13 research outputs found
Heterogeneous Change Point Inference
We propose HSMUCE (heterogeneous simultaneous multiscale change-point
estimator) for the detection of multiple change-points of the signal in a
heterogeneous gaussian regression model. A piecewise constant function is
estimated by minimizing the number of change-points over the acceptance region
of a multiscale test which locally adapts to changes in the variance. The
multiscale test is a combination of local likelihood ratio tests which are
properly calibrated by scale dependent critical values in order to keep a
global nominal level alpha, even for finite samples. We show that HSMUCE
controls the error of over- and underestimation of the number of change-points.
To this end, new deviation bounds for F-type statistics are derived. Moreover,
we obtain confidence sets for the whole signal. All results are non-asymptotic
and uniform over a large class of heterogeneous change-point models. HSMUCE is
fast to compute, achieves the optimal detection rate and estimates the number
of change-points at almost optimal accuracy for vanishing signals, while still
being robust. We compare HSMUCE with several state of the art methods in
simulations and analyse current recordings of a transmembrane protein in the
bacterial outer membrane with pronounced heterogeneity for its states. An
R-package is available online
Fully-Automatic Multiresolution Idealization for Filtered Ion Channel Recordings: Flickering Event Detection
We propose a new model-free segmentation method, JULES, which combines recent
statistical multiresolution techniques with local deconvolution for
idealization of ion channel recordings. The multiresolution criterion takes
into account scales down to the sampling rate enabling the detection of
flickering events, i.e., events on small temporal scales, even below the filter
frequency. For such small scales the deconvolution step allows for a precise
determination of dwell times and, in particular, of amplitude levels, a task
which is not possible with common thresholding methods. This is confirmed
theoretically and in a comprehensive simulation study. In addition, JULES can
be applied as a preprocessing method for a refined hidden Markov analysis. Our
new methodolodgy allows us to show that gramicidin A flickering events have the
same amplitude as the slow gating events. JULES is available as an R function
jules in the package clampSeg
Heterogeneous Idealization of Ion Channel Recordings -- Open Channel Noise
We propose a new model-free segmentation method for idealizing ion channel
recordings. This method is designed to deal with heterogeneity of measurement
errors. This in particular applies to open channel noise which, in general, is
particularly difficult to cope with for model-free approaches. Our methodology
is able to deal with lowpass filtered data which provides a further
computational challenge. To this end we propose a multiresolution testing
approach, combined with local deconvolution to resolve the lowpass filter.
Simulations and statistical theory confirm that the proposed idealization
recovers the underlying signal very accurately at presence of heterogeneous
noise, even when events are shorter than the filter length. The method is
compared to existing approaches in computer experiments and on real data. We
find that it is the only one which allows to identify openings of the PorB
porine at two different temporal scales. An implementation is available as an R
package
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Analysis of patchclamp recordings: model-free multiscale methods and software.
Analysis of patchclamp recordings is often a challenging issue. We give practical guidance how such recordings can be analyzed using the model-free multiscale idealization methodology JSMURF, JULES, and HILDE. We provide an operational manual how to use the accompanying software available as an R-package and as a graphical user interface. This includes selection of the right approach and tuning of parameters. We also discuss advantages and disadvantages of model-free approaches in comparison to hidden Markov model approaches and explain how they complement each other
High-resolution experimental and computational electrophysiology reveals weak β-lactam binding events in the porin PorB
Abstract The permeation of most antibiotics through the outer membrane of Gram-negative bacteria occurs through porin channels. To design drugs with increased activity against Gram-negative bacteria in the face of the antibiotic resistance crisis, the strict constraints on the physicochemical properties of the permeants imposed by these channels must be better understood. Here we show that a combination of high-resolution electrophysiology, new noise-filtering analysis protocols and atomistic biomolecular simulations reveals weak binding events between the β-lactam antibiotic ampicillin and the porin PorB from the pathogenic bacterium Neisseria meningitidis. In particular, an asymmetry often seen in the electrophysiological characteristics of ligand-bound channels is utilised to characterise the binding site and molecular interactions in detail, based on the principles of electro-osmotic flow through the channel. Our results provide a rationale for the determinants that govern the binding and permeation of zwitterionic antibiotics in porin channels
An antibiotic-resistance conferring mutation in a neisserial porin:Structure, ion flux, and ampicillin binding
Gram-negative bacteria cause the majority of highly drug-resistant bacterial infections. To cross the outer membrane of the complex Gram-negative cell envelope, antibiotics permeate through porins, trimeric channel proteins that enable the exchange of small polar molecules. Mutations in porins contribute to the development of drug-resistant phenotypes. In this work, we show that a single point mutation in the porin PorB from Neisseria meningitidis, the causative agent of bacterial meningitis, can strongly affect the binding and permeation of beta-lactam antibiotics. Using X-ray crystallography, high-resolution electrophysiology, atomistic biomolecular simulation, and liposome swelling experiments, we demonstrate differences in drug binding affinity, ion selectivity and drug permeability of PorB. Our work further reveals distinct interactions between the transversal electric field in the porin eyelet and the zwitterionic drugs, which manifest themselves under applied electric fields in electrophysiology and are altered by the mutation. These observations may apply more broadly to drug-porin interactions in other channels. Our results improve the molecular understanding of porin-based drug-resistance in Gram-negative bacteria