RESUMO
An accurate force calculation with the Poisson-Boltzmann equation is challenging, as it requires the electric field on the molecular surface. Here we present a calculation of the electric field on the solute-solvent interface that is exact for piecewise linear variations of the potential and analyze four different alternatives to compute the force using a boundary element method. We performed a verification exercise for two cases: the isolated and two interacting molecules. Our results suggest that the boundary element method outperforms the finite difference method, as the latter needs a much finer mesh than in solvation energy calculations to get acceptable accuracy in the force, whereas the same surface mesh as in a standard energy calculation is appropriate for the boundary element method. Among the four evaluated alternatives of force calculation, we saw that the most accurate one is based on the Maxwell stress tensor. However, for a realistic application, like the barnase-barstar complex, the approach based on variations of the energy functional, which is less accurate, gives equivalent results. This analysis is useful toward using the Poisson-Boltzmann equation for force calculations in applications where high accuracy is key, for example, to feed molecular dynamics models or to enable the study of the interaction between large molecular structures, like viruses adsorbed onto substrates.
RESUMO
Electrostatic interactions are crucial for the assembly, disassembly and stability of proteinaceous viral capsids. Moreover, at the molecular scale, elucidating the organization and structure of the capsid proteins in response to an approaching nanoprobe is a major challenge in biomacromolecular research. Here, we report on a generalized electrostatic model, based on the Poisson-Boltzmann equation, that quantifies the subnanometric electrostatic interactions between an AFM tip and a proteinaceous capsid from molecular snapshots. This allows us to describe the contributions of specific amino acids and atoms to the interaction force. We show validation results in terms of total electrostatic forces with previous semi-empirical generalized models at available length scales (d > 1 nm). Then, we studied the interaction of the Zika capsid with conical and spherical AFM tips in a tomography-type analysis to identify the most important residues and atoms, showing the localized nature of the interaction. This method can be employed for the interpretation of force microscopy experiments in fundamental virological characterization and in diverse nanomedicine applications, where specific regions of the protein cages are aimed to electrostatically interact with molecular sized functionalized inhibitors, or tailoring protein-cage functional properties for nucleic acid delivery.
Assuntos
Infecção por Zika virus , Zika virus , Capsídeo/química , Proteínas do Capsídeo/química , Humanos , Microscopia de Força Atômica , Eletricidade Estática , Tomografia , VírionRESUMO
RNA is a functionally rich molecule with multilevel, hierarchical structures whose role in the adsorption to molecular substrates is only beginning to be elucidated. Here, we introduce a multiscale simulation approach that combines a tractable coarse-grained RNA structural model with an interaction potential of a structureless flat adsorbing substrate. Within this approach, we study the specific role of stem-hairpin and multibranch RNA secondary structure motifs on its adsorption phenomenology. Our findings identify a dual regime of adsorption for short RNA fragments with and without the secondary structure and underline the adsorption efficiency in both cases as a function of the surface interaction strength. The observed behavior results from an interplay between the number of contacts formed at the surface and the conformational entropy of the RNA molecule. The adsorption phenomenology of RNA seems to persist also for much longer RNAs as qualitatively observed by comparing the trends of our simulations with a theoretical approach based on an ideal semiflexible polymer chain.
RESUMO
Three-dimensional RNA domain reconstruction is important for the assembly, disassembly and delivery functionalities of a packed proteinaceus capsid. However, to date, the self-association of RNA molecules is still an open problem. Recent chemical probing reports provide, with high reliability, the secondary structure of diverse RNA ensembles, such as those of viral genomes. Here, we present a method for reconstructing the complete 3D structure of RNA genomes, which combines a coarse-grained model with a subdomain composition scheme to obtain the entire genome inside proteinaceus capsids based on secondary structures from experimental techniques. Despite the amount of sampling involved in the folded and also unfolded RNA molecules, advanced microscope techniques can provide points of anchoring, which enhance our model to include interactions between capsid pentamers and RNA subdomains. To test our method, we tackle the satellite tobacco mosaic virus (STMV) genome, which has been widely studied by both experimental and computational communities. We provide not only a methodology to structurally analyze the tertiary conformations of the RNA genome inside capsids, but a flexible platform that allows the easy implementation of features/descriptors coming from both theoretical and experimental approaches.
Assuntos
Capsídeo/química , Genoma Viral , Estrutura Secundária de Proteína , Vírus de RNA/química , Vírus de RNA/genética , RNA Viral/genética , Vírus Satélite do Mosaico do Tabaco/genética , Proteínas do Capsídeo/genética , Modelos Moleculares , Conformação de Ácido Nucleico , Vírus Satélite do Mosaico do Tabaco/químicaRESUMO
Molecular simulations of large biological systems, such as viral capsids, remains a challenging task in soft matter research. On one hand, coarse-grained (CG) models attempt to make the description of the entire viral capsid disassembly feasible. On the other hand, the permanent development of novel molecular dynamics (MD) simulation approaches, like enhanced sampling methods, attempt to overcome the large time scales required for such simulations. Those methods have a potential for delivering molecular structures and properties of biological systems. Nonetheless, exploring the process on how a viral capsid disassembles by all-atom MD simulations has been rarely attempted. Here, we propose a methodology to analyze the disassembly process of viral capsids from a free energy perspective, through an efficient combination of dynamics using coarse-grained models and Poisson-Boltzmann simulations. In particular, we look at the effect of pH and charge of the genetic material inside the capsid, and compute the free energy of a disassembly trajectory precalculated using CG simulations with the SIRAH force field. We used our multiscale approach on the Triatoma virus (TrV) as a test case, and find that even though an alkaline environment enhances the stability of the capsid, the resulting deprotonation of the genetic material generates a Coulomb-type electrostatic repulsion that triggers disassembly.