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 .     

Oscillatory dynamics protect enzymes and possibly cells against toxic substances

We have used the oscillating peroxidase-oxidase (PO) reaction as a model system to study how oscillatory dynamics may affect the influence of toxic reaction intermediates on enzyme stability. In the peroxidase-oxidase reaction reactive intermediates, such as hydrogen peroxide, superoxide, and hydroxyl radical are formed. Such intermediates inactivate many cellular macromolecules such as proteins and nucleic acids. These reaction intermediates also react with peroxidase itself to form an inactive enzyme. The fact that the PO reaction shows bistability between an oscillatory and a steady state gives us a unique possibility to compare such inactivation when the system is in one of these two states. We show that inactivation of peroxidase is slower when the system is in an oscillatory state, and using numerical simulations we provide evidence that oscillatory dynamics lower the average concentration of the reactive intermediates.     

Greenhouse gas abatement — toward Pareto-optimal decisions under uncertainty

This paper examines the economic logic of integrated assessment — balancing the costs against the benefits of greenhouse gas abatement. Stylized facts are employed in a multiregion computable general equilibrium model with a public good. The percentage shares of global emissions are determined outside the model — based upon some form of international agreement — and emission rights are tradeable between regions. The analysis is confined to Pareto-optimal (cooperative) solutions. We focus on the sensitivity of initial decisions to low-probability, high-consequence scenarios associated with cumulative emissions. For simplicity, there are only two regions, two tradeable goods, two time periods, and two states-of-world. With the particular form of public good model adopted here (production rather than utility function impacts), it turns out that a Pareto-optimal hedging strategy is indepedent of the emission shares allocated to each region. Equity issues may be separated from those of economic efficiency. Similar results extend to cases in which there are additional regions, tradeable goods, time periods, and states-of-world.Presented at the Conference on the Economics of Global Environmental Change, Birmingham University, May 9–11, 1994. This research was funded by the Electric Power Research Institute (EPRI). The views presented here are solely those of the individual authors, and do not necessarily represent the views of EPRI or its members.     

Ab initio excited-state dynamics of the photoactive yellow protein chromophore

The photoisomerization mechanism of the neutral form of the photoactive yellow protein (PYP) chromophore is investigated using ab initio quantum chemistry and first-principles nonadiabatic molecular dynamics (ab initio multiple spawning or AIMS). We identify the nature of the two lowest-lying excited states, characterize the short-time behavior of molecules excited directly to S2, and explain the origin of the experimentally observed wavelength-dependent photoisomerization quantum yield.     

Conformational analysis and electronic structure of acetanilide

The calculations of the electronic structure and conformational analysis of the acetanilide were carried out using the CNDO/2 method. The results show that the endo form is 1.2 Kcal/mole more stable than the exo form. The most stable conformation of the exo isomer corresponds to the dihedral angle of 90 ° between the phenyl and acetamide plane, whereas the minimum energy conformation of the endo isomer corresponds to the dihedral angle 50 °–60 °. A comparison of the calculated and experimental dipole moments suggests also the dihedral angle of 50 °–60 °. A comparison with experiment indicates that this molecular orbital method is good for conformational analysis and gives electronic structure which is compatible with spectroscopic measurement. The calculated conformational analysis and electronic structure of the acetanilide are in excellent agreement with experiments.We thank Professor J. P. Green for helpful discussions. This research was supported by a grant from the National Institute of Mental Health (MH-17489-01).     

Hydrophilic interaction chromatography using amino and silica columns for the determination of polar pharmaceuticals and impurities

Hydrophilic interaction chromatography (HILIC) is described as a useful alternative to reversed-phase chromatography for applications involving polar compounds. In the HILIC mode, an aqueous-organic mobile phase is used with a polar stationary phase to provide normal-phase retention behavior. Silica and amino columns with aqueous-acetonitrile mobile phases offer potential for use in the HILIC mode. An examination of the retention and separation of several pyrimidines, purines, and amides on silica and amino columns from three manufacturers revealed that mobile phases should contain a buffer or acid for pH control to achieve similar and reproducible results among columns from different sources. Amino columns may also be used in an anion-exchange mode, which provides an advantage for some applications. In some cases, silica can provide different selectivity and better separation than an amino column. Example applications include: low-molecular-mass organic acids and amides as impurities in non-polar drug substances, 5-fluorouracil in 5-fluorocytosine, guanine in acyclovir, and different selectivity for polar basic compounds compared to an ion-pairing system.