RESUMEN
The immunoglobulin (Ig)-like domain is found in a broad range of proteins with diverse functional roles. While an essential ß-sandwich fold is maintained, considerable structural variations exist and are critical for functional diversity. The Rib-domain family, primarily found as tandem-repeat modules in the surface proteins of Gram-positive bacteria, represents another significant structural variant of the Ig-like fold. However, limited structural and functional exploration of this family has been conducted, which significantly restricts the understanding of its evolution and significance within the Ig superclass. In this work, a high-resolution crystal structure of a Rib domain derived from the probiotic bacterium Limosilactobacillus reuteri is presented. This protein, while sharing significant structural similarity with homologous domains from other bacteria, exhibits a significantly increased thermal resistance. The potential structural features contributing to this stability are discussed. Moreover, the presence of two copper-binding sites, with one positioned on the interface, suggests potential functional roles that warrant further investigation.
Asunto(s)
Proteínas Bacterianas , Limosilactobacillus reuteri , Modelos Moleculares , Limosilactobacillus reuteri/química , Limosilactobacillus reuteri/metabolismo , Cristalografía por Rayos X , Proteínas Bacterianas/química , Proteínas Bacterianas/metabolismo , Proteínas Bacterianas/genética , Secuencia de Aminoácidos , Sitios de Unión , Pared Celular/metabolismo , Pared Celular/química , Dominios Proteicos , Cobre/química , Cobre/metabolismo , Estabilidad Proteica , Proteínas de la Membrana/química , Proteínas de la Membrana/metabolismo , Proteínas de la Membrana/genéticaRESUMEN
The immunoglobulin fold (Ig fold) domain is a super-secondary structural motif consisting of a sandwich with two layers of ß-sheets that is present in many proteins with very diverse biological functions covering a wide range of physiological processes. This domain presents a modular architecture built with ß strands connected by variable length loops that has a highly conserved structural core of four ß-strands and quite variable ß-sheet extensions in the two sandwich layers that enable both divergent and convergent evolutionary mechanisms in the known Ig fold proteome. The central role of this Ig fold's structural plasticity in the evolutionary success of antibodies in our immune system is well established. Nature has also utilized this Ig fold in all domains of life in many different physiological contexts that go way beyond the immune system. Here we will present a structural and functional overview of the utilization of the Ig fold in different biological processes and in different cellular contexts to highlight some of the innumerable ways that this structural motif can interact in multidomain proteins to enable their diversity of functions. This includes shareable specific protein structure visualizations behind those functions that serve as starting points for further explorations of the biomolecular interactions spanning the Ig fold proteome. This overview also highlights how this Ig fold is being utilized through natural adaptation, engineering, and even building from scratch for a range of biotechnological applications.
Asunto(s)
Pliegue de Proteína , Proteoma , AnticuerposRESUMEN
Akkermansia muciniphila is a kind of beneficial microorganism colonized in the human gut. A. muciniphila is closely related to human intestinal health and has a good effect on diseases related to intestinal metabolism. The proteins encoded by the Amuc_1098-Amuc_1102 gene cluster, which are related to the formation and assembly of the pilus, are highly expressed in the membrane protein components of A. muciniphila. In this paper, we report the crystal structure of Amuc_1102 at a resolution of 1.75 Å, which adopts an immunoglobulin (Ig)-like fold. Amuc_1102 shares a similar fold to three archaeal proteins related to type IV pilus (T4P)-like structure, Pilin, FlaF, and FlaG, indicating a similar function. Amuc_1102 exists as a trimer both in the crystal structure and in solution, which differs from the assemblies of Pilin, FlaF, and FlaG. This study provides a structural basis for the elucidation of the T4P formation of A. muciniphila.
