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Fast viral dynamics revealed by microsecond time-resolved cryo-EM

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Coupling fast triplet-triplet energy transfer (TTET) between xanthone and naphthylalanine to the helix-coil equilibrium in alanine-based peptides allowed the observation of local equilibrium fluctuations in alpha-helices on the nanoseconds to microseconds ...

2009

Solute energy based REMD

Molecular dynamics (MD) simulations have increasingly contributed to the understanding of biomolecular processes, allowing for predictions of thermodynamic and structural properties. Unfortunately, the holy grail of protein structure prediction was soon fo ...

EPFL2008

Diffusion-limited unbinding of small peptides from PDZ domains

Paolo De Los Rios, Francesco Piazza

PDZ domains are typical examples of binding motifs mediating the formation of protein-protein assemblies in many different cells. A quantitative characterization of the mechanisms intertwining structure, chemistry, and dynamics with the PDZ function repres ...

2007

A Novel Hamiltonian Replica Exchange MD Protocol to Enhance Protein Conformational Space Sampling

Ivano Tavernelli

Limited searching in the conformational space is one of the major obstacles for investigating protein dynamics by numerical approaches. For this reason, classical all-atom mol. dynamics (MD) simulations of proteins tend to be confined to local energy min., ...

2006

Dynamics of antibodies from cryo-electron tomography

Paolo De Los Rios, Francesco Piazza

The issue of protein dynamics and its implications in the biological function of proteins are arousing greater and greater interest in molecular biology. In cryo-electron tomography experiments one takes several snapshots of a given biological macromolecul ...

Elsevier2005

Evolutionarily Conserved Functional Mechanics across Pepsin-like and Retroviral Aspartic Proteases

Ursula Röthlisberger, Michele Cascella, Paolo Carloni

The biol. function of the aspartic protease from HIV-1 has recently been related to the conformational flexibility of its structural scaffold. Here, we use a multistep strategy to investigate whether the same mechanism affects the functionality in the peps ...

2005

Single-particle electron microscopy (EM) combined with biochemical measurements revealed the molecular shape of SAP97 and a monomer-dimer transition that depended on the N-terminal L27 domain. Overexpression of SAP97 drove GluR1 to synapses, potentiated AM ...

Elsevier2004

Freezing immunoglobulins to see them move

Paolo De Los Rios, Francesco Piazza

The issue of protein dynamics and its implications in the biological function of proteins are arousing greater and greater interest in different fields of molecular biology. In cryo-electron tomography experiments one may take several snapshots of a given ...

National Academy of Sciences2004

Protein dynamics, thermal stability, and free-energy landscapes: A molecular dynamics investigation

Ivano Tavernelli

Proteins have a complex free-energy landscape because of their rich topol. and the nature of their nonbonded interaction potential. This has important consequences because the roughness of the landscape affects the ease with which a chain folds and also de ...

2003

The mechanism that allows proteins with the same fold to be different in their dynamic and stability properties is poorly understood. We report here the results of mol. dynamics (MD) simulations on rubredoxin (Rd) from hyperthermophilic and mesophilic bact ...

2001