- Time-dependent density functional theory for biomolecules
- Computational methods for molecular dynamics simulation of biomolecules
- Fluorescent protein photophysics
R Nifosì, Y Luo
Origin of the Anomalous Two-Photon Absorption in Fluorescent Protein DsRed
Journal of Physical Chemistry B
(Letter) 111, 505 (2007).
The red fluorescent protein DsRed displays a two-photon excitation band around 760 nm which is not accompanied by any feature in the corresponding one-photon spectral region (380 nm). By means of time-dependent density functional theory we are able to explain such effect, as arising from an electronic excitation of the DsRed chromophore with ability to couple with a charge-transfer state, through an effective two-photon absorption channel.
- R Nifosì, V Tozzini `` Cis-trans photolsomerization of the chromophore in the green fluorescent protein variant E2GFP: A molecular dynamics study'', Chemical Physicsi 323, 358 (2006).
By force-field molecular dynamics simulations we investigate the dynamics of cis-trans photoisomerization of the chromophore in the GFP mutant E2GFP (F64L/S65T/T203Y), and the rearrangements that allow the protein structure to accommodate the trans form of the chromophore. We find that in this new configuration the chromophore is less well coordinated with the Surrounding protein matrix. From this configuration the simulated trans-cis photoisomerization of the chromophore and the associated non-radiative decay are faster than in the cis-trans case
T Laino, R Nifosì, V
Relationship between structure and optical properties
in Green Fluorescent Proteins: A quantum mechanical study of the
298, 17 (2004).
The present paper reports the first quantum mechanical modeling of a
realistic chromophore environment of the green fluorescent proteins
(GFPs). Based on density functional theory (DFT) and semiempirical
calculation, we studied the effect of each amino acid in close contact
with the chromophore and derived a quantitative and predictive
relationship between structure and optical properties. On the basis of
this relationship, the structural, optical and vibrational properties
of the different states of wild-type GFP and of two mutants, EGFP
(F64L/S65T) and E2GFP (F64L/S65T/T203Y), are then
specifically studied. This approach can be applied to infer some
structural features of spectroscopic states for which no structural
data is available, such as the dark states involved in GFP
R Nifosì, V Tozzini ``Molecular
dynamics simulations of enhanced green fluorescent proteins: Effects of
F64L, S65T and T203Y mutations on the ground-state proton equilibria'',
51, 378 (2003).
R Nifosì, A Ferrari, C Arcangeli,
V Tozzini, V Pellegrini, and F Beltram ``Photoreversible Dark State in
a Tristable Green Fluorescent Protein Variant'', J Phys Chem B 107,
The reversible photoinduced structural changes of a green fluorescent
protein (GFP) mutant and their opticalcontrol are reported. A photoreversible
optically inactive configuration is demonstrated with the absorption peak
at 365 nm, which is consistent with a photoisomerization pathway associated
with hydrogen-bond breakingin the chromophore environment. We show that
this state is involved in the switching dynamics recently discovered in
these molecules and we determine the transition rates of the reversible
photoconversion processes.These experiments combine to provide the framework
for the implementation and optimization of efficient room-temperature GFP-based
all-optical memories that use the fluorescent properties of these proteins.
V Tozzini and R Nifosì, ``Ab
Initio Molecular Dynamics of the GFP Chromophore: An Insight into the Photoinduced
Dynamics of the Green Fluorescent Proteins'', J Phys Chem B 105,
We present an ab initio molecular dynamics study of the chromophore
of Green Fluorescent Protein (GFP) in the four relevant protonation states.
Ground state geometries, electronic structures and vibrational spectra
are calculated. Patterns of vibrations are assigned to recently detected
Raman bands. These results provide insight into the correlation between
vibrational frequencies and optical absorption wavelengths of the GFP chromophore,
observed upon mutations of its environment. An intramolecular mode-coupling
mechanism is suggested, which rationalizes the coherent dynamics recently
revealed by ultrafast pump-and-probe optical spectroscopy. This mechanism
is tested by a simulation mimicking the dynamics subsequent to the electronic
excitation, which shows internal energy transfer between high and low frequency
C Reyes, R Nifosì and P A Kollman,
``Molecular Dynamics and Binding Specificity Analysis of the BIV Tat-TAR
Complex'', Biophys J 80, 2833 (2001).
We have performed molecular dynamics (MD) simulations, with particle-mesh
Ewald, explicit waters and counterions, and binding specificity analyses
combined molecular mechanics and continuum solvent (MM-PBSA) on the BIV
Tat peptide-TAR RNA complex. The solution structure for the complex was
solved independently by Patel and co-workers and Puglisi and co-workers.
We investigated the differences in both structures and trajectories, particularly
in the formation of the U-A-U base triple, the dynamic flexibility of the
Tat peptide and the interactions at the binding interface. We observed
a decrease in RMSD in comparing the final average RNA structures and initial
RNA structures of both trajectories, which suggests the convergence of
the RNA structures to a MD equilibrated RNA structure. We also calculated
the relative binding of different Tat peptide mutants to TAR RNA and found
qualitative agreement with experimental studies.
R Nifosì, C Reyes and P A Kollman,
``Molecular Dynamics Studies of HIV-1 TAR and its Complex with Argininamide'',
Acid Res 28, 4944 (2000).
The dynamic behavior of HIV-1 TAR and its complex with argininamide
is investigated by means of molecular dynamics simulations starting from
NMR structures, with explicit inclusion of water and periodic boundary
conditions particle mesh Ewald representation of the electrostatic energy.
During simulations of free and argininamide-bound TAR, local structural
patterns, as determined by NMR experiments, were reproduced. An interdomain
motion was observed in the simulations of free TAR, which is absent in
the case of bound TAR, leading to the conclusion that the free conformation
of TAR is intrinsically more flexible than the bound conformation. In particular,
in the bound conformation the TAR-argininamide interface is very well ordered,
as a result of the formation of a U·A·U base triple, which
imposes structural constraints on the global conformation of the molecule.
Free energy analysis, which includes solvation contributions, was used
to evaluate the influence of van der Waals and electrostatic terms on formation
of the complex and on the conformational rearrangement from free to bound
E Strepparola, R Nifosì
and M P Tosi, ``Ground-state structure and thermodynamics of Yukawa Bose
fluids in dimensionality D=3 and D=2'', J Phys: Condens Matter 10,
We evaluate the structure and the thermodynamic properties (internal
energy, pressure and compressibility) of zero-temperature fluids of Bose
particles interacting via the Yukawa potential in dimensionality D = 3
and D = 2. These systems provide simplified models for nuclear matter in
D = 3 and for assemblies of flux lines in high- superconductors in D =
2. Our calculations are based on the dielectric formalism, with short-range
correlations being treated in the self-consistent scheme of Singwi et al.
In both dimensionalities our results for the ground-state energy demonstrate
a crucial role of short-range correlations and are in good agreement with
those of variational and diffusion Monte Carlo studies over extended ranges
of values for the system parameters (reduced DeBoer length and reduced
particle density). Reasonable agreement is also found for the pressure
with the available diffusion Monte Carlo data in D = 2. The extent of the
deviations from the compressibility sum rule in the theory is assessed
for both dimensionalities. On all the above grounds it appears that the
present approach is quite accurate for the high-density fluid and provides
a useful starting point for fully quantitative studies of the low-density
R Nifosì, S Conti and
M P Tosi,``Dynamic exchange-correlation potentials for the electron gas
in dimensionality D=3 and D=2``, Phys Rev B 58, 12758
Recent progress in the formulation of a fully dynamical local
approximation to time-dependent Density Functional Theory appeals to the
longitudinal and transverse components of the exchange and correlation
kernel in the linear current-density response of the homogeneous fluid
at long wavelength. Both components are evaluated for the electron gas
in dimensionality $D=3$ and $D=2$ by an approximate decoupling in the equation
of motion for the current density, which accounts for processes of excitation
of two electron-hole pairs. Each electron-hole pair is treated in the random
phase approximation, but the role of exchange and correlation is also examined;
in addition, final-state exchange processes are included phenomenologically
so as to satisfy the exactly known high-frequency behaviours of the kernel.
The transverse and longitudinal spectra involve the same decay channels
and are similar in shape. A two-plasmon threshold in the spectrum for two-pair
excitations in $D=3$ leads to a sharp minimum in the real part of the exchange
and correlation kernel at twice the plasma frequency. In $D=2$ the same
mechanism leads to a broad spectral peak and to a broad minimum in the
real part of the kernel, as a consequence of the dispersion law of the
plasmon vanishing at long wavelength. The numerical results have been fitted
to simple analytic functions.