Asunto(s)
Archaea/metabolismo , Proteínas Bacterianas/química , Cristalografía por Rayos X/métodos , Fimbrias Bacterianas/química , Inmunoglobulinas/química , Proteínas de la Membrana/química , Akkermansia/química , Akkermansia/metabolismo , Archaea/química , Proteínas Bacterianas/metabolismo , Fimbrias Bacterianas/metabolismo , Humanos , Inmunoglobulinas/metabolismo , Proteínas de la Membrana/metabolismo , Proteínas Recombinantes/química , Proteínas Recombinantes/aislamiento & purificaciónRESUMEN
The glycoprotein uromodulin (UMOD) is the most abundant protein in human urine and forms filamentous homopolymers that encapsulate and aggregate uropathogens, promoting pathogen clearance by urine excretion. Despite its critical role in the innate immune response against urinary tract infections, the structural basis and mechanism of UMOD polymerization remained unknown. Here, we present the cryo-EM structure of the UMOD filament core at 3.5 Å resolution, comprised of the bipartite zona pellucida (ZP) module in a helical arrangement with a rise of ~65 Å and a twist of ~180°. The immunoglobulin-like ZPN and ZPC subdomains of each monomer are separated by a long linker that interacts with the preceding ZPC and following ZPN subdomains by ß-sheet complementation. The unique filament architecture suggests an assembly mechanism in which subunit incorporation could be synchronized with proteolytic cleavage of the C-terminal pro-peptide that anchors assembly-incompetent UMOD precursors to the membrane.
Asunto(s)
Uromodulina , Microscopía por Crioelectrón , Humanos , Modelos Moleculares , Polimerizacion , Conformación Proteica en Lámina beta , Dominios Proteicos , Uromodulina/química , Uromodulina/metabolismo , Uromodulina/ultraestructuraRESUMEN
FimA is the main structural subunit of adhesive type 1 pili from uropathogenic Escherichia coli strains. Up to 3000 copies of FimA assemble to the helical pilus rod through a mechanism termed donor strand complementation, in which the incomplete immunoglobulin-like fold of each FimA subunit is complemented by the N-terminal extension (Nte) of the next subunit. The Nte of FimA, which exhibits a pseudo-palindromic sequence, is inserted in an antiparallel orientation relative to the last ß-strand of the preceding subunit in the pilus. The resulting subunit-subunit interactions are extraordinarily stable against dissociation and unfolding. Alternatively, FimA can fold to a self-complemented monomer with anti-apoptotic activity, in which the Nte inserts intramolecularly into the FimA core in the opposite, parallel orientation. The FimA monomers, however, show dramatically lower thermodynamic stability compared with FimA subunits in the assembled pilus. Using self-complemented FimA variants with reversed, pseudo-palindromic extensions, we demonstrate that the high stability of FimA polymers is primarily caused by the specific interactions between the side chains of the Nte residues and the FimA core and not by the antiparallel orientation of the donor strand alone. In addition, we demonstrate that nonequilibrium two-state folding, a hallmark of FimA with the Nte inserted in the pilus rod-like, antiparallel orientation, only depends on the identity of the inserted Nte side chains and not on Nte orientation.
Asunto(s)
Escherichia coli/metabolismo , Proteínas Fimbrias/metabolismo , Fimbrias Bacterianas/metabolismo , Pliegue de Proteína , Multimerización de Proteína , Escherichia coli/química , Escherichia coli/genética , Proteínas Fimbrias/química , Proteínas Fimbrias/genética , Fimbrias Bacterianas/química , Fimbrias Bacterianas/genética , Dominios ProteicosRESUMEN
In this paper we show that the fuzzy oil drop model represents a general framework for describing the generation of hydrophobic cores in proteins and thus provides insight into the influence of the water environment upon protein structure and stability. The model has been successfully applied in the study of a wide range of proteins, however this paper focuses specifically on domains representing immunoglobulin-like folds. Here we provide evidence that immunoglobulin-like domains, despite being structurally similar, differ with respect to their participation in the generation of hydrophobic core. It is shown that ß-structural fragments in ß-barrels participate in hydrophobic core formation in a highly differentiated manner. Quantitatively measured participation in core formation helps explain the variable stability of proteins and is shown to be related to their biological properties. This also includes the known tendency of immunoglobulin domains to form amyloids, as shown using transthyretin to reveal the clear relation between amyloidogenic properties and structural characteristics based on the fuzzy oil drop model.