126 research outputs found
InferenceMAP: Mapping of Single-Molecule Dynamics with Bayesian Inference
Single-particle tracking (SPT) grants unprecedented insight into cellular
function at the molecular scale [1]. Throughout the cell, the movement of
single-molecules is generally heterogeneous and complex. Hence, there is an
imperative to understand the multi-scale nature of single-molecule dynamics in
biological systems. We have previously shown that with high-density SPT,
spatial maps of the parameters that dictate molecule motion can be generated to
intricately describe cellular environments [2,3,4]. To date, however, there
exist no publically available tools that reconcile trajectory data to generate
the aforementioned maps. We address this void in the SPT community with
InferenceMAP: an interactive software package that uses a powerful Bayesian
method to map the dynamic cellular space experienced by individual
biomolecules.Comment: 56 page
Mapping the energy and diffusion landscapes of membrane proteins at the cell surface using high-density single-molecule imaging and Bayesian inference: application to the multi-scale dynamics of glycine receptors in the neuronal membrane
Protein mobility is conventionally analyzed in terms of an effective
diffusion. Yet, this description often fails to properly distinguish and
evaluate the physical parameters (such as the membrane friction) and the
biochemical interactions governing the motion. Here, we present a method
combining high-density single-molecule imaging and statistical inference to
separately map the diffusion and energy landscapes of membrane proteins across
the cell surface at ~100 nm resolution (with acquisition of a few minutes).
When applying these analytical tools to glycine neurotransmitter receptors
(GlyRs) at inhibitory synapses, we find that gephyrin scaffolds act as shallow
energy traps (~3 kBT) for GlyRs, with a depth modulated by the biochemical
properties of the receptor-gephyrin interaction loop. In turn, the inferred
maps can be used to simulate the dynamics of proteins in the membrane, from the
level of individual receptors to that of the population, and thereby, to model
the stochastic fluctuations of physiological parameters (such as the number of
receptors at synapses). Overall, our approach provides a powerful and
comprehensive framework with which to analyze biochemical interactions in
living cells and to decipher the multi-scale dynamics of biomolecules in
complex cellular environments.Comment: 23 pages, 4 figure
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