Essence of Small Molecule-Mediated Control of Hydroxyapatite Growth: Free Energy Calculations of Amino Acid Side Chain Analogues

Abstract

Much effort has been exerted to unravel the bone biomineralization mechanism by which the growth of plate-shaped crystals of hydroxyapatite (HAP) is regulated within a fibrillar collagen matrix. Acidic noncollagenous acidic proteins (NCPs) bearing a large number of carboxylate and phosphorylate amino acid residues are effective regulators of HAP crystal morphology. To reveal the energetic and structural essence of the growth-regulation mechanism, we performed here advanced molecular dynamics simulations to obtain adsorption free energies of side chain analogues (SCAs) of acidic and uncharged polar amino acids as well as the corresponding zwitterionic backbone (BB) fragment and compared the results to those for the entire amino acid molecule. We observed that negatively charged SCAs (phosphoserine in two protonation states, aspartate and glutamate) and the zwitterionic BB preferentially bind to the HAP (100) surface compared to the (001) face, consistent with [100] being the preferred growth direction for plate-shaped HAP crystals. Charged SCAs and zwitterionic BB bind via the formation of salt bridges between the −COO– group and Ca2+ ions on the surface, or hydrogen bonds between the −NH3 + and surface PO4 3– ions, and adsorption of uncharged, polar serine SCA was thermodynamically unfavorable. Intriguingly, however, binding free energies depend on the number of charged groups rather than simply on net charge. Thus, zwitterionic (net neutral) BB adsorbed more strongly than monovalent Asp and Glu or uncharged Ser SCAs. Second, it was more difficult for larger molecules to adsorb presumably because of less favorable enthalpic and entropic contributions required to penetrate the tightly bound surface water layer. Accordingly, Asp adsorbed more strongly than homoionic Glu, and the sum of the SCA and BB binding affinities was greater than that of the entire amino acid molecule. The present results shed light on some previously unidentified subtle effects that the number of charged motifs rather than net charge and molecule size control a delicate balance of molecule–surface and water–surface interactions. These results should help understand the mechanisms of NCP-mediated HAP crystal growth in bone biomineralization and have broad implications for the design of new peptides and small molecules for biomimetic crystal synthesis.

Structure–Activity Relationships of Hydroxyapatite-Binding Peptides

“…The model HBPs studied here possess mainly hydrophilic amino acid side chain residues, of which lysine, glutamic acid, and phosphoserine are charged, while asparagine and serine are polar, neutral amino acid residues. All these residues may interact with the calcium, phosphate, and hydroxide ions on the HAP surface through electrostatic interactions or H-bonding. − Here, we have explored the effects of HBPs on Ca-PO 4 nucleation, phase transition from amorphous Ca-PO 4 to crystalline HAP, and crystal growth (morphology modification) to further probe any potential structure–activity relationship of HBPs.…”

Quantitatively Identifying the Roles of Interfacial Water and Solid Surface in Governing Peptide Adsorption

“…Details about the setup of running parameters for umbrella sampling can be found in our previous studies. 23,33 Decomposition of PMF. The free energy can be also written as 56…”

“…13 The strong interactions between the water layer and the outermost Ca 2+ and PO 4 3− ions on the surface significantly impede the exchange of water molecules residing in the adsorption layer with the bulk phase. 33,34 The second interface model of interest is the graphene− water system, which traditionally serves as a good model for a hydrophobic interface, and the graphene hydrophobic environment plays a key role in the adsorption of small molecules and large biomolecules on the surface. 35 Many applications of graphene, for example, in nanotechnology and chemical biosensors, rely on its interaction with peptides and proteins in an aqueous system.…”

“…38 By contrast, in terms of free energy calculations for side chains of amino acid adsorptions on surfaces, serine, as a polar amino acid, displays unfavorable interaction with the HAP surface, but strongly binds with the graphene surface. 33 These two residues are, therefore, selected as the basic unit of tripeptide to compare the distinct behavior at two interfaces in view of free energy profiles. Additionally, valine, with similar molecular size to serine is chosen to represent a nonpolar amino acid for investigating the effect of polarity on peptide adsorption.…”

Predicting binding affinities of nitrogen-containing bisphosphonates on hydroxyapatite surface by molecular dynamics

“…[14,15] Molecular simulations are useful for studying interactions between organic molecules and biomineral surfaces. [18][19][20][21][22][23][24] HAP has also been used to environment. [31][32][33] The third issue is that simulations have calculated the binding energies rather than binding free energies of NBPs to HAP surfaces.…”