23 research outputs found
Molecular Models of Nanodiscs
Nanodiscs
are discoloidal proteinālipid particles that self-assemble
from a mixture of lipids and membrane scaffold proteins. They form
a highly soluble membrane mimetic that closely resembles a native-like
lipid environment, unlike micelles. Nanodiscs are widely used for
experimental studies of membrane proteins. In this work, we present
a new method for building arbitrary nanodiscs using a combination
of the Martini coarse-grained and all-atom force fields. We model
the basic membrane scaffold protein MSP1 and its extended versions,
such as MSP1E1 and MSP1E2, using a crystal structure of human apolipoprotein
Apo-I. We test our method by generating nanodiscs of different sizes
and compositions, including nanodiscs with embedded membrane proteins,
such as bacteriorhodopsin, outer membrane protein X, and the glucose
transporter. We show that properties of our nanodiscs are in general
agreement with experimental data and previous computational studies
Parameterization of Palmitoylated Cysteine, Farnesylated Cysteine, Geranylgeranylated Cysteine, and Myristoylated Glycine for the Martini Force Field
Peripheral membrane proteins go through
various post-translational
modifications that covalently bind fatty acid tails to specific amino
acids. These post-translational modifications significantly alter
the lipophilicity of the modified proteins and allow them to anchor
to biological membranes. Over 1000 different proteins have been identified
to date that require such membraneāprotein interactions to
carry out their biological functions, including members of the Src
and Ras superfamilies that play key roles in cell signaling and carcinogenesis.
We have used all-atom simulations with the CHARMM36 force field to
parameterize four of the most common post-translational modifications
for the Martini 2.2 force field: palmitoylated cysteine, farnesylated
cysteine, geranylgeranylated cysteine, and myristoylated glycine.
The parameters reproduce the key features of clusters of configurations
of the different anchors in lipid membranes as well as the waterāoctanol
partitioning free energies of the anchors, which are crucial for the
correct reproduction of the expected biophysical behavior of peripheral
membrane proteins at the membraneāwater interface. Implementation
in existing Martini setup tools facilitates the use of the new parameters
Microsecond Molecular Dynamics Simulations of Lipid Mixing
Molecular
dynamics (MD) simulations of membranes are often hindered by the slow
lateral diffusion of lipids and the limited time scale of MD. In order
to study the dynamics of mixing and characterize the lateral distribution
of lipids in converged mixtures, we report microsecond-long all-atom
MD simulations performed on the special-purpose machine Anton. Two
types of mixed bilayers, POPE:POPG (3:1) and POPC:cholesterol (2:1),
as well as a pure POPC bilayer, were each simulated for up to 2 Ī¼s.
These simulations show that POPE:POPG and POPC:cholesterol are each
fully miscible at the simulated conditions, with the final states
of the mixed bilayers similar to a random mixture. By simulating three
POPE:POPG bilayers at different NaCl concentrations (0, 0.15, and
1 M), we also examined the effect of salt concentration on lipid mixing.
While an increase in NaCl concentration is shown to affect the area
per lipid, tail order, and lipid lateral diffusion, the final states
of mixing remain unaltered, which is explained by the largely uniform
increase in Na<sup>+</sup> ions around POPE and POPG. Direct measurement
of water permeation reveals that the POPE:POPG bilayer with 1 M NaCl
has reduced water permeability compared with those at zero or low
salt concentration. Our calculations provide a benchmark to estimate
the convergence time scale of all-atom MD simulations of lipid mixing.
Additionally, equilibrated structures of POPE:POPG and POPC:cholesterol,
which are frequently used to mimic bacterial and mammalian membranes,
respectively, can be used as starting points of simulations involving
these membranes
Improving Internal Peptide Dynamics in the Coarse-Grained MARTINI Model: Toward Large-Scale Simulations of Amyloid- and Elastin-like Peptides
We present an extension of the coarse-grained MARTINI
model for
proteins and apply this extension to amyloid- and elastin-like peptides.
Atomistic simulations of tetrapeptides, octapeptides, and longer peptides
in solution are used as a reference to parametrize a set of pseudodihedral
potentials that describe the internal flexibility of MARTINI peptides.
We assess the performance of the resulting model in reproducing various
structural properties computed from atomistic trajectories of peptides
in water. The addition of new dihedral angle potentials improves agreement
with the contact maps computed from atomistic simulations significantly.
We also address the question of which parameters derived from atomistic
trajectories are transferable between different lengths of peptides.
