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Granulocyte-colony stimulating factor (GCSF) is a widely used therapeutic protein to treat neutropenia. GCSF has an increased propensity to aggregate if the pH is increased above 5.0. Although GCSF is very well experimentally characterized, the exact pH-dependent aggregation mechanism of GCSF is still under debate. This study aimed to model the complex pH-dependent aggregation behavior of GCSF using state-of-the-art simulation techniques. The conformational stability of GCSF was investigated by performing metadynamics simulations, while the protein-protein interactions were investigated using coarse-grained (CG) simulations of multiple GCSF monomers. The CG simulations were directly compared with small-angle X-ray (SAXS) data. The metadynamics simulations demonstrated that the orientations of Trp residues in GCSF are dependent on pH. The conformational change of Trp residues is due to the loss of Trp-His interactions at the physiological pH, which in turn may increase protein flexibility. The helical structure of GCSF was not affected by the pH conditions of the simulations. Our CG simulations indicate that at pH 4.0, the colloidal stability may be more important than the conformational stability of GCSF. The electrostatic potential surface and CG simulations suggested that the basic residues are mainly responsible for colloidal stability as deprotonation of these residues causes a reduction of the highly positively charged electrostatic barrier close to the aggregation-prone long loop regions.

Connexin channels play numerous essential roles in virtually every organ by mediating solute exchange between adjacent cells, or between cytoplasm and extracellular milieu. Our understanding of the structure-function relationship of connexin channels relies on X-ray crystallographic data for human connexin 26 (hCx26) intercellular gap junction channels. Comparison of experimental data and molecular dynamics simulations suggests that the published structures represent neither fully-open nor closed configurations. To facilitate the search for alternative stable configurations, we developed a coarse grained (CG) molecular model of the hCx26 hemichannel and studied its responses to external electric fields. When challenged by a field of 0.06 V/nm, the hemichannel relaxed toward a novel configuration characterized by a widened pore and an increased bending of the second transmembrane helix (TM2) at the level of the conserved Pro87. A point mutation that inhibited such transition in our simulations impeded hemichannel opening in electrophysiology and dye uptake experiments conducted on HeLa tranfectants. These results suggest that the hCx26 hemichannel uses a global degree of freedom to transit between different configuration states, which may be shared among the whole connexin family.

Abstract: The ability of a highly coarse‐grained polymer model is explored to simulate the impact of carbon black (CB) filler concentration on the rheological properties of unvulcanized styrene–butadiene melts—an intermediate stage in the production of styrene–butadiene rubber (SBR) commonly used in tyres. Responsive particle dynamics (RaPiD), previously used to study dilute polymeric systems, models entire polymers as single particles interacting through a combination of conservative interactions and transient entanglement‐mimicking forces. The simulation parameters are tuned to the linear rheology of the unfilled melt, as measured using a rubber process analyzer (RPA). For the filled compounds, only the interaction between the polymers and fillers is varied. On top of excluded volume interactions, a slight attraction (≈0.1 kBT) between polymers and fillers is required to attain agreement with RPA measurements. The physical origins of the small strength of this interaction are discussed. This method offers potential for future numerical investigations of filled melts. [ABSTRACT FROM AUTHOR]

Connexin channels play numerous essential roles in virtually every organ by mediating solute exchange between adjacent cells, or between cytoplasm and extracellular milieu. Our understanding of the structure-function relationship of connexin channels relies on X-ray crystallographic data for human connexin 26 (hCx26) intercellular gap junction channels. Comparison of experimental data and molecular dynamics simulations suggests that the published structures represent neither fully-open nor closed configurations. To facilitate the search for alternative stable configurations, we developed a coarse grained (CG) molecular model of the hCx26 hemichannel and studied its responses to external electric fields. When challenged by a field of 0.06 V/nm, the hemichannel relaxed toward a novel configuration characterized by a widened pore and an increased bending of the second transmembrane helix (TM2) at the level of the conserved Pro87. A point mutation that inhibited such transition in our simulations impeded hemichannel opening in electrophysiology and dye uptake experiments conducted on HeLa tranfectants. These results suggest that the hCx26 hemichannel uses a global degree of freedom to transit between different configuration states, which may be shared among the whole connexin family. [ABSTRACT FROM AUTHOR]

