Parallel tempering Monte Carlo simulations of lysozyme orientation on charged surfaces

Xie, Yun; Zhou, Jian; Jiang, Shaoyi

doi:10.1063/1.3305244

Cited by 88 publications

(162 citation statements)

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“…The effects of salt on protein conformation and consequently on adsorption properties were investigated in the simulations. Similar united residue models for peptide chains were used in several other papers (Evers et al 2012;Knotts et al 2005Knotts et al , 2008Skepö, 2008;Xie et al 2010). In two of these studies, short-range attraction potentials were added to model the binding of statherin protein on pure hydrophobic, charged, and mixed surfaces (Skepö, 2008), and the binding of β-casein on hydrophobic and charged surfaces (Evers et al 2012).…”

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

confidence: 99%

“…The PTMC method has been applied to protein-surface interactions in several studies, including prediction of the binding orientations of proteins (Xie et al 2010), and investigation of thermal and mechanical properties of proteins tethered on surfaces using a hybrid PTMC method with MD (Knotts et al 2005). Xie et al (2010) compared the performance of the PTMC method with that of conventional serial Metropolis MC simulations of lysozyme on charged surfaces using the same parameters. Figure 11a shows the distribution of the orientations of the lysozyme on a negatively charged surface obtained from the different MC methods.…”

Section: Al-mekhnaqimentioning

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.

197

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: Al-mekhnaqimentioning

confidence: 99%

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

Ozboyaci

Kokh

Corni

et al. 2016

Quart. Rev. Biophys.

197

199

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show abstract

“…More generally, the search for a global minimum in the enzyme-surface interaction energy landscape is a classic way to handle the question of protein orientation on a surface [165], and can be addressed via several modeling schemes such as parallel tempering Monte Carlo [166], docking via Brownian Dynamics Simulations [167], or MD simulations [168]. In their recent study on β-galactosidase grafted on a hydrophilic surface, Li et al used coarse-grain MD simulations to probe the enzyme orientation and its catalytic activity as a function of the surface's hydrophilicity [169].…”

Section: Modelingmentioning

confidence: 99%

Controlling Redox Enzyme Orientation at Planar Electrodes

et al. 2018

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Abstract:Redox enzymes, which catalyze reactions involving electron transfers in living organisms, are very promising components of biotechnological devices, and can be envisioned for sensing applications as well as for energy conversion. In this context, one of the most significant challenges is to achieve efficient direct electron transfer by tunneling between enzymes and conductive surfaces. Based on various examples of bioelectrochemical studies described in the recent literature, this review discusses the issue of enzyme immobilization at planar electrode interfaces. The fundamental importance of controlling enzyme orientation, how to obtain such orientation, and how it can be verified experimentally or by modeling are the three main directions explored. Since redox enzymes are sizable proteins with anisotropic properties, achieving their functional immobilization requires a specific and controlled orientation on the electrode surface. All the factors influenced by this orientation are described, ranging from electronic conductivity to efficiency of substrate supply. The specificities of the enzymatic molecule, surface properties, and dipole moment, which in turn influence the orientation, are introduced. Various ways of ensuring functional immobilization through tuning of both the enzyme and the electrode surface are then described. Finally, the review deals with analytical techniques that have enabled characterization and quantification of successful achievement of the desired orientation. The rich contributions of electrochemistry, spectroscopy (especially infrared spectroscopy), modeling, and microscopy are featured, along with their limitations.

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“…Zhou et al [22] also investigated the orientation and conformation of cytochrome c adsorbed on self-assembled monolayers (SAMs) by a combined MC and MD simulation approach. Xie et al [23] applied the parallel tempering Monte Carlo (PTMC) algorithm to identify the globalminimum-energy orientation of a protein adsorbed on a surface accurately and efficiently in a single simulation. The PTMC method was also applied to study the adsorption of lysozyme [24] and protein G [25].…”

Section: Introductionmentioning

confidence: 99%