18,022 research outputs found
Collective Molecular Dynamics in Proteins and Membranes
The understanding of dynamics and functioning of biological membranes and in
particular of membrane embedded proteins is one of the most fundamental
problems and challenges in modern biology and biophysics. In particular the
impact of membrane composition and properties and of structure and dynamics of
the surrounding hydration water on protein function is an upcoming hot topic,
which can be addressed by modern experimental and computational techniques.
Correlated molecular motions might play a crucial role for the understanding
of, for instance, transport processes and elastic properties, and might be
relevant for protein function. Experimentally that involves determining
dispersion relations for the different molecular components, i.e., the length
scale dependent excitation frequencies and relaxation rates. Only very few
experimental techniques can access dynamical properties in biological materials
on the nanometer scale, and resolve dynamics of lipid molecules, hydration
water molecules and proteins and the interaction between them. In this context,
inelastic neutron scattering turned out to be a very powerful tool to study
dynamics and interactions in biomolecular materials up to relevant nanosecond
time scales and down to the nanometer length scale. We review and discuss
inelastic neutron scattering experiments to study membrane elasticity and
protein-protein interactions of membrane embedded proteins
Coarse-grained simulation of transmembrane peptides in the gel phase
We use Dissipative Particle Dynamics simulations, combined with parallel tempering and umbrella sampling, to investigate the potential of mean force between model transmembrane peptides in the various phases of a lipid bilayer, including the low-temperature gel phase.
The observed oscillations in the effective interaction between peptides are consistent with the different structures of the surrounding lipid phases
Exploring emergent properties in cellular homeostasis using OnGuard to model K+ and other ion transport in guard cells
It is widely recognized that the nature and characteristics of transport across eukaryotic membranes are so complex as to defy intuitive understanding. In these circumstances, quantitative mathematical modeling is an essential tool, both to integrate detailed knowledge of individual transporters and to extract the properties emergent from their interactions. As the first, fully integrated and quantitative modeling environment for the study of ion transport dynamics in a plant cell, OnGuard offers a unique tool for exploring homeostatic properties emerging from the interactions of ion transport, both at the plasma membrane and tonoplast in the guard cell. OnGuard has already yielded detail sufficient to guide phenotypic and mutational studies, and it represents a key step toward ‘reverse engineering’ of stomatal guard cell physiology, based on rational design and testing in simulation, to improve water use efficiency and carbon assimilation. Its construction from the HoTSig libraries enables translation of the software to other cell types, including growing root hairs and pollen. The problems inherent to transport are nonetheless challenging, and are compounded for those unfamiliar with conceptual ‘mindset’ of the modeler. Here we set out guidelines for the use of OnGuard and outline a standardized approach that will enable users to advance quickly to its application both in the classroom and laboratory. We also highlight the uncanny and emergent property of OnGuard models to reproduce the ‘communication’ evident between the plasma membrane and tonoplast of the guard cell
Inferring diffusion in single live cells at the single molecule level
The movement of molecules inside living cells is a fundamental feature of
biological processes. The ability to both observe and analyse the details of
molecular diffusion in vivo at the single molecule and single cell level can
add significant insight into understanding molecular architectures of diffusing
molecules and the nanoscale environment in which the molecules diffuse. The
tool of choice for monitoring dynamic molecular localization in live cells is
fluorescence microscopy, especially so combining total internal reflection
fluorescence (TIRF) with the use of fluorescent protein (FP) reporters in
offering exceptional imaging contrast for dynamic processes in the cell
membrane under relatively physiological conditions compared to competing single
molecule techniques. There exist several different complex modes of diffusion,
and discriminating these from each other is challenging at the molecular level
due to underlying stochastic behaviour. Analysis is traditionally performed
using mean square displacements of tracked particles, however, this generally
requires more data points than is typical for single FP tracks due to
photophysical instability. Presented here is a novel approach allowing robust
Bayesian ranking of diffusion processes (BARD) to discriminate multiple complex
modes probabilistically. It is a computational approach which biologists can
use to understand single molecule features in live cells.Comment: combined ms (1-37 pages, 8 figures) and SI (38-55, 3 figures
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