Literature DB >> 26587623

GolP-CHARMM: First-Principles Based Force Fields for the Interaction of Proteins with Au(111) and Au(100).

Louise B Wright1, P Mark Rodger1, Stefano Corni2, Tiffany R Walsh3.   

Abstract

Computational simulation of peptide adsorption at the aqueous gold interface is key to advancing the development of many applications based on gold nanoparticles, ranging from nanomedical devices to smart biomimetic materials. Here, we present a force field, GolP-CHARMM, designed to capture peptide adsorption at both the aqueous Au(111) and Au(100) interfaces. The force field, compatible with the bio-organic force field CHARMM, is parametrized using a combination of experimental and first-principles data. Like its predecessor, GolP (Iori, F.; et al. J. Comput. Chem.2009, 30, 1465), this force field contains terms to describe the dynamic polarization of gold atoms, chemisorbing species, and the interaction between sp(2) hybridized carbon atoms and gold. A systematic study of small molecule adsorption at both surfaces using the vdW-DF functional (Dion, M.; et al. Phys. Rev. Lett.2004, 92, 246401-1. Thonhauser, T.; et al. Phys. Rev. B2007, 76, 125112) is carried out to fit and test force field parameters and also, for the first time, gives unique insights into facet selectivity of gold binding in vacuo. Energetic and spatial trends observed in our DFT calculations are reproduced by the force field under the same conditions. Finally, we use the new force field to calculate adsorption energies, under aqueous conditions, for a representative set of amino acids. These data are found to agree with experimental findings.

Entities:  

Year:  2013        PMID: 26587623     DOI: 10.1021/ct301018m

Source DB:  PubMed          Journal:  J Chem Theory Comput        ISSN: 1549-9618            Impact factor:   6.006


  23 in total

Review 1.  Force fields for simulating the interaction of surfaces with biological molecules.

Authors:  Lewis Martin; Marcela M Bilek; Anthony S Weiss; Serdar Kuyucak
Journal:  Interface Focus       Date:  2016-02-06       Impact factor: 3.906

2.  Perspectives on the simulation of protein-surface interactions using empirical force field methods.

Authors:  Robert A Latour
Journal:  Colloids Surf B Biointerfaces       Date:  2014-06-30       Impact factor: 5.268

3.  Parameterization of an interfacial force field for accurate representation of peptide adsorption free energy on high-density polyethylene.

Authors:  Tigran M Abramyan; James A Snyder; Jeremy A Yancey; Aby A Thyparambil; Yang Wei; Steven J Stuart; Robert A Latour
Journal:  Biointerphases       Date:  2015-06-27       Impact factor: 2.456

4.  Effects of Orientation on the Stability and Affinity of Antibody-GNP Conjugation.

Authors:  Fatemeh Ramezani
Journal:  Protein J       Date:  2019-04       Impact factor: 2.371

5.  Ubiquitin immobilized on mesoporous MCM41 silica surfaces - Analysis by solid-state NMR with biophysical and surface characterization.

Authors:  Nurit Adiram-Filiba; Avital Schremer; Eli Ohaion; Merav Nadav-Tsubery; Tammi Lublin-Tennenbaum; Keren Keinan-Adamsky; Gil Goobes
Journal:  Biointerphases       Date:  2017-05-31       Impact factor: 2.456

6.  Control of protein orientation on gold nanoparticles.

Authors:  Wayne Lin; Thomas Insley; Marcus D Tuttle; Lingyang Zhu; Deborah A Berthold; Petr Král; Chad M Rienstra; Catherine J Murphy
Journal:  J Phys Chem C Nanomater Interfaces       Date:  2015-08-18       Impact factor: 4.126

7.  NanoEHS beyond Toxicity - Focusing on Biocorona.

Authors:  Sijie Lin; Monika Mortimer; Ran Chen; Aleksandr Kakinen; Jim E Riviere; Thomas P Davis; Feng Ding; Pu Chun Ke
Journal:  Environ Sci Nano       Date:  2017-06-01

Review 8.  Understanding interactions between biomolecules and two-dimensional nanomaterials using in silico microscopes.

Authors:  Serena H Chen; David R Bell; Binquan Luan
Journal:  Adv Drug Deliv Rev       Date:  2022-05-19       Impact factor: 17.873

9.  Surface-site reactivity in small-molecule adsorption: A theoretical study of thiol binding on multi-coordinated gold clusters.

Authors:  Elvis C M Ting; Tatiana Popa; Irina Paci
Journal:  Beilstein J Nanotechnol       Date:  2016-01-18       Impact factor: 3.649

10.  Protein-Ligand Interaction Detection with a Novel Method of Transient Induced Molecular Electronic Spectroscopy (TIMES): Experimental and Theoretical Studies.

Authors:  Tiantian Zhang; Tao Wei; Yuanyuan Han; Heng Ma; Mohammadreza Samieegohar; Ping-Wei Chen; Ian Lian; Yu-Hwa Lo
Journal:  ACS Cent Sci       Date:  2016-10-24       Impact factor: 14.553

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.