PROTEIN STRUCI'URE MODELLING OF THE BACTERIAL LIGHT-HARVESTING COMPLEX

Abstract Protein structure modelling offers a method of obtaining 3-dimensional information that can be tested and used to plan mutagenesis experiments when a crystallographically determined structure is not available. At its simplest a model may consist of little more than a secondary structure prediction coupled with a determination of the likely regions of transmembrane/membrane surface/globular configuration. These methods can yield an interesting topology map of the protein, which places the residues in their likely positions with respect to, for example, the membrane interface. If it is a member of a large family of related proteins then aligned protein sequences can be used to predict the residues that have an important function as these. will be largely conserved in the alignments. Using all these methods a model can be constructed (using for example, the Nicholson Molecular Modelling Kit) to visualize the proposed structure in three dimensions following the premise of good design, that is, avoiding obvious steric clashes, packing of helices in a realistic manner, observing the correct H-bond lengths, etc . In this latter exercise the review of Chothia ( Annu. Rev. Biochem . 53 , 537–572, 1984) of the principles of protein structure is particularly helpful as it clearly sets out how proteins pack and their preferred configuration. There is a wealth of information about individual amino acid conformational preferences and observed frequencies of occurrence in known protein structures, which can help decide how the residues in the model can be oriented.
In this article we have collated the various protein models of the bacterial light-harvesting complexes and present our own model, which is a synthesis of the available biophysical data and theoretical predictions, and show its performance in explaining recent results of site-directed mutants of the LHI and LH2 light-harvesting complexes of Rhodobacter sphaeroides .     

Molecular cluster decay viewed as escape from a potential of mean force

We show that evaporation from a quasistable molecular cluster may be treated as a kinetic problem involving the stochastically driven escape of a molecule from a potential of mean force. We derive expressions for the decay rate, and a relationship between the depth of the potential and the change in system free energy upon loss of a molecule from the cluster. This establishes a connection between kinetic and thermodynamic treatments of evaporation, but also reveals differences in the prefactor in the rate expression. We perform constant energy molecular dynamics simulations of cluster dynamics to calculate potentials of mean force, friction coefficients and effective temperatures for use in the kinetic analysis, and to compare the results with the directly observed escape rates. We also use the simulations to estimate the escape rates by a probabilistic analysis. It is much more efficient to calculate the decay rate by the methods we have developed than it is to monitor escape directly, making these approaches potentially useful for the assessment of molecular cluster stability.     

Multiphoton ionization detected by fourier-transform mass spectrometry

Ions produced by multiphoton ionization (MPI) of naphthalene, fluoranthene and triphenylene have been detected by Fourier-transform mass spectrometry (FT MS). Paret ions are produced very efficiently at 250 and 222 nm with pulse energies as low as 1 mJ. With FT MS a complete, high-resolution mass spectrum is obtained for each laser pulse.     

The concerted addition of HBr to aryl alkynes; orthogonal pi bond selectivity

In a weakly acidic solution, the addition of HBr to 1-phenylprop-1-yne produces predominantly the anti-Markovnikov product. In this paper, we consider five possible explanations for this behavior and conclude that the concerted addition is occurring on the acetylenic pi bond orthogonal to the extended aromatic pi system. The electronic effect of the distal methyl group and the steric hindrance of the coplanar phenyl ring combine to promote bromide attack at the beta carbon. Attack on this pi bond is insensitive to the electronic effect of meta and para substituents on the ring but is very (sterically) sensitive toward all ortho substituents.     

Dynamic interaction of theory and experiment: total determination of the gas-phase molecular structure of tri-tert-butylphosphine oxide (OPBut3)

A new method to aid the determination of structures of sterically crowded molecules in the gas phase by dynamically linking the gas-phase electron diffraction (GED) refinement process with computational methods has been developed. The procedure involves refining the heavy-atom skeleton of the molecule using the GED data while continually updating the light-atom positions during the refinement using computational methods, in this case molecular mechanics. This removes errors associated with the assumption of local symmetry for the light-atom groups, which can affect the final values of the heavy-atom parameters. The refinement of the molecular structure of tri-tert-butyl phosphine oxide has been used to illustrate this new technique, which we call the DYNAMITE (DYNAMic Interaction of Theory and Experiment) method. Re-examination of the structure using this method has resulted in a shorter P-O distance than was found in a less sophisticated anaylsis, and is consistent with the molecule being regarded as O=PBut3, rather than O(-)-P+But3.     

ADVENTITIOUS INTERCONVERSION OF cis- AND trans-UROCANIC ACID BY LABORATORY LIGHT

Urocanic acid (UCA) is a chromophore in the stratum corneum. Ultraviolet radiation (ultraviolet B) has been shown to suppress mammalian cell-mediated immunity. The photoisomerization of trans -UCA to cis -UCA was proposed as the initiator of the suppression process. Cis -urocanic acid has been demonstrated to suppress immunity by a variety of experiments. Investigators should be aware that laboratory illumination may be capable of interconverting trans -UCA and cis -UCA during experimental manipulations. This possible inadvertent contamination of one isomer by the other may influence results. We demonstrated that fluorescent lamps, daylight, sunlight and incandescent lamps were able to bring about isomerization. Window glass and container materials of plastic and clear glass did not filter out effective wavelengths, but three commercial plastic diffusers on fluorescent fixtures prevented the isomerization. Because the molar extinction coefficient (ɛ) for cis -UCA is less than that of trans -UCA, we have exposed 0.1 m M trans -UCA to ambient light and monitored the change in absorbance. A method is given to calculate the percentage of trans and cis isomers from the absorbance at 277 nm when the initial purity and absorbance are known. Using this procedure, we validated the molar extinction coefficient of cis -UCA.     

Tandem purification of mouse IgM monoclonal antibodies produced in vitro using anion-exchange and gel fast protein liquid chromatography

A tandem chromatographic procedure was used to isolate rapidly mouse IgM monoclonal antibodies produced by cultivation of hybridomas in vitro. Hybridoma culture supernatants containing mouse IgM monoclonal antibodies were first chromatographed on an anion-exchange Mono Q column connected to a fast protein liquid chromatography system. This anion-exchange step offers the advantage of obtaining IgM antibodies in a concentrated form. The IgM-rich fractions from the Mono Q column were then injected on a gel filtration Superose 6 column equilibrated with a low-ionic strength buffer and eluted with a high-ionic strength buffer. Assessment of the purity of isolated IgM monoclonal antibodies was performed by sodium dodecyl sulphate polyacrylamide gel electrophoresis together with a Coomassie Brillant Blue R 250 staining technique. Assessment of the immunoreactivity of isolated IgM monoclonal antibodies was performed by an enzyme linked immunosorbent assay using a solid phase adsorbed antigen against which IgM monoclonal antibodies were directed. The chromatographic procedures described allows the rapid isolation of mouse IgM monoclonal antibodies produced in vitro at a high degree of purity and in an immunoreactive state.