2 research outputs found
Multi-Conformation Monte Carlo: A Method for Introducing Flexibility in Efficient Simulations of Many-Protein Systems
We
present a novel multi-conformation Monte Carlo simulation method
that enables the modeling of protein–protein interactions and
aggregation in crowded protein solutions. This approach is relevant
to a molecular-scale description of realistic biological environments,
including the cytoplasm and the extracellular matrix, which are characterized
by high concentrations of biomolecular solutes (e.g., 300–400
mg/mL for proteins and nucleic acids in the cytoplasm of Escherichia coli). Simulation of such environments
necessitates the inclusion of a large number of protein molecules.
Therefore, computationally inexpensive methods, such as rigid-body
Brownian dynamics (BD) or Monte Carlo simulations, can be particularly
useful. However, as we demonstrate herein, the rigid-body representation
typically employed in simulations of many-protein systems gives rise
to certain artifacts in protein–protein interactions. Our approach
allows us to incorporate molecular flexibility in Monte Carlo simulations
at low computational cost, thereby eliminating ambiguities arising
from structure selection in rigid-body simulations. We benchmark and
validate the methodology using simulations of hen egg white lysozyme
in solution, a well-studied system for which extensive experimental
data, including osmotic second virial coefficients, small-angle scattering
structure factors, and multiple structures determined by X-ray and
neutron crystallography and solution NMR, as well as rigid-body BD
simulation results, are available for comparison
Direct Evidence of Conformational Changes Associated with Voltage Gating in a Voltage Sensor Protein by Time-Resolved X‑ray/Neutron Interferometry
The
voltage sensor domain (VSD) of voltage-gated cation (e.g.,
Na<sup>+</sup>, K<sup>+</sup>) channels central to neurological signal
transmission can function as a distinct module. When linked to an
otherwise voltage-insensitive, ion-selective membrane pore, the VSD
imparts voltage sensitivity to the channel. Proteins homologous with
the VSD have recently been found to function themselves as voltage-gated
proton channels or to impart voltage sensitivity to enzymes. Determining
the conformational changes associated with voltage gating in the VSD
itself in the absence of a pore domain thereby gains importance. We
report the direct measurement of changes in the scattering-length
density (SLD) profile of the VSD protein, vectorially oriented within
a reconstituted phospholipid bilayer membrane, as a function of the
transmembrane electric potential by time-resolved X-ray and neutron
interferometry. The changes in the experimental SLD profiles for both
polarizing and depolarizing potentials with respect to zero potential
were found to extend over the entire length of the isolated VSD’s
profile structure. The characteristics of the changes observed were
in qualitative agreement with molecular dynamics simulations of a
related membrane system, suggesting an initial interpretation of these
changes in terms of the VSD’s atomic-level 3-D structure