Efficient Sampling and Characterization of Free Energy Landscapes of Ion–Peptide Systems

Stable Binding Conformations of Polymaleic and Polyacrylic Acids at a Calcite Surface in the Presence of Countercations: A Metadynamics Study

Elucidating the stable binding conformations of additives at the surface of CaCO3 crystals is essential to biomineralization, scale inhibition, and materials technology. However, accomplishing this by experimental means is rather difficult. In this study, molecular dynamics simulations based on a metadynamics approach were conducted to elucidate the stable binding conformations of a deprotonated polymaleic acid (PMA) additive and two deprotonated poly(acrylic acid) (PAA) additives with different polymerization degrees in the presence of various countercations at a hydrated calcite (104) surface. The simulated free-energy surfaces suggested the existence of several slightly different stable binding conformations for each additive. The appearance of these distinct binding conformations is speculated to originate from different balances of interactions between the additive, the calcite surface, and the countercations. The binding conformations and binding stabilities at the calcite surface were affected by the countercations, with Ca2+ ions producing a more pronounced effect than Na+ ions. Furthermore, the simulation results suggested that the binding stability at the calcite surface was higher for the PMA additive than for the PAA additives, and the PAA additive with a polymerization degree of 10 displayed a binding stability that was similar to or lower than that of the PAA additive with a polymerization degree of 5. The present simulation method provides a new strategy for analyzing the binding conformations of complex additives at material surfaces, developing additives that stably bind to these surfaces, and designing additives to control crystal growth.

Three Reasons Why Aspartic Acid and Glutamic Acid Sequences Have a Surprisingly Different Influence on Mineralization

Understanding the role of polymers rich in aspartic acid (Asp) and glutamic acid (Glu) is the key to gaining precise control over mineralization processes. Despite their chemical similarity, experiments revealed a surprisingly different influence of Asp and Glu sequences. We conducted molecular dynamics simulations of Asp and Glu peptides in the presence of calcium and chloride ions to elucidate the underlying phenomena. In line with experimental differences, in our simulations, we indeed find strong differences in the way the peptides interact with ions in solution. The investigated Asp pentapeptide tends to pull a lot of ions into its vicinity, and many structures with clusters of calcium and chloride ions on the surface of the peptide can be observed. Under the same conditions, comparatively fewer ions can be found in proximity of the investigated Glu pentapeptide, and the structures are characterized by single calcium ions bound to multiple carboxylate groups. Based on our simulation data, we identified three reasons contributing to these differences, leading to a new level of understanding additive-ion interactions.

Influence of Calcium Binding on Conformations and Motions of Anionic Polyamino Acids. Effect of Side Chain Length

Investigation of the effect of CaCl2 salt on conformations of two anionic poly(amino acids) with different side chain lengths, poly-(α-l glutamic acid) (PGA) and poly-(α-l aspartic acid) (PASA), was performed by atomistic molecular dynamics (MD) simulations. The simulations were performed using both unbiased MD and the Hamiltonian replica exchange (HRE) method. The results show that at low CaCl2 concentration adsorption of Ca2+ ions lead to a significant chain size reduction for both PGA and PASA. With the increase in concentration, the chains sizes partially recover due to electrostatic repulsion between the adsorbed Ca2+ ions. Here, the side chain length becomes important. Due to the longer side chain and its ability to distance the charged groups with adsorbed ions from both each other and the backbone, PGA remains longer in the collapsed state as the CaCl2 concentration is increased. The analysis of the distribution of the mineral ions suggests that both poly(amino acids) should induce the formation of mineral with the same structure of the crystal cell.

Understanding and modelling the interactions of peptides with membranes: from partitioning to self-assembly

Atomic detail simulations are starting to reveal how flexible polypeptides interact with fluid lipid bilayers. These insights are transforming our understanding of one of the fundamental processes in biology: membrane protein folding and assembly. Advanced molecular dynamics (MD) simulation techniques enable accurate prediction of protein structure, folding pathways and assembly in microsecond-timescales. Such simulations show how membrane-active peptides self-assemble in cell membranes, revealing their binding, folding, insertion, and aggregation, while at the same time providing atomic resolution details of peptide-lipid interactions. Essential to the impact of simulations are experimental approaches that enable calibration and validation of the computational models and techniques. In this review, we summarize the current development of applying unbiased atomic detail MD simulations and the relation to experimental techniques, to study peptide folding and provide our perspective of the field.

Cations in motion: QM/MM studies of the dynamic and electrostatic roles of H+ and Mg2+ ions in enzyme reactions

Here we discuss current trends in the simulations of enzymatic reactions focusing on phosphate catalysis. The mechanistic details of the proton transfers coupled to the phosphate cleavage is one of the key challenges in QM/MM calculations of these and other enzyme catalyzed reactions. The lack of experimental information offers both an opportunity for computations as well as often unresolved controversies. We discuss the example of small GTPases including the important human Ras protein. The high dimensionality and chemical complexity of these reactions demand carefully chosen computational techniques both in terms of the underlying quantum chemical theory and the sampling of the conformational ensemble. We also point out the important role of Mg²⁺ ions, and recent advances in their transient involvement in the catalytic mechanisms.