Fabio Lapenta
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View article: Structural flexibility of the human vault protein revealed by high-resolution cryo-EM and molecular dynamics simulations
Structural flexibility of the human vault protein revealed by high-resolution cryo-EM and molecular dynamics simulations Open
Vaults are massive ribonucleoprotein complexes, highly conserved and abundant in eukaryotic cells, yet with unclear function. Their thin-walled barrel-shape architecture is composed of two symmetrical, antiparallel half-shells, each contai…
View article: Preorganized cyclic modules facilitate the self-assembly of protein nanostructures
Preorganized cyclic modules facilitate the self-assembly of protein nanostructures Open
Modular protein cages can self-assemble from multiple preorganized modules. We implemented an intein-mediated cyclization that enhanced the structural stability and definition of protein–protein interaction surfaces.
View article: The avidin‐theophylline complex: A structural and computational study
The avidin‐theophylline complex: A structural and computational study Open
The interaction between avidin and its counterpart biotin is one of central importance in biology and has been reproposed and studied at length. However, the binding pocket of avidin is prone to promiscuous binding, able to accommodate eve…
View article: Intrinsically disordered ectodomain modulates ion permeation through a metal transporter
Intrinsically disordered ectodomain modulates ion permeation through a metal transporter Open
The function of many channels and transporters is enriched by the conformational plasticity of intrinsically disordered regions (IDRs). Copper transporter 1 (Ctr1) is the main entry point for Cu(I) ions in eukaryotes and contains IDRs both…
View article: Modelling data for article "Intrinsically disordered ectodomain modulates ion permeation through a metal transporter"
Modelling data for article "Intrinsically disordered ectodomain modulates ion permeation through a metal transporter" Open
Full-length hCtr1 models used to perform classical molecular dynamics (MD) simulations described in the article "Intrinsically disordered ectodomain modulates ion permeation through a metal transporter" by Aupič et al. The zipped file cont…
View article: Modelling data for article "Intrinsically disordered ectodomain modulates ion permeation through a metal transporter"
Modelling data for article "Intrinsically disordered ectodomain modulates ion permeation through a metal transporter" Open
Full-length hCtr1 models used to perform classical molecular dynamics (MD) simulations described in the article "Intrinsically disordered ectodomain modulates ion permeation through a metal transporter" by Aupič et al. The zipped file cont…
View article: Metal ion–regulated assembly of designed modular protein cages
Metal ion–regulated assembly of designed modular protein cages Open
Coiled-coil (CC) dimers are versatile, customizable building modules for the design of diverse protein architectures unknown in nature. Incorporation of dynamic self-assembly, regulated by a selected chemical signal, represents an importan…
View article: A nanobody toolbox targeting dimeric coiled-coil modules for functionalization of designed protein origami structures
A nanobody toolbox targeting dimeric coiled-coil modules for functionalization of designed protein origami structures Open
Significance Coiled-coil dimers are structural motifs which occur frequently in natural proteins. They consist of two α-helices which wind around each other to form a supercoil and can be used as versatile modules for the construction of d…
View article: Author Correction: Self-assembly and regulation of protein cages from pre-organised coiled-coil modules
Author Correction: Self-assembly and regulation of protein cages from pre-organised coiled-coil modules Open
A Correction to this paper has been published: https://doi.org/10.1038/s41467-021-21969-9
View article: Coiled-coil heterodimers with increased stability for cellular regulation and sensing SARS-CoV-2 spike protein-mediated cell fusion
Coiled-coil heterodimers with increased stability for cellular regulation and sensing SARS-CoV-2 spike protein-mediated cell fusion Open
Coiled-coil (CC) dimer-forming peptides are attractive designable modules for mediating protein association. Highly stable CCs are desired for biological activity regulation and assay. Here, we report the design and versatile applications …
View article: IN VIVO SELF-ASSEMBLING COILED-COIL-BASED PROTEIN ORIGAMI
IN VIVO SELF-ASSEMBLING COILED-COIL-BASED PROTEIN ORIGAMI Open
Proteins are complex biopolymers that fold in a large array of nanostructures. Although resolved natural protein structures span over a large conformational landscape, a much wider sampling space, formed by polypeptides that nature has not…
View article: Structure–Activity Relationship in Monosaccharide-Based Toll-Like Receptor 4 (TLR4) Antagonists
Structure–Activity Relationship in Monosaccharide-Based Toll-Like Receptor 4 (TLR4) Antagonists Open
The structure–activity relationship was investigated in a series of synthetic TLR4 antagonists formed by a glucosamine core linked to two phosphate esters and two linear carbon chains. Molecular modeling showed that the compounds with 10, …
View article: Coiled coil protein origami: from modular design principles towards biotechnological applications
Coiled coil protein origami: from modular design principles towards biotechnological applications Open
This review illustrates the current state in designing coiled-coil-based proteins with an emphasis on coiled coil protein origami structures and their potential.
View article: CC-protein-origami
CC-protein-origami Open
Dataset includes:Topologies-circular-permutations-TCO.xlsx – List of topologies and circular permutations in fileCC-protein-origami.fasta – List of all the design sequences in fasta format.all-atom-models.zip – representative models genera…
View article: Escherichia coli DnaE Polymerase Couples Pyrophosphatase Activity to DNA Replication
Escherichia coli DnaE Polymerase Couples Pyrophosphatase Activity to DNA Replication Open
DNA Polymerases generate pyrophosphate every time they catalyze a step of DNA elongation. This elongation reaction is generally believed as thermodynamically favoured by the hydrolysis of pyrophosphate, catalyzed by inorganic pyrophosphata…