5 research outputs found
PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data
We describe PTRAJ and its successor
CPPTRAJ, two complementary,
portable, and freely available computer programs for the analysis
and processing of time series of three-dimensional atomic positions
(i.e., coordinate trajectories) and the data therein derived. Common
tools include the ability to manipulate the data to convert among
trajectory formats, process groups of trajectories generated with
ensemble methods (e.g., replica exchange molecular dynamics), image
with periodic boundary conditions, create average structures, strip
subsets of the system, and perform calculations such as RMS fitting,
measuring distances, B-factors, radii of gyration, radial distribution
functions, and time correlations, among other actions and analyses.
Both the PTRAJ and CPPTRAJ programs and source code are freely available
under the GNU General Public License version 3 and are currently distributed
within the AmberTools 12 suite of support programs that make up part
of the Amber package of computer programs (see http://ambermd.org). This overview describes the general design, features, and history
of these two programs, as well as algorithmic improvements and new
features available in CPPTRAJ
Improved Generalized Born Solvent Model Parameters for Protein Simulations
The
generalized Born (GB) model is one of the fastest implicit
solvent models, and it has become widely adopted for Molecular Dynamics
(MD) simulations. This speed comes with trade-offs, and many reports
in the literature have pointed out weaknesses with GB models. Because
the quality of a GB model is heavily affected by empirical parameters
used in calculating solvation energy, in this work we have refit these
parameters for GB-Neck, a recently developed GB model, in order to
improve the accuracy of both the solvation energy and effective radii
calculations. The data sets used for fitting are significantly larger
than those used in the past. Comparing to other pairwise GB models
like GB-OBC and the original GB-Neck, the new GB model (GB-Neck2)
has better agreement with Poisson–Boltzmann (PB) in terms of
reproducing solvation energies for a variety of systems ranging from
peptides to proteins. Secondary structure preferences are also in
much better agreement with those obtained from explicit solvent MD
simulations. We also obtain near-quantitative reproduction of experimental
structure and thermal stability profiles for several model peptides
with varying secondary structure motifs. Extension to nonprotein systems
will be explored in the future
Reliable Oligonucleotide Conformational Ensemble Generation in Explicit Solvent for Force Field Assessment Using Reservoir Replica Exchange Molecular Dynamics Simulations
Molecular dynamics force field development
and assessment requires
a reliable means for obtaining a well-converged conformational ensemble
of a molecule in both a time-efficient and cost-effective manner.
This remains a challenge for RNA because its rugged energy landscape
results in slow conformational sampling and accurate results typically
require explicit solvent which increases computational cost. To address
this, we performed both traditional and modified replica exchange
molecular dynamics simulations on a test system (alanine dipeptide)
and an RNA tetramer known to populate A-form-like conformations in
solution (single-stranded rGACC). A key focus is on providing the
means to demonstrate that convergence is obtained, for example, by
investigating replica RMSD profiles and/or detailed ensemble analysis
through clustering. We found that traditional replica exchange simulations
still require prohibitive time and resource expenditures, even when
using GPU accelerated hardware, and our results are not well converged
even at 2 μs of simulation time per replica. In contrast, a
modified version of replica exchange, reservoir replica exchange in
explicit solvent, showed much better convergence and proved to be
both a cost-effective and reliable alternative to the traditional
approach. We expect this method will be attractive for future research
that requires quantitative conformational analysis from explicitly
solvated simulations
Computational Assessment of Potassium and Magnesium Ion Binding to a Buried Pocket in GTPase-Associating Center RNA
An
experimentally well-studied model of RNA tertiary structures
is a 58mer rRNA fragment, known as GTPase-associating center (GAC)
RNA, in which a highly negative pocket walled by phosphate oxygen
atoms is stabilized by a chelated cation. Although such deep pockets
with more than one direct phosphate to ion chelation site normally
include magnesium, as shown in one GAC crystal structure, another
GAC crystal structure and solution experiments suggest potassium at
this site. Both crystal structures also depict two magnesium ions
directly bound to the phosphate groups comprising this controversial
pocket. Here, we used classical molecular dynamics simulations as
well as umbrella sampling to investigate the possibility of binding
of potassium versus magnesium inside the pocket and to better characterize
the chelation of one of the binding magnesium ions outside the pocket.
The results support the preference of the pocket to accommodate potassium
rather than magnesium and suggest that one of the closely binding
magnesium ions can only bind at high magnesium concentrations, such
as might be present during crystallization. This work illustrates
the complementary utility of molecular modeling approaches with atomic-level
detail in resolving discrepancies between conflicting experimental
results
Self-Tensioning Aquatic Caddisfly Silk: Ca<sup>2+</sup>-Dependent Structure, Strength, and Load Cycle Hysteresis
Caddisflies are aquatic relatives
of silk-spinning terrestrial
moths and butterflies. Casemaker larvae spin adhesive silk fibers
for underwater construction of protective composite cases. The central
region of Hesperophylax sp. H-fibroin
contains a repeating pattern of three conserved subrepeats, all of
which contain one or more (SX)<sub><i>n</i></sub> motifs
with extensively phosphorylated serines. Native silk fibers were highly
extensible and displayed a distinct yield point, force plateau, and
load cycle hysteresis. FTIR spectroscopy of native silk showed a conformational
mix of random coil, β-sheet, and turns. Exchanging multivalent
ions with Na<sup>+</sup> EDTA disrupted fiber mechanics, shifted the
secondary structure ratios from antiparallel β-sheet toward
random coil and turns, and caused the fibers to shorten, swell in
diameter, and disrupted fiber birefringence. The EDTA effects were
reversed by restoring Ca<sup>2+</sup>. Molecular dynamic simulations
provided theoretical support for a hypothetical structure in which
the (pSX)<sub><i>n</i></sub> motifs may assemble into two-
and three-stranded, Ca<sup>2+</sup>-stabilized β-sheets