The modified coarse-grained model shows reasonable transferability
of parameters for the amyloid- and elastin-like peptides. In addition,
the improved coarse-grained model is also applied to investigate the
self-assembly of Ī²-sheet forming peptides on the microsecond
time scale. The octapeptides SNNFGAIL and (GV)<sub>4</sub> are used
to examine peptide aggregation in different environments, in water,
and at the waterāoctane interface. At the interface, peptide
adsorption occurs rapidly, and peptides spontaneously aggregate in
favor of stretched conformers resembling Ī²-strands
Antimicrobial Peptide Simulations and the Influence of Force Field on the Free Energy for Pore Formation in Lipid Bilayers
Due to antimicrobial resistance,
the development of new drugs to
combat bacterial and fungal infections is an important area of research.
Nature uses short, charged, and amphipathic peptides for antimicrobial
defense, many of which disrupt the lipid membrane in addition to other
possible targets inside the cell. Computer simulations have revealed
atomistic details for the interactions of antimicrobial peptides and
cell-penetrating peptides with lipid bilayers. Strong interactions
between the polar interface and the charged peptides can induce bilayer
deformations ā including membrane rupture and peptide stabilization
of a hydrophilic pore. Here, we performed microsecond-long simulations
of the antimicrobial peptide CM15 in a POPC bilayer expecting to observe
pore formation (based on previous molecular dynamics simulations).
We show that caution is needed when interpreting results of equilibrium
peptide-membrane simulations, given the length of time single trajectories
can dwell in local energy minima for 100ās of ns to microseconds.
While we did record significant membrane perturbations from the CM15
peptide, pores were not observed. We explain this discrepancy by computing
the free energy for pore formation with different force fields. Our
results show a large difference in the free energy barrier (ca. 40
kJ/mol) against pore formation predicted by the different force fields
that would result in orders of magnitude differences in the simulation
time required to observe spontaneous pore formation. This explains
why previous simulations using the Berger lipid parameters reported
pores induced by charged peptides, while with CHARMM based models
pores were not observed in our long time-scale simulations. We reconcile
some of the differences in the distance dependent free energies by
shifting the free energy profiles to account for thickness differences
between force fields. The shifted curves show that all the models
describe small defects in lipid bilayers in a consistent manner, suggesting
a common physical basis
The Role of Atomic Polarization in the Thermodynamics of Chloroform Partitioning to Lipid Bilayers
In spite of extensive research and use in medical practice,
the
precise molecular mechanism of volatile anesthetic action remains
unknown. The distribution of anesthetics within lipid bilayers and
potential targeting to membrane proteins is thought to be central
to therapeutic function. Therefore, obtaining a molecular level understanding
of volatile anesthetic partitioning into lipid bilayers is of vital
importance to modern pharmacology. In this study we investigate the
partitioning of the prototypical anesthetic, chloroform, into lipid
bilayers and different organic solvents using molecular dynamics simulations
with potential models ranging from simplified coarse-grained MARTINI
to additive and polarizable CHARMM all-atom force fields. Many volatile
anesthetics display significant inducible dipole moments, which correlate
with their potency, yet the exact role of molecular polarizability
in their stabilization within lipid bilayers remains unknown. We observe
that explicit treatment of atomic polarizability makes it possible
to accurately reproduce solvation free energies in solvents with different
polarities, allowing for quantitative studies in heterogeneous molecular
distributions, such as lipid bilayers. We calculate the free energy
profiles for chloroform crossing lipid bilayers to reveal a role of
polarizability in modulating chloroform partitioning thermodynamics
via the chloroform-induced dipole moment and highlight competitive
binding to the membrane core and toward the glycerol backbone that
may have significant implications for understanding anesthetic action
Two-Dimensional Potentials of Mean Force of Nile Red in Intact and Damaged Model Bilayers. Application to Calculations of Fluorescence Spectra
Fluorescent dyes revolutionized and
expanded our understanding
of biological membranes. The interpretation of experimental fluorescence
data in terms of membrane structure, however, requires detailed information
about the molecular environment of the dyes. Nile red is a fluorescent
molecule whose excitation and emission maxima depend on the polarity
of the solvent. It is mainly used as a probe to study lipid microenvironments,
for example in imaging the progression of damage to the myelin sheath
in multiple sclerosis. In this study, we determine the position and
orientation of Nile red in lipid bilayers by calculating two-dimensional
Potential of Mean Force (2D-PMF) profiles in a defect-free 1-palmitoyl-2-oleoyl-<i>sn</i>-glycero-3-phosphocholine (POPC) bilayer and in damaged
bilayers containing two mixtures of the oxidized lipid 1-palmitoyl-2-(9ā²-oxo-nonanoyl)-<i>sn</i>-glycero-3-phosphocholine and POPC. From 2D-PMF simulations
we obtain positions and orientations of Nile Red corresponding to
the minimum on the binding free energy surface in three different
membrane environments with increasing amounts of water, mimicking
damage in biological tissue. Using representative snapshots from the
simulations, we use combined quantum mechanical/molecular mechanical
(QM/MM) models to calculate the emission spectrum of Nile red as a
function of its local solvation environment. The results of QM and
QM/MM computations are in qualitative agreement with the experimentally
observed shift in fluorescence for the dye moving from aqueous solution
to the more hydrophobic environment of the lipid interiors. The range
of the conformation dependent values of the computed absorption-emission
spectra and the lack of solvent relaxation effects in the QM/MM calculations
made it challenging to delineate specific differences between the
intact and damaged bilayers
Going Backward: A Flexible Geometric Approach to Reverse Transformation from Coarse Grained to Atomistic Models
The conversion of
coarse-grained to atomistic models is an important
step in obtaining insight about atomistic scale processes from coarse-grained
simulations. For this process, called backmapping or reverse transformation,
several tools are available, but these commonly require libraries
of molecule fragments or they are linked to a specific software package.
