DPD Simulation of Protein Conformations: From α-Helices to β-Structures

Prediction of the Critical Micelle Concentration of Nonionic Surfactants by Dissipative Particle Dynamics Simulations

Micellization of surfactant solutions is a ubiquitous phenomenon in natural systems and technological processes, and its theoretical description represents one of the cornerstone problems in the physical chemistry of colloidal systems. However, successful attempts of quantitative modeling confirmed by experimental data remains limited. We show, for the first time, that the dissipative particle dynamics with rigorously defined soft repulsion interaction and rigidity parameters is capable of predicting micellar self-assembly of nonionic surfactants. This is achieved due to a novel approach suggested for defining the interaction parameters by fitting to the infinite dilution activity coefficients of binary solutions formed by reference compounds that represent coarse-grained fragments of surfactant molecules. Using this new parametrization scheme, we obtained quantitative agreement with the experimental critical micelle concentration and aggregation number for several typical surfactants of different chemical structures. The proposed approach can be extended to various colloidal and polymeric systems beyond nonionic surfactant solutions.

Computational Insights into Dynamics of Protein Aggregation and Enzyme-Substrate Interactions

In this Perspective, the roles of protein dynamics have been discussed in the aggregation of amyloid beta (Aβ) peptides and formation of enzyme-substrate complexes of beta-secretase (BACE1) and insulin-degrading enzyme (IDE). The studies regarding the influence of individual amino acid residues and specific regions on the structures and oligomerization of early Aβ aggregates and computations of their translational and rotational diffusion coefficients and order parameters exhibited that even the short-time-scale molecular dynamics simulations can reproduce certain experimental parameters with reasonable accuracy. The simulations elucidating the enzyme-substrate interactions of BACE1 and IDE successfully showed that the chemical nature and length of the substrates influence the dynamics and plasticity of both the enzyme and substrate. An atomic-level understanding of these processes will advance our efforts to develop therapeutic strategies for several deadly diseases through the design of small molecules with antiaggregation properties and substrate-specific "designer" forms of enzymes.