Atomistic Simulations of Wimley–White Pentapeptides: Sampling of Structure and Dynamics in Solution

Understanding the Interaction Between Oligopeptide and Water in Aqueous Solution Using Temperature-Dependent Near-Infrared Spectroscopy

Investigating the interaction between oligopeptide and water is essential for understanding the structure, dynamics and function of proteins. Temperature-dependent near-infrared (NIR) spectroscopy and independent component analysis (ICA) were employed to study the interaction between oligopeptide and water in aqueous solution. The NIR spectra of two homo-oligopeptides, penta-aspartic acid (D₅) and penta-lysine (K₅), in aqueous solution of different concentration were measured at different temperature (30-90 ℃). Independent component analysis was performed to extract the spectral information that changes with temperature. The independent components (ICs) representing the spectral information of NH and CH₂ groups were obtained. Compared with D₅, the two groups in K₅ change significantly at higher temperature. The result may suggest that K₅ has stronger interaction with water than D₅. Moreover, three ICs that contain the spectral information of the water species with no (S₀), one (S₁), and two (S₂) hydrogen-bonds were obtained. It was shown that the spectral intensity of S₀ and S₁ increases while that of S₂ decreases with the temperature, and the changes of oligopeptide solutions are weaker than those of pure water. The results indicate that water structure is sensitive to temperature and the oligopeptide in aqueous solution improves the thermal stability of the water species. When oligopeptide is added, the spectral intensity of S₀ and S₂ decreases and that of S₁ increases for D₅ solution, but the intensity of all the three species decreases for K₅ solution. Furthermore, the concentration effect of K₅ was found to be stronger than D₅. The result may reveal that D₅ combines with water molecule through forming one hydrogen bond but K₅ interacts with water through a different way.

Critical Comparison of Biomembrane Force Fields: Protein-Lipid Interactions at the Membrane Interface

Molecular dynamics (MD) simulations offer the possibility to study biological processes at high spatial and temporal resolution often not reachable by experiments. Corresponding biomolecular force field parameters have been developed for a wide variety of molecules ranging from inorganic ligands and small organic molecules over proteins and lipids to nucleic acids. Force fields have typically been parametrized and validated on thermodynamic observables and structural characteristics of individual compounds, e.g. of soluble proteins or lipid bilayers. Less strictly, due to the added complexity and missing experimental data to compare to, force fields have hardly been tested on the properties of mixed systems, e.g. on protein-lipid systems. Their selection and combination for mixed systems is further complicated by the partially differing parametrization strategies. Additionally, the presence of other compounds in the system may shift the subtle balance of force field parameters. Here, we assessed the protein-lipid interactions as described in the four atomistic force fields GROMOS54a7, CHARMM36 and the two force field combinations Amber14sb/Slipids and Amber14sb/Lipid14. Four observables were compared, focusing on the membrane-water interface: the conservation of the secondary structure of transmembrane proteins, the positioning of transmembrane peptides relative to the lipid bilayer, the insertion depth of side chains of unfolded peptides absorbed at the membrane interface, and the ability to reproduce experimental insertion energies of Wimley-White peptides at the membrane interface. Significant differences between the force fields were observed that affect e.g. membrane insertion depths and tilting of transmembrane peptides.

Dihedral angle entropy measures for intrinsically disordered proteins

Protein stability is based on a delicate balance between energetic and entropic factors. Intrinsically disordered proteins (IDPs) interacting with a folded partner protein in the act of binding can order the IDP to form the correct functional interface by decrease in the overall free energy. In this work, we evaluate the part of the entropic cost of ordering an IDP arising from their dihedral states. The IDP studied is a leucine zipper dimer that we simulate with molecular dynamics and find that it does show disorder in six phi and psi dihedral angles of the N terminal sequence of one monomer. Essential to ascertain is the degree of disorder in the IDP, and we do so by considering the entire, discretized probability distribution function of N dihedrals with M conformers per dihedral. A compositional clustering method is introduced, whereby the NS = N(M) states are formed from the Cartesian product of each dihedral's conformational space. Clustering is carried out with a version of a k-means algorithm that accounts for the circular nature of dihedral angles. For the 12 dihedrals each found to have three conformers, among the resulting 531441 states, their populations show that the first 100 (500) most populated states account for ∼65% (∼90%) of the entire population, indicating that there are strong dependencies among the dihedrals' conformations. These state populations are used to evaluate a Kullback-Leibler divergence entropy measure and obtain the dihedral configurational entropy S. At 300 K, TS ∼ 3 kcal/mol, showing that IDP entropy, while roughly half that would be expected from independently distributed dihedrals, can be a decisive contributor to the free energy of this IDP binding and ordering.

