1,132 research outputs found
pmx Webserver: A User Friendly Interface for Alchemistry
Full text linkWith
the increase of available computational power and improvements
in simulation algorithms, alchemical molecular dynamics based free
energy calculations have developed into routine usage. To further
facilitate the usability of alchemical methods for amino acid mutations,
we have developed a web based infrastructure for obtaining hybrid
protein structures and topologies. The presented webserver allows
amino acid mutation selection in five contemporary molecular mechanics
force fields. In addition, a complete mutation scan with a user defined
amino acid is supported. The output generated by the webserver is
directly compatible with the Gromacs molecular dynamics engine and
can be used with any of the alchemical free energy calculation setup.
Furthermore, we present a database of input files and precalculated
free energy differences for tripeptides approximating a disordered
state of a protein, of particular use for protein stability studies.
Finally, the usage of the webserver and its output is exemplified
by performing an alanine scan and investigating thermodynamic stability
of the Trp cage mini protein. The webserver is accessible at http://pmx.mpibpc.mpg.d
Quantifying Asymmetry of Multimeric Proteins
Full text linkA large
number of proteins assemble as homooligomers. These homooligomers
accomplish their function either symmetrically or asymmetrically.
If asymmetry is prevalent in a structure ensemble, the asymmetric
motion will occur in any of the subunits. Many computational analysis
tools implicitly use ensemble averages to determine protein motions,
e.g., principle component analysis. Therefore, taken together, this
approach results in a loss of the asymmetric signal and a false symmetric
output, rendering it impossible to analyze asymmetric motions with
available tools. A first step toward understanding asymmetric systems
is the quantification of asymmetry. Only a few tools exist to calculate
asymmetry quantitatively, such as the continuous symmetry measure
(CSM). In this study, we present an extension of CSM delivering additional
information about the subunit contributions to the overall asymmetry.
Furthermore, we introduce an algorithm termed the functional asymmetry
measure (FAME). FAME is based on an algorithm that predicts functionally
relevant motions of a protein (PLS-FMA) and thus allows calculating
asymmetry in relation to protein function. To validate our developed
algorithm, we applied it to two different potassium channels, TREK-2
and KcsA, as well as to the unfolding mechanism of the carrier protein
Transthyretin. For both potassium channel systems, an artificial asymmetric
motion was introduced to benchmark the algorithm in addition to demonstrate
the interpretation potential of the results. Therefore, the degree
of overall as well as subunit based asymmetry for KcsA was quantified
using CSM as the provided extension requires more than two subunits.
The functional modes of asymmetric TREK-2 motions were recovered and
their asymmetry was quantified using FAME as a dimeric protein is
the simplest application. FAME was further used to study the asymmetry
of the unfolding pathway of Transthyretin. We show the ability of
both algorithms to correctly predict asymmetry. The tools are available
online and can be applied to most homooligomeric systems
Mechanism of mechanosensitive gating of the TREK-2 potassium channel.
Full text linkhttps://doi.org/10.1016/j.bpj.2018.01.03
On the importance of statistics in molecular simulations for thermodynamics, kinetics and simulation box size
Full text linkComputational simulations, akin to wetlab experimentation, are subject to statistical fluctuations. Assessing the magnitude of these fluctuations, that is, assigning uncertainties to the computed results, is of critical importance to drawing statistically reliable conclusions. Here, we use a simulation box size as an independent variable, to demonstrate how crucial it is to gather sufficient amounts of data before drawing any conclusions about the potential thermodynamic and kinetic effects. In various systems, ranging from solvation free energies to protein conformational transition rates, we showcase how the proposed simulation box size effect disappears with increased sampling. This indicates that, if at all, the simulation box size only minimally affects both the thermodynamics and kinetics of the type of biomolecular systems presented in this work
Alchemical Free Energy Calculations for Nucleotide Mutations in Protein–DNA Complexes
Full text linkNucleotide sequence dependent interactions between proteins and DNA are responsible for a wide range of gene regulatory functions. Accurate and generalizable methods to evaluate the strength of protein-DNA binding have been long sought after. While numerous computational approaches have been developed, most of them require fitting parameters to experimental data to a certain degree, e.g. machine learning algorithms or knowledge based statistical potentials. Molecular dynamics based free energy calculations offer a robust, system independent, first principles based method to calculate free energy differences upon nucleotide mutation. We present an automated procedure to setup alchemical MD based calculations to evaluate free energy changes occurring due to a nucleotide mutation in DNA. We further use these methods to perform a large scale mutation scan comprising 397 nucleotide mutation cases in 16 protein-DNA complexes. The obtained prediction accuracy reaches 5.6 kJ/mol average unsigned deviation from experiment. Subsequently, we utilize the MD based free energy calculations to construct protein-DNA binding profiles for a zinc finger protein Zif268. The calculation results compare remarkably well with the experimentally determined binding profiles. The software automating structure and topology setup for alchemical calculations is a part of pmx package; the utilities are also made available online: http://pmx.mpibpc.mpg.de/dna_webserver.html
Molecular dynamics simulations reveal the importance of amyloid-beta oligomer β-sheet edge conformations in membrane permeabilization
Full text linkOligomeric aggregates of the amyloid-beta peptide(1-42) (Aβ42) are regarded as a primary cause of cytotoxicity related to membrane damage in Alzheimer’s disease. However, a dynamical and structural characterization of pore-forming Aβ42 oligomers at atomic detail has not been feasible. Here, we used Aβ42 oligomer structures previously determined in a membrane-mimicking environment as putative model systems to study the pore formation process in phospholipid bilayers with all-atom molecular dynamics simulations. Multiple Aβ42 oligomer sizes, conformations, and N-terminally truncated isoforms were investigated on the multi-μs time scale. We found that pore formation and ion permeation occur via edge conductivity and exclusively for β-sandwich structures that feature exposed side-by-side β-strand pairs formed by residues 9-21 of Aβ42. The extent of pore formation and ion permeation depends on the insertion depth of hydrophilic residues 13-16 (HHQK domain) and thus on subtle differences in the overall stability, orientation, and conformation of the aggregates in the membrane. Additionally, we determined that backbone carbonyl and polar side-chain atoms from the edge strands directly contribute to the coordination sphere of the permeating ions. Furthermore, point mutations that alter the number of favorable side-chain contacts correlate with the ability of the Aβ42 oligomer models to facilitate ion permeation in the bilayer center. Our findings suggest that membrane-inserted, layered β-sheet edges are a key structural motif in pore-forming Aβ42 oligomers independent of their size and play a pivotal role in aggregate-induced membrane permeabilization
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