Facet-Specific Adsorption of Tripeptides at Aqueous Au Interfaces: Open Questions in Reconciling Experiment and Simulation

Hughes, Zak E.; Raji, K.; Walsh, Tiffany R.

doi:10.1021/acs.langmuir.6b04558

Cited by 29 publications

(36 citation statements)

References 84 publications

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“…Since there have been no MD studies of the peptides on a mercury surface, we can only compare our results to studies with the adsorption of peptides on other metallic surfaces. A similar interfacial behavior was found for an His‐rich octapeptide on a Au(111) surface as well as for other peptides and proteins . An enhanced adsorption of the protein tagged with His residues compared to its wild‐type form was also observed .…”

Section: Resultsmentioning

confidence: 99%

“…This illustrates that even a relatively high positive voltage cannot fully repel the positively charged residues from the surface. Metadynamics studies on the adsorption of the amino acids and tripeptides on a Au(111) surface revealed [36] that adsorption free energies of both histidine forms are very similar, 13 kJ.mol À 1 (for protonated histidine) and 11 kJ.mol À 1 (for non-protonated histidine), thus explaining the similarities in the adsorption behavior of the HIE and HIP states of the H-wire.…”

Section: H-wire Conformation In Watermentioning

confidence: 99%

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Structures of Peptidic H‐wires at Mercury Surface: Molecular Dynamics Study

et al. 2019

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Biopolymer immobilization strategies, self‐assembly systems and adsorption phenomenon in general are crucial for the development of methods that work on the basis of the surface‐detection principle, including electrochemistry. A mechanistic view into the interaction of biopolymers with electrode surfaces is also important for studying fundamental and dynamic processes such as electron/proton transport. In this sense, the utilization of new approaches for investigating the interfacial behavior of immobilized biomolecular architectures is a permanent focus. Here we use a molecular dynamics (MD) approach to simulate the structural changes and metallic surface interactions of a model 21‐mer peptide of His (H) and Ala (A), A3(HA2)6, a peptidic proton wire (H‐wire). This H‐wire was previously proposed for the electrochemical study of proton transfer at mercury electrodes (Langmuir, 2018, 34, 6997). The rigid solid mercury mono‐atomic layer (α‐mercury lattice model) was used systematically in all our simulations. The calculations were performed in a simulation box with 1, 16 and 32 H‐wire strands attached covalently to the mercury layer via the thiol group of a cysteinamide residue appended to the H‐wire C‐terminus. The internal alpha‐helical configuration of H‐wires was maintained by the presence of 2,2,2‐trifluoroethanol. It was shown that both the surface density of H‐wires and the protonation state of His residues play a decisive role in the structural stability and orientation of the peptide to the surface, whereas the applied voltage only has a mild effect on it, especially in case of 16 and 32 H‐wire strand configurations. The MD simulations presented here could be used for the further investigation of other peptides at metallic surfaces and for electrochemical analyses of structural changes of surface‐attached peptides that depend on their protonation states and other external factors.

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Section: Resultsmentioning

confidence: 99%

Section: H-wire Conformation In Watermentioning

confidence: 99%

Structures of Peptidic H‐wires at Mercury Surface: Molecular Dynamics Study

et al. 2019

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“…[6][7][8][9][10][11] While experimental efforts to resolve the molecular-level structure of the biotic/abiotic interface are evolving, at present molecular dynamics (MD) simulations can provide a key complementary approach to elucidate the structure and interactions of biomolecules adsorbed at aqueous metal interfaces. 5,7,[12][13][14][15][16][17][18][19][20][21][22][23][24][25][26][27][28] However, the quality of information that can be obtained from molecular simulation is dependent on the model, including the force-field (FF); i.e., how adequately we can capture and describe the interactions between all components of the interface.…”

Section: Introductionmentioning

confidence: 99%

“…23,31,32 For example, there is a strong body of evidence (primarily drawn from molecular simulation sources) that water is more strongly ordered at the (100) surface of noble metals than at the (111) surface, which is reported to confer differences in the adsorption modes of (bio)molecules at the (111) and (100) metal interfaces. [16][17][18][19]23,27,33 Density functional theory (DFT) calculations have predicted that, in vacuo, a single molecule of water adsorbs more strongly at the interface of Pd, and Pt, than to Au and Ag. [34][35][36][37][38] This might lead to a more strongly bound, and ordered, first layer of liquid water molecules at the Pd(111) interface compared with the Au/Ag(111) interface, 33,[39][40][41] which is likely to affect how (bio)molecules adsorb to these different aqueous metal interfaces.…”

