A Brownian Dynamics Study of the Initial Stages of Hen Egg-White Lysozyme Adsorption at a Solid Interface

Ravichandran, Sarangan; Madura, Jeffry D.; Talbot, J.

doi:10.1021/jp010223r

Cited by 110 publications

(109 citation statements)

References 22 publications

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“…The authors pointed out that the simplified description of the molecules would not work with proteins that are not globular, or that have an anisotropic charge distribution. In a separate study, Ravichandran et al (2001) investigated the early stages of the adsorption process and the binding orientations of HEWL on a positively charged surface with a full atomic detail representation of the protein. Although HEWL has an overall positive charge, it could bind to the charged surface due to the non-uniform distribution of the charges on the protein.…”

Section: Coarse-grained Molecular Mechanics Modeling Of Protein-surfamentioning

confidence: 99%

“…BD has been used in many studies of adsorption of proteins on surfaces with CG (Ravichandran & Talbot, 2000) and all-atom (Ravichandran et al 2001) representations of the proteins. Simplified BD simulation methods designed for CG models have been proposed (De la Torre et al 2009;Gorba & Helms, 2003) and one (Gorba & Helms, 2003) was tested for the diffusional dynamics of cytochrome c on a charged surface.…”

Section: Brownian Dynamicsmentioning

confidence: 99%

See 1 more Smart Citation

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

Ozboyaci

Kokh

Corni

et al. 2016

Quart. Rev. Biophys.

193

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: Coarse-grained Molecular Mechanics Modeling Of Protein-surfamentioning

confidence: 99%

Section: Brownian Dynamicsmentioning

confidence: 99%

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

Ozboyaci

Kokh

Corni

et al. 2016

Quart. Rev. Biophys.

193

199

View full text Add to dashboard Cite

show abstract

“…However, there is no obvious positively charge patch on the protein surface that might be expected to interact with the negatively charged mica surface. This highlights the importance of performing molecular modelling, which allows structural relaxation in the molecule to occur; models built on the concept of rigid proteins are likely to fail to capture the essence of the process [15,17].…”

Section: Molecular Dynamics Simulationsmentioning

confidence: 99%

Protein adsorption mechanisms on solid surfaces: lysozyme-on-mica

Mulheran

Kubiak

2009

Molecular Simulation

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A methodology for discovering the mechanisms and dynamics of protein clustering on solid surfaces is reviewed and complemented by atomistic molecular dynamics (MD) simulations. In situ atomic force microscopy images of the early stages of protein film formation are quantitatively compared with Monte Carlo simulations, using cluster statistics to differentiate various growth models. We have studied lysozyme adsorption on mica as a model system, finding that all surface-supported clusters are mobile with diffusion constant inversely related to cluster size. Furthermore, our results suggest that protein monomers diffusing to the surface from solution only adhere to the bare surface with a finite probability. Fully atomistic MD simulations reveal that the lysozyme does indeed have a preferred orientation for binding to the surface, so that proteins with incorrect orientations move away from the surface rather than towards it. Agreement with experimental studies in the literature for the residues involved in the surface adsorption is found.

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“…Emphasis was put on the role of the protein structure on protein adsorption. Ravichandran et al [51,52] used Brownian dynamics to study lysozyme (represented as charged spherical molecule) adsorption at a positively charged surface, and its mobility in the adsorbed state. Dickinson's group have performed numerous Brownian dynamics simulations in order to study different aspects of protein adsorption, including the displacement of the protein monolayer by competitive adsorption; [53] the analysis of a multi-subunit continuum model aimed to shed some light onto the deformation of globular proteins at a surface; [54] and they have used networks of spherical particles to simulate the gel-type nature of adsorbed protein layers.…”

Section: Neutron Reflectivitymentioning

confidence: 99%