Development of a Tuned Interfacial Force Field Parameter Set for the Simulation of Protein Adsorption to Silica Glass

Snyder, James A.; Abramyan, Tigran M.; Yancey, Jeremy A.; Thyparambil, Aby A.; Wei, Yang; Stuart, Steven J.; Latour, Robert A.

doi:10.1007/s13758-012-0056-4

Cited by 17 publications

(23 citation statements)

References 58 publications

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“…The Dual-FF (Biswas et al 2012), (discussed in more detail in Sec.7·5) was optimized to reproduce the experimental binding energies of TGTG-X-GTGT peptides, with X = N, D, G, K, F,T, W and V, on hydroxylated quartz (100) and glass surfaces in MD simulations (Snyder et al 2012). In the Dual-FF, CHARMM parameters were used for biomolecules, while interfacial parameters, such as partial charges and Lennard-Jones parameters for silica-peptide and silica-water interactions, were tuned to obtain the best agreement with peptide adsorption energies.…”

Section: (2012)mentioning

confidence: 99%

Modeling and simulation of protein–surface interactions: achievements and challenges

Ozboyaci

Kokh

Corni

et al. 2016

Quart. Rev. Biophys.

191

199

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Abstract. Understanding protein-inorganic surface interactions is central to the rational design of new tools in biomaterial sciences, nanobiotechnology and nanomedicine. Although a significant amount of experimental research on protein adsorption onto solid substrates has been reported, many aspects of the recognition and interaction mechanisms of biomolecules and inorganic surfaces are still unclear. Theoretical modeling and simulations provide complementary approaches for experimental studies, and they have been applied for exploring protein-surface binding mechanisms, the determinants of binding specificity towards different surfaces, as well as the thermodynamics and kinetics of adsorption. Although the general computational approaches employed to study the dynamics of proteins and materials are similar, the models and force-fields (FFs) used for describing the physical properties and interactions of material surfaces and biological molecules differ. In particular, FF and water models designed for use in biomolecular simulations are often not directly transferable to surface simulations and vice versa. The adsorption events span a wide range of time-and length-scales that vary from nanoseconds to days, and from nanometers to micrometers, respectively, rendering the use of multi-scale approaches unavoidable. Further, changes in the atomic structure of material surfaces that can lead to surface reconstruction, and in the structure of proteins that can result in complete denaturation of the adsorbed molecules, can create many intermediate structural and energetic states that complicate sampling. In this review, we address the challenges posed to theoretical and computational methods in achieving accurate descriptions of the physical, chemical and mechanical properties of protein-surface systems. In this context, we discuss the applicability of different modeling and simulation techniques ranging from quantum mechanics through all-atom molecular mechanics to coarse-grained approaches. We examine uses of different sampling methods, as well as free energy calculations. Furthermore, we review computational studies of protein-surface interactions and discuss the successes and limitations of current approaches.

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Section: (2012)mentioning

confidence: 99%

Modeling and simulation of protein–surface interactions: achievements and challenges

Ozboyaci

Kokh

Corni

et al. 2016

Quart. Rev. Biophys.

191

199

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“…My group has primarily focused on the use of umbrella sampling, often in combination with REMD, to provide adequate sampling over both the designated solute's position over a surface and its conformational phase space, as briefly summarized below. Readers are again referred to publications of our methods to see the specific details that we have used to address each of these three steps [54,69,70]. …”

Section: Methodsmentioning

confidence: 99%

“…We are presently developing new modules for the LAMMPS simulation program (Large-scale Atomic/Molecular Massively Parallel Simulator; from Sandia National Laboratories) for this same purpose. We then used the modified simulation program to adjust nonbonded parameters of the IFF force field (i.e., partial charges, L–J well depth) to correct deviations found from step (1) until adsorption free energy values for each peptide were within about 0.5 kcal/mol of their respective target benchmark data set values [70]. …”

Section: Methodsmentioning

confidence: 99%

Perspectives on the simulation of protein–surface interactions using empirical force field methods

Latour

2014

Colloids and Surfaces B: Biointerfaces

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Protein–surface interactions are of fundamental importance for a broad range of applications in the fields of biomaterials and biotechnology. Present experimental methods are limited in their ability to provide a comprehensive depiction of these interactions at the atomistic level. In contrast, empirical force field based simulation methods inherently provide the ability to predict and visualize protein–surface interactions with full atomistic detail. These methods, however, must be carefully developed, validated, and properly applied before confidence can be placed in results from the simulations. In this perspectives paper, I provide an overview of the critical aspects that I consider being of greatest importance for the development of these methods, with a focus on the research that my combined experimental and molecular simulation groups have conducted over the past decade to address these issues. These critical issues include the tuning of interfacial force field parameters to accurately represent the thermodynamics of interfacial behavior, adequate sampling of these types of complex molecular systems to generate results that can be comparable with experimental data, and the generation of experimental data that can be used for simulation results evaluation and validation.

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“…This method successfully reproduced the free energy of adsorption on hydrophobic SAMs without affecting the same measure over hydrophilic SAMs. The Dual-FF approach has also been applied to silica [57] and high-density polyethylene [58] to reproduce experimental adsorption data. While this solution achieves the goal of reproducing the desired experimental data, it is a practical solution, which neglects the possibility of underlying errors in the parametrization of the surface.…”

Section: Interfacial Force Fields and Surface Modelsmentioning

confidence: 99%

Force fields for simulating the interaction of surfaces with biological molecules

et al. 2016

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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.

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Development of a Tuned Interfacial Force Field Parameter Set for the Simulation of Protein Adsorption to Silica Glass

Cited by 17 publications

References 58 publications

Modeling and simulation of protein–surface interactions: achievements and challenges

Modeling and simulation of protein–surface interactions: achievements and challenges

Perspectives on the simulation of protein–surface interactions using empirical force field methods

Force fields for simulating the interaction of surfaces with biological molecules

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