Publication

Contrasting the excited-state dynamics of the photoactive yellow protein chromophore: Protein versus solvent environments

Publications associées (37)

Tuning the Excited-State Dynamics of GFP-Inspired Imidazolone Derivatives

The excited-state dynamics of five derivatives of the GFP-chromophore, which differ by the position and nature of their substituents, has been investigated in solvents of various viscosity and polarity and in rigid media using femtosecond-resolved spectros ...

2010

Temperature Dependence of Normal Mode Reconstructions of Protein Dynamics

Paolo De Los Rios, Francesco Piazza

Normal mode (NM) analysis is a widely used technique for reconstructing conformational changes of proteins from the knowledge of native structures. In this Letter, we investigate to what extent NMs capture the salient features of the dynamics over a range ...

American Physical Society2009

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

Ultrafast UV photon echo peak shift and fluorescence up conversion studies of non-polar solvation dynamics

Majed Chergui, Frank van Mourik, Andrea Cannizzo, Ahmad Ajdar Zadeh Oskouei

The authors present photon echo peak shift and femtosecond fluorescence up-conversion studies of nonpolar solvation dynamics of a simple nonpolar dye p-terphenyl in EtOH and cyclohexane, using excitation in the UV range at 290 nm. The UV fluorescence up-co ...

2008

Single molecule detection on surfaces

Marcel Leutenegger

Monitoring biological relevant reactions on the single molecule level based on fluorescence spectroscopy techniques has become one of the most promising approaches for understanding a variety of phenomena in biophysics, biochemistry and life science. By ap ...

EPFL2007

Excited-State Dynamics of Donor−Acceptor Bridged Systems Containing a Boron−Dipyrromethene Chromophore: Interplay between Charge Separation and Reorientational Motion

Natalie Renuka Banerji, Eric Vauthey

The excited-state dynamics of a series of electron donor−acceptor bridged systems (DABS) consisting of a boron−dipyrromethene chromophore covalently linked to a dinitro-substituted triptycene has been investigated using femtosecond time-resolved spectrosco ...

2007

Solvent effects on the ultrafast dynamics of the retinal chromophore of bacteriorhodopsin

Goran Zgrablic

Photo-induced excited-state reactions stand in the center of function of the photosensitive biological systems. These reactions can be accompanied by structural changes of the chromophore (for example isomerization) which are influenced by the nearest envi ...

EPFL2006

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

Solvent and protein effects on the structure and dynamics of the rhodopsin chromophore

Ursula Röthlisberger, Leonardo Guidoni

The structure and dynamics of the retinal chromophore of rhodopsin are investigated systematically in different environments (vacuum, methanol soln., and protein binding pocket) and with different computational approaches (classical, quantum, and hybrid qu ...

2005

Influence of the protein environment on spectroscopy and ultrafast dynamics of retinal in bacteriorhodopsin

Selma Schenkl

The environment is important for the exact course of a chemical reaction. As an example of the strong influence of the environment on the reaction, this work studies the isomerization reaction of the chromophore retinal in the binding pocket of the protein ...

EPFL2004

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