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Aptamer Conformational Dynamics Modulate Neurotransmitter Sensing in Nanopores

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The exquisite structural and optical characteristics of single-walled carbon nanotubes (SWCNTs), combined with the tunable specificities of proteins and peptides, can be exploited to strongly benefit technologies with applications in fields ranging from bi ...

Amer Chemical Soc2017

Protein-protein structure prediction by scoring molecular dynamics trajectories of putative poses

Bruno Emanuel Ferreira De Sousa Correia, Stefano Zamuner

The prediction of protein-protein interactions and their structural configuration remains a largely unsolved problem. Most of the algorithms aimed at finding the native conformation of a protein complex starting from the structure of its monomers are based ...

Wiley-Blackwell2016

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

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

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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

All-atom simulations of crowding effects on ubiquitin dynamics

Matteo Dal Peraro, Luciano Andres Abriata, Enrico Spiga

It is well-known that crowded environments affect the stability of proteins, with strong biological and biotechnological implications; however, beyond this, crowding is also expected to affect the dynamic properties of proteins, an idea that is hard to pro ...

Iop Publishing Ltd2013

Structure and Substrate-Induced Conformational Changes of the Secondary Citrate/Sodium Symporter CitS Revealed by Electron Crystallography

Henning Paul-Julius Stahlberg

The secondary Na+/citrate symporter CitS of Klebsiella pneumoniae is the best-characterized member of the 2-hydroxycarboxylate transporter family. The recent projection structure gave insight into its overall structural organization. Here, we present the t ...

Elsevier BV2013

Free-energy landscape of protein oligomerization from atomistic simulations

Alessandro Barducci, Michele Parrinello

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

Macromolecular Symmetric Assembly Prediction Using Swarm Intelligence Dynamic Modeling

Matteo Dal Peraro, Matteo Thomas Degiacomi

Proteins often assemble in multimeric complexes to perform a specific biologic function. However, trapping these high-order conformations is difficult experimentally. Therefore, predicting how proteins assemble using in silico techniques can be of great he ...

Cell Press2013

Understanding mol. recognition is of fundamental importance in applications such as therapeutics, chem. catalysis and sensor design. The most common recognition motifs involve biol. macromols. such as antibodies and aptamers. The key to biorecognition cons ...

2013