ProMetCS: An Atomistic Force Field for Modeling Protein−Metal Surface Interactions in a Continuum Aqueous Solvent

Kokh, Daria B.; Corni, Stefano; Winn, Peter J.; Hoefling, Martin; Gottschalk, Kay E.; Wade, Rebecca C.

doi:10.1021/ct100086j

Cited by 60 publications

(105 citation statements)

References 78 publications

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“…The strong binding of aromatic (most pronounced for Tyr and Trp) and sulfur-containing amino acids (Met) observed in the experiments supports the conclusion of Kokh et al that adsorption on an uncharged or weakly charged Au surface is driven primarily by van der Waals and chemical interactions. [22] This result also indicates that the force-field parameters derived by Iori et al [36] and used in the present calculations represent the interaction between biomolecules and the Au surface in a reasonable manner and can be applied to the simulation of protein adsorption. Points of disagreement may result from inaccuracies in the theoretical description of the system, some bias introduced by the experimental system, or a combination thereof.…”

Section: Wwwchemeurjorgsupporting

confidence: 65%

“…Simulation of amino acid binding to gold: The ProMetCS protein-metal continuum solvent model [22] was used to compute adsorption free energies of amino acids on an AuA C H T U N G T R E N N U N G (111) surface. In this model, the interaction energy of a biomolecule with a metal surface is described by three main terms: van der Waals energy (which also includes weak chemical binding of aromatic residues and sulfur atoms to gold), adsorbate-metal electrostatic interaction energy (taken into account only for the charged side chains), and desolvation energy.…”

Section: His-blip Binding To Gold Islands and Continuous Gold Sur-a Cmentioning

confidence: 99%

“…Simulation of adsorption using free energy calculations: The ProMetCS model [22] for protein-metal interactions was used to compute the adsorption free energies of amino acids on an atomically flat AuA C H T U N G T R E N N U N G (111) surface. All amino acid conformations were obtained from MD simulations of capped amino acids [41] on Au.…”

Section: Spr Binding Measurementsmentioning

confidence: 99%

“…The experimental results were compared with adsorption energies for amino acids, calculated using a protein-metal continuum solvent model (ProMetCS). [22] …”

Section: Introductionmentioning

confidence: 99%

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A Quantitative, Real‐Time Assessment of Binding of Peptides and Proteins to Gold Surfaces

Cohavi

Reichmann

Abramovich

et al. 2010

Chemistry A European J

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Interactions of peptides and proteins with inorganic surfaces are important to both natural and artificial systems; however, a detailed understanding of such interactions is lacking. In this study, we applied new approaches to quantitatively measure the binding of amino acids and proteins to gold surfaces. Real-time surface plasmon resonance (SPR) measurements showed that TEM1-β-lactamase inhibitor protein (BLIP) interacts only weakly with Au nanoparticles (NPs). However, fusion of three histidine residues to BLIP (3H-BLIP) resulted in a significant increase in the binding to the Au NPs, which further increased when the histidine tail was extended to six histidines (6H-BLIP). Further increasing the number of His residues had no effect on the binding. A parallel study using continuous (111)-textured Au surfaces and single-crystalline, (111)-oriented, Au islands by ellipsometry, FTIR, and localized surface plasmon resonance (LSPR) spectroscopy further confirmed the results, validating the broad applicability of Au NPs as model surfaces. Evaluating the binding of all other natural amino acid homotripeptides fused to BLIP (except Cys and Pro) showed that aromatic and positively-charged residues bind preferentially to Au with respect to small aliphatic and negatively charged residues, and that the rate of association is related to the potency of binding. The binding of all fusions was irreversible. These findings were substantiated by SPR measurements of synthesized, free, soluble tripeptides using Au-NP-modified SPR chips. Here, however, the binding was reversible allowing for determination of binding affinities that correlate with the binding potencies of the related BLIP fusions. Competition assays performed between 3H-BLIP and the histidine tripeptide (3 His) suggest that Au binding residues promote the adsorption of proteins on the surface, and by this facilitate the irreversible interaction of the polypeptide chain with Au. The binding of amino acids to Au was simulated by using a continuum solvent model, showing agreement with the experimental values. These results, together with the observed binding potencies and kinetics of the BLIP fusions and free peptides, suggest a binding mechanism that is markedly different from biological protein-protein interactions.

