4.7 Article

A Classical Potential to Model the Adsorption of Biological Molecules on Oxidized Titanium Surfaces

Journal

JOURNAL OF CHEMICAL THEORY AND COMPUTATION
Volume 7, Issue 2, Pages 473-484

Publisher

AMER CHEMICAL SOC
DOI: 10.1021/ct1004388

Keywords

-

Funding

  1. Deutsche Forschungsgemeinschaft (DFG) [CI 144/2-1]
  2. EU-FP7-NMP [229205]

Ask authors/readers for more resources

The behavior of titanium implants in physiological environments is governed by the thin oxide layer that forms spontaneously on the metal surface and mediates the interactions with adsorbate molecules. In order to study the adsorption of biomolecules on titanium in a realistic fashion, we first build up a model of an oxidized Ti surface in contact with liquid water by means of extensive first-principles molecular dynamics simulations. Taking the obtained structure as reference, we then develop a classical potential to model the Ti/TiOx/water interface. This is based on the mapping with Coulomb and Lennard-Jones potentials of the adsorption energy landscape of single water and ammonia molecules on the rutile TiO2(110) surface. The interactions with arbitrary organic molecules are obtained via standard combination rules to established biomolecular force fields. The transferability of our potential to the case of organic molecules adsorbing on the oxidized Ti surface is checked by comparing the classical potential energy surfaces of representative systems to quantum mechanical results at the level of density functional theory. Moreover, we calculate the heat of immersion of the TiO2 rutile surface and the detachment force of a single tyrosine residue from steered molecular dynamics simulations, finding good agreement with experimental reference data in both cases. As a first application, we study the adsorption behavior of the Arg-Gly-Asp (RGD) peptide on the oxidized titanium surface, focusing particularly on the calculation of the free energy of desorption.

Authors

I am an author on this paper
Click your name to claim this paper and add it to your profile.

Reviews

Primary Rating

4.7
Not enough ratings

Secondary Ratings

Novelty
-
Significance
-
Scientific rigor
-
Rate this paper

Recommended

Article Mathematics, Applied

Mathematical aspects of catalyst positioning in lithium/air batteries

Thuong-Huyen Nguyen, Dinh Nho Hao, Peter Maass, Lucio Colombi Ciacchi

INVERSE PROBLEMS (2020)

Article Materials Science, Multidisciplinary

Strong Macroscale Supercrystalline Structures by 3D Printing Combined with Self-Assembly of Ceramic Functionalized Nanoparticles

Berta Domenech, Alvin T. L. Tan, Hans Jelitto, Eduardo Zegarra Berodt, Malte Blankenburg, Oliver Focke, Jaclyn Cann, C. Cem Tasan, Lucio Colombi Ciacchi, Martin Mueller, Kaline P. Furlan, A. John Hart, Gerold A. Schneider

ADVANCED ENGINEERING MATERIALS (2020)

Review Engineering, Chemical

A review of contact force models between nanoparticles in agglomerates, aggregates, and films

Stefan Christian Endres, Lucio Colombi Ciacchi, Lutz Maedler

Summary: The desire to optimize the production and performance of nanoparticle structured materials has driven the development of increasingly accurate and fundamental models, presenting challenging multiscale modeling problems. Particle assemblies at nanoscale form complex aggregates and agglomerates, requiring new contact models at the primary particle level. Ambient conditions such as humidity have a significant effect on the final structure of materials due to capillary and solvation forces.

JOURNAL OF AEROSOL SCIENCE (2021)

Article Chemistry, Physical

Lessons from a Challenging System: Accurate Adsorption Free Energies at the Amino Acid/ZnO Interface

Monika Michaelis, Massimo Delle Piane, Dirk Rothenstein, Carole C. Perry, Lucio Colombi Ciacchi

Summary: In this study, four challenges hindering the understanding of ZnO/biomolecule interfaces at the atomic scale were overcome. The adsorption free energies predicted showed remarkable agreement with experimental measurements, revealing the mechanism of interactions between ZnO surface and amino acids.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2021)

Article Chemistry, Physical

Water Reactions on Reconstructed Rutile TiO2: A Density Functional Theory/Density Functional Tight Binding Approach

Filippo Balzaretti, Verena Gupta, Lucio Colombi Ciacchi, Balint Aradi, Thomas Frauenheim, Susan Koeppen

Summary: The reactive interaction of water with rutile remains a challenge to atomistic modeling techniques, but can be partly described by density functional tight binding. However, improvements are needed to accurately predict the low dissociation propensity of H2O. A reliable description of water surface reactivity is crucial for understanding the nonstoichiometric reconstruction of the Ti-rich (001) facet.

JOURNAL OF PHYSICAL CHEMISTRY C (2021)

Article Multidisciplinary Sciences

Identification of a HTT-specific binding motif in DNAJB1 essential for suppression and disaggregation of HTT

S. M. Ayala Mariscal, M. L. Pigazzini, Y. Richter, M. Ozel, I. L. Grothaus, J. Protze, K. Ziege, M. Kulke, M. ElBediwi, J. V. Vermaas, L. Colombi Ciacchi, S. Koppen, F. Liu, J. Kirstein

Summary: Huntington's disease is a neurodegenerative disorder caused by aggregation-prone mutant HTT protein. The trimeric chaperone complex formed by Hsc70, DNAJB1, and Apg2 can suppress and reverse the aggregation of HTTExon1Q(48) by binding to the HTT protein's poly-proline region through DNAJB1. The mutation of the conserved H244 in DNAJB1's HBM specifically affects the suppression and disaggregation of HTT fibrils, highlighting the importance of this interaction site for Huntington's disease.

NATURE COMMUNICATIONS (2022)

Article Biochemistry & Molecular Biology

N-glycosylation modulates enzymatic activity of Trypanosoma congolense trans-sialidase

Jana Rosenau, Isabell Louise Grothaus, Yikun Yang, Nilima Dinesh Kumar, Lucio Colombi Ciacchi, Sorge Kelm, Mario Waespy

Summary: This study reveals how N-glycans affect the enzymatic activity and structural stability of recombinant TS enzyme TconTS1 in Trypanosoma congolense. The removal of N-glycans decreases substrate affinity but has no impact on the conversion rate. Interactions between N-glycans and amino acids in the catalytic site may lead to conformational changes, enhancing substrate accessibility and enzyme-substrate complex stability.

JOURNAL OF BIOLOGICAL CHEMISTRY (2022)

Article Chemistry, Medicinal

Exploration, Representation, and Rationalization of the Conformational Phase Space of N-Glycans

Isabell Louise Grothaus, Giovanni Bussi, Lucio Colombi Ciacchi

Summary: Despite their biological relevance, structure-property relationships in N-glycans are currently not well understood. In this study, a novel enhanced-sampling scheme was developed to explore the highly multidimensional compositional and conformational phase spaces of N-glycans. The results reveal the effect of chemical substitutions on the conformational ensemble of selected glycans and assess the structure-prediction capabilities of commonly used force fields.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2022)

Article Chemistry, Physical

Protein conformational changes at the oil/water-interface induced by premix membrane emulsification

Tobias Wollborn, Monika Michaelis, Lucio Colombi Ciacchi, Udo Fritsching

Summary: This study provides evidence that beta-lactoglobulin proteins undergo conformational changes during membrane emulsification processes. The shear stress applied during oil droplet fragmentation causes the protein to transition into a more stable, partially unfolded interfacial state.

JOURNAL OF COLLOID AND INTERFACE SCIENCE (2022)

Review Biotechnology & Applied Microbiology

Biomolecule-mimetic nanomaterials for photothermal and photodynamic therapy of cancers: Bridging nanobiotechnology and biomedicine

Peng He, Guozheng Yang, Danzhu Zhu, Hao Kong, Yendry Regina Corrales-Urena, Lucio Colombi Ciacchi, Gang Wei

Summary: This review presents recent advances in the biomolecule-mimetic synthesis of functional nanomaterials for photothermal therapy (PTT) and photodynamic therapy (PDT) of cancers. It introduces different biomimetic synthesis methods and discusses the advantages of each method. The review also explores the synthesis of nanomaterials using biomolecules and discusses how to regulate the structure and functions of the obtained biomimetic nanomaterials. Additionally, potential applications of biomimetic nanomaterials for both PTT and PDT of cancers are demonstrated and discussed.

JOURNAL OF NANOBIOTECHNOLOGY (2022)

Article Materials Science, Multidisciplinary

Atomistic simulations of chitosan as a possible carrier system for miRNA transport

Alexander Avdoshin, Vladimir Naumov, Lucio Colombi Ciacchi, Stanislav Ignatov, Susan Koeppen

Summary: MicroRNA (miRNA) holds great potential as a new high-tech pharmacological agent and requires protective drug delivery carriers. Chitosan, with its useful properties such as mucoadhesion, ease of modification, low cost, and biocompatibility, is a promising material for these carriers. Molecular dynamics simulations of chitosan/miRNA complexes demonstrated that the protonation and acetylation degree of chitosan influenced the formation and adsorption properties of the complexes.

MATERIALS ADVANCES (2023)

Meeting Abstract Biochemistry & Molecular Biology

Modulation of multidrug resistance protein 1-mediated export processes by the antiviral drug ritonavir

Christian Arend, Isabell Louise Grothaus, Mario Waespy, Lucio Colombi Ciacchi, Ralf Dringen

JOURNAL OF NEUROCHEMISTRY (2022)

Meeting Abstract Biophysics

Monosaccharide puckering influences N-glycan conformational phase space distribution

Isabell L. Grothaus, Giovanni Bussi, Lucio Colombi Ciacchi

EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS (2021)

Meeting Abstract Biochemistry & Molecular Biology

Role of N-glycosylation on structure-function relations of Trypanosoma congolense trans-sialidase

Isabell L. Grothaus, Jana Rosenau, Nilima Dinesh Kumar, Lucio Colombi Ciacchi, Sorge Kelm, Mario Waespy

GLYCOBIOLOGY (2020)

Article Chemistry, Multidisciplinary

Bio-interfactants as double-sided tapes for graphene oxide

Felipe Macul Perez, Yendry Regina Corrales Urena, Klaus Rischka, Welchy Leite Cavalcanti, Paul-Ludwig Michael Noeske, Arta Anushirwan Safari, Gang Wei, Lucio Colombi Ciacchi

NANOSCALE (2019)

No Data Available