LitCovid-sentences  

PMC:7605337 / 13003-19979 JSONTXT 8 Projects

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Id Subject Object Predicate Lexical cue
T64 0-14 Sentence denotes MD Simulations
T65 15-148 Sentence denotes The crystal structure of nCOV-2019 in the complex with hACE2 (pdb id:6M0J)17 as well as the SARS-COV complex with human ACE2 (pdb id:
T66 149-305 Sentence denotes 6ACJ)33 were obtained from RCSB (www.rcsb.org).34 The RBD domain of nCOV-2019 comprises 194 residues (333–526) and SARS-COV includes 190 residues (323–512).
T67 306-392 Sentence denotes ACE2 protein contains 597 residues (19–615) in the complex structure for both systems.
T68 393-648 Sentence denotes All the structures including nCOV-2019, SARS-COV, and all 21 alanine substitutions of nCOV-2019 were prepared and solvated in GROMACS.35 A TIP3P water model was used for the solvent and Param99SB-ILDN AMBER force field36,37 was used for all the complexes.
T69 649-842 Sentence denotes A few counter ions were added to each system to neutralize the charges on the RBD and ACE2 as the PBSA method for binding energy calculation is known to be problematic with high ionic strength.
T70 843-885 Sentence denotes Each system contained about 260,000 atoms.
T71 886-978 Sentence denotes It is important to note that, none of the RBD/ACE2 complexes studied here were glycosylated.
T72 979-1098 Sentence denotes The glycosylation sites on RBD are far from the binding interface and do not interfere with the binding of RBD to ACE2.
T73 1099-1279 Sentence denotes Moreover, there are nine Cys residues at the RBD of nCOV-2019 and eight of them form four pairs of disulfide bonds (Cys336-Cys361, Cys379-Cys432, Cys391-Cys525, and Cys480-Cys488).
T74 1280-1372 Sentence denotes In total, 5000 steps of energy minimizations were done using the steepest descent algorithm.
T75 1373-1527 Sentence denotes In all steps, the LINCS algorithm was used to constrain all bonds containing hydrogen atoms and a time step of 2 fs was used as the integration time step.
T76 1528-1586 Sentence denotes Equilibration of all systems was performed in three steps.
T77 1587-1963 Sentence denotes In the first step, 100,000 steps of simulation were performed using a velocity-rescaling thermostat to maintain the temperature at 310 K with a 0.1 ps coupling constant in an NVT ensemble under periodic boundary conditions and harmonic restraints on the backbone and side-chain atoms of the complex.38 A velocity rescaling thermostat was used in all other steps of simulation.
T78 1964-2284 Sentence denotes In the next step, we performed 300,000 steps in the isothermal-isobaric NPT ensemble at a temperature of 310 K and pressure of 1 bar using a Berendsen barostat.39 This was done through decreasing the force constant of the restraint on the backbone and side-chain atoms of the complex from 1000 to 100 and finally to 10 .
T79 2285-2405 Sentence denotes The Berendsen barostat was only used for the equilibration step because of its usefulness in rapidly correcting density.
T80 2406-2543 Sentence denotes In the next step, the restraints were removed, and the systems were subjected to 1,000,000 steps of MD simulation under the NPT ensemble.
T81 2544-2814 Sentence denotes In the production run, harmonic restraints were removed and all the systems were simulated using a NPT ensemble where the pressure was maintained at 1 bar using the Parrinello-Rahman barostat40 with a compressibility of 4.5 × 10–5bar–1 and a coupling constant of 0.5 ps.
T82 2815-3317 Sentence denotes It is important to note that the Berendsen barostat was only used for the equilibration step as it was shown that this barostat can cause unrealistic temperature gradients.41 The production run lasted for 500 ns for SARS-COV and nCOV-2019 complexes and 300 ns for all the mutants with a 2 fs timestep and the particle-mesh Ewald42 for long range electrostatic interactions using the GROMACS 2018.3 package.43 All mutant systems were constructed as described before and ran for 300 ns of production run.
