Details of charge distribution in stable viral capsid

We present the results of Molecular Dynamics simulations of a viral capsid with the aim to analyse ion distribution on the capsid's surface that defines its stability. Two systems were modelled, a stable capsid with neutralising number of ions and an unstable capsid with low number of ions. For the ion distribution analysis the capsid's structure was identical and fixed in both simulations. It was then released for the stability analysis. The ion distribution demonstrated two types of the local regions on the inner surface of the capsid's wall: highly occupied with chloride ions in both systems despite a largely uniform electrostatic potential everywhere on the surface, and the regions that loose almost all chloride ions in the unstable capsid. The latter regions are located close to the cracks that are formed when the capsid is destabilised and thus could initiate the collapse of the capsid

Study of the effectiveness of various cannabinoid receptor 1 (CB1) agonists using molecular docking and molecular dynamics modeling

The binding of a series of small organic molecules, acting as agonists of the cannabinoid receptor CB1, was investigated by means of three methods of computational chemistry. Binding modes were predicted by means of molecular docking, and binding free energy was estimated via docking, molecular-mechanics Poisson-Boltzmann surface area method, and multistate Bennett acceptance ratio. No evident correlation was observed for the molecules between the experimental characteristics of affinity and three computed binding free energy estimates. The reasons for the discrepancy were discussed

Reconstruction and validation of entire virus model with complete genome from mixed resolution cryo-EM density

It is very difficult to reconstruct computationally a large biomolecular complex in its biological entirety from experimental data. The resulting atomistic model should not contain gaps structurally and it should yield stable dynamics. We, for the first time, reconstruct from published incomplete cryo-EM density a complete MS2 virus at atomistic resolution, that is, the capsid with the genome, and validate the result by all-atom Molecular Dynamics with explicit water. The available experimental data includes a high resolution protein capsid and an inhomogeneously resolved genome map. For the genomic RNA, apart from 16 hairpins with atomistic resolution, the strands near the capsid’s inner surface were resolved up to the nucleic backbone level, and the innermost density was completely unresolved. As a result, only 242 nucleotides (out of 3569) were positioned, while only a fragmented backbone was outlined for the rest of the genome, making a detailed model reconstruction necessary. For model reconstruction, in addition to the available atomistic structure information, we extensively used the predicted secondary structure of the genome (base pairing). The technique was based on semi-automatic building of relatively large strands of RNA with subsequent manual positioning over the traced backbone. The entire virus structure (capsid+genome) was validated by a Molecular Dynamics run in physiological solution with ions at standard conditions confirming the stability of the model

A hybrid molecular dynamics/fluctuating hydrodynamics method for modelling liquids at multiple scales in space and time

A new 3D implementation of a hybrid model based on the analogy with two-phase hydrodynamics has been developed for the simulation of liquids at microscale. The idea of the method is to smoothly combine the atomistic description in the molecular dynamics zone with the Landau-Lifshitz fluctuating hydrodynamics representation in the rest of the system in the framework of macroscopic conservation laws through the use of a single "zoom-in" user-defined function s that has the meaning of a partial concentration in the two-phase analogy model. In comparison with our previous works, the implementation has been extended to full 3D simulations for a range of atomistic models in GROMACS from argon to water in equilibrium conditions with a constant or a spatially variable function s. Preliminary results of simulating the diffusion of a small peptide in water are also reported

Protein-ligand dissociation rate constant from all-atom simulation

Dissociation of a ligand isoniazid from a protein catalase was investigated using all-atom Molecular Dynamics (MD) simulations. Random Acceleration MD (τ-RAMD) was used where a random artificial force applied to the ligand facilitates its dissociation. We have suggested an approach to extrapolate such obtained dissociation times to the zero-force limit that was never attempted before, thus allowing direct comparison with experimentally measured values. We have found that our calculated dissociation time was equal to 36.1 seconds with statistically significant values distributed in the interval 0.2-72.0 s, that quantitatively matches the experimental value of 50 ± 8 seconds despite the extrapolation over nine orders of magnitude in time

In search of an optimal acid-base indicator for examining surfactant micelles:Spectrophotometric studies and molecular dynamics simulations

