Computational Techniques at the Organic−Inorganic Interface in Biomineralization

Harding, John C. S.; Duffy, Dorothy M.; Sushko, Maria L.; Rodger, P. Mark; Quigley, David A.; Elliott, James M.

doi:10.1021/cr078278y

Cited by 108 publications

(97 citation statements)

References 407 publications

(587 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In subsequent stages of the trajectory, these clusters grow similarly and ions tend to re-organize, suggesting that the system evolves towards poly-organized HAp. This multi-nucleation behaviour is fully consistent with previous studies devoted to investigating HAp crystal growth 28 and differs from that displayed in Fig. 1, which shows the preferential nucleation around the DNA template.…”

Section: Computational Designsupporting

confidence: 91%

Mineralization of DNA into nanoparticles of hydroxyapatite

et al. 2014

View full text Add to dashboard Cite

show abstract

“…The underlying source of these differences is undoubtedly the unique adsorption behavior of polypeptides at surfaces (16). Polypeptide binding to an oppositely charged surface requires crossing a series of kinetic barriers, such as displacement of shielding counterions, configurational relaxation of the polymer, and coordination with oppositely charged sites on the crystal to reach the final collapsed state in which the polypeptide residues form specific bonds to lattice sites (16).…”

mentioning

confidence: 99%

“…Polypeptide binding to an oppositely charged surface requires crossing a series of kinetic barriers, such as displacement of shielding counterions, configurational relaxation of the polymer, and coordination with oppositely charged sites on the crystal to reach the final collapsed state in which the polypeptide residues form specific bonds to lattice sites (16). In contrast, at like-charged surfaces, polypeptide solutions containing di-and trivalent counterions exhibit fluctuating polarizations that can diminish the double-layer repulsion between like-charged objects, allowing the van der Waals attraction to dominate (16,17). This effect can lead to polypeptide clustering (dictated by the balance of enthalpic gain and entropic cost of aggregation) as well as nonspecific binding to the surface.…”

mentioning

confidence: 99%

Subnanometer atomic force microscopy of peptide–mineral interactions links clustering and competition to acceleration and catastrophe

Friddle

Weaver

Qiu³

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

138

View full text Add to dashboard Cite

In vitro observations have revealed major effects on the structure, growth, and composition of biomineral phases, including stabilization of amorphous precursors, acceleration and inhibition of kinetics, and alteration of impurity signatures. However, deciphering the mechanistic sources of these effects has been problematic due to a lack of tools to resolve molecular structures on mineral surfaces during growth. Here we report atomic force microscopy investigations using a system designed to maximize resolution while minimizing contact force. By imaging the growth of calciumoxalate monohydrate under the influence of aspartic-rich peptides at single-molecule resolution, we reveal how the unique interactions of polypeptides with mineral surfaces lead to acceleration, inhibition, and switching of growth between two distinct states. Interaction with the positively charged face of calcium-oxalate monohydrate leads to formation of a peptide film, but the slow adsorption kinetics and gradual relaxation to a well-bound state result in time-dependent effects. These include a positive feedback between peptide adsorption and step inhibition described by a mathematical catastrophe that results in growth hysteresis, characterized by rapid switching from fast to near-zero growth rates for very small reductions in supersaturation. Interactions with the negatively charged face result in formation of peptide clusters that impede step advancement. The result is a competition between accelerated solute attachment and inhibition due to blocking of the steps by the clusters. The findings have implications for control of pathological mineralization and suggest artificial strategies for directing crystallization.biomineralization | calcium oxalate monohydrate | crystal growth | peptide adsorption | molecular resolution

show abstract

“…1,4,55 It is, however, understood that usage of the bulk value ∆µ = ∆µ coex as the driving force to nucleation may be unsuitable for the description of the microscopic particle attachment process. 56 An alternative value ∆µ fit ( β, f ) can be obtained via a two parameter fit of Eq. (14), allowing the appropriate value of ∆µ to be determined by the microscopic dynamics of the system.…”

Section: E Choice Of ∆µmentioning

confidence: 99%

Nucleation barrier reconstruction via the seeding method in a lattice model with competing nucleation pathways