T83 3318-3425 Sentence denotes In addition, the simulation time for a few mutants (Y449A, T478I, Y489A, and S494P) was extended to 500 ns.
T84 3427-3467 Sentence denotes Gibbs Free Energy and Correlated Motions
T85 3468-3874 Sentence denotes The last 400 ns of simulation was used to explore the dominant motions in SARS-COV, nCOV-2019 and the mutations with extended simulation, and last 200 ns for all other mutants using principal component analysis (PCA) as part of the quasiharmonic analysis method.44 For this method the rotational and translational motions of RBD of all systems were eliminated by fitting to a reference (crystal) structure.
T86 3875-4118 Sentence denotes Next, 4000 snapshots from the last 400 ns of SARS-COV, nCOV-2019 and mutations with extended simulation time, and 2000 snapshots from last 200 ns of all other mutant systems were taken to generate the covariance matrix between Cα atoms of RBD.
T87 4119-4205 Sentence denotes In the mutant systems with production run, the last 400 ns was used for this analysis.
T88 4206-4539 Sentence denotes Diagonalization of this matrix resulted in a diagonal matrix of eigenvalues and their corresponding eigenvectors.43,45 The first eigenvector which indicate the first principal component was used to visualize the dominant global motions of all complexes through porcupine plots using the (PorcupinePlot.tcl) script in visual MD (VMD).
T89 4540-4642 Sentence denotes The principal components were used to calculate and plot the approximate free energy landscape (aFEL).
T90 4643-5003 Sentence denotes We refer to the FEL produced by this approach to be approximate in that the ensemble with respect to the first few PC’s (lowest frequency quasiharmonic modes) is not close to convergence, but the analysis can still provide valuable information and insight. g_sham, g_covar, and g_anaeig functions in GROMACS35 were used to obtain principal components and aFEL.
T91 5004-5255 Sentence denotes The dynamic cross-correlation maps (DCCM) were obtained using the MD_TASK package to identify the correlated motions of RBD residues.46 In DCCM, the cross-correlation matrix Cij is obtained from displacement of backbone Cα atoms at a time interval Δt.
T92 5256-5433 Sentence denotes The DCCM was constructed using the last 400 ns of SARS-COV and nCOV-2019 and the extended mutant systems and last 200 ns of all other mutant systems with a 100 ps time interval.
T93 5434-5565 Sentence denotes Hydrogen bonds were analyzed in VMD where the distance cutoff was 3.2Å and the angle cutoff between the donor and acceptor was 30°.
T94 5567-5649 Sentence denotes Binding Free Energy from Molecular Mechanics Poisson-Boltzmann Surface Area Method
T95 5650-6025 Sentence denotes The molecular mechanics Poisson-Boltzmann surface area (MMPBSA) method was applied to calculate the binding energy between RBD and ACE2 in all complexes.47,48 For SARS-COV and nCOV-2019, 200 snapshots of the last 400 ns and for the mutant systems and 100 snapshots of the last 200 ns simulation were used for the calculation of binding free energies with an interval of 2 ns.
T96 6026-6223 Sentence denotes Simulation for a few mutant systems (Y449A, T478I, Y489A, and S494P) was extended to 400 ns, and the binding energies were calculated for the last 400 ns to assess the convergence of free energies.
T97 6224-6307 Sentence denotes The binding free energy of a ligand–receptor complex can be calculated as:1 2 3 4 5
T98 6308-6515 Sentence denotes In these equations, ΔEMM, ΔGbind, solv, and −TΔS are calculated in the gas phase. ΔEMM is the gas phase molecular mechanical energy changes which includes covalent, electrostatic, and van der Waals energies.
T99 6516-6720 Sentence denotes Based on previous studies, the entropy change during binding is small and neglected in these calculations.48−50 ΔGbind, solv is the solvation free energy which comprises the polar and nonpolar components.
T100 6721-6854 Sentence denotes The polar solvation is calculated using the MMPBSA method by setting a value of 80 and 2 for solvent and solute dielectric constants.
T101 6855-6976 Sentence denotes The nonpolar free energy is simply estimated from the solvent accessible surface area (SASA) of the solute from the eq 5.