Section: Introductionmentioning

confidence: 99%

Distinct Differences in Peptide Adsorption on Palladium and Gold: Introducing a Polarizable Model for Pd(111)

Hughes

Walsh

2018

J. Phys. Chem. C

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Materials-binding peptides offer promising routes to the production of tailored Pd nanomaterials in aqueous media, enabling the optimization of catalytic properties. However, the atomic-scale details needed to make these advances are relatively scarce and challenging to obtain. Molecular simulations can provide key insights into the structure of peptides adsorbed at the aqueous Pd interface, provided that the forcefield can appropriately capture the relevant bio-interface interactions. Here, we introduce and apply a new polarizable force field, PdP-CHARMM, for the simulation of biomolecule-Pd binding under aqueous conditions. PdP-CHARMM was parametrized with density functional theory (DFT) calculations, using a process compatible with similar polarizable force-fields created for Ag and Au surfaces, ultimately enabling a direct comparison of peptide binding modes across these metal substrates. As part of our process for developing PdP-CHARMM, we provide an extensive study of the performance of ten different dispersion-inclusive DFT functionals in recovering biomolecule-Pd(111) binding. We use the functional with best all-round performance to create PdP-CHARMM. We then employ PdP-CHARMM and metadynamics simulations to estimate the adsorption free energy for a range of amino acids at the aqueous Pd(111) interface. Our findings suggest that only His and Met favor direct contact with the Pd substrate, which we attribute to a remarkably robust interfacial solvation layering. Replica-exchange with solute tempering molecular dynamics simulations of two experimentally-identified Pd-binding peptides also indicate surface contact to be chiefly mediated by His and Met residues at aqueous Pd(111). Adsorption of these two peptides was also predicted for the Au(111) interface, revealing distinct differences in both the solvation structure and modes of peptide adsorption at the Au and Pd interfaces. We propose that this sharp contrast in peptide binding is largely due to the differences in interfacial solvent structuring. 2

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“…For example, thermal hysteresis proteins, a group of serum proteins commonly present in organisms living in cold environments, bind to specific faces of ice crystals to enable their antifreeze activity 13,14 . Recent theoretical studies point to the possibility of facet-dependent selective binding of amino acids, peptides, proteins, and DNA to crystal surfaces containing metals [15][16][17][18][19] . Here, we experimentally prove the concept that facet engineering may be utilized to tune the nanocrystal-biomolecule association for refining biological applications of crystalline nanomaterials.…”

mentioning

confidence: 99%

Nanocrystal facet modulation to enhance transferrin binding and cellular delivery

Zhang

Jing

et al. 2020

Nat Commun

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Binding of biomolecules to crystal surfaces is critical for effective biological applications of crystalline nanomaterials. Here, we present the modulation of exposed crystal facets as a feasible approach to enhance specific nanocrystal-biomolecule associations for improving cellular targeting and nanomaterial uptake. We demonstrate that facet-engineering significantly enhances transferrin binding to cadmium chalcogenide nanocrystals and their subsequent delivery into cancer cells, mediated by transferrin receptors, in a complex biological matrix.Competitive adsorption experiments coupled with theoretical calculations reveal that the (100) facet of cadmoselite and (002) facet of greenockite preferentially bind with transferrin via inner-sphere thiol complexation. Molecular dynamics simulation infers that facet-dependent transferrin binding is also induced by the differential affinity of crystal facets to water molecules in the first solvation shell, which affects access to exposed facets. Overall, this research underlines the promise of facet engineering to improve the efficacy of crystalline nanomaterials in biological applications.

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Facet-Specific Adsorption of Tripeptides at Aqueous Au Interfaces: Open Questions in Reconciling Experiment and Simulation

Cited by 29 publications

References 84 publications

Structures of Peptidic H‐wires at Mercury Surface: Molecular Dynamics Study

Structures of Peptidic H‐wires at Mercury Surface: Molecular Dynamics Study

Distinct Differences in Peptide Adsorption on Palladium and Gold: Introducing a Polarizable Model for Pd(111)

Nanocrystal facet modulation to enhance transferrin binding and cellular delivery

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