Prediction of cis/trans isomerization in proteins using PSI-BLAST profiles and secondary structure information

BACKGROUND: The majority of peptide bonds in proteins are found to occur in the trans conformation. However, for proline residues, a considerable fraction of Prolyl peptide bonds adopt the cis form. Proline cis/trans isomerization is known to play a critical role in protein folding, splicing, cell signaling and transmembrane active transport. Accurate prediction of proline cis/trans isomerization in proteins would have many important applications towards the understanding of protein structure and function. RESULTS: In this paper, we propose a new approach to predict the proline cis/trans isomerization in proteins using support vector machine (SVM). The preliminary results indicated that using Radial Basis Function (RBF) kernels could lead to better prediction performance than that of polynomial and linear kernel functions. We used single sequence information of different local window sizes, amino acid compositions of different local sequences, multiple sequence alignment obtained from PSI-BLAST and the secondary structure information predicted by PSIPRED. We explored these different sequence encoding schemes in order to investigate their effects on the prediction performance. The training and testing of this approach was performed on a newly enlarged dataset of 2424 non-homologous proteins determined by X-Ray diffraction method using 5-fold cross-validation. Selecting the window size 11 provided the best performance for determining the proline cis/trans isomerization based on the single amino acid sequence. It was found that using multiple sequence alignments in the form of PSI-BLAST profiles could significantly improve the prediction performance, the prediction accuracy increased from 62.8% with single sequence to 69.8% and Matthews Correlation Coefficient (MCC) improved from 0.26 with single local sequence to 0.40. Furthermore, if coupled with the predicted secondary structure information by PSIPRED, our method yielded a prediction accuracy of 71.5% and MCC of 0.43, 9% and 0.17 higher than the accuracy achieved based on the singe sequence information, respectively. CONCLUSION: A new method has been developed to predict the proline cis/trans isomerization in proteins based on support vector machine, which used the single amino acid sequence with different local window sizes, the amino acid compositions of local sequence flanking centered proline residues, the position-specific scoring matrices (PSSMs) extracted by PSI-BLAST and the predicted secondary structures generated by PSIPRED. The successful application of SVM approach in this study reinforced that SVM is a powerful tool in predicting proline cis/trans isomerization in proteins and biological sequence analysis

2Statistically significant dependence of the Xaa-Pro peptide bond conformation on secondary structure and amino acid sequence

BACKGROUND: A reliable prediction of the Xaa-Pro peptide bond conformation would be a useful tool for many protein structure calculation methods. We have analyzed the Protein Data Bank and show that the combined use of sequential and structural information has a predictive value for the assessment of the cis versus trans peptide bond conformation of Xaa-Pro within proteins. For the analysis of the data sets different statistical methods such as the calculation of the Chou-Fasman parameters and occurrence matrices were used. Furthermore we analyzed the relationship between the relative solvent accessibility and the relative occurrence of prolines in the cis and in the trans conformation. RESULTS: One of the main results of the statistical investigations is the ranking of the secondary structure and sequence information with respect to the prediction of the Xaa-Pro peptide bond conformation. We observed a significant impact of secondary structure information on the occurrence of the Xaa-Pro peptide bond conformation, while the sequence information of amino acids neighboring proline is of little predictive value for the conformation of this bond. CONCLUSION: In this work, we present an extensive analysis of the occurrence of the cis and trans proline conformation in proteins. Based on the data set, we derived patterns and rules for a possible prediction of the proline conformation. Upon adoption of the Chou-Fasman parameters, we are able to derive statistically relevant correlations between the secondary structure of amino acid fragments and the Xaa-Pro peptide bond conformation

Detection of discriminative sequence patterns in the neighborhood of proline cis peptide bonds and their functional annotation

<p>Abstract</p> <p>Background</p> <p>Polypeptides are composed of amino acids covalently bonded via a peptide bond. The majority of peptide bonds in proteins is found to occur in the <it>trans </it>conformation. In spite of their infrequent occurrence, <it>cis </it>peptide bonds play a key role in the protein structure and function, as well as in many significant biological processes.</p> <p>Results</p> <p>We perform a systematic analysis of regions in protein sequences that contain a proline <it>cis </it>peptide bond in order to discover non-random associations between the primary sequence and the nature of proline <it>cis/trans </it>isomerization. For this purpose an efficient pattern discovery algorithm is employed which discovers regular expression-type patterns that are overrepresented (i.e. appear frequently repeated) in a set of sequences. Four types of pattern discovery are performed: i) exact pattern discovery, ii) pattern discovery using a chemical equivalency set, iii) pattern discovery using a structural equivalency set and iv) pattern discovery using certain amino acids' physicochemical properties. The extracted patterns are carefully validated using a specially implemented scoring function and a significance measure (i.e. log-probability estimate) indicative of their specificity. The score threshold for the first three types of pattern discovery is 0.90 while for the last type of pattern discovery 0.80. Regarding the significance measure, all patterns yielded values in the range [-9, -31] which ensure that the derived patterns are highly unlikely to have emerged by chance. Among the highest scoring patterns, most of them are consistent with previous investigations concerning the neighborhood of <it>cis </it>proline peptide bonds, and many new ones are identified. Finally, the extracted patterns are systematically compared against the PROSITE database, in order to gain insight into the functional implications of <it>cis </it>prolyl bonds.</p> <p>Conclusion</p> <p><it>Cis </it>patterns with matches in the PROSITE database fell mostly into two main functional clusters: family signatures and protein signatures. However considerable propensity was also observed for targeting signals, active and phosphorylation sites as well as domain signatures.</p

