Functional Molecular Crystals in Biology

Rationalizing the Influence of Small-Molecule Dopants on Guanine Crystal Morphology

Many spectacular optical phenomena in animals are produced by reflective assemblies of guanine crystals. The crystals comprise planar H-bonded layers of π-stacked molecules with a high in-plane refractive index. By preferentially expressing the highly reflective π-stacked (100) crystal face and controlling its cross-sectional shape, organisms generate a diverse array of photonic superstructures. How is this precise control over crystal morphology achieved? Recently, it was found that biogenic guanine crystals are composites, containing high quantities of hypoxanthine and xanthine in a molecular alloy. Here, we crystallized guanine in the presence of these dopants and used computations to rationalize their influence on the crystal morphology and energy. Exceptional quantities of hypoxanthine are incorporated into kinetically favored solid solutions, indicating that fast crystallization kinetics underlies the heterogeneous compositions of biogenic guanine crystals. We find that weakening of H-bonding interactions by additive incorporation elongates guanine crystals along the stacking direction-the opposite morphology of biogenic crystals. However, by modulation of the strength of competing in-plane H-bonding interactions, additive incorporation strongly influences the cross-sectional shape of the crystals. Our results suggest that small-molecule H-bond disrupting additives may be simultaneously employed with π-stack blocking additives to generate reflective platelet crystal morphologies exhibited by organisms.

Understanding the Solid-State Structure of Riboflavin through a Multitechnique Approach

Crystalline riboflavin (vitamin B2) performs an important biological role as an optically functional material in the tapetum lucidum of certain animals, notably lemurs and cats. The tapetum lucidum is a reflecting layer behind the retina, which serves to enhance photon capture and vision in low-light settings. Motivated by the aim of rationalizing its biological role, and given that the structure of biogenic solid-state riboflavin remains unknown, we have used a range of experimental and computational techniques to determine the solid-state structure of synthetic riboflavin. Our multitechnique approach included microcrystal XRD, powder XRD, three-dimensional electron diffraction (3D-ED), high-resolution solid-state 13C NMR spectroscopy, and dispersion-augmented density functional theory (DFT-D) calculations. Although an independent report of the crystal structure of riboflavin was published recently, our structural investigations reported herein provide a different interpretation of the intermolecular hydrogen-bonding arrangement in this material, supported by all the experimental and computational approaches utilized in our study. We also discuss, more generally, potential pitfalls that may arise in applying DFT-D geometry optimization as a bridging step between structure solution and Rietveld refinement in the structure determination of hydrogen-bonded materials from powder XRD data. Finally, we report experimental and computational values for the refractive index of riboflavin, with implications for its optical function.

Biomineralization and Properties of Guanine Crystals

Guanine crystals with unique optical properties in organisms have been extensively studied and the biomineralization principles of guanine are being established. This review summarizes the fundamental physicochemical properties (solubility, tautomers, bands, and refractivity), polymorphs, morphology of biological and synthetic forms, and the reported biomineralization principles of guanine (selective recrystallization of amorphous precursor, preassembled scaffolds, additives, twinning, hypoxanthine doping, fluorescence, and assembly). The biomineralization principles of guanine will be helpful for the synthesis of guanine crystals with excellent properties and the design of functional organic materials for drugs, dyes, organic semiconductors, etc.

Brilliant whiteness in shrimp from ultra-thin layers of birefringent nanospheres

A fundamental question regarding light scattering is how whiteness, generated from multiple scattering, can be obtained from thin layers of materials. This challenge arises from the phenomenon of optical crowding, whereby, for scatterers packed with filling fractions higher than ~30%, reflectance is drastically reduced due to near-field coupling between the scatterers. Here we show that the extreme birefringence of isoxanthopterin nanospheres overcomes optical crowding effects, enabling multiple scattering and brilliant whiteness from ultra-thin chromatophore cells in shrimp. Strikingly, numerical simulations reveal that birefringence, originating from the spherulitic arrangement of isoxanthopterin molecules, enables intense broadband scattering almost up to the maximal packing for random spheres. This reduces the thickness of material required to produce brilliant whiteness, resulting in a photonic system that is more efficient than other biogenic or biomimetic white materials which operate in the lower refractive index medium of air. These results highlight the importance of birefringence as a structural variable to enhance the performance of such materials and could contribute to the design of biologically inspired replacements for artificial scatterers like titanium dioxide.

Guanine crystal formation by bacteria

BACKGROUND

Guanine crystals are organic biogenic crystals found in many organisms. Due to their exceptionally high refractive index, they contribute to structural color and are responsible for the reflective effect in the skin and visual organs in animals such as fish, reptiles, and spiders. Occurrence of these crystals in animals has been known for many years, and they have also been observed in eukaryotic microorganisms, but not in prokaryotes.

RESULTS

In this work, we report the discovery of extracellular crystals formed by bacteria and reveal that they are composed of guanine monohydrate. This composition differs from that of biogenic guanine crystals found in other organisms, mostly composed of β anhydrous guanine. We demonstrate the formation of these crystals by Aeromonas and other bacteria and investigate the metabolic traits related to their synthesis. In all cases studied, the presence of the bacterial guanine crystals correlates with the absence of guanine deaminase, which could lead to guanine accumulation providing the substrate for crystal formation.