Membrane fusion is critical to eukaryotic cellular function and crucial to the entry of enveloped viruses such as influenza and human immunodeficiency virus. Influenza viral entry in the host cell is mediated by a 20-23 amino acid long sequence, called the fusion peptide (FP). Recently, possible structures for the fusion peptide (ranging from an inverted V shaped alpha-helical structure to an alpha-helical hairpin, or to a complete alpha-helix) and their implication in the membrane fusion initiation have been proposed. Despite the large number of studies devoted to the structure of the FP, the mechanism of action of this peptide remains unclear with several mechanisms having been suggested, including the induction of local disorder, promoting membrane curvature, and/or altering local membrane composition.In recent years, several research groups have employed atomistic and/or coarse-grained molecular dynamics (MD) simulations to investigate the matter.In all previous works, the behaviour of a single FP monomer was studied, while in this manuscript, we use a simplified model of a tripeptide (TP) monomer of FP (TFP) instead of a single FP monomer because each Influenza Hemagglutinin contains three FP molecules in the biological system. In this manuscript we report findings targeted at understanding the fusogenic properties and the collective behaviour of these trimers of FP peptides on a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine model membrane. Here we show how the TFP monomers self-assemble into differently sized oligomers in the presence of the membrane. We measure the perturbation to the structure of the phospholipid membrane caused by the presence of these TFP oligomers. Our work (i) shows how self-assembly of TFP in the presence of the membrane induces non negligible deformation to the membrane and (ii) could be a useful starting point to stimulate discussion and further work targeted to fusion pore formation.

Viral channel forming proteins (VCPs) have been discovered in the late 70s and are found in many viruses to date. Usually they are small and have to assemble to form channels which depolarize the lipid membrane of the host cells. Structural information is just about to emerge for just some of them. Thus, computational methods play a pivotal role in generating plausible structures which can be used in the drug development process. In this review the accumulation of structural data is introduced from a historical perspective. Computational performances and their predictive power are reported guided by biological questions such as the assembly, mechanism of function and drug–protein interaction of VCPs. An outlook of how coarse grained simulations can contribute to yet unexplored issues of these proteins is given. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov. [ABSTRACT FROM AUTHOR]

Segmented thermoplastic polyurethanes, polyureas and polyurethaneureas (TPU) based on a given hard segment and two chemically different soft segments display interesting microphase morphologies and thermal, mechanical and surface properties. In these systems the final TPU morphology is mainly controlled by the structure, amount and molecular weight of the soft segment oligomers and the nature and extent of specific intermolecular interactions between the mixed soft segments themselves and with the urethane hard segments. These interactions lead to variable compatibilities between the soft and hard segments resulting in interesting TPU morphologies. The proper choice of the two chemically different soft blocks provides more flexibility in controlling the extent of microphase separation, size and shape of the microphase domains and offers new possibilities for controlling the properties of TPUs. In this study coarse grained computer simulations were carried out to better understand the nature of intermolecular interactions and to elucidate the equilibrium microphase morphologies of TPUs with two different soft segments at 300 K. Model TPU systems investigated are comprised of poly(tetramethylene oxide) (PTMO) or poly(hexylethyl carbonate) (PHEC) and polydimethylsiloxane (PDMS) or polyisobutylene (PIB) soft segments with molecular weights in the range of 500–2500 g/mol. Hard segments consisted, in all cases, of diphenylmethane diisocyanate (MDI) based urethane repeat units and ranged from 25 to 50% by weight. Through coarse grained Dissipative Particle Dynamics (DPD) simulations it was demonstrated that by varying the composition and the chain lengths of the soft and hard blocks, quite different morphologies from homogeneous (or mixed) to gradient and to completely microphase separated structures were attainable. As expected, fairly hydrophobic soft blocks such as PIB and PDMS favored strong microphase separation when compared with relatively hydrophilic PHEC and PTMO segments. For comparison, morphologies of the TPUs based on single soft segments (PTMO, PHEC, PDMS and PEO) with varying molecular weights and hard segment contents were also simulated. [ABSTRACT FROM AUTHOR]