We report on combined experimental and theoretical investigations of the water/micelle interface of cationic, anionic, zwitterionic, and non-ionic surfactants using a new hydrophobic acid-base indicator 2,6-dinitro-4-n-dodecylphenol. The indices of the so-called apparent ionization constant, pKa app, of the indicator fixed in the micellar pseudophase are determined by the spectrophotometric method. The data allows estimating the Stern layer's electrostatic potential of the ionic micelles Ψ. Molecular Dynamics modeling was used to locate the dye molecule and, in particular, its ionizing group OH→O– within the micelles of the studied surfactants. The comparison of the Ψ values estimated using 2,6-dinitro-4-n-dodecylphenol with both our computer simulation and literature experimental results reveals obstacles in monitoring electrical interfacial potentials. In particular, the Ψ values of the surfactant micelles with alkylammonium groups determined via 2,6-dinitro-4-n-dodecylphenol are overestimated. The reason is specific interactions of the indicator anion with the surfactant head groups. For anionic surfactants, however, this indicator is quite suitable, which is confirmed by the location of HA and A– equilibrium forms in the pseudophase

All-atom molecular dynamics simulations of entire virus capsid reveal the role of ion distribution in capsid’s stability

Present experimental methods do not have sufficient resolution to investigate all processes in virus particles at atomistic details. We report the results of molecular dynamics simulations and analyze the connection between the number of ions inside an empty capsid of PCV2 virus and its stability. We compare the crystallographic structures of the capsids with unresolved N-termini and without them in realistic conditions (room temperature and aqueous solution) and show that the structure is preserved. We find that the chloride ions play a key role in the stability of the capsid. A low number of chloride ions results in loss of the native icosahedral symmetry, while an optimal number of chloride ions create a neutralizing layer next to the positively charged inner surface of the capsid. Understanding the dependence of the capsid stability on the distribution of the ions will help clarify the details of the viral life cycle that is ultimately connected to the role of packaged viral genome inside the capsid

Association of novel monomethine cyanine dyes with bacteriophage MS2:A fluorescence study

Novel monomethine cyanine dyes Cl-YO, F-YO, Cl-YO-Et, Cl-YO-Bu, and YO-Pent were evaluated as agents to detect and characterise a small virus, the MS2 bacteriophage, using the dye and virus intrinsic fluorescence, kinetic and thermal properties, chemical denaturation, and molecular docking and quantum chemistry modelling. The examined compounds demonstrated enhanced fluorescence responses and high affinities (~1 μM−1) for the intact bacteriophage at physiological ionic strength. The linear Scatchard plots revealed the existence of one binding mode for most dyes. Strong evidence that the cyanines bind to the bacteriophage external surface were obtained, although the possibility of the dye penetration through the virus shell and subsequent complexation with the viral RNA was also tested. The main arguments in favour of the former were that i) the fluorescence of the MS2-bound fluorophores decreased under the influence of protein denaturants, urea and guanidine hydrochloride; ii) the fluorescence responses of the dyes to MS2 and bovine serum albumin were similar; and (iii) one order of magnitude higher sensitivity of the dyes to the yeast RNA was found. Simple docking studies suggested that one cyanine molecule is trapped in a cleft formed by three proteins composing the virus shell. Significant role of electrostatic forces in the stabilisation of the dye-MS2 complexes at low ionic strength (10 mM) was demonstrated, while the influence of steric, hydrophobic, and van-der-Waals interactions was expected to increase at physiological ionic strength. The spectral properties of the novel cyanine dyes compared to other fluorophores demonstrated higher sensitivity of the cyanines to MS2, rendering them promising agents for the investigation of the changes in the virus structure under the influence of heat (Cl-YO-Et, Cl-YO-Bu), denaturants (Cl-YO, F-YO), and ionic strength (all the compounds)

Analysis of Waterman’s Method in the Case of Layered Scatterers

The method suggested by Waterman has been widely used in the last years to solve various light scattering problems. We analyze the mathematical foundations of this method when it is applied to layered nonspherical (axisymmetric) particles in the electrostatic case. We formulate the conditions under which Waterman’s method is applicable, that is, when it gives an infinite system of linear algebraic equations relative to the unknown coefficients of the field expansions which is solvable (i.e., the inverse matrix exists) and solutions of the truncated systems used in calculations converge to the solution of the infinite system. The conditions obtained are shown to agree with results of numerical computations. Keeping in mind the strong similarity of the electrostatic and light scattering cases and the agreement of our conclusions with the numerical calculations available for homogeneous and layered scatterers, we suggest that our results are valid for light scattering as well