Conformational ensembles

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Related publications (27)

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

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

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

Nonlinear Plasmonic Nanorulers

Olivier Martin, Jérémy Butet

The evaluation of distances as small as few nanometers using optical waves Is a very challenging task that can pave the way for the development of new applications in biotechnology and nanotechnology. In this article, we propose a new measurement method ba ...

Amer Chemical Soc2014

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

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

All-atom simulations of crowding effects on ubiquitin dynamics

Matteo Dal Peraro, Enrico Spiga, Luciano Andres Abriata

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

Characterization of Molecular Determinants of the Conformational Stability of Macrophage Migration Inhibitory Factor: Leucine 46 Hydrophobic Pocket

Ursula Röthlisberger, Hilal Lashuel, Florence Pojer, Bruno Claude Daniel Fauvet, Michele Cascella, Marilisa Neri, Magdalena Zweckstetter, Hajer Ouertatani-Sakouhi, Farah El Turk, Min Kyu Cho, Amer Ashrafi

Macrophage Migration Inhibitory Factor (MIF) is a key mediator of inflammatory responses and innate immunity and has been implicated in the pathogenesis of several inflammatory and autoimmune diseases. The oligomerization of MIF, more specifically trimer f ...

Public Library of Science2012

Statistical Analysis of Ion Mobility Spectrometry. II. Adaptively Biased Methods and Shape Correlations

Yury Tsybin

Following a recent effort [J. Am. Soc. Mass Spectrom. 23, 386-396 (2012)], we continue to explore computational methodologies for generating molecular conformations to support collisional cross sections suggested by ion mobility measurements. Here, adaptiv ...

2012

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