The salt dependent radius of gyration of a polyelectrolyte in aqueous solution is calculated in an environment where the polyelectrolyte is surrounded by a permeable membrane that exchanges only solvent particles with the bulk. We obtain additionally the scaling exponent of the gyration radius as a function of the polymerization degree, and find that the polyelectrolyte retains a stretched conformation during the condensation and re-expansion process, indicating that these effects are of an electrostatic nature. The solvent quality is also shown to affect the polyelectrolyte conformation, especially for the poor solvent case. These results are obtained using a hybridized Monte Carlo technique with the coarse-grained, dissipative particle dynamics method with fluctuating number of solvent particles. The full range of the electrostatic interactions is included in the simulations, using the Ewald sum method, and the counterions and solvent molecules are included explicitly. In the complex systems mentioned above, the electrostatic interactions and the solvent quality play a key role in understanding phenomena that do not occur in uncharged systems. Our results are compared and validated with the behavior of some biomolecules under similar environments. [ABSTRACT FROM AUTHOR]

Granulocyte-colony stimulating factor (GCSF) is a widely used therapeutic protein to treat neutropenia. GCSF has an increased propensity to aggregate if the pH is increased above 5.0. Although GCSF is very well experimentally characterized, the exact pH-dependent aggregation mechanism of GCSF is still under debate. This study aimed to model the complex pH-dependent aggregation behavior of GCSF using state-of-the-art simulation techniques. The conformational stability of GCSF was investigated by performing metadynamics simulations, while the protein-protein interactions were investigated using coarse-grained (CG) simulations of multiple GCSF monomers. The CG simulations were directly compared with small-angle X-ray (SAXS) data. The metadynamics simulations demonstrated that the orientations of Trp residues in GCSF are dependent on pH. The conformational change of Trp residues is due to the loss of Trp-His interactions at the physiological pH, which in turn may increase protein flexibility. The helical structure of GCSF was not affected by the pH conditions of the simulations. Our CG simulations indicate that at pH 4.0, the colloidal stability may be more important than the conformational stability of GCSF. The electrostatic potential surface and CG simulations suggested that the basic residues are mainly responsible for colloidal stability as deprotonation of these residues causes a reduction of the highly positively charged electrostatic barrier close to the aggregation-prone long loop regions., Competing Interests: The authors declare that there are no known conflicts of interest. The financial support of the research or personal relationships do not have any significant impact on the outcomes reported in this works., (© 2022 The Authors. Published by Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology.)

We use coarse-grained molecular dynamics simulations to study a single di block polyelectrolyte chain in solution. We analyze the conformational properties of the chain and localization of counterions as a function of the charge fraction, backbone stiffness, Bjerrum length, and counterion valence. The interplay between the excluded-volume effects and the electrostatic interactions among charged residues leads to variation in block−polyelectrolyte architecture. Our computational findings indicate that varying such system properties lead to nontrivial effects and can be a powerful mechanism to tune the conformational properties of block polyelectrolytes. Unlabelled Image • We study the conformational properties of single diblock polyelectrolyte chain in aqueous solution using coarse- grained Langevin dynamics simulations. • We investigate the dependence of the basic properties such as the radius of gyration, the mean end-to-end distance and the pair correlation function on system variables such as charged residues, rigidity, dielectrics, and counterion valence for block polyelectrolytes with diblock architectures. • Our computational studies show how the such properties of block polyelectrolytes can be tuned by varying such system properties. [ABSTRACT FROM AUTHOR]