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Title: Atomic-Scale Quantification of Interfacial Binding between Peptides and Inorganic Crystals: The Case of Calcium Carbonate Binding Peptide on Aragonite

Abstract

Using a specific explicitly solvated interface model between a calcium carbonate binding peptide and crystalline aragonite, we investigate the electronic structure, atomic bonding, solvation effect, and the role of hydrogen bonding on the cohesion, stability, and functionality of this complex hybrid system using density functional calculation. The large interface model is strategically constructed using a stepwise procedure followed by ab initio molecular dynamics to obtain the optimal conformation. The calculated data on the electronic structure and bonding are analyzed in terms of three structural parts: aragonite, peptide, and water. Next, we focus on the binding between aragonite (001) surface and the peptide mediated by water. Finally, specific interatomic bonding between the amino acids in peptide and the (001) surface of aragonite is quantified. A single quantum mechanical metric, the total bond order density (TBOD), infers the dynamic interplay of different competing interactions. Four amino acids HIS1, ARG6, MET7, and TRP11 in the peptide sequence have strong interfacial Ca–O bonding and O···H hydrogen bonding between aragonite and peptide. The calculated Young’s modulus 33.37 GPa is in line with the measured value for nacre. Our approach for interfacial study between aragonite and a calcium carbonate binding peptide offers a broad perspective formore » probing complex interactions between the biomimetic interfaces. Finally, TBOD can be used as an effective parameter in ranking the efficacy of peptide–surface interactions and in providing a programmable design for bio-inspired material interfaces based on computational means.« less

Authors:
 [1];  [2];  [3]; ORCiD logo [1]
  1. Univ. of Missouri, Kansas City, MO (United States). Dept. of Physics and Astronomy
  2. Univ. of Kansas, Lawrence, KS (United States). Dept. of Mechanical Engineering
  3. Univ. of Kansas, Lawrence, KS (United States). Dept. of Civil, Environmental, and Architectural Engineering
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES)
OSTI Identifier:
1483664
Grant/Contract Number:  
SC0008176; AC03-76SF00098
Resource Type:
Accepted Manuscript
Journal Name:
Journal of Physical Chemistry. C
Additional Journal Information:
Journal Volume: 121; Journal Issue: 51; Journal ID: ISSN 1932-7447
Publisher:
American Chemical Society
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY

Citation Formats

Poudel, Lokendra, Tamerler, Candan, Misra, Anil, and Ching, Wai-Yim. Atomic-Scale Quantification of Interfacial Binding between Peptides and Inorganic Crystals: The Case of Calcium Carbonate Binding Peptide on Aragonite. United States: N. p., 2017. Web. doi:10.1021/acs.jpcc.7b10004.
Poudel, Lokendra, Tamerler, Candan, Misra, Anil, & Ching, Wai-Yim. Atomic-Scale Quantification of Interfacial Binding between Peptides and Inorganic Crystals: The Case of Calcium Carbonate Binding Peptide on Aragonite. United States. https://doi.org/10.1021/acs.jpcc.7b10004
Poudel, Lokendra, Tamerler, Candan, Misra, Anil, and Ching, Wai-Yim. Tue . "Atomic-Scale Quantification of Interfacial Binding between Peptides and Inorganic Crystals: The Case of Calcium Carbonate Binding Peptide on Aragonite". United States. https://doi.org/10.1021/acs.jpcc.7b10004. https://www.osti.gov/servlets/purl/1483664.
@article{osti_1483664,
title = {Atomic-Scale Quantification of Interfacial Binding between Peptides and Inorganic Crystals: The Case of Calcium Carbonate Binding Peptide on Aragonite},
author = {Poudel, Lokendra and Tamerler, Candan and Misra, Anil and Ching, Wai-Yim},
abstractNote = {Using a specific explicitly solvated interface model between a calcium carbonate binding peptide and crystalline aragonite, we investigate the electronic structure, atomic bonding, solvation effect, and the role of hydrogen bonding on the cohesion, stability, and functionality of this complex hybrid system using density functional calculation. The large interface model is strategically constructed using a stepwise procedure followed by ab initio molecular dynamics to obtain the optimal conformation. The calculated data on the electronic structure and bonding are analyzed in terms of three structural parts: aragonite, peptide, and water. Next, we focus on the binding between aragonite (001) surface and the peptide mediated by water. Finally, specific interatomic bonding between the amino acids in peptide and the (001) surface of aragonite is quantified. A single quantum mechanical metric, the total bond order density (TBOD), infers the dynamic interplay of different competing interactions. Four amino acids HIS1, ARG6, MET7, and TRP11 in the peptide sequence have strong interfacial Ca–O bonding and O···H hydrogen bonding between aragonite and peptide. The calculated Young’s modulus 33.37 GPa is in line with the measured value for nacre. Our approach for interfacial study between aragonite and a calcium carbonate binding peptide offers a broad perspective for probing complex interactions between the biomimetic interfaces. Finally, TBOD can be used as an effective parameter in ranking the efficacy of peptide–surface interactions and in providing a programmable design for bio-inspired material interfaces based on computational means.},
doi = {10.1021/acs.jpcc.7b10004},
journal = {Journal of Physical Chemistry. C},
number = 51,
volume = 121,
place = {United States},
year = {2017},
month = {12}
}

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Figures / Tables:

Table 1 Table 1: Total energy (TE), surface binding energy (BE) and TBOD for interface models

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Figures/Tables have been extracted from DOE-funded journal article accepted manuscripts.