Force fields for simulating the interaction of surfaces with biological molecules

Abstract

The interaction of biomolecules with solid interfaces is of fundamental importance to several emerging biotechnologies such as medical implants, anti-fouling coatings and novel diagnostic devices. Many of these technologies rely on the binding of peptides to a solid surface, but a full understanding of the mechanism of binding, as well as the effect on the conformation of adsorbed peptides, is beyond the resolution of current experimental techniques. Nanoscale simulations using molecular mechanics offer potential insights into these processes. However, most models at this scale have been developed for aqueous peptide and protein simulation, and there are no proven models for describing biointerfaces. In this review, we detail the current research towards developing a non-polarizable molecular model for peptide-surface interactions, with a particular focus on fitting the model parameters as well as validation by choice of appropriate experimental data.

POP1 might be recruiting its type‐Ia interface for NLRP3‐mediated PYD‐PYD interaction: Insights from MD simulation

“…Although the computational predictions are reliable in envisaging the functional aspects of biological macromolecules (the arbitrated biochemical interactions), the accuracy of prediction depends on selective algorithm, scoring function, and accessible hardware. Moreover, the initial conformation of protein structure or, protein‐counterpart complex also plays an imperative role in governing the biomolecular interactions . To understand the PYD‐PYD interaction between POP1 and NLRP3 PYD , we considered the high‐resolution experimental structures and manually docked them referring to ASC PYD dimeric/trimeric conformation and interaction modes of other PYD‐PYD studies .…”

“…Moreover, the initial conformation of protein structure or, protein-counterpart complex also plays an imperative role in governing the biomolecular interactions. [43][44][45][46] To understand the PYD-PYD interaction between POP1 and NLRP3 PYD , we considered the high-resolution experimental structures and manually docked them referring to ASC PYD dimeric/trimeric conformation and interaction modes of other PYD-PYD studies. [19][20][21][22][23][24] The modeled heterodimeric and trimeric complexes were simulated up to 100 and 80 ns, respectively.…”

Organic–inorganic interface simulation for new material discoveries

“…CHARMM, CVFF, PCFF, CHARMM‐METAL, and INTERFACE are the popular FFs employed to study the interface. More detailed information on interface FFs can be found in some recent reviews …”

Integrated multiscale biomaterials experiment and modelling: a perspective

“…Two major factors are deriving models for interactions between proteins and charged surfaces, and identifying and modelling the structures that enable mineralcollagen interaction in bone. A substantial advance is presented by Martin et al [25] in the former area, with a transformative new framework for this type of simulation. In the latter area, Smith et al [26] present an integrated modelling and experimental study that seemingly argues against the hypotheses that mineral and collagen interact mechanically in a significant way in bone without the action of additional supporting protein structures.…”