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All-atom simulations of crowding effects on ubiquitin dynamics

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Molecular Effects of Concentrated Solutes on Protein Hydration, Dynamics, and Electrostatics

Matteo Dal Peraro, Luciano Andres Abriata, Enrico Spiga

Most studies of protein structure and function are performed in dilute conditions, but proteins typically experience high solute concentrations in their physiological scenarios and biotechnological applications. High solute concentrations have well-known e ...

Cell Press2016

Optimization of Conformational Dynamics in an Epistatic Evolutionary Trajectory

Luciano Andres Abriata

The understanding of protein evolution depends on the ability to relate the impact of mutations on molecular traits to organismal fitness. Biological activity and robustness have been regarded as important features in shaping protein evolutionary landscape ...

Oxford Univ Press2016

Assessing the potential of atomistic molecular dynamics simulations to probe reversible protein-protein recognition and binding

Matteo Dal Peraro, Luciano Andres Abriata

Protein-protein recognition and binding are governed by diffusion, noncovalent forces and conformational flexibility, entangled in a way that only molecular dynamics simulations can dissect at high resolution. Here we exploited ubiquitin's noncovalent dime ...

Nature Publishing Group2015

One of the fundamental challenges of physical biology is to understand the relationship between protein dynamics and function. At physiological temperatures, functional motions arise from the complex interplay of thermal motions of proteins and their envir ...

Amer Assoc Advancement Science2015

Centrioles are evolutionarily conserved cylindrical cell organelleswith characteristic radial symmetry. Despite their considerable size (400 nm x 200 nm, in humans), genetic studies suggest that relatively few protein components are involved in their assem ...

Portland Press Ltd2015

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This work examines the conformational ensemble involved in beta-hairpin folding by means of advanced molecular dynamics simulations and dimensionality reduction. A fully atomistic description of the protein and the surrounding solvent molecules is used, an ...

Amer Chemical Soc2015

Dissecting the Effects of Concentrated Carbohydrate Solutions on Protein Diffusion, Hydration, and Internal Dynamics

Matteo Dal Peraro, Luciano Andres Abriata, Francesco Piazza, Enrico Spiga

We present herein a thorough description of the effects of high glucose concentrations on the diffusion, hydration and internal dynamics of ubiquitin, as predicted from extensive molecular dynamics simulations on several systems described at fully atomisti ...

Amer Chemical Soc2014

Real-Time Monitoring of Protein Conformational Changes Using a Nano-Mechanical Sensor

Giovanni Dietler, Paolo De Los Rios, Sandor Kasas, Giovanni Longo, Dusan Vobornik, Fabrizio Benedetti, Livan Bladimir Alonso Sarduy

Proteins can switch between different conformations in response to stimuli, such as pH or temperature variations, or to the binding of ligands. Such plasticity and its kinetics can have a crucial functional role, and their characterization has taken center ...

Public Library of Science2014

We study the equilibrium liquid structure and dynamics of dilute and concentrated bovine eye lens alpha-crystallin solutions, using small-angle X-ray scattering, static and dynamic light scattering, viscometry, molecular dynamics simulations, and mode-coup ...

Natl Acad Sciences2014

Multiscale simulations of protein dynamics

Enrico Spiga

Characteristic timescales associated with the function of biomolecules, like proteins, range from femtoseconds up to minutes, whereas their corresponding spatial extent ranges from few ̊A to μm when associating in large macromolecular complexes. Moreover, ...

EPFL2013