Effect of confinement on DNA, solvent and counterion dynamics in a model biological nanopore

The application of recent advances in nanopore technology to high-throughput DNA sequencing requires a more detailed understanding of solvent, ion and DNA interactions occurring within these pores. Here we present a combination of atomistic and coarse-grained modeling studies of the dynamics of short single-stranded DNA (ssDNA) homopolymers within the alpha-hemolysin pore, for the two single-stranded homopolymers poly(dA)40 and poly(dC)40. Analysis of atomistic simulations along with the per-residue decomposition of protein-DNA interactions in these simulations gives new insight into the very complex issues that have yet to be fully addressed with detailed MD simulations. We discuss a modification of the solvent properties and ion distribution around DNA within nanopore confinement and put it into the general framework of counterion condensation theory. There is a reasonable agreement in computed properties from our all-atom simulations and the resulting predictions from analytical theories with experimental data, and our equilibrium results here support the conclusions from our previous non-equilibrium Brownian dynamics studies with a recently developed BROMOC protocol that cations are the primary charge carriers through alpha-hemolysin nanopores under an applied voltage in the presence of ssDNA. Clustering analysis led to an identification of distinct conformational states of captured polymer and depth of the current blockade. Therefore, our data suggest that confined polymer may act as a flickering gate, thus contributing to excess noise phenomena. We also discuss the extent of water structuring due to nanopore confinement and the relationship between the conformational dynamics of a captured polymer and the distribution of blocked current.

Exploring the Free Energy Landscape of Solutes Embedded in Lipid Bilayers

Free energy calculations are vital for our understanding of biological processes on an atomistic scale and can offer insight to various mechanisms. However, in some cases, degrees of freedom (DOFs) orthogonal to the reaction coordinate have high energy barriers and/or long equilibration times, which prohibit proper sampling. Here we identify these orthogonal DOFs when studying the transfer of a solute from water to a model membrane. Important DOFs are identified in bulk liquids of different dielectric nature with metadynamics simulations and are used as reaction coordinates for the translocation process, resulting in two- and three-dimensional space of reaction coordinates. The results are in good agreement with experiments and elucidate the pitfalls of using one-dimensional reaction coordinates. The calculations performed here offer the most detailed free energy landscape of solutes embedded in lipid bilayers to date and show that free energy calculations can be used to study complex membrane translocation phenomena.

Lipid bilayer membrane affinity rationalizes inhibition of lipid peroxidation by a natural lignan antioxidant

Lipid peroxidation is a degenerative oxidative process that modifies the structure of membranes, influencing their biological functions. Lignans, natural polyphenolic antioxidants widely distributed in plants, can prevent this membrane damage by free-radical scavenging. Here, we rationalize the difference in lipid peroxidation inhibition activity of argenteane, a natural dilignan isolated from wild nutmeg, and 3,3'-dimethoxy-1,1'-biphenyl-2,2'-diol, which represents the central part of argenteane responsible for its antioxidant activity. Although both compounds have the same capacity to scavenge free radicals, argenteane is a more active inhibitor of lipid peroxidation. We show that both compounds penetrate into DOPC and PLPC lipid bilayers and adopt similar positions and orientations, which therefore does not explain the difference in their lipid peroxidation inhibition activity. However, free energy profiles indicate that argenteane has a significantly higher affinity to the lipid bilayer, and thus a higher effective concentration to scavenge radicals formed during lipid peroxidation. This finding explains the higher activity of argenteane to inhibit lipid peroxidation.