Publications by Duccio Malinverni

Data-driven large-scale genomic analysis reveals an intricate phylogenetic and functional landscape in J-domain proteins

Paolo De Los Rios, Duccio Malinverni, Alessandro Barducci, Stefano Zamuner, Mathieu Rebeaud

The 70-kD heat shock protein (Hsp70) chaperone system is a central hub of the proteostasis network that helps maintain protein homeostasis in all organisms. The recruitment of Hsp70 to perform different and specific cellular functions is regulated by the J ...

National Academy of Sciences2023

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

Statistical Analysis of Protein Sequences: A Coevolutionary Study of Molecular Chaperones

Duccio Malinverni

Recent advances in DNA sequencing technologies led to the accumulation of enormous quantities of genetic information available in public databases. This rapid growth of available biological datasets calls for quantitative analysis tools and concomitantly o ...

EPFL2018

Modeling Hsp70/Hsp40 interaction by multi-scale molecular simulations and co-evolutionary sequence analysis

Paolo De Los Rios, Duccio Malinverni, Alessandro Barducci

The interaction between the Heat Shock Proteins 70 and 40 is at the core of the ATPase regulation of the chaperone machinery that maintains protein homeostasis. However, the structural details of the interaction are still elusive and contrasting models hav ...

Elife Sciences Publications Ltd2017

New Techniques for Ancient Proteins: Direct Coupling Analysis Applied on Proteins Involved in Iron Sulfur Cluster Biogenesis

Paolo De Los Rios, Duccio Malinverni

Direct coupling analysis (DCA) is a powerful statistical inference tool used to study protein evolution. It was introduced to predict protein folds and protein-protein interactions, and has also been applied to the prediction of entire interactomes. Here, ...

2017

Evolution of an intricate J-protein network driving protein disaggregation in eukaryotes

Paolo De Los Rios, Duccio Malinverni, Alessandro Barducci

Hsp70 participates in a broad spectrum of protein folding processes extending from nascent chain folding to protein disaggregation. This versatility in function is achieved through a diverse family of J-protein cochaperones that select substrates for Hsp70 ...

Elife Sciences Publications Ltd2017

Large-Scale Conformational Transitions and Dimerization Are Encoded in the Amino-Acid Sequences of Hsp70 Chaperones

Paolo De Los Rios, Duccio Malinverni, Alessandro Barducci

Hsp70s are a class of ubiquitous and highly conserved molecular chaperones playing a central role in the regulation of proteostasis in the cell. Hsp70s assist a myriad of cellular processes by binding unfolded or misfolded substrates during a complex bioch ...

Public Library Science2015

Addressing Conditioning Data in Multiple-Point Statistics Simulation Algorithms Based on a Multiple Grid Approach

Duccio Malinverni

Multiple-point statistics (MPS) allows simulations reproducing structures of a conceptual model given by a training image (TI) to be generated within a stochastic framework. In classical implementations, fixed search templates are used to retrieve the patt ...

Springer Heidelberg2014