RESUMEN
The first step in gene identification problem based on genomic signal processing is to convert character strings into numerical sequences. These numerical sequences are then analysed spectrally or using digital filtering techniques for the period-3 peaks, which are present in exons (coding areas) and absent in introns (non-coding areas). In this paper, we have shown that single-indicator sequences can be generated by encoding schemes based on physico-chemical properties. Two new methods are proposed for generating single-indicator sequences based on hydration energy and dipole moments. The proposed methods produce high peak at exon locations and effectively suppress false exons (intron regions having greater peak than exon regions) resulting in high discriminating factor, sensitivity and specificity.
Asunto(s)
Secuencia de Bases , Exones , Genómica/métodos , IntronesRESUMEN
Photosystem II (PS II) of thylakoid membrane of photosynthetic organisms has drawn attention of researchers over the years because it is the only system on Earth that provides us with oxygen that we breathe. In the recent past, structure of PS II has been the focus of research in plant science. The report of X-ray crystallographic structure of PS II complex by the research groups of James Barber and So Iwata in UK is a milestone in the area of research in photosynthesis. It follows the pioneering and elegant work from the laboratories of Horst Witt and W. Saenger in Germany, and J. Shen in Japan. It is time to analyze the historic events during the long journey made by the researchers to arrive at this point. This review makes an attempt to critically review the growth of the advancement of concepts and knowledge on the photosystem in the background of technological development. We conclude the review with perspectives on research and technology that should reveal the complete story of PS II of thylakoid in the future.
Asunto(s)
Oxígeno/metabolismo , Complejo de Proteína del Fotosistema II/química , Complejo de Proteína del Fotosistema II/metabolismo , Plantas/enzimología , Clorofila/metabolismo , Luz , Relación Estructura-ActividadRESUMEN
The DI protein of photosystem II (PS II) complex of a microalga Chaetosphaeridium globosum has been theoretically modelled from its sequence using comparative modeling with known backbone structure of DI protein from bacterium Thermosynechococcus vulcanus as template. The model is built with missing loops and all side chains, which are not resolved in the structure of the template. The structure of the tetramanganese cluster (TMC) and the ligand forming side chains have been subjected to modeling studies in order to gather more information useful to understanding of the water splitting reactions. Earlier models of TMC have been scrutinized and an insight into the manganese coordination sphere has been provided.
Asunto(s)
Manganeso/química , Streptophyta/enzimología , Secuencia de Aminoácidos , Calcio/química , Cristalografía por Rayos X/métodos , Cianobacterias/metabolismo , Ligandos , Modelos Moleculares , Modelos Teóricos , Conformación Molecular , Datos de Secuencia Molecular , Oxígeno/química , Complejo de Proteína del Fotosistema II , Unión Proteica , Estructura Secundaria de Proteína , Estructura Terciaria de Proteína , Homología de Secuencia de Aminoácido , Agua/químicaRESUMEN
A model is proposed for the organization of chlorophyll-protein complex in photosystem II (PS II) of higher plants. The rates of exciton migration and exciton trapping have been computed using stochastic method to find out the photochemical efficiency of the dimeric PS II. Three dimeric PS II units are assumed to form a group, as transfer of the exciton to the light harvesting bed of the nearest neighbour on either side may only be effective. A relationship has been deduced between the fractions of the reaction centre traps closed and the number of jumps (J) required by the exciton for trapping. The photochemical efficiency and fluorescence quantum yield are computed using J as the parameter in an empirical equation.
Asunto(s)
Clorofila/química , Proteínas del Complejo del Centro de Reacción Fotosintética/química , Dimerización , Luz , Complejos de Proteína Captadores de Luz , Modelos Biológicos , Modelos Estadísticos , Complejo de Proteína del Fotosistema II , Unión Proteica , Espectrometría de FluorescenciaRESUMEN
Based on the experimental data and homologous sites in Protein Data Bank (PDB) a model for metal binding sites in D1/D2 heterodimer has been proposed. On searching for tetranuclear and binuclear Mn binding sites in the PDB, a suitable sequence homology in thermolysin and D1 could be observed. From the homology and site-directed mutagenesis data, a model for binuclear Mn-Ca or Mn-Mn has been built and it is extended to a tetranuclear Mn centre.