In addition, the methods are usually restricted to specific molecules
and to a specific force field. Here, we present an alternative method,
consisting of geometric projection and subsequent force-field based
relaxation. This method is designed to be simple and flexible, and
offers a generic solution for resolution transformation. For simple
systems, the conversion only requires a list of particle correspondences
on the two levels of resolution. For special cases, such as nondefault
protonation states of amino acids and virtual sites, a target particle
list can be specified. The mapping uses simple building blocks, which
list the particles on the different levels of resolution. For conversion
to higher resolution, the initial model is relaxed with several short
cycles of energy minimization and position-restrained MD. The reconstruction
of an atomistic backbone from a coarse-grained model is done using
a new dedicated algorithm. The method is generic and can be used to
map between any two particle based representations, provided that
a mapping can be written. The focus of this work is on the coarse-grained
MARTINI force field, for which mapping definitions are written to
allow conversion to and from the higher-resolution force fields GROMOS,
CHARMM, and AMBER, and to and from a simplified three-bead lipid model.
Together, these offer the possibility to simulate mesoscopic membrane
structures, to be transformed to MARTINI and subsequently to an atomistic
model for investigation of detailed interactions. The method was tested
on a set of systems ranging from a simple, single-component bilayer
to a large proteināmembraneāsolvent complex. The results
demonstrate the efficiency and the efficacy of the new approach
Computational Lipidomics with <i>insane</i>: A Versatile Tool for Generating Custom Membranes for Molecular Simulations
For simulations of
membranes and membrane proteins, the generation
of the lipid bilayer is a critical step in the setup of the system.
Membranes comprising multiple components pose a particular challenge,
because the relative abundances need to be controlled and the equilibration
of the system may take several microseconds. Here we present a comprehensive
method for building membrane containing systems, characterized by
simplicity and versatility. The program uses preset, coarse-grain
lipid templates to build the membrane, and also allows on-the-fly
generation of simple lipid types by specifying the headgroup, linker,
and lipid tails on the command line. The resulting models can be equilibrated,
after which a relaxed atomistic model can be obtained by reverse transformation.
For multicomponent membranes, this provides an efficient means for
generating equilibrated atomistic models. The method is called <i>insane</i>, an acronym for INSert membrANE. The program has
been made available, together with the complementary method for reverse
transformation, at http://cgmartini.nl/. This work highlights
the key features of <i>insane</i> and presents a survey
of properties for a large range of lipids as a start of a computational
lipidomics project
Conformational Changes of the Antibacterial Peptide ATP Binding Cassette Transporter McjD Revealed by Molecular Dynamics Simulations
The
ATP binding cassette (ABC) transporters form one of the largest
protein superfamilies. They use the energy of ATP hydrolysis to transport
chemically diverse ligands across membranes. An alternating access
mechanism in which the transporter switches between inward- and outward-facing
conformations has been proposed to describe the translocation process.
One of the main open questions in this process is the degree of opening
of the transporter at different stages of the transport cycle, as
crystal structures and biochemical data have suggested a wide range
of distances between nucleotide binding domains. Recently, the crystal
structure of McjD, an antibacterial peptide ABC transporter from <i>Escherichia coli</i>, revealed a new occluded intermediate state
of the transport cycle. The transmembrane domain is closed on both
sides of the membrane, forming a cavity that can accommodate its ligand,
MccJ25, a lasso peptide of 21 amino acids. In this work, we investigate
the degree of opening of the transmembrane cavity required for ligand
translocation. By means of steered molecular dynamics simulations,
the ligand was pulled from the internal cavity to the extracellular
side. This resulted in an outward-facing state. Comparison with existing
outward-facing crystal structures shows a smaller degree of opening
in the simulations, suggesting that the large conformational changes
in some crystal structures may not be necessary even for a large substrate
like MccJ25