The presence of surfaces influences the fibril formation kinetics of peptides and proteins. We present a systematic study of the aggregation kinetics of amyloidogenic peptides caused by different ...surfaces using molecular simulations of model peptides and thioflavin T fluorescence experiments. Increasing the monomer–surface attraction affects the nucleation and growth of small oligomers in a nonlinear manner: Weakly attractive surfaces lead to retardation; strongly attractive surfaces lead to acceleration. Further, the same type of surface either accelerates or retards growth, depending on the bulk propensity of the peptide to form fibrils: An attractive surface retards fibril formation of peptides with a high tendency for fibril formation, while the same surface accelerates fibril formation of peptides with a low propensity for fibril formation. The surface effect is thus determined by the relative association propensity of peptides for the surface compared to bulk and by the surface area to protein concentration ratio. This rationalization is in agreement with the measured fibrillar growth of α-synuclein from Parkinson and amyloid β peptide from Alzheimer disease in the presence of surface area introduced in a controlled way in the form of nanoparticles. These findings offer molecular insight into amyloid formation kinetics in complex environments and may be used to tune fibrillation properties in diverse systems.
Cellular uptake through endocytosis is crucial for drug delivery and nanomedicine. However, the conditions under which passive endocytosis (i.e., not ATP driven) takes place are not well understood. ...We report MD simulations of the passive uptake of ligand-coated nanoparticles with varying size, shape, coverage, and membrane-binding strength. We find that the efficiency of passive endocytosis is higher for spherocylindrical particles than for spheres and that endocytosis is suppressed for particles with sharp edges.
Curvature sensing is an essential ability of biomolecules to preferentially localize to membrane regions of a specific curvature. It has been shown that amphipathic helices (AHs), helical peptides ...with both hydrophilic and hydrophobic regions, could sense a positive membrane curvature. The origin of this AH sensing has been attributed to their ability to exploit lipid-packing defects that are enhanced in regions of positive curvature. In this study, we revisit an alternative framework where AHs act as sensors of local internal stress within the membrane, suggesting the possibility of an AH sensing a negative membrane curvature. Using molecular dynamics simulations, we gradually tuned the hydrophobicity of AHs, thereby adjusting their insertion depth so that the curvature preference of AHs is switched from positive to negative. This study suggests that highly hydrophobic AHs could preferentially localize proteins to regions of a negative membrane curvature.
Cell-penetrating and some antimicrobial peptides can translocate across lipid bilayers without disrupting the membrane structure. However, the molecular properties required for efficient ...translocation are not fully understood. We employed the Metropolis Monte Carlo method together with coarse-grained models to systematically investigate free-energy landscapes associated with the translocation of secondary amphiphilic peptides. We studied α-helical peptides with different length, amphiphilicity, and distribution of hydrophobic content and found a common translocation path consisting of adsorption, tilting, and insertion. In the adsorbed state, the peptides are parallel to the membrane plane, whereas, in the inserted state, the peptides are perpendicular to the membrane. Our simulations demonstrate that, for all tested peptides, there is an optimal ratio of hydrophilic/hydrophobic content at which the peptides cross the membrane the easiest. Moreover, we show that the hydrophobicity of peptide termini has an important effect on the translocation barrier. These results provide general guidance to optimize peptides for use as carriers of molecular cargos or as therapeutics themselves.
The transport of molecules across cell membranes is vital for proper cell function and effective drug delivery. While most cell membranes naturally possess an asymmetric lipid composition, research ...on membrane transport predominantly uses symmetric lipid membranes. The permeation through the asymmetric membrane is then calculated as a sum of the inverse permeabilities of leaflets from symmetric bilayers. In this study, we examined how two types of amphiphilic molecules translocate across both asymmetric and symmetric membranes. Using computer simulations with both coarse-grained and atomistic force fields, we calculated the free energy profiles for the passage of model amphiphilic peptides and a lipid across various membranes. Our results consistently demonstrate that while the free energy profiles for asymmetric membranes with a small differential stress concur with symmetric ones in the region of lipid headgroups, the profiles differ around the center of the membrane. In this region, the free energy for the asymmetric membrane transitions between the profiles for two symmetric membranes. In addition, we show that peptide permeability through an asymmetric membrane cannot always be predicted from the permeabilities of the symmetric membranes. This indicates that using symmetric membranes falls short in providing an accurate depiction of peptide translocation across asymmetric membranes.
Coarse grained molecular dynamics simulations have been crucial for investigating the dynamics of nanoparticle uptake by cell membranes via ligand-receptor interactions. These models have enabled ...researchers to evaluate the effects of nanoparticle size, shape, and ligand distribution on cellular uptake. However, when pair potentials are used to represent ligand-receptor interactions, the number of receptors interacting with one ligand, valency, may vary. We demonstrate that the curvature of a nanoparticle, strength of ligand-receptor interactions, and ligand or receptor concentration change the valency, ranging from 3.4 to 5.1 in this study. Such a change in valency can create inaccurate comparisons between nanoparticles or even result in the uptake of smaller nanoparticles than would be expected. To rectify this inconsistency, we propose the adoption of a model based on bond formation and use it to determine the extent to which previous studies may have been affected. This work recommends avoiding pair potentials for modeling ligand-receptor interactions to ensure methodological consistency in nanoparticle studies.
Biological membranes present a major obstacle for the delivery of therapeutic agents into cells. Some peptides have been shown to translocate across the membrane spontaneously, and they could be thus ...used as drug-carriers. However, the advantageous peptide properties for the translocation remain unclear. Of particular interest is the effect of a proline-induced kink in α-helical peptides, because the kink was previously reported to both increase and decrease the antimicrobial activity. The antimicrobial activity of peptides could be related to their translocation across the membrane as is the case of the buforin 2 peptide investigated here. Using computer simulations with two independent models, we consistently showed that the presence of the kink has (1) no effect on the translocation barrier, (2) reduces the peptide affinity to the membrane, and (3) disfavors the transmembrane state. Moreover, we were able to determine that these effects are mainly caused by the peptide increased polarity, not the increased flexibility of the kink. The provided molecular understanding can be utilized for the design of cell-penetrating and drug-carrying peptides.
PDF