Lifanov

Vorselaars

Quigley

2016

The Journal of Chemical Physics

Self Cite

View full text Add to dashboard Cite

We study a three-species analogue of the Potts lattice gas model of nucleation from solution in a regime where partially disordered solute is a viable thermodynamic phase. Using a multicanonical sampling protocol, we compute phase diagrams for the system, from which we determine a parameter regime where the partially disordered phase is metastable almost everywhere in the temperature-fugacity plane. The resulting model shows non-trivial nucleation and growth behaviour, which we examine via multidimensional free energy calculations. We consider the applicability of the model in capturing the multi-stage nucleation mechanisms of polymorphic biominerals (e.g., CaCO 3 ). We then quantitatively explore the kinetics of nucleation in our model using the increasingly popular "seeding" method. We compare the resulting free energy barrier heights to those obtained via explicit free energy calculations over a wide range of temperatures and fugacities, carefully considering the propagation of statistical error. We find that the ability of the "seeding" method to reproduce accurate free energy barriers is dependent on the degree of supersaturation, and severely limited by the use of a nucleation driving force ∆µ computed for bulk phases. We discuss possible reasons for this in terms of underlying kinetic assumptions, and those of classical nucleation theory. C 2016 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution (CC BY) license

show abstract

“…Young's moduli, molar ratio of shell constituents, viscosity, osmolarity, crystalinity, topography and other read-outs are frequently changing on different length scales. Computational methods are currently developed for a number of biomineralization proteins and their interactions with mineral phases [189]. As outlined in Fig.…”

Section: Experimental Tools For Studying Mollusc Chitin Synthasesmentioning

confidence: 99%

Species-specific shells: Chitin synthases and cell mechanics in molluscs

Weiss¹

2012

Zeitschrift Für Kristallographie - Crystalline Materials

View full text Add to dashboard Cite

Abstract. The size, morphology and species-specific texture of mollusc shell biominerals is one of the unresolved questions in nature. In search of molecular control principles, chitin has been identified by Weiner and Traub (FEBS Lett. 1980, 111 : 311-316) as one of the organic compounds with a defined co-organization with mineral phases. Chitin fibers can be aligned with certain mineralogical axes of crystalline calcium carbonate in a speciesspecific manner. These original observations motivated the functional characterization of chitin forming enzymes in molluscs. The full-length cDNA cloning of mollusc chitin synthases identified unique myosin domains as part of the biological control system. The potential impact of molecular motors and other conserved domains of these complex transmembrane enzymes on the evolution of shell biomineralization is investigated and discussed in this article. Chitin in organisms Chitin in extracellular matrices of cellsIn the end of the 19th century, there was a hot debate regarding the chemical nature of chitin. It lasted until acetylated glucosamine was found in alkaline melts of the carapace of diverse arthropods in contrast to tunicate cellulose [1], and "mycosin" of fungi in contrast to "fungal cellulose" (reviewed by [2]). Today, fungi are well accepted as one of the most prominent groups of eukaryotic organisms which contain chitin as part of their extracellular matrix [3]. Since chitin is usually associated with proteins, complex carbohydrates and sometimes mineral phases, it remains a challenge until today to characterize the diversity of cell walls and integuments in both, uni-and multicellular organisms [4][5][6][7][8][9]. One of the best examples for naturally pure chitin are cell wall appendices of diatoms [10,11], and some enzymes involved in their formation have recently been identified [12,13]. As originally determined by fiber diffraction studies [14-17], three major modifications of chitin are distinguished: a-, b-, and g-chitin [18,19], which differ from each other by the arrangement and molar fractions of differently oriented poly-N-acetylated linear b(1!4) glucosamine (i.e. chitobiose homopolymer, Fig. 1) backbones. They assemble into fiber crystals which are stabilized by H-bonds in either two or three dimensions [4,20,21]. Squids such as the European Squid Loligo vulgaris or the Humboldt squid Dosidicus gigas, which are members of the molluscan class Cephalopoda, perform the biosynthesis of different chitin polymorphs in a tissuespecific manner. The chitinous organs are associated with different sets of proteins [22]. The N-acetyl-glucosamine (GlcNAc) chains are assembled into fibrils and hierarchical structures in order to accomodate specific functions such as mechanical stiffness and strength [23,24]. This is important for the functional design, e.g. of insect exoskeletons and additional functions such as structural colours and adhesive micro-pillar appendages [25,26].A major achievement is the abundant information regarding primary structures of enzyme...

show abstract

Computational Techniques at the Organic−Inorganic Interface in Biomineralization

Cited by 108 publications

References 407 publications

Mineralization of DNA into nanoparticles of hydroxyapatite

Subnanometer atomic force microscopy of peptide–mineral interactions links clustering and competition to acceleration and catastrophe

Nucleation barrier reconstruction via the seeding method in a lattice model with competing nucleation pathways

Species-specific shells: Chitin synthases and cell mechanics in molluscs

Contact Info

Product

Resources

About