Asunto(s)
Eucariontes/química , Proteínas del Complejo del Centro de Reacción Fotosintética , Secuencia de Aminoácidos , Sitios de Unión , Calcio/química , Bases de Datos Factuales , Ligandos , Manganeso/química , Modelos Moleculares , Datos de Secuencia Molecular , Mutagénesis Sitio-Dirigida , Unión Proteica , Homología de Secuencia de AminoácidoRESUMEN
Membrane spanning regions of 43 kDa and 47 kDa antenna proteins of photosystem II of thylakoid membranes are theoretically predicted. Prediction of topology of chlorophyll-a and beta-carotene molecules in the proteins and interaction of the proteins with 33 kDa extrinsic protein on the lumenal side of thylakoid membrane is based on the findings reported earlier. Each antenna protein is predicted to have six transmembrane alpha-helices with twelve chlorophyll-a and five beta-carotene molecules binding to it. Both N- and C- terminal ends are proposed to be on the stromal side of thylakoid membrane. The proposed structural model conforms to the reported experimental results from the literature.
Asunto(s)
Proteínas de la Membrana/química , Proteínas del Complejo del Centro de Reacción Fotosintética/química , Estructura Secundaria de Proteína , Sitios de Unión , Clorofila/análisis , Clorofila A , Membranas Intracelulares/química , Complejos de Proteína Captadores de Luz , Modelos Moleculares , Peso Molecular , Complejo de Proteína del Fotosistema II , beta Caroteno/análisisRESUMEN
Secondary structures, functionally important residues, antigenic sites, membrane spanning segments and hydropathicity of light harvesting chlorophyll a/b binding polypeptides (LHC) are predicted by theoretical methods from the amino acid sequence of the polypeptides. The reported structural features of the Pea LHC (Lhcb 1 gene product) from electron crystallographic studies have been compared by alignment with other types of chlorophyll a/b binding polypeptides for structural prediction. Fifteen conserved residues D85, D89, E113, H116, E/Q133, E/Q181, E189, D/N233, E252, N/H255, Q/E269, E/D/Q280, N281, H285, D288 (number indicates position in the aligned sequence), are identified which are potential ligands to Mg2+ of chlorophylls. Three amino acid residues D89, E/Q131 and D/N 233 are proposed as ligands to chlorophylls b2, a7 and b2 respectively, for which ligands are not identified in electron crystallographic study.
Asunto(s)
Clorofila/metabolismo , Proteínas del Complejo del Centro de Reacción Fotosintética/química , Estructura Secundaria de Proteína , Secuencia de Aminoácidos , Sitios de Unión , Complejos de Proteína Captadores de Luz , Datos de Secuencia Molecular , Homología de Secuencia de AminoácidoRESUMEN
Chou-Fasman method was modified to account for amphipathic nature of Gly and hydrophobic environment. The modified method shows improvement in prediction accuracy from 35 to 70% and can be applied to predict the conformation of D1, D2 polypeptides of reaction centre II of thylakoid, which are analogous to L and M respectively. Possible sites for Mn binding to D1/D2 heterodimer are postulated.
Asunto(s)
Proteínas Bacterianas , Clorofila , Proteínas de Plantas , Aminoácidos , Complejos de Proteína Captadores de Luz , Modelos Moleculares , Modelos Estadísticos , Proteínas del Complejo del Centro de Reacción Fotosintética , Conformación ProteicaRESUMEN
A model for evolution of oxygen evolving reaction center II of higher plant initiating from a chlorophyll--quinone complex is proposed. The reaction center gradually incorporates pheophytin, Fe and Mn to finally achieve oxidation of water to oxygen. The structural and functional pattern during evolution is proposed to descend from higher order of symmetry to lower one.