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An Atomistic View on the Mechanism of Diatom Peptide-Guided Biomimetic Silica Formation.

ABSTRACT: Deciphering nature's remarkable way of encoding functions in its biominerals holds the potential to enable the rational development of nature-inspired materials with tailored properties. However, the complex processes that convert solution-state precursors into solid biomaterials remain largely unknown. In this study, an unconventional approach is presented to characterize these precursors for the diatom-derived peptides R5 and synthetic Silaffin-1A₁ (synSil-1A₁). These molecules can form defined supramolecular assemblies in solution, which act as templates for solid silica structures. Using a tailored structural biology toolbox, the structure-function relationships of these self-assemblies are unveiled. NMR-derived constraints are employed to enable a recently developed fractal-cluster formalism and then reveal the architecture of the peptide assemblies in atomistic detail. Finally, by monitoring the self-assembly activities during silica formation at simultaneous high temporal and residue resolution using real-time spectroscopy, the mechanism is elucidated underlying template-driven silica formation. Thus, it is demonstrated how to exercise morphology control over bioinorganic solids by manipulating the template architectures. It is found that the morphology of the templates is translated into the shape of bioinorganic particles via a mechanism that includes silica nucleation on the solution-state complexes' surfaces followed by complete surface coating and particle precipitation.

SUBMITTER: Kozak F

PROVIDER: S-EPMC11321707 | biostudies-literature | 2024 Aug

REPOSITORIES: biostudies-literature

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An Atomistic View on the Mechanism of Diatom Peptide-Guided Biomimetic Silica Formation.

Kozak Fanny F Brandis Dörte D Pötzl Christopher C Epasto Ludovica M LM Reichinger Daniela D Obrist Dominik D Peterlik Herwig H Polyansky Anton A Zagrovic Bojan B Daus Fabian F Geyer Armin A Becker Christian Fw CF Kurzbach Dennis D

Advanced science (Weinheim, Baden-Wurttemberg, Germany) 20240614 30

Deciphering nature's remarkable way of encoding functions in its biominerals holds the potential to enable the rational development of nature-inspired materials with tailored properties. However, the complex processes that convert solution-state precursors into solid biomaterials remain largely unknown. In this study, an unconventional approach is presented to characterize these precursors for the diatom-derived peptides R5 and synthetic Silaffin-1A<sub>1</sub> (synSil-1A<sub>1</sub>). These mol ...[more]

PMID: 38874418

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Project description:Peptides were identified during degradation of the diatom Thalassiosira weissflogii with and without the use of the enzyme trypsin. This allows comparison of protein degradation occurring within the experiment (no trypsin added; peptides already present due to in situ degradation) and the protein still available for future degradation (peptides released from protein when trypsin is added during analysis). Over the 12-day degradation experiment 31% of the particulate organic carbon was depleted and there was no preferential degradation of the overall protein pool. However, there was distinct differentiation in the cellular location, secondary structure and modifications of the peptides that were either degraded or remained. During the initial period of rapid algal decay and bacterial growth, intracellular components from the cytoplasm were selectively consumed, resulting in the accumulation of membrane-associated proteins and peptides in the detrital pool. Accompanying this was an increase in the importance of membrane-bound ɑ-helix motifs. At the end of the 12 day experiment, the natural bacterial assemblage was focusing on degradation of membrane-associated proteins, which was the dominant source of peptides in both the residual pool (released by trypsin) and the actively degraded pool (no trypsin added). Methylated arginine, a post-translationally modified amino acid that is produced within the diatom prior to senescence, is found in high amounts within the detrital peptide pool, suggesting a link between in-cell modification and resistance to immediate degradation. Another modification - asparagine deamidation - appears to occur during degradation and deamidated peptides also accumulate within the detritus. The bacterial community decomposing the algal material was rich in proteobacteria, and employed a growth approach focusing on accumulation of solubilized material across their membranes and on DNA replication. At this early stage of diagenesis, no changes in bulk amino acids (THAA) were observed, yet a peptidomic approach allowed us to observe the differential changes in diatom protein preservation by discriminating between intracellular location, secondary structure, and modifications status.

Dataset Information

An Atomistic View on the Mechanism of Diatom Peptide-Guided Biomimetic Silica Formation.

Publications

An Atomistic View on the Mechanism of Diatom Peptide-Guided Biomimetic Silica Formation.

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