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_b 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_p) from ubiquitin, protein G, bovine pancreatic trypsin inhibitor, and barstar C42/80A were successfully reproduced using the SPC/E_b 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_bT model was also developed with temperature-dependent bond-length tuning to facilitate reproduction of the experimental τ_p 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>_a 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^–1 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>_{60 MPa} – <i>X</i>_{0.1 MPa} where <i>X</i> = <i>E</i>_conf, Δ<i>μ</i>, <i>TS</i>, or <i>G</i>. Δ<i>G</i> = Δ<i>E</i>_conf+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 Mg²⁺ 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>_Nu are defined by O^β-P^γ-O^w and P^γ-O^w, respectively, where O^w 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>_ex), solvent accessible surface area (SASA) and isothermal compressibility (<i>κ_T</i>).

<p>Units: <i>V</i>_ex (10⁴ ų), SASA (10⁴ Ų), <i>κ_T</i>, (GPa⁻¹). Δ = <i>X</i>_{60 MPa} – <i>X</i>_{0.1 MPa} where <i>X</i> = <i>V</i>_ex, SASA, or <i>κ_T</i>. The value after “±” indicates standard deviation.</p

Number of salt bridges formed between secondary structures and subdomains.

<p>Salt bridges ^abetween distinct helices or strands, ^bbetween a helix/strand and a loop, ^cbetween distinct loops, ^dwithin helix or strand. ^eSalt bridges between ATP and a residue. ^fInter and ^gintra subdomain salt bridge. ^hThe 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 Mg²⁺ 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