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Section: Wwwchemeurjorgsupporting

confidence: 65%

Section: His-blip Binding To Gold Islands and Continuous Gold Sur-a Cmentioning

confidence: 99%

Section: Spr Binding Measurementsmentioning

confidence: 99%

“…The experimental results were compared with adsorption energies for amino acids, calculated using a protein-metal continuum solvent model (ProMetCS). [22] …”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

A Quantitative, Real‐Time Assessment of Binding of Peptides and Proteins to Gold Surfaces

Cohavi

Reichmann

Abramovich

et al. 2010

Chemistry A European J

Self Cite

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“…Results show that GoIP-CHARMM computed adsorption energies for individual amino acids compare well with experimental trends. For faster simulations, this potential has recently been coupled with an implicit solvent model ProMetCS, where water and ion molecules are now represented at a continuum level [103].…”

Section: Classical Biological-metal Modelsmentioning

confidence: 99%

Biomediated Atomic Metal Nanoclusters: Synthesis and Theory

Griep¹,

West²,

Sellers³

et al. 2015

Handbook of Nanoparticles

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Fluorescent metal nanoclusters are an emerging class of multifunctional materials engineered at the singleatom level, with dimensions approaching the Fermi wavelength of electrons that offer competitive functionalities of traditional semiconductor QDs including tunable emission, ease of conjugation, extended photostability, and high quantum yield. With the additional advantages of being composed of nontoxic/ biocompatible materials, function with a fraction of the metal content, greatly reduced size for enhanced cellular uptake, opportunity for two-photon absorption at biologically relevant wavelengths, and demonstrated renal evacuation efficacy for in vivo applications, metal nanoclusters hold substantial promise. More recently the development of hybrid atomic cluster synthesis routes has expanded the materials' multifunctional capabilities. This chapter will summarize the current high-yield synthesis and functionalization strategies for producing monodisperse pure metal and hybrid nanocluster materials from both wet chemistry and newly developed biomediated nanocluster synthesis methodologies, involving protein and DNA hosts. The role of the bio-host and surface functional groups on the nanoclusters formation, stability, and physical properties will be detailed through recent experimental and theoretical simulation efforts.

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Experimental characterization and simulation of amino acid and peptide interactions with inorganic materials

Schwaminger

Blank-Shim

Borkowska-Panek

et al. 2017

Engineering in Life Sciences

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Inspired by nature, many applications and new materials benefit from the interplay of inorganic materials and biomolecules. A fundamental understanding of complex organic–inorganic interactions would improve the controlled production of nanomaterials and biosensors to the development of biocompatible implants for the human body. Although widely exploited in applications, the interaction of amino acids and peptides with most inorganic surfaces is not fully understood. To date, precisely characterizing complex surfaces of inorganic materials and analyzing surface–biomolecule interactions remain challenging both experimentally and computationally. This article reviews several approaches to characterizing biomolecule–surface interactions and illustrates the advantages and disadvantages of the methods presented. First, we explain how the adsorption mechanism of amino acids/peptides to inorganic surfaces can be determined and how thermodynamic and kinetic process constants can be obtained. Second, we demonstrate how this data can be used to develop models for peptide–surface interactions. The understanding and simulation of such interactions constitute a basis for developing molecules with high affinity binding domains in proteins for bioprocess engineering and future biomedical technologies.

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ProMetCS: An Atomistic Force Field for Modeling Protein−Metal Surface Interactions in a Continuum Aqueous Solvent

Cited by 60 publications

References 78 publications

A Quantitative, Real‐Time Assessment of Binding of Peptides and Proteins to Gold Surfaces

A Quantitative, Real‐Time Assessment of Binding of Peptides and Proteins to Gold Surfaces

Biomediated Atomic Metal Nanoclusters: Synthesis and Theory

Experimental characterization and simulation of amino acid and peptide interactions with inorganic materials

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