Beta-sheet aggregation is a critical phenomenon in protein folding and stability, often associated with amyloid formation and protein misfolding diseases. The aggregation of beta-sheets is primarily driven by intermolecular hydrogen bonding, hydrophobic interactions, and aromatic stacking forces. These structural and chemical properties make beta-sheets particularly prone to aggregation under certain conditions, leading to the formation of stable and often pathological protein assemblies.
One of the key factors contributing to beta-sheet aggregation is the extensive hydrogen bonding network that characterizes this secondary structure. Beta-sheets form through hydrogen bonds between the amide (NH) and carbonyl (C=O) groups of adjacent polypeptide strands. When multiple beta-sheets come into close proximity, these interactions extend beyond the individual protein molecules, creating intermolecular hydrogen bonds that stabilize large aggregated structures. This extended hydrogen bonding network facilitates the formation of insoluble, stacked beta-sheet aggregates, a hallmark of amyloid fibrils.
In addition to hydrogen bonding, hydrophobic interactions play a significant role in beta-sheet aggregation. Beta-strands often expose hydrophobic residues on one or both faces of the sheet. When these hydrophobic regions interact, they tend to cluster together to minimize exposure to the aqueous environment, leading to a process known as hydrophobic collapse. This stabilizes beta-sheet aggregates and drives their self-assembly into larger, insoluble fibrillar structures. Such hydrophobic interactions are particularly important in protein misfolding diseases, where mutations or environmental conditions promote beta-sheet-rich aggregates that resist degradation.
Aromatic residues within beta-sheets, such as phenylalanine, tyrosine, and tryptophan, further contribute to aggregation through π-π stacking interactions. These aromatic interactions allow beta-strands to stack in an ordered manner, enhancing the stability of the aggregated structure. This mechanism is especially relevant in amyloid fibrils, where β-strands align perpendicular to the fibril axis, forming the characteristic cross-β structure. The stacking of aromatic side chains reinforces the stability and insolubility of these fibrils, making them highly resistant to proteolytic degradation.
Moreover, the structural rigidity of beta-sheets compared to other secondary structures, such as alpha-helices, makes them more prone to aggregation. The relatively flat and extended conformation of beta-sheets allows them to stack efficiently, unlike the more compact and sterically hindered alpha-helices. This stacking ability increases the likelihood of intermolecular interactions and enhances aggregation potential. In some cases, charged amino acids within beta-sheets contribute to aggregation through salt bridge formation or electrostatic complementarity, further stabilizing the aggregated state.
Another important factor is the kinetic accessibility of beta-sheet structures. Unlike alpha-helices, which are stabilized by internal hydrogen bonds and compact folding, beta-sheets have an extended conformation that can readily adopt aggregation-prone intermediates. Under physiological or pathological conditions, proteins with beta-sheet-rich regions may misfold, exposing hydrophobic residues and facilitating aggregation. This tendency is particularly evident in neurodegenerative diseases such as Alzheimer’s, Parkinson’s, and Huntington’s, where misfolded proteins form beta-sheet-rich amyloid fibrils.
Chain A: MHLNPAEKEKLQIFLASELALKRKARGLKLNYPEAVAIITSFIMEGARDGKTVAMLMEEGKHVLTRDDVMEGVPEMIDDIQAEATFPDGTKLVTVHNPIS
Chain B:
NYIVPGEYRVAEGEIEINAGREKTTIRVSNTGDRPIQVGSHIHFVEVNKELLFDRAEGIGRRLNIPSGTAARFEPGEEMEVELTELGGNREVFGISDLTNGSVDNKELILQRAKELGYKGVE
Chain C:
MKINRQQYAESYGPTVGDQVRLADTDLWIEVEKDYTTYGDEANFGGGKVLREGMGENGTYTRTENVLDLLLTNALILDYTGIYKADIGVKDGYIVGIGKGGNPDIMDGVTPNMIVGTATEVIAAEGKIVTAGGIDTHVHFINPDQVDVALANGITTLFGGGTGPAEGSKATTVTPGPWNIEKMLKSTEGLPINVGILGKGHGSSIAPIMEQIDAGAAGLKIHEDWGATPASIDRSLTVADEADVQVAIHSDTLNEAGFLEDTLRAINGRVIHSFHVEGAGGGHAPDIMAMAGHPNVLPSSTNPTRPFTVNTIDEHLDMLMVCHHLKQNIPEDVAFADSRIRPETIAAEDILHDLGIISMMSTDALAMGRAGEMVLRTWQTADKMKKQRGPLAEEKNGSDNFRAKRYVSKYTINPAIAQGIAHEVGSIEEGKFADLVLWEPKFFGVKADRVIKGGIIAYAQIGDPSASIPTPQPVMGRRMYGTVGDLIHDTNITFMSKSSIQQGVPAKLGLKRRIGTVKNCRNIGKKDMKWNDVTTDIDINPETYEVKVDGEVLTCEPVKELPMAQRYFLF
Urease is a nickel-dependent enzyme produced by Sporosarcina pasteurii, catalyzing the hydrolysis of urea into ammonia and carbon dioxide. This reaction increases environmental pH, making S. pasteurii particularly useful in biomineralization processes such as microbial-induced calcium carbonate precipitation (MICP). The enzyme plays a crucial role in cementation applications, including biocement and self-healing concrete, as well as in bioremediation efforts. Urease from S. pasteurii was selected due to its significance in biotechnology, particularly for enhancing the efficiency of MICP in engineered living materials.
Using the pBLAST tool to identify homologous sequences, urease from S. pasteurii exhibits a large number of homologs across different bacterial species. Many species of Bacillus, Pseudomonas, and other ureolytic bacteria contain urease sequences with high similarity, indicating the widespread conservation of this enzyme. The Clustal Omega tool allows for multiple sequence alignment, revealing highly conserved active site residues necessary for nickel binding and enzymatic function.
Sporosarcina pasteurii urease belongs to the urease enzyme family, classified under the amidohydrolase superfamily. It is part of the ureC family, which encompasses urease catalytic subunits across various bacterial and fungal species. The enzyme functions as a multi-subunit complex, typically consisting of UreA, UreB, and UreC subunits, with UreC containing the active site. Conserved structural motifs in this family contribute to the enzyme’s stability and catalytic activity, making it a well-studied model for urease function and application.
Klebsiella aerogenes Yersinia enterocolitica W22703 Brucella abortus 2308 Mycobacterium tuberculosis Helicobacter pylori Helicobacter pylori Helicobacter pylori 26695 Canavalia ensiformis Canavalia ensiformis Canavalia ensiformis Canavalia ensiformis Helicobacter mustelae 12198 Cajanus cajan Cajanus cajan