Extraction of consensus protein patterns in regions containing non-proline cis peptide bonds and their functional assessment

<p>Abstract</p> <p>Background</p> <p>In peptides and proteins, only a small percentile of peptide bonds adopts the <it>cis </it>configuration. Especially in the case of amide peptide bonds, the amount of <it>cis </it>conformations is quite limited thus hampering systematic studies, until recently. However, lately the emerging population of databases with more 3D structures of proteins has produced a considerable number of sequences containing non-proline <it>cis </it>formations (<it>cis</it>-nonPro).</p> <p>Results</p> <p>In our work, we extract regular expression-type patterns that are descriptive of regions surrounding the <it>cis</it>-nonPro formations. For this purpose, three types of pattern discovery are performed: i) exact pattern discovery, ii) pattern discovery using a chemical equivalency set, and iii) pattern discovery using a structural equivalency set. Afterwards, using each pattern as predicate, we search the Eukaryotic Linear Motif (ELM) resource to identify potential functional implications of regions with <it>cis</it>-nonPro peptide bonds. The patterns extracted from each type of pattern discovery are further employed, in order to formulate a pattern-based classifier, which is used to discriminate between <it>cis</it>-nonPro and <it>trans</it>-nonPro formations.</p> <p>Conclusions</p> <p>In terms of functional implications, we observe a significant association of <it>cis</it>-nonPro peptide bonds towards ligand/binding functionalities. As for the pattern-based classification scheme, the highest results were obtained using the structural equivalency set, which yielded 70% accuracy, 77% sensitivity and 63% specificity.</p

Development of analytical methods for the characterization of tempera paintings at micro- and nano-scale and their deterioration and biodeterioration processes

Egg (the whole, the yolk or the white) is a natural product used since ancient times as tempera painting medium mainly in Europe and the Mediterranean Basin countries. In addition, egg is a complex multicomponent microstructured system susceptible of being influenced by the pigments that compose the paints, as well as a source of nutrient susceptible of biodeterioration. Modifying effect of artists' pigments on the binding medium as well as, the microbial biodeterioration are responsible for changes in the structure and composition of the binding medium and, consequently, on the physico-chemical properties of the paint. For this purpose, analytical techniques such as Fourier transform infrared spectroscopy - attenuated total reflection (FTIR-ATR) was used for the chemical characterization, Field emission scanning microscopy (FESEM) and Atomic force microscopy - nanoindentation (AFM-nanoindentation) were run for morphological and mechanical characterization of the deterioration processes resulted from the pigment-binder interactions involved in tempera painting. On the other hand, the current research report the application of the voltammetry of microparticles (VMP), complemented with FTIR-ATR, FESEM and AFM-nanoindentation techniques to monitor the deterioration of a series of tempera reconstructed model paint specimens under the action of different biological agents. This methodology would be of application for identifying the type of biological agent causing deterioration of painting, which is an important problem affecting cultural heritage. The analysis of biodeterioration processes is complicated by the fact that the action of microorganisms can affect both pigment and binding media. The deterioration of pictorial specimens by Acremonium chrysogenum, Aspergillus niger, Mucor rouxii, Penicillium chrysogenum and Trichoderma pseudokoningii fungi and Arthrobacter oxydans, Bacillus amyloliquefaciens and Streptomyces cellulofans bacteria was tested using sample-modified graphite electrodes immersed into aqueous electrolytes. Finally, the study carried out by means of FTIR-ATR, FESEM and AFM-nanoindentation confirms that egg proteins attached to the pigment grains changes their secondary structures. The results obtained also confirm that proteins and phospholipids are prevalently established linkages with the solid particles of pigment whereas triglycerides should be integrated in the complex binding network responsible for the cohesion of the paint film. Interactions between egg components with solid pigment particles are described and correlated with micromorphology and mechanical properties determined at micro- and nano-scale on the reconstructed model paint specimens. As a result of the crossing of VMP data with the results obtained by means of FTIR, FESEM and AFM-nanoindentation, the voltammetric signals obtained were associated to the electrochemical reduction of pigments and different complexes associated to the binding media. These results were particularly relevant in the study of biodeterioration, to allowing the electrochemical monitoring of biological attack.El huevo (entero, yema o clara) es un producto natural utilizado desde la antigüedad como medio aglutinante en la pintura al temple, principalmente en Europa y los países de la cuenca mediterránea. Además, el huevo es un complejo sistema multicomponente microestructurado susceptible de ser alterado por los pigmentos que componen las pinturas, así como fuente de nutrientes susceptible de biodeterioro. El efecto de los pigmentos sobre el medio aglutinante, así como el biodeterioro microbiano son responsables de cambios en la estructura y composición del medio aglutinante y, por consiguiente, en las propiedades fisicoquímicas de la pintura. Es por esto que, se utilizaron técnicas analíticas como la Espectroscopía Infrarroja por Transformada de Fourier en modo Reflexión Total Atenuada (FTIR-ATR), para la caracterización química de los procesos de deterioro resultantes de las interacciones pigmento-aglutinante en la pintura al temple. Así mismo, se utilizó Microscopía Electrónica de Emisión de Barrido (FESEM) para el estudio morfológico de las muestras, y para el estudio de las propiedades mecánicas Microscopía de Fuerza Atómica en modo Nanoindentación (AFM-nanoindentación). Por otro lado, la presente investigación propone el uso de la Voltamperometría de Micropartículas (VMP), en conjunto con otras técnicas de análisis como FTIR-ATR, FESEM y AFM-nanoindentación para el estudio del biodeterioro producido por hongos y bacