Publications related to Protein superfamily

New protein–protein interactions designed by a computer

Creating protein interactions through computational design is a key challenge in the fields of both basic and translational biology. An approach that uses the machine-learned fingerprints of protein-surface features was used to produce synthetic proteins t ...

2023

A molecular device for the redox quality control of GroEL/ES substrates

Camille Véronique Bernadette Goemans

Hsp60 chaperonins and their Hsp10 cofactors assist protein folding in all living cells, constituting the paradigmatic example of molecular chaperones. Despite extensive investigations of their structure and mechanism, crucial questions regarding how these ...

2023

Cellularization across eukaryotes: Conserved mechanisms and novel strategies

Omaya Pierre Dudin

Many eukaryotes form multinucleated cells during their devel-opment. Some cells persist as such during their lifetime, others choose to cleave each nucleus individually using a specialized cytokinetic process known as cellularization. What is cellula-rizat ...

CURRENT BIOLOGY LTD2023

Hierarchy of the Components in Spray-Dried, Protein-Excipient Particles Using DNP-Enhanced NMR Spectroscopy

David Lyndon Emsley, Pierrick Berruyer, Andrea Bertarello, Baptiste Busi

Protein-based drugs are becoming increasingly important, but there are challenges associated with their formulation (for example, formulating stable inhalable aerosols while maintaining the proper long-term stability of the protein). Determining the morpho ...

Washington2023

J-domain protein chaperone circuits in proteostasis and disease

Paolo De Los Rios, Duccio Malinverni, Ruobing Zhang

The J-domain proteins (JDP) form the largest protein family among cellular chaperones. In cooperation with the Hsp70 chaperone system, these co-chaperones orchestrate a plethora of distinct functions, including those that help maintain cellular proteostasi ...

ELSEVIER SCIENCE LONDON2022

A generic framework for hierarchical de novo protein design

Bruno Emanuel Ferreira De Sousa Correia, Zander Harteveld, Jaume Bonet Martinez, Fabian Sesterhenn, Stéphane Rosset, Che Yang

De novo protein design enables the exploration of novel sequences and structures absent from the natural protein universe. De novo design also stands as a stringent test for our understanding of the underlying physical principles of protein folding and may ...

NATL ACAD SCIENCES2022

Correlations from structure and phylogeny combine constructively in the inference of protein partners from sequences

Anne-Florence Raphaëlle Bitbol, Nicola Dietler, Andonis Samuel Rene Gerardos

Inferring protein-protein interactions from sequences is an important task in computational biology. Recent methods based on Direct Coupling Analysis (DCA) or Mutual Information (MI) allow to find interaction partners among paralogs of two protein families ...

San Francisco2022

Extracting phylogenetic dimensions of coevolution reveals hidden functional signals

Anne-Florence Raphaëlle Bitbol

Despite the structural and functional information contained in the statistical coupling between pairs of residues in a protein, coevolution associated with function is often obscured by artifactual signals such as genetic drift, which shapes a protein's ph ...

NATURE PORTFOLIO2022

Protein language models trained on multiple sequence alignments learn phylogenetic relationships

Anne-Florence Raphaëlle Bitbol, Damiano Sgarbossa, Umberto Lupo

Self-supervised neural language models with attention have recently been applied to biological sequence data, advancing structure, function and mutational effect prediction. Some protein language models, including MSA Transformer and AlphaFold's EvoFormer, ...

NATURE PORTFOLIO2022

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Protein superfamily

New protein–protein interactions designed by a computer

A molecular device for the redox quality control of GroEL/ES substrates

Cellularization across eukaryotes: Conserved mechanisms and novel strategies

Hierarchy of the Components in Spray-Dried, Protein-Excipient Particles Using DNP-Enhanced NMR Spectroscopy

J-domain protein chaperone circuits in proteostasis and disease

A generic framework for hierarchical de novo protein design

Towards automating de novo protein design for novel functionalities: controlling protein folds and protein-protein interactions

Correlations from structure and phylogeny combine constructively in the inference of protein partners from sequences

Extracting phylogenetic dimensions of coevolution reveals hidden functional signals

Protein language models trained on multiple sequence alignments learn phylogenetic relationships

Graph Chatbot

Chat with Graph Search

Towards automating de novo protein design for novel functionalities: controlling protein folds and protein-protein interactions

New protein–protein interactions designed by a computer

A generic framework for hierarchical de novo protein design

Protein language models trained on multiple sequence alignments learn phylogenetic relationships

Hierarchy of the Components in Spray-Dried, Protein-Excipient Particles Using DNP-Enhanced NMR Spectroscopy

Correlations from structure and phylogeny combine constructively in the inference of protein partners from sequences

A molecular device for the redox quality control of GroEL/ES substrates

Cellularization across eukaryotes: Conserved mechanisms and novel strategies

J-domain protein chaperone circuits in proteostasis and disease

Extracting phylogenetic dimensions of coevolution reveals hidden functional signals