Molecular simulation of protein-surface interactions: Benefits, problems, solutions, and future directions (Review)

Latour, Robert A.

doi:10.1116/1.2965132

Cited by 159 publications

(186 citation statements)

References 132 publications

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“…Potentially relevant issues about some approximations implicit in these nonbonded potentials should be noted [28]. The first one is the above-mentioned point charge approximation to account for the local dipoles.…”

Section: (A) the Mathematical Model: The Force Fieldmentioning

confidence: 99%

Molecular modelling of protein adsorption on the surface of titanium dioxide polymorphs

Raffaini

2012

Phil. Trans. R. Soc. A.

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This paper reports a molecular modelling study of the adsorption of protein subdomains with unlike secondary structures on different surfaces of ceramic titanium dioxide (TiO 2 ), forming a passivating film on titanium biomaterials that provides the interface between the bulk metal and the physiological environment, affecting its biocompatibility and performance. Using molecular dynamics methods, we study the effect of the nanoscale structure of the common TiO 2 polymorphs (rutile, anatase and brookite) on the adsorption of an albumin subdomain and on two connected fibronectin modules, respectively containing a-helices and b-sheets. We find that the larger protein subdomain shows a stronger adsorption, as expected because of its size, but also that the three surfaces behave differently. In particular, brookite shows the weakest adsorption, whereas anatase leads to the strongest intrinsic adsorption, in particular for the fibronectin modules. Moreover, the simulations indicate a significant conformational change of the adsorbed protein subdomains with extensive surface nanopatterning. These results show that classical molecular dynamics methods can provide useful information about the influence of nanostructure and topology on protein physisorption at a fixed surface chemistry.

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Section: (A) the Mathematical Model: The Force Fieldmentioning

confidence: 99%

Molecular modelling of protein adsorption on the surface of titanium dioxide polymorphs

Raffaini

2012

Phil. Trans. R. Soc. A.

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“…Therefore careful conformational sampling is an indispensable tool for ensuring meaningful results [17][18][19][20][21][22][23][24][25][26][27][28][29] , since insufficient sampling may give rise to misleading conclusions. The challenge of extensive conformational sampling is made more acute by the need to use an explicit description of liquid water, 30,31 since spatial structuring of interfacial solvent is thought to be a key determinant in peptide-materials binding. 26,30 However, this requirement to describe liquid water at the molecular level leads to inefficiencies in conventional advanced sampling methods such as temperature-based replica-exchange MD.…”

Section: Introductionmentioning

confidence: 99%

What makes a good graphene-binding peptide? Adsorption of amino acids and peptides at aqueous graphene interfaces

2015

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Investigation of the non-covalent interaction of biomolecules with aqueous graphene interfaces is a rapidly expanding area. However, reliable exploitation of these interfaces in many applications requires that the links between the sequence and binding of the adsorbed peptide structures be clearly established. Molecular dynamics (MD) simulations can play a key role in elucidating the conformational ensemble of peptides adsorbed at graphene interfaces, helping to elucidate these rules in partnership with experimental characterisation. We apply our recently-developed polarisable force-field for biomolecule-graphene interfaces, GRAPPA, in partnership with advanced simulation approaches, to probe the adsorption behaviour of peptides at aqueous graphene. First we determine the free energy of adsorption of all twenty naturally occurring amino acids (AAs) via metadynamics simulations, providing a benchmark for interpreting peptide-graphene adsorption studies. From these free energies, we find that strong-binding amino acids have flat and/or compact side chain groups, and we relate this behaviour to the interfacial solvent structuring. Second, we apply replica exchange with solute tempering simulations to efficiently and widely sample the conformational ensemble of two experimentally-characterised peptide sequences, P1 and its alanine mutant P1A3, in solution and adsorbed on graphene. For P1 we find a significant minority of the conformational ensemble possesses a helical structure, both in solution and when adsorbed, while P1A3 features mostly extended, random-coil conformations. In solution this helical P1 configuration is stabilised through favourable intra-peptide interactions, while the adsorbed structure is stabilised via interaction of four strongly-binding residues, identified from our metadynamics simulations, with the aqueous graphene interface. Our findings rationalise the performance of the P1 sequence as a known graphene binder.

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“…146,147 The interaction between proteins and hydroxyapatite surfaces plays an important role in many applications, namely medicine, pharmacy, nanodevices, biosensors, and bioengineering. 148 In particular, in the biomaterials field, its study is fundamental to learn more about the biomineralization process in vivo, 149 to test the material performance in biological environment, 150 or to check its ability as inorganic carrier for biomolecules. 151,152 Although protein adsorption on solid surfaces has been widely studied for decades, its mechanisms are still far from being fully understood.…”

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confidence: 99%

Evolving application of biomimetic nanostructured hydroxyapatite

Roveri¹,

Iafisco²

2010

NSA

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By mimicking Nature, we can design and synthesize inorganic smart materials that are reactive to biological tissues. These smart materials can be utilized to design innovative thirdgeneration biomaterials, which are able to not only optimize their interaction with biological tissues and environment, but also mimic biogenic materials in their functionalities. The biomedical applications involve increasing the biomimetic levels from chemical composition, structural organization, morphology, mechanical behavior, nanostructure, and bulk and surface chemical-physical properties until the surface becomes bioreactive and stimulates cellular materials. The chemical-physical characteristics of biogenic hydroxyapatites from bone and tooth have been described, in order to point out the elective sides, which are important to reproduce the design of a new biomimetic synthetic hydroxyapatite. This review outlines the evolving applications of biomimetic synthetic calcium phosphates, details the main characteristics of bone and tooth, where the calcium phosphates are present, and discusses the chemical-physical characteristics of biomimetic calcium phosphates, methods of synthesizing them, and some of their biomedical applications.

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Molecular simulation of protein-surface interactions: Benefits, problems, solutions, and future directions (Review)

Cited by 159 publications

References 132 publications

Molecular modelling of protein adsorption on the surface of titanium dioxide polymorphs

Molecular modelling of protein adsorption on the surface of titanium dioxide polymorphs

What makes a good graphene-binding peptide? Adsorption of amino acids and peptides at aqueous graphene interfaces

Evolving application of biomimetic nanostructured hydroxyapatite

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