Occurrence and chirality of oscillaxanthin

The quantitative carotenoid composition of natural blooms of Oscillatoria rubescens and O. agardhii is reported and compared with previous isolations. Chemical or enzymatic conversion of oscillaxanthin to the chiral aglycone failed. CD-correlation of oscillaxanthin hexaacetate with (2S,2′S)-bacterioruberin, (2′R)-plectaniaxanthin and (2′R)-plectaniaxanthin-2′-β-D-glucoside tetraacetate support the 2R,2′R-configuration for oscillaxanthin.     

CD correlation of C-2′substituted monocyclic carotenoids

The scope and limitation of circular dichroism (CD) correlations of several C-2′ substituted monocyclic monochiral, homodichiral and heterodichiral carotenoids have been investigated, aiming at the assignment of absolute configuration at C-2′ by using the diester and 2′-β-d-tetraacetylglucosyl derivative of (2′R)-plectaniaxanthin and a synthetic chiral C₄₅-carotene as key references. The correlations are based on the additivity hypothesis, the conformational rule and a comparison of CD spectra, preferably conservative ones. Quantitative aspects of the conformational rule are considered. Substituent effects at C-2′ and C-1′ have been studied. Absolute configurations are suggested for (2′)-phleixanthophyll (3S,2′S)-2′-hydroxyflexixanthin, (3R,2′S)-myxoxanthophyll, (3S,2′S-4-ketomyxoxanthophyll (3R,2′S)-myxol-2′-O-methyl methylpentoside and (2R,2′S)-Cp. 473 from relevant CD correlations. The chiralities of (2′S)-4-ketophleixanthophyll and (2R,6R,2′S)-A.g. 471 are suggested from biogenetic considerations. A chemosystematic consideration of chirality and source is included.     

Numerical taxonomy of psychrotrophic lactic acid bacteria from prepacked meat and meat products

Ninety-four strains of lactic acid bateria isolated from refrigerated, prepacked meat and meat products were together with 59 reference strains of Brochothrix, Lactobacillus, Leuconostoc, Pediococcus and Streptococcus phenotypically classfied, using 96 unit characters. Data were examined using Simple Matching (S_SM) or Jaccard coefficient (S_J), and unweighted pair group algorithm with arithmetic averages. Twenty-three clusters with two or more members were defined at the 84% S_SM-similarity level which corresponded to the S_J-similarity level of 61%. Based on S_SM, most field strains were included in nine clusters, and with three unsignificant exceptions these contained no reference strains. The field clusters were designated Carnobacterium piscicola (cluster 1; 5% of field isolates), Carnobacterium divergens(cluster 2; 9% of field isolates), Leuconostoc (cluster 9; 18% of field isolates) and Lactobacillus (cluster 4, 10, 11, 12, 13 and 14; together 60% of field isolates). The Lactobacillus clusters had many features in common with cluster II of Shaw & Harding (1984). Phenotypical characteristics of major clusters are given. The S_SM and S_J based classifications basically coincided for the field strains; the exception was cluster 4 which now were split in two parts. Fourteen clusters were made up of mainly reference strains (S_SM). Most of them included more than one type strain on species level; exceptions were Brochothrix thermosphacta (cluster 3), Lactobacillus salivarius (cluster 17) and Leuconostoc mesenteroides (cluster 18). Several rearrangements were seen amongst the clusters of the reference strains when S_J, instead of S_SM, was used for clustering.     

Network analysis of a proposed exit pathway for protons to the P-side of cytochrome c oxidase

Cytochrome c Oxidase (CcO) reduces O₂, the terminal electron acceptor, to water in the aerobic, respiratory electron transport chain. The energy released by O₂ reductions is stored by removing eight protons from the high pH, N-side, of the membrane with four used for chemistry in the active site and four pumped to the low pH, P-side. The proton transfers must occur along controllable proton pathways that prevent energy dissipating movement towards the N-side. The CcO N-side has well established D- and K-channels to deliver protons to the protein interior. The P-side has a buried core of hydrogen-bonded protonatable residues designated the Proton Loading Site cluster (PLS cluster) and many protonatable residues on the P-side surface, providing no obvious unique exit. Hydrogen bond pathways were identified in Molecular Dynamics (MD) trajectories of Rb. sphaeroides CcO prepared in the P_R state with the heme a₃ propionate and Glu286 in different protonation states. Grand Canonical Monte Carlo sampling of water locations, polar proton positions and residue protonation states in trajectory snapshots identify a limited number of water mediated, proton paths from PLS cluster to the surface via a (P-exit) cluster of residues. Key P-exit residues include His93, Ser168, Thr100 and Asn96. The hydrogen bonds between PLS cluster and P-exit clusters are mediated by a water wire in a cavity centered near Thr100, whose hydration can be interrupted by a hydrophobic pair, Leu255B (near Cu_A) and Ile99. Connections between the D channel and PLS via Glu286 are controlled by a second, variably hydrated cavity.

Calculated coupling of electron and proton transfer in the photosynthetic reaction center of Rhodopseudomonas viridis.

