Publications de Alessandro Barducci

Publications associées (19)

Free-energy landscape of protein oligomerization from atomistic simulations

In the realm of protein-protein interactions, the assembly process of homooligomers plays a fundamental role because the majority of proteins fall into this category. A comprehensive understanding of this multistep process requires the characterization of ...

National Academy of Sciences2013

Efficient conversion of chemical energy into mechanical work by Hsp70 chaperones

Paolo De Los Rios, Alessandro Barducci, Salvatore Assenza, Alberto Stefano Sassi

Hsp70 molecular chaperones are abundant ATP-dependent nanomachines that actively reshape non-native, misfolded proteins and assist a wide variety of essential cellular processes. Here, we combine complementary theoretical approaches to elucidate the struct ...

2019

Structural and energetic basis for hybridization limits in high-density DNA monolayers

Alessandro Barducci

High-density monolayers (HDMs) of single-strand (ss) DNA are important nanoscale platforms for the fabrication of sensors and for mechanistic studies of enzymes on surfaces. Such systems can be used, for example, to monitor gene expression, and for the con ...

Royal Society of Chemistry2013

The allosteric communication pathways in KIX domain of CBP

Alessandro Barducci

Allosteric regulation plays an important role in a myriad of bio-macromolecular processes. Specifically, in a protein, the process of allostery refers to the transmission of a local perturbation, such as ligand binding, to a distant site. Decades after the ...

National Academy of Sciences2013

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

Paolo De Los Rios, Alessandro Barducci, Duccio Malinverni

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

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

Paolo De Los Rios, Alessandro Barducci, Duccio Malinverni

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

Hsp70 chaperones are non-equilibrium machines that achieve ultra-affinity by energy consumption

Paolo De Los Rios, Alessandro Barducci

70-kDa Heat shock proteins are ATP-driven molecular chaperones that perform a myriad of essential cellular tasks. Although structural and biochemical studies have shed some light on their functional mechanism, the fundamental issue of the role of energy co ...

Elife Sciences Publications Ltd2014

The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems

Alessandro Barducci

The OPEP coarse-grained protein model has been applied to a wide range of applications since its first release 15 years ago. The model, which combines energetic and structural accuracy and chemical specificity, allows the study of single protein properties ...

Royal Society of Chemistry2014

Function, evolution, and structure of J-domain proteins

Paolo De Los Rios, Alessandro Barducci

Hsp70 chaperone systems are very versatile machines present in nearly all living organisms and in nearly all intracellular compartments. They function in many fundamental processes through their facilitation of protein (re)folding, trafficking, remodeling, ...

2019

Effect of the Synaptic Plasma Membrane on the Stability of the Amyloid Precursor Protein Homodimer

Matteo Dal Peraro, Alessandro Barducci, Thomas Lemmin, Martina Audagnotto

The proteolytic cleavage of the transmembrane (TM) domain of the amyloid precursor protein (APP) releases amyloid-beta (A beta) peptides, which accumulation in the brain tissue is an early indicator of Alzheimer's disease. We used multiscale molecular dyna ...

Amer Chemical Soc2016

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

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

Single-molecule spectroscopy reveals chaperone-mediated expansion of substrate protein

Alessandro Barducci

Molecular chaperones are an essential part of the machinery that avoids protein aggregation and misfolding in vivo. However, understanding the molecular basis of how chaperones prevent such undesirable interactions requires the conformational changes withi ...

National Academy of Sciences2014

DNA-segment-capture model for loop extrusion by structural maintenance of chromosome (SMC) protein complexes

Paolo De Los Rios, Alessandro Barducci

Cells possess remarkable control of the folding and entanglement topology of long and flexible chromosomal DNA molecules. It is thought that structural maintenance of chromosome (SMC) protein complexes play a crucial role in this, by organizing long DNAs i ...

2019

Molecular dissection of amyloid disaggregation by human HSP70

Paolo De Los Rios, Alessandro Barducci

The molecular steps that lead to the disaggregation of amyloid fibrils are shown to involve the synergistic action of HSP70 and its co-chaperones DNAJB1 and HSP110. ...

NATURE RESEARCH2020

Accuracy of Current All-Atom Force-Fields in Modeling Protein Disordered States

Alessandro Barducci

Molecular Dynamics (MD) plays a fundamental role in characterizing protein disordered states that are emerging as crucial actors in many biological processes. Here we assess the accuracy of three current force-fields in modeling disordered peptides by comb ...

Amer Chemical Soc2015

Quantifying the role of chaperones in protein translocation by computational modeling

Paolo De Los Rios, Alessandro Barducci, Salvatore Assenza

2015

Non-equilibrium conformational dynamics in the function of molecular chaperones

Paolo De Los Rios, Alessandro Barducci

Why do chaperones need ATP hydrolysis to help proteins reach their native, functional states? In this review, we highlight the most recent experimental and theoretical evidences suggesting that ATP hydrolysis allows molecular chaperones to escape the bound ...

Elsevier2015

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

Paolo De Los Rios, Alessandro Barducci, Duccio Malinverni

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

Theoretical and Experimental Characterization of Amino-PEG-Phosphonate-Terminated Polyphosphorhydrazone Dendrimers: Influence of Size and PEG Capping on Cytotoxicity Profiles

Alessandro Barducci

The synthesis of new series of PPH (poly(phosphorhydrazone)) dendrimers with amino-PEG phosphonates or the corresponding amino-PEG phosphonic acids as terminal groups is presented, from generations 1-3. The size of PEG-terminated dendrimers is experimental ...

Wiley-Blackwell2015