pH modulates the quinone position in the photosynthetic reaction center from Rhodobacter sphaeroides in the neutral and charge separated states

'Double water exclusion': a hypothesis refining the O-ring theory for the hot spots at protein interfaces

Motivation: The O-ring theory reveals that the binding hot spot at a protein interface is surrounded by a ring of residues that are energetically less important than the residues in the hot spot. As this ring of residues is served to occlude water molecules from the hot spot, the O-ring theory is also called ‘water exclusion’ hypothesis. We propose a ‘double water exclusion’ hypothesis to refine the O-ring theory by assuming the hot spot itself is water-free. To computationally model a water-free hot spot, we use a biclique pattern that is defined as two maximal groups of residues from two chains in a protein complex holding the property that every residue contacts with all residues in the other group.

Methods and Results: Given a chain pair A and B of a protein complex from the Protein Data Bank (PDB), we calculate the interatomic distance of all possible pairs of atoms between A and B. We then represent A and B as a bipartite graph based on these distance information. Maximal biclique subgraphs are subsequently identified from all of the bipartite graphs to locate biclique patterns at the interfaces. We address two properties of biclique patterns: a non-redundant occurrence in PDB, and a correspondence with hot spots when the solvent-accessible surface area (SASA) of a biclique pattern in the complex form is small. A total of 1293 biclique patterns are discovered which have a non-redundant occurrence of at least five, and which each have a minimum two and four residues at the two sides. Through extensive queries to the HotSprint and ASEdb databases, we verified that biclique patterns are rich of true hot residues. Our algorithm and results provide a new way to identify hot spots by examining proteins' structural data.

Availability: The biclique mining algorithm is available at http://www.ntu.edu.sg/home/jyli/dwe.html.

Contact:jyli@ntu.edu.sg

Supplementary information:Supplementary data are available at Bioinformatics online.

Spectrally silent light induced conformation change in photosynthetic reaction centers

Spectrally silent conformation change after photoexcitation of photosynthetic reaction centers isolated from Rhodobacter sphaeroides R-26 was observed by the optical heterodyne transient grating technique. The signal showed spectrally silent structural change in photosynthetic reaction centers followed by the primary P+BPh- charge separation and this change remains even after the charge recombination. Without bound quinone to the RC, the conformation change relaxes with about 28micros lifetime. The presence of quinone at the primary quinone (QA) site may suppress this conformation change. However, a weak relaxation with 30-40micros lifetime is still observed under the presence of QA, which increases up to 40micros as a function of the occupancy of the secondary quinone (QB) site.

Average electron tunneling route of the electron transfer in protein media

We present a new theoretical method to determine and visualize the average tunneling route of the electron transfer (ET) in protein media. In this, we properly took into account the fluctuation of the tunneling currents and the quantum-interference effect. The route was correlated with the electronic factor <TDA(2)> in the case of ET by the elastic tunneling mechanism. We expanded <TDA(2)> by the interatomic tunneling currents <Jab(2)>'s. Incorporating the quantum-interference effect into the mean-square interatomic tunneling currents, denoted as <Jab(2)>, we could express <TDA(2)> as a sum of variant Planck's over 2pi(2)<Jab(2)>. Drawing the distribution of <Jab(2)> on the protein structure, we obtain the <Jab(2)> map which visually represents which parts of bonds and spaces most significantly contribute to <TDA(2)>. We applied this method to the ET from the bacteriopheophytin anion to the primary quinone in the bacterial photosynthetic reaction center of Rhodobacter sphaeroides. We obtained <Jab(2)>'s by a combined method of molecular dynamics simulations and quantum chemical calculations. In calculating <Jab(2)>, we found that much destructive interference works among the interatomic tunneling currents even after taking the average. We drew the <Jab(2)> map by a pipe model where atoms a and b are connected by a pipe with width proportional to the magnitude of <Jab(2)>. We found that two groups of <Jab(2)>'s, which are mutually coupled with high correlation in each group, have broad pipes and form the average tunneling routes, called Trp route and Met route. Each of the two average tunneling routes is composed of a few major pathways in the Pathways model which are fused at considerable part to each other. We also analyzed the average tunneling route for the ET by the inelastic tunneling mechanism.

Investigating the mechanisms of photosynthetic proteins using continuum electrostatics

Computational methods based on continuum electrostatics are widely used in theoretical biochemistry to analyze the function of proteins. Continuum electrostatic methods in combination with quantum chemical and molecular mechanical methods can help to analyze even very complex biochemical systems. In this article, applications of these methods to proteins involved in photosynthesis are reviewed. After giving a short introduction to the basic concepts of the continuum electrostatic model based on the Poisson-Boltzmann equation, we describe the application of this approach to the docking of electron transfer proteins, to the comparison of isofunctional proteins, to the tuning of absorption spectra, to the analysis of the coupling of electron and proton transfer, to the analysis of the effect of membrane potentials on the energetics of membrane proteins, and to the kinetics of charge transfer reactions. Simulations as those reviewed in this article help to analyze molecular mechanisms on the basis of the structure of the protein, guide new experiments, and provide a better and deeper understanding of protein functions.

The fe2+ site of photosynthetic reaction centers probed by multiple scattering x-ray absorption fine structure spectroscopy: improving structure resolution in dry matrices

We report on the x-ray absorption fine structure of the Fe(2+) site in photosynthetic reaction centers from Rhodobacter sphaeroides. Crystallographic studies show that Fe(2+) is ligated with four N(epsilon) atoms from four histidine (His) residues and two O(epsilon) atoms from a Glu residue. By considering multiple scattering contributions to the x-ray absorption fine structure function, we improved the structural resolution of the site: His residues were split into two groups, characterized by different Fe-N(epsilon) distances, and two distinct Fe-O(epsilon) bond lengths resolved. The effect of the environment was studied by embedding the reaction centers into a polyvinyl alcohol film and into a dehydrated trehalose matrix. Incorporation into trehalose caused elongation in one of the two Fe-N(epsilon) distances, and in one Fe-O(epsilon) bond length, compared with the polyvinyl alcohol film. The asymmetry detected in the cluster of His residues and its response to incorporation into trehalose are ascribed to the hydrogen bonds between two His residues and the quinone acceptors. The structural distortions observed in the trehalose matrix indicate a strong interaction between the reaction-centers surface and the water-trehalose matrix, which propagates deeply into the interior of the protein. The absence of matrix effects on the Debye-Waller factors is brought back to the static heterogeneity and rigidity of the ligand cluster.

Crystal structure of cyanobacterial photosystem II at 3.0 A resolution: a closer look at the antenna system and the small membrane-intrinsic subunits

Photosystem II (PSII) is a homodimeric protein-cofactor complex embedded in the thylakoid membrane that catalyses light-driven charge separation accompanied by the water splitting reaction during oxygenic photosynthesis. In the first part of this review, we describe the current state of the crystal structure at 3.0 A resolution of cyanobacterial PSII from Thermosynechococcus elongatus [B. Loll et al., Towards complete cofactor arrangement in the 3.0 A resolution structure of photosystem II, Nature 438 (2005) 1040-1044] with emphasis on the core antenna subunits CP43 and CP47 and the small membrane-intrinsic subunits. The second part describes first the general theory of optical spectra and excitation energy transfer and how the parameters of the theory can be obtained from the structural data. Next, structure-function relationships are discussed that were identified from stationary and time-resolved experiments and simulations of optical spectra and energy transfer processes.