Based on new Rhodopseudomonas (Rp.) viridis reaction center (RC) coordinates with a reliable structure of the secondary acceptor quinone (QB) site, a continuum dielectric model and finite difference technique have been used to identify clusters of electrostatically interacting ionizable residues. Twenty-three residues within a distance of 25 A from QB (QB cluster) have been shown to be strongly electrostatically coupled to QB, either directly or indirectly. An analogous cluster of 24 residues is found to interact with QA (QA cluster). Both clusters extend to the cytoplasmic surface in at least two directions. However, the QB cluster differs from the QA cluster in that it has a surplus of acidic residues, more strong electrostatic interactions, is less solvated, and experiences a strong positive electrostatic field arising from the polypeptide backbone. Consequently, upon reduction of QA or QB, it is the QB cluster, and not the QA cluster, which is responsible for substoichiometric proton uptake at neutral pH. The bulk of the changes in the QB cluster are calculated to be due to the protonation of a tightly coupled cluster of the three Glu residues (L212, H177, and M234) within the QB cluster. If the lifetime of the doubly reduced state QB2- is long enough, Asp M43 and Ser L223 are predicted to also become protonated. The calculated complex titration behavior of the strongly interacting residues of the QB cluster and the resulting electrostatic response to electron transfer may be a common feature in proton-transferring membrane protein complexes.     

Incorporating protein conformational flexibility into the calculation of pH-dependent protein properties.

A method for combining calculations of residue pKa's with changes in the position of polar hydrogens has been developed. The Boltzmann distributions of proton positions in hydroxyls and neutral titratable residues are found in the same Monte Carlo sampling procedure that determines the amino acid ionization states at each pH. Electrostatic, Lennard-Jones potentials, and torsion angle energies are considered at each proton position. Many acidic and basic residues are found to have significant electrostatic interactions with either a water- or hydroxyl-containing side chain. Protonation state changes are coupled to reorientation of the neighboring hydroxyl dipoles, resulting in smaller free energy differences between neutral and ionized residues than when the protein is held rigid. Multiconformation pH titration gives better agreement with the experimental pKa's for triclinic hen egg lysozyme than conventional rigid protein calculations. The hydroxyl motion significantly increases the protein dielectric response, making it sensitive to the composition of the local protein structure. More than one conformer per residue is often found at a given pH, providing information about the distribution of low-energy lysozyme structures.     

The importance of the protein in controlling the electrochemistry of heme metalloproteins: methods of calculation and analysis

 The importance of electrostatic effects in determining the free energy of redox reactions in proteins such as cytochromes and iron-sulfur complexes is well established. Several theoretical techniques have been used to analyze how the protein and its environment combine to produce the observed electrochemical midpoints. The free energy of changing the cofactor charge is influenced by the distribution of charges and dipoles in the protein, solvent and ions surrounding the protein, and by the redistribution of these charges and dipoles coupled to the reaction. An outline of a consistent view for calculating these effects will be presented and compared with other theoretical models. Heme redox potentials in yeast cytochrome c and the cytochrome subunit of photosynthetic reaction centers will be calculated to show how these protein structures produce the observed electrochemistry. Received, accepted: 26 November 1996     

Radical-pair energetics and decay mechanisms in reaction centers containing anthraquinones, naphthoquinones or benzoquinones in place of ubiquinone

In reaction centers from Rhodobacter sphaeroides (formerly called Rhodopseudomonas sphaeroides), light causes an electron-transfer reaction that forms the radical pair state (P+I-, or PF) from the initial excited singlet state (P) of a bacteriochlorophyll dimer (P). Subsequent electron transfer to a quinone (Q) produces the state P+Q-. Back electron transfer can regenerate P from P+Q-, giving rise to 'delayed' fluorescence that decays with approximately the same lifetime as P+Q-. The free-energy difference between P+Q- and P can be determined from the initial amplitude of the delayed fluorescence. In the present work, we extracted the native quinone (ubiquinone) from Rps. sphaeroides reaction centers, and replaced it by various anthraquinones, naphthoquinones, and benzoquinones. We found a rough correlation between the halfwave reduction potential (E1/2) of the quinone used for reconstitution (as measured polarographically in dimethylformamide) and the apparent free energy of the state P+Q- relatively to P. As the E1/2 of the quinone becomes more negative, the standard free-energy gap between P+Q- and P decreases. However, the correlation is quantitatively weak. Apparently, the effective midpoint potentials (Em) of the quinones in situ depend subtly on interactions with the protein environment in the reaction center. Using the value of the Em for ubiquinone determined in native reaction centers as a reference, and the standard free energies determined for P+Q- in reaction centers reconstituted with other quinones, the effective Em values of 12 different quinones in situ are estimated. In native reaction centers, or in reaction centers reconstituted with quinones that give a standard free-energy gap of more than about 0.8 eV between P+Q- and P*, charge recombination from P+Q- to the ground state (PQ) occurs almost exclusively by a temperature-insensitive mechanism, presumably electron tunneling. When reaction centers are reconstituted with quinones that give a free-energy gap between P+Q- and P* of less than 0.8 with quinones that give a free-energy gap between P+Q- and P* of less than 0.8 eV, part or all of the decay proceeds through a thermally accessible intermediate. There is a linear relationship between the log of the rate constant for the decay of P+Q- via the intermediate state and the standard free energy of P+Q-. The higher the free energy, the faster the decay. The kinetic and thermodynamic properties of the intermediate appear not to depend strongly on the quinone used for reconstitution, indicating that the intermediate is probably not simply an activated form of P+Q-.(ABSTRACT TRUNCATED AT 400 WORDS)