CONCLUSIONS

Our finding of the hitherto unknown guanine crystal occurrence in prokaryotes extends the range of organisms that produce these crystals to a new domain of life. Bacteria constitute a novel and more accessible model to study the process of guanine crystal formation and assembly. This discovery opens countless chemical and biological questions, including those about the functional and adaptive significance of their production in these microorganisms. It also paves the road for the development of simple and convenient processes to obtain biogenic guanine crystals for diverse applications.

Revisiting biocrystallization: purine crystalline inclusions are widespread in eukaryotes

Despite the widespread occurrence of intracellular crystalline inclusions in unicellular eukaryotes, scant attention has been paid to their composition, functions, and evolutionary origins. Using Raman microscopy, we examined >200 species from all major eukaryotic supergroups. We detected cellular crystalline inclusions in 77% species out of which 80% is composed of purines, such as anhydrous guanine (62%), guanine monohydrate (2%), uric acid (12%) and xanthine (4%). Our findings shifts the paradigm assuming predominance of calcite and oxalates. Purine crystals emerge in microorganisms in all habitats, e.g., in freshwater algae, endosymbionts of reef-building corals, deadly parasites, anaerobes in termite guts, or slime molds. Hence, purine biocrystallization is a general and ancestral eukaryotic process likely present in the last eukaryotic common ancestor (LECA) and here we propose two proteins omnipresent in eukaryotes that are likely in charge of their metabolism: hypoxanthine-guanine phosphoribosyl transferase and equilibrative nucleoside transporter. Purine crystalline inclusions are multifunctional structures representing high-capacity and rapid-turnover reserves of nitrogen and optically active elements, e.g., used in light sensing. Thus, we anticipate our work to be a starting point for further studies spanning from cell biology to global ecology, with potential applications in biotechnologies, bio-optics, or in human medicine.

The Non-Classical Crystallization Mechanism of a Composite Biogenic Guanine Crystal

Spectacular colors and visual phenomena in animals are produced by light interference from highly reflective guanine crystals. Little is known about how organisms regulate crystal morphology to tune the optics of these systems. By following guanine crystal formation in developing spiders, a crystallization mechanism is elucidated. Guanine crystallization is a "non-classical," multistep process involving a progressive ordering of states. Crystallization begins with nucleation of partially ordered nanogranules from a disordered precursor phase. Growth proceeds by orientated attachment of the nanogranules into platelets which coalesce into single crystals, via progressive relaxation of structural defects. Despite their prismatic morphology, the platelet texture is retained in the final crystals, which are composites of crystal lamellae and interlamellar sheets. Interactions between the macromolecular sheets and the planar face of guanine appear to direct nucleation, favoring platelet formation. These findings provide insights on how organisms control the morphology and optical properties of molecular crystals.

Real-Space Crystal Structure Analysis by Low-Dose Focal-Series TEM Imaging of Organic Materials with Near-Atomic Resolution

Structural analysis of beam-sensitive materials by transmission electron microscopy (TEM) represents a significant challenge, as high-resolution TEM (HRTEM) requires high electron doses that limit its applicability to stable inorganic materials. Beam-sensitive materials, e.g., organic crystals, must be imaged under low dose conditions, leading to problematic contrast interpretation and loss of fine structural details. Here, HRTEM imaging of organic crystalline materials with near-atomic resolution of up to 1.6 Å is described, which enables real-space studies of crystal structures, as well as observation of co-existing polymorphs, crystal defects, and atoms. This is made possible by a low-dose focal-series reconstruction methodology, which provides HRTEM images where contrast reflects true object structure and can be performed on contemporary cryo-EM instruments available to many research institutions. Copper phthalocyanine (CuPc), a perchlorinated analogue of CuPc, and indigo crystalline films are imaged. In the case of indigo crystals, co-existing polymorphs and individual atoms (carbonyl oxygen) can be observed. In the case of CuPc, several polymorphs are observed, including a new one, for which the crystal structure is found based on direct in-focus imaging, accomplishing real-space crystal structure elucidation. Such direct analysis can be transformative for structure studies of organic materials.

Biogenic Guanine Crystals Are Solid Solutions of Guanine and Other Purine Metabolites

Highly reflective crystals of the nucleotide base guanine are widely distributed in animal coloration and visual systems. Organisms precisely control the morphology and organization of the crystals to optimize different optical effects, but little is known about how this is achieved. Here we examine a fundamental question that has remained unanswered after over 100 years of research on guanine: what are the crystals made of? Using solution-state and solid-state chemical techniques coupled with structural analysis by powder XRD and solid-state NMR, we compare the purine compositions and the structures of seven biogenic guanine crystals with different crystal morphologies, testing the hypothesis that intracrystalline dopants influence the crystal shape. We find that biogenic "guanine" crystals are not pure crystals but molecular alloys (aka solid solutions and mixed crystals) of guanine, hypoxanthine, and sometimes xanthine. Guanine host crystals occlude homogeneous mixtures of other purines, sometimes in remarkably large amounts (up to 20% of hypoxanthine), without significantly altering the crystal structure of the guanine host. We find no correlation between the biogenic crystal morphology and dopant content and conclude that dopants do not dictate the crystal morphology of the guanine host. The ability of guanine crystals to host other molecules enables animals to build physiologically "cheaper" crystals from mixtures of metabolically available purines, without impeding optical functionality. The exceptional levels of doping in biogenic guanine offer inspiration for the design of mixed molecular crystals that incorporate multiple functionalities in a single material.