128 research outputs found
Revisiting the optical properties of the FMO protein
We review the optical properties of the FMO complex as found by spectroscopic studies of the Qy band over the last two decades. This article emphasizes the different methods used, both experimental and theoretical, to elucidate the excitonic structure and dynamics of this pigment–protein complex
Structural, spectroscopic and catalytic activity studies on glutathione reductase reconstituted with FAD analogues
Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/66378/1/j.1432-1033.1991.tb16100.x.pd
Superradiance Transition in Photosynthetic Light-Harvesting Complexes
We investigate the role of long-lasting quantum coherence in the efficiency
of energy transport at room temperature in Fenna-Matthews-Olson photosynthetic
complexes. The excitation energy transfer due to the coupling of the light
harvesting complex to the reaction center ("sink") is analyzed using an
effective non-Hermitian Hamiltonian. We show that, as the coupling to the
reaction center is varied, maximal efficiency in energy transport is achieved
in the vicinity of the superradiance transition, characterized by a segregation
of the imaginary parts of the eigenvalues of the effective non-Hermitian
Hamiltonian. Our results demonstrate that the presence of the sink (which
provides a quasi--continuum in the energy spectrum) is the dominant effect in
the energy transfer which takes place even in absence of a thermal bath. This
approach allows one to study the effects of finite temperature and the effects
of any coupling scheme to the reaction center. Moreover, taking into account a
realistic electric dipole interaction, we show that the optimal distance from
the reaction center to the Fenna-Matthews-Olson system occurs at the
superradiance transition, and we show that this is consistent with available
experimental data.Comment: 9 page
Functional Subsystems and Quantum Redundancy in Photosynthetic Light Harvesting
The Fenna-Matthews-Olson (FMO) antennae complex, responsible for light
harvesting in green sulfur bacteria, consists of three monomers, each with
seven chromophores. Here we show that multiple subsystems of the seven
chromophores can transfer energy from either chromophore 1 or 6 to the reaction
center with an efficiency matching or in many cases exceeding that of the full
seven chromophore system. In the FMO complex these functional subsystems
support multiple quantum pathways for efficient energy transfer that provide a
built-in quantum redundancy. There are many instances of redundancy in nature,
providing reliability and protection, and in photosynthetic light harvesting
this quantum redundancy provides protection against the temporary or permanent
loss of one or more chromophores. The complete characterization of functional
subsystems within the FMO complex offers a detailed map of the energy flow
within the FMO complex, which has potential applications to the design of more
efficient photovoltaic devices
Origin of Long Lived Coherences in Light-Harvesting Complexes
A vibronic exciton model is developed to investigate the origin of long lived
coherences in light-harvesting complexes. Using experimentally determined
parameters and uncorrelated site energy fluctuations, the model predicts
oscillations in the nonlinear spectra of the Fenna-Matthews-Olson (FMO) complex
with a dephasing time of 1.3 ps at 77 K. These oscillations correspond to the
coherent superposition of vibronic exciton states with dominant contributions
from vibrational excitations on the same pigment. Purely electronic coherences
are found to decay on a 200 fs timescale.Comment: 4 pages, 2 figure
How to do an evaluation: pitfalls and traps
The recent literature is replete with papers evaluating computational tools (often those operating on 3D structures) for their performance in a certain set of tasks. Most commonly these papers compare a number of docking tools for their performance in cognate re-docking (pose prediction) and/or virtual screening. Related papers have been published on ligand-based tools: pose prediction by conformer generators and virtual screening using a variety of ligand-based approaches. The reliability of these comparisons is critically affected by a number of factors usually ignored by the authors, including bias in the datasets used in virtual screening, the metrics used to assess performance in virtual screening and pose prediction and errors in crystal structures used
How to do an evaluation: pitfalls and traps
The recent literature is replete with papers evaluating computational tools (often those operating on 3D structures) for their performance in a certain set of tasks. Most commonly these papers compare a number of docking tools for their performance in cognate re-docking (pose prediction) and/or virtual screening. Related papers have been published on ligand-based tools: pose prediction by conformer generators and virtual screening using a variety of ligand-based approaches. The reliability of these comparisons is critically affected by a number of factors usually ignored by the authors, including bias in the datasets used in virtual screening, the metrics used to assess performance in virtual screening and pose prediction and errors in crystal structures used
Accommodating a Non-Conservative Internal Mutation by WaterMediated Hydrogen-Bonding Between β-Sheet Strands: A Comparison of Human and Rat Type B (Mitochondrial) Cytochrome b5
Mammalian type B (mitochondrial) cytochromes b5 exhibit greater amino acid sequence diversity than their type A (microsomal) counterparts, as exemplified by the type B proteins from human (hCYB5B) and rat (rCYB5B). The comparison of X-ray crystal structures of hCYB5B and rCYB5B reported herein reveals a striking difference in packing involving the five-stranded β-sheet, attributable to fully buried residue 21 in strand β4. The greater bulk of Leu21 in hCYB5B in comparison to Thr21 in rCYB5B results in a substantial displacement of the first two residues in β5, and consequent loss of two of the three hydrogen bonds between β5 and β4. Hydrogen-bonding between the residues is instead mediated by two well-ordered, fully buried water molecules. In a 10 ns molecular dynamics simulation, one of the buried water molecules in the hCYB5B structure exchanged readily with solvent via intermediates having three water molecules sandwiched between β4 and β5. When the buried water molecules were removed prior to a second 10 ns simulation, β4 and β5 formed persistent hydrogen bonds identical to those in rCYB5B, but the Leu21 side chain was forced to adopt a rarely observed conformation. Despite the apparently greater ease of water access to the interior of hCYB5B than of rCYB5B suggested by these observations, the two proteins exhibit virtually identical stability, dynamic and redox properties. The results provide new insight into the factors stabilizing the cytochrome b5 fold
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