MassCCS: A High-Performance Collision Cross-Section Software for Large Macromolecular Assemblies.

Ion mobility mass spectrometry (IM-MS) techniques have become highly valued as a tool for structural characterization of biomolecular systems since they yield accurate measurements of the rotationally averaged collision cross-section (CCS) against a buffer gas. Despite its enormous potential, IM-MS data interpretation is often challenging due to the conformational isomerism of metabolites, lipids, proteins, and other biomolecules in the gas phase. Therefore, reliable and fast CCS calculations are needed to help interpret IM-MS data. In this work, we present MassCCS, a parallelized open-source code for computing CCS of molecules ranging from small organic compounds to massive protein assemblies at the trajectory method level of description using atomic and molecular buffer gas particles. The performance of the code is comparable to other available software for small molecules and proteins but is significantly faster for larger macromolecular assemblies. We performed extensive tests regarding accuracy, performance, and scalability with system size and number of CPU cores. MassCCS has proven highly accurate and efficient, with execution times under a few minutes, even for large (84.87 MDa) virus capsid assemblies with very modest computational resources. MassCCS is freely available at https://github.com/cces-cepid/massccs.

Adsorption of lysozyme into a charged confining pore.

Several applications arise from the confinement of proteins on surfaces because their stability and biological activity are enhanced. It is also known that the way in which a protein adsorbs on the surface is important for its biological function since its active sites should not be obstructed. In this study, the adsorption properties of hen egg-white lysozyme, HEWL, into a negatively charged silica pore is examined by employing a coarse-grained model and constant-pH Monte Carlo simulations. The role of electrostatic interactions is taken into account via including the Debye-Hückel potentials into the Cα structure-based model. We evaluate the effects of pH, salt concentration, and pore radius on the protein preferential orientation and spatial distribution of its residues regarding the pore surface. By mapping the residues that stay closer to the pore surface, we find that the increase of pH leads to orientational changes of the adsorbed protein when the solution pH gets closer to the HEWL isoelectric point. Under these conditions, the pKa shift of these important residues caused by the adsorption into the charged confining surface results in a HEWL charge distribution that stabilizes the adsorption in the observed protein orientation. We compare our observations to the results of the pKa shift for HEWL available in the literature and to some experimental data.

Monte Carlo simulations and mean-field modeling of electric double layers at weakly and moderately charged spherical macroions.

Monte Carlo simulations are employed to determine the differential capacitance of an electric double layer formed by small size-symmetric anions and cations in the vicinity of weakly to moderately charged macroions. The influence of interfacial curvature is deduced by investigating spherical macroions, ranging from flat to moderately curved. We also calculate the differential capacitance using a previously developed mean-field model where, in addition to electrostatic interactions, the excluded volumes of the ions are taken into account using either the lattice-gas or the Carnahan-Starling equation of state. For both equations of state, we compare the mean-field model for arbitrary curvature with a recently developed second-order curvature expansion. Our Monte Carlo simulations predict an increase in the differential capacitance with growing macroion curvature if the surface charge density is small, whereas for moderately charged macroions the differential capacitance passes through a local minimum. Both mean-field models tend to somewhat overestimate the differential capacitance as compared with Monte Carlo simulations. At the same time, they do reproduce the curvature dependence of the differential capacitance, especially for small surface charge density. Our study suggests that the quality of mean-field modeling does not worsen when weakly or moderately charged macroions exhibit spherical curvature.

Critical adsorption of multiple polyelectrolytes onto a nanosphere: splitting the adsorption-desorption transition boundary.

Employing extensive Monte Carlo computer simulations, we investigate in detail the properties of multichain adsorption of charged flexible polyelectrolytes (PEs) onto oppositely charged spherical nanoparticles (SNPs). We quantify the conditions of critical adsorption-the phase-separation curve between the adsorbed and desorbed states of the PEs-as a function of the SNP surface-charge density and the concentration of added salt. We study the degree of fluctuations of the PE-SNP electrostatic binding energy, which we use to quantify the emergence of the phase subtransitions, including a series of partially adsorbed PE configurations. We demonstrate how the phase-separation adsorption-desorption boundary shifts and splits into multiple subtransitions at low-salt conditions, thereby generalizing and extending the results for critical adsorption of a single PE onto the SNP. The current findings are relevant for finite concentrations of PEs around the attracting SNP, such as the conditions for PE adsorption onto globular proteins carrying opposite electric charges.

pH and Charged Mutations Modulate Cold Shock Protein Folding and Stability: A Constant pH Monte Carlo Study.

The folding and stability of proteins is a fundamental problem in several research fields. In the present paper, we have used different computational approaches to study the effects caused by changes in pH and for charged mutations in cold shock proteins from Bacillus subtilis (Bs-CspB). First, we have investigated the contribution of each ionizable residue for these proteins to their thermal stability using the TKSA-MC, a Web server for rational mutation via optimizing the protein charge interactions. Based on these results, we have proposed a new mutation in an already optimized Bs-CspB variant. We have evaluated the effects of this new mutation in the folding energy landscape using structure-based models in Monte Carlo simulation at constant pH, SBM-CpHMC. Our results using this approach have indicated that the charge rearrangements already in the unfolded state are critical to the thermal stability of Bs-CspB. Furthermore, the conjunction of these simplified methods was able not only to predict stabilizing mutations in different pHs but also to provide essential information about their effects in each stage of protein folding.

Modeling the camel-to-bell shape transition of the differential capacitance using mean-field theory and Monte Carlo simulations.

Mean-field electrostatics is used to calculate the differential capacitance of an electric double layer formed at a planar electrode in a symmetric 1:1 electrolyte. Assuming the electrolyte is also ion-size symmetric, we derive analytic expressions for the differential capacitance valid up to fourth order in the surface charge density or surface potential. Our mean-field model accounts exclusively for electrostatic interactions but includes an arbitrary non-ideality in the mixing entropy of the mobile ions. The ensuing criterion for the camel-to-bell shape transition of the differential capacitance is analyzed using commonly used mixing models (one based on a lattice gas and the other based on the Carnahan-Starling equation of state) and compared with Monte Carlo simulations. We observe a reasonable agreement between all our mean-field models and the simulation data for the camel-to-bell shape transition. The absolute value of the differential capacitance for an uncharged (or weakly charged) electrode is, however, not reproduced by our mean-field approaches, not even upon introducing a Stern layer with a thickness equal of the ion radius. We show that, if a Stern layer is introduced, its thickness dependence on the ion size is non-monotonic or, depending on the salt concentration, even inversely proportional.

Differential capacitance of an electric double layer with asymmetric solvent-mediated interactions: mean-field theory and Monte Carlo simulations.

The differential capacitance of an electrical double layer is directly affected by properties of the electrolyte solution such as temperature, salt concentration, ionic size, and solvent structure. In the present work, we employ a mean-field approach and Monte Carlo simulations to investigate how the inclusion of asymmetric solvent-mediated ion-ion and ion-surface interactions affects the differential capacitance. We focus on a charged flat electrode immersed in an electrolyte solution of monovalent ions at physiological concentration in a uniform dielectric background. Solvent-mediated anion-anion, anion-cation and cation-cation interactions are modeled on the basis of Yukawa potentials with three independent strengths that add to Coulomb and excluded volume pair-potentials, the latter accounted for through a lattice gas approach. We use the three interaction strengths to produce and analyze asymmetric profiles of the differential capacitance as function of the electrode's surface charge density. While solvent-mediated anion-anion and cation-cation interactions mainly affect the behavior at medium charge densities of the electrode, anion-cation repulsion increases the differential capacitance of a weakly charged electrode. We present a simple phenomenological model to rationalize this finding. Most importantly, because the added solvent-mediated interaction potential is comparatively soft, our mean-field model is able to qualitatively - and in some cases quantitatively - reproduce all Monte Carlo simulation results, even at high surface charge densities of the electrode.

Critical adsorption of periodic and random polyampholytes onto charged surfaces.

How different are the properties of critical adsorption of polyampholytes and polyelectrolytes onto charged surfaces? How important are the details of polyampholyte charge distribution on the onset of critical adsorption transition? What are the scaling relations governing the dependence of critical surface charge density on salt concentration in the surrounding solution? Here, we employ Metropolis Monte Carlo simulations and uncover the scaling relations for critical adsorption for quenched periodic and random charge distributions along the polyampholyte chains. We also evaluate and discuss the dependence of the adsorbed layer width on solution salinity and details of the charge distribution. We contrast our findings to the known results for polyelectrolyte adsorption onto oppositely charged surfaces, in particular, their dependence on electrolyte concentration.

Conformational properties of block-polyampholytes adsorbed on charged cylindrical surfaces.

Polyampholytes are polymers that have positive and negative monomers along their chain. The adsorption of polyampholytes on charged surfaces has been the subject of a large number of theoretical, computational and experimental studies due to its importance in a variety of bio and nanothechnological systems. However, computational studies focusing on interaction between polyampholytes and cylindrical charged surfaces are rather scarce. This study, therefore, aims to investigate the conformational properties of block-polyampholytes in the presence of a negatively charged cylinder by means of Metropolis Monte Carlo simulations. Adopting a simplified model in which the electrolyte solution is treated at the Debye-Hückel level, the effects of the ionic strength, the linear charge density of the cylinder and the block length on monomers distributions have been investigated. It was found that increasing the salt concentration promotes a transition from a conformation characterized by large loops to a necklace-like conformation parallel to the surface. It was also shown that, at low cylinder charge density, the increase in salt concentration and the length of the blocks lead to a change in the orientation of the adsorbed chain.

Role of ion hydration for the differential capacitance of an electric double layer.

The influence of soft, hydration-mediated ion-ion and ion-surface interactions on the differential capacitance of an electric double layer is investigated using Monte Carlo simulations and compared to various mean-field models. We focus on a planar electrode surface at physiological concentration of monovalent ions in a uniform dielectric background. Hydration-mediated interactions are modeled on the basis of Yukawa potentials that add to the Coulomb and excluded volume interactions between ions. We present a mean-field model that includes hydration-mediated anion-anion, anion-cation, and cation-cation interactions of arbitrary strengths. In addition, finite ion sizes are accounted for through excluded volume interactions, described either on the basis of the Carnahan-Starling equation of state or using a lattice gas model. Both our Monte Carlo simulations and mean-field approaches predict a characteristic double-peak (the so-called camel shape) of the differential capacitance; its decrease reflects the packing of the counterions near the electrode surface. The presence of hydration-mediated ion-surface repulsion causes a thin charge-depleted region close to the surface, which is reminiscent of a Stern layer. We analyze the interplay between excluded volume and hydration-mediated interactions on the differential capacitance and demonstrate that for small surface charge density our mean-field model based on the Carnahan-Starling equation is able to capture the Monte Carlo simulation results. In contrast, for large surface charge density the mean-field approach based on the lattice gas model is preferable.