17 research outputs found
Water Model Tuning for Improved Reproduction of Rotational Diffusion and NMR Spectral Density
A water model for molecular simulation was optimized
to improve the reproduction of translational and rotational diffusion
of pure water and proteins. The SPC/E<sub>b</sub> model was developed
from the original SPC/E model with a slight increase of the O–H
bond length of 1%. This tuning has significantly improved the translational
and rotational diffusion when compared to the experimental values,
whereas only small changes were observed in the other thermodynamic
properties examined. The overall tumbling correlation times (τ<sub>p</sub>) from ubiquitin, protein G, bovine pancreatic trypsin inhibitor,
and barstar C42/80A were successfully reproduced using the SPC/E<sub>b</sub> model. Calculated site-specific spectral densities of the
main chain amide bond rotation in ubiquitin and protein G were in
good agreement with those derived from nuclear magnetic resonance
reduced spectral density mapping. The SPC/E<sub>bT</sub> model was
also developed with temperature-dependent bond-length tuning to facilitate
reproduction of the experimental τ<sub>p</sub> around room temperature
Computational Assignment of the Histidine Protonation State in (6-4) Photolyase Enzyme and Its Effect on the Protonation Step
The
initial step to resolving the controversy regarding the repair
mechanism of the pyrimidine (6-4) pyrimidone photoproduct DNA lesion
is to determine the protonation state of the two conserved active
site histidine residues (His365 and His369 in Drosophila
melanogaster) in the (6-4) photolyase enzyme ((6-4)
PHR). Both His residues were experimentally determined to be crucial
for catalysis. Most previous theoretical studies assumed the presence
of protonated His365 in the active site, which would transfer its
proton to N3′ of the lesion as the first step in repair; however,
other empirical/semiempirical p<i>K</i><sub>a</sub> calculations
suggested the presence of two neutral His residues in the active site.
Here, we conduct molecular dynamics simulations (MD) of the (6-4)
PHR/DNA complex on the basis of the X-ray crystal structure to investigate
all combinations of the three possible protonation states of each
His. The MD results show that HIP365 (both ND1 and NE2 protonated)
and HID369 (only ND1 protonated) are the most probable protonation
states in the active site. Furthermore, we employ quantum mechanics-cluster
and quantum mechanical/molecular mechanical (QM/MM) approaches to
investigate the protonation of N3′, starting with three plausible
complexes resulting from MD (HIP365/HID369, HID365/HIE369, and HID365/HIP369).
Surprisingly, protonation of the N3′ atom is found to be feasible
starting from all three protonation states: protonated HIP365 transfers
the proton via a barrierless step, and in the other cases of neutral
HID365, the proton is transferred from O4′ of the lesion via
His365 through an energy barrier of ∼80 kJ mol<sup>–1</sup> in both complexes. These results might explain the conservation
of repair activity over a wide range of pH values
ColDock: Concentrated Ligand Docking with All-Atom Molecular Dynamics Simulation
We propose a simple but efficient
and accurate method to generate
protein–ligand complex structures, called Concentrated ligand
Docking (ColDock). This method consists of multiple independent molecular
dynamics simulations in which ligands are initially distributed randomly
around a protein at relatively high concentration (∼100 mM).
This condition significantly increases the probability of the ligand
exploring the protein surface, which induces spontaneous ligand binding
to the correct binding sites within a 100 ns MD. After clustering
of the protein-bound ligand poses, representatives of the populationally
dominant clusters are considered as predicted ligand poses. We applied
ColDock to four cases starting from holo protein structures and showed
that ColDock can generate “correct” ligand poses very
similar to the crystal complex structures. Correct ligand poses are
also well reproduced in three out of four cases started from apo structures,
with the exception being a case with an initially closed binding pocket.
The results indicate that ColDock can be used as a protein–ligand
docking as long as the ligand binding pocket is initially open. Plausible
protein–ligand complex structures can be easily generated by
conducting the ColDock procedure using standard MD simulation software
Energy differences between 60 and 0.1
<p>Unit: kcal/mol. Δ<i>X</i> = <i>X</i><sub>60 MPa</sub> – <i>X</i><sub>0.1 MPa</sub> where <i>X</i> = <i>E</i><sub>conf</sub>, Δ<i>μ</i>, <i>TS</i>, or <i>G</i>. Δ<i>G</i> = Δ<i>E</i><sub>conf</sub>+ΔΔ<i>μ</i> − <i>T</i>Δ<i>S</i>. ΔΔ<i>G</i> is the difference from Δ<i>G</i> of Ac1Q.</p
Mechanism of Deep-Sea Fish α-Actin Pressure Tolerance Investigated by Molecular Dynamics Simulations
<div><p>The pressure tolerance of monomeric α-actin proteins from the deep-sea fish <i>Coryphaenoides armatus</i> and <i>C. yaquinae</i> was compared to that of non-deep-sea fish <i>C. acrolepis</i>, carp, and rabbit/human/chicken actins using molecular dynamics simulations at 0.1 and 60 MPa. The amino acid sequences of actins are highly conserved across a variety of species. The actins from <i>C. armatus</i> and <i>C. yaquinae</i> have the specific substitutions Q137K/V54A and Q137K/L67P, respectively, relative to <i>C. acrolepis</i>, and are pressure tolerant to depths of at least 6000 m. At high pressure, we observed significant changes in the salt bridge patterns in deep-sea fish actins, and these changes are expected to stabilize ATP binding and subdomain arrangement. Salt bridges between ATP and K137, formed in deep-sea fish actins, are expected to stabilize ATP binding even at high pressure. At high pressure, deep-sea fish actins also formed a greater total number of salt bridges than non-deep-sea fish actins owing to the formation of inter-helix/strand and inter-subdomain salt bridges. Free energy analysis suggests that deep-sea fish actins are stabilized to a greater degree by the conformational energy decrease associated with pressure effect.</p></div
Arrangement of the water molecule expected to initiate nucleophilic attack on the γ-phosphate of ATP.
<p>The arrangement of non-deep-sea fish actins (A) and deep-sea fish actins (B). Green spheres show water molecules expected to be nucleophilic water for ATP hydrolysis. Red spheres indicate the water molecules coordinated to Mg<sup>2+</sup> and those bridging the expected nucleophilic water and H161 with hydrogen bonds. Black dotted lines show typical hydrogen bonds formed during the MD simulation. Angle <i>θ</i> and distance <i>d</i><sub>Nu</sub> are defined by O<sup>β</sup>-P<sup>γ</sup>-O<sup>w</sup> and P<sup>γ</sup>-O<sup>w</sup>, respectively, where O<sup>w</sup> represents the oxygen of the expected nucleophilic water (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0085852#pone-0085852-g001" target="_blank">Figure 1C</a> for the definition of the other atoms).</p
The root mean-square fluctuation (RMSF) per residue at 60 MPa.
<p>The RMSF was calculated by best-fitting the backbone heavy atoms of each snapshot to the average structure. Secondary structure and subdomain assignments are also shown.</p
Effect of high pressure on excluded volume (<i>V</i><sub>ex</sub>), solvent accessible surface area (SASA) and isothermal compressibility (<i>κ<sub>T</sub></i>).
<p>Units: <i>V</i><sub>ex</sub> (10<sup>4</sup> Å<sup>3</sup>), SASA (10<sup>4</sup> Å<sup>2</sup>), <i>κ<sub>T</sub></i>, (GPa<sup>−1</sup>). Δ = <i>X</i><sub>60 MPa</sub> – <i>X</i><sub>0.1 MPa</sub> where <i>X</i> = <i>V</i><sub>ex</sub>, SASA, or <i>κ<sub>T</sub></i>. The value after “±” indicates standard deviation.</p
Number of salt bridges formed between secondary structures and subdomains.
<p>Salt bridges <sup>a</sup>between distinct helices or strands, <sup>b</sup>between a helix/strand and a loop, <sup>c</sup>between distinct loops, <sup>d</sup>within helix or strand. <sup>e</sup>Salt bridges between ATP and a residue. <sup>f</sup>Inter and <sup>g</sup>intra subdomain salt bridge. <sup>h</sup>The sum of “Secondary structure”+“ATP” or “Subdomains”+“ATP”. The value after “±” indicates standard deviation.</p
Structure of monomeric actin.
<p>(A) Subdomain arrangement. Subdomains 1, 2, 3 and 4 are shown in cyan, red, yellow and green, respectively. The pink sphere represents Mg<sup>2+</sup> at the active site. (B) Positions of substituted residues in <i>C. yaquinae</i> actin as compared to rabbit/chicken actin. The residues shown in red and cyan in the licorice model represent the specific substitutions in deep-sea fish actins and those of terrestrial animals and shallow-water fish species, respectively. (C) Chemical formula of ATP. Oxygen atoms in the phosphate tail of ATP are distinguished by α, β, and γ.</p