Interaction of calcite (104) surfaces with a peptide molecule (Jianwei Wang and Udo Becker)
A change in crystal morphology induced by additives indicates the nature of interactions between additives and crystal surface sites. In biomineralization, many experimental results prompt an atomistic scale understanding of how surface morphology of a biomineral depends on the details of the location and configuration of adsorbates and the energetics of the adsorption. This understanding could provide important insights on how organisms control and mediate inorganic deposits. We apply large-scale molecular dynamics simulations that take into account the effect of dynamical fluctation of hydrogen bonding networks of water molecules and reorientation of organic molecules. The free energies and free energy barriers are calculated using Umbrella sampling technique for the adsorption and desorption of peptide moledules at calcite (104) surface sites. These free energies are fed into a surface growth model using a kinetic Monte-Carlo approach that operates at longer time scales. The results from these simulations can be verified by in situ atomically resolved microscopic experiments.
The three movies/animations below are from molecular dynamics simulations of calcite (104) surfaces with a peptide molecule (ARG-VAL-PRO), using the Gromacs molecular dynamics package. The three surfaces are: (a) a polar step, (b) a non-polar step (a so-called periodic bond chain), and (c) a flat surface. (a) The carboxyl gropu of the peptide is stronglly bonded to a Ca2+ ion at the polar step whereas the (positively charge) amino group bonds to carbonate sites only occasionally. (b) A relatively weak interaction is observed at the non-polar step, resulting in rare bonding events with immediate detachement. (c) No specific bonding site is found on the flat (104) surface such that the biomolecule predominantly stays in solution. Green balls are Ca2+ ions, red balls are O atoms of CO32-, cyan balls are C atoms of CO32-, dark grey balls are H atoms of the peptide, and blue balls are N atoms of the peptide. Thin red and grey butterflies are water molecules.
Interaction of polypeptide network with Calcite (Subhashis Biswas and Udo Becker)
My main research project is on biomineralization. Biomineralization is selective uptake and formation of inorganic minerals on organic matrix/template under strict biological conditions. This is governed by interfacial matching of electrostatic potential, lattice energy, topography and stereochemistry. Calcite, silica, magnetite, apatite are examples of biominerals that form on hard body exoskeleton of coccolithophores, diatoms, trigeminal nerve of trout fish, bone and teeth respectively. My work is focused on calcite and apatite. Calcite is a Calcite is a rhombohedral polymorph of calcium carbonate (CaCO3). The mineral (calcite) deposition on the exoskeleton of the organism can be related to its DNA pattern, and hence, to the protein sequence that forms the hard body exoskeleton. Our first objective is to find suitable orientations of amino-acid residues in these peptide chains, where these peptide chains align themselves parallel to the calcite surface or parallel to a step on these surfaces. Various sequences of small-chain (3-aminoacid) peptide residues on both polar and non-polar surface steps on calcite (104) faces have been studied. The residue with the highest adsorption energy of the ones that we studied is Phe-leu-lys4- with total adsorption energy of -1.071eV (non-polar calcite surface step) or –0.3571 eV/residue. For the interaction of a 12-amino acid long peptide chain in alkaline conditions with polar steps, we calculate an adsorption energy of –0.09824 eV/amino acid residue and -0.1978 eV/amino acid residue when the peptide residue is neutral (acidic condition and non-polar step). The12-amino acid long peptide chain with alternating glycine and alanine shows better parallel alignment.
In order to understand the nucleating mechanism of inorganic mineral surfaces on organic templates during biomineralization, we are studying the growth and nucleation of calcium carbonates on two and three-dimensional peptide-chain networks. Scientists have focused on synthetic bioorganic templates, such as polymers, β-pleated polyamino acids entrapped in gelatin self-assembled monolayers on gold substrates, and Langmuir films. In the case of Langmuir monolayers, the amphiphilic molecules can be designed in such a way that they act as artificial two-dimensional nuclei for the promotion of crystal nucleation. Such films have been used as templates to direct the crystal nucleation and growth of calcium carbonate. This is the starting point of our molecular dynamics simulations. After deriving a pure-core potential set for fast molecular dynamics simulations, we have created different two-dimensional networks of amide-containing phospholipids that serve as templates for Ca carbonate seed formation. By varying the distance and structural arrangement of the amphipilic molecules in the two-dimensional network, we can control the seed formation. The water content and concentrations of Ca2+ and CO32- were also varied below the Langmuir film.
We applied pressure on both side of the two-dimensional amphiphilic molecule on the film, and increased the pressure until the disruption of the film. The pressure-area curve matched the experimental data. We studied the Langmuir film interaction with calcite surface on (1 0 4), (1 0 0) and (0 0 1) direction, and observed the effect of phosphate group interaction with calcium and carbonate up to first 3-4 layers in (0 0 1) direction.
The ultimate goal of this project is to provide systematic insight into template and, thus, seed formation control from a theoretical point of view. Ultimately, we want to understand which carbonate will form with which surface at the interface depending on the template provided. Our work with apatite is currently also in progress. We plan to study interaction of polypeptide on apatite and hydroxyapatite. The apatite that grows on teeth and bone are carbonated apatite with non-stoichiometric inclusions of hydroxides. We are building a force field for apatite/hydroxyapatite, and then we would study interaction of small and big chain polypeptides containing specific functional groups in the amino acid side chain, with different apatite surfaces.
Interaction of polypeptide with Hydroxyapatite (Subhashis Biswas and Udo Becker in collaboration with Sharon Segvich, David Kohn, University of Michigan School of Dentistry)
Understanding the interaction between organic molecules and inorganic surfaces is an important aspect in the development of functional bone tissue engineered substitutes. Specifically, the microenvironment on hydroxyapatite and carbonated apatite surfaces can influence cellular behavior positively by influencing cell adhesion, spreading, and growth or negatively by promoting cell death (apoptosis). Through observation of nature’s bone mineralization process, biomimetic techniques of precipitating bone-like mineral on polymeric scaffolding have been developed. Soaking a biodegradable, 3D scaffold in a supersaturated solution that contains similar ion concentrations to that of human serum at body temperature (37C) will heterogeneously precipitate a carbonated apatite phase onto the scaffold. This carbonated apatite layer can be used as a platform for biomolecular delivery of proteins, growth factors, peptides, etc. The focus of this project is to develop force fields for hydroxyapatite and carbonated apatite in order to perform molecular simulations of peptides on predominant face planes of both minerals. Peptides contain strings of amino acids that, in a certain configuration, can trigger cellular behavior such as adhesion, secretion of signaling factors, and initiation of signaling cascades.
The interaction of peptide with hydroxyapatite surface is studied with empirical methods using potentials of apatite and force-field. To develop a force-field, first we have to build a potential energy file .This is the GULP file, (General Utility Lattice Program). The potential energy file consists of the lattice parameters, fractional coordinates and occupancies of the atoms in the lattice. The charges on the different atoms are also specified. The charges can be variable, and that can be mentioned in the gulp file. Then there are interaction parameters and potentials among the different atoms in the lattice.
For apatite, we have interactions between phosphorous and oxygen, Calcium and oxygen. We have to keep in mind that there are two different types of oxygen, oxygen in the phosphate group and oxygen of the hydroxide. We assign two different types of potentials to them. The potential that is used here is Buckingham potential and Lenard-Jones potential. The constants A and C is obtained by running the GULP program ,also the bond stretch terms for different types of oxygen and phosphorus in Harmonic and Morse potential is obtained.
This potential file now has to be incorporated in the Cerius Program as a Force field file .When we would run the simulation between peptide and hydroxyapatite, this empirical force-field will provide necessary interaction parameters to the models for minimum energy conformation.
In the Cerius software, we incorporate the constants for off-diagonal van der Waals, bonded interactions, bond-stretch terms, and angle bend terms. Then we save the force field file, reload it, and calculate interaction energies for all the different possible atom interactions using this force-field. We calculate the same using Universal force field, and obtained apparently same result. Thus we can be assured and satisfied with this force-field and use it for our future energy minimizations and molecular dynamics with peptides and hydroxyapatite.
Current study involves the interaction of 3 different peptides on hydoxyapatite (010) surface step. The peptides are E7PRGDT, RGD and RGE. We studied the mineral-peptide interaction with only one layer of hydroxyapatite moving, top 3 layers of mineral moving and the whole hydroxyapatite surface moving.
Reference: 1) Potential energy for apatite paper
2) GULP - a computer program for the symmetry adapted simulation of solids, J.D. Gale, JCS Faraday Trans., 93, 629 (1997)