the human leucocyte antigen (HLA), which plays a crucial role in the adaptive immune system by presenting peptides for recognition by the αβ T‐cell receptor (TCR). The role that the peptide plays in tuning HLA flexibility during TCR recognition is potentially crucial in determining the functional outcome of an immune response, with obvious relevance to the growing list of immunotherapies that target the T‐cell compartment. We have applied high‐pressure/temperature perturbation experiments, combined with molecular dynamics simulations, to explore the drivers that affect molecular flexibility for a series of different peptide–HLA complexes. We find that different peptide sequences affect peptide–HLA flexibility in different ways, with the peptide cargo tuning a network of correlated motions throughout the pHLA complex, including in areas remote from the peptide‐binding interface, in a manner that could influence T‐cell antigen discrimination

    bicop: A command for fitting bivariate ordinal regressions with residual dependence characterized by a copula function and normal mixture marginals

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    In this article, we describe a new Stata command, bicop, for fitting a model consisting of a pair of ordinal regressions with a flexible residual distribution, with each marginal distribution specified as a two-part normal mixture, and stochastic dependence governed by a choice of copula functions. The bicop command generalizes the existing biprobit and bioprobit commands, which assume a bivariate normal residual distribution. We present and explain the bicop estimation command and the available postestimation commands using data on financial well-being from the UK Understanding Society Panel Survey

    A Comparison of Recall and Diary Food Expenditure Data

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    Recall food expenditure data, which is the basis of a great deal of empirical work, is believed to suffer from considerable measurement error. Diary records are believed to be more accurate. We study an unusual data set that collects recall and diary data from the same households and so allows a direct comparison of the two methods of data collection. The diary data imply measurement errors in recall food expenditure data that are substantial, and which do not have the properties of classical measurement error. However, we also present evidence that the diary measures are themselves imperfect

    Understanding Society Innovation Panel Wave 6: results from methodological experiments

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    This paper presents some preliminary findings from Wave 6 of the Innovation Panel (IP6) of Understanding Society: The UK Household Longitudinal Study. Understanding Society is a major panel survey in the UK. In March 2013, the sixth wave of the Innovation Panel went into the field. IP6 used a mixed-mode design, using on-line interviews and face-to-face interviews. This paper describes the design of IP6, the experiments carried and the preliminary findings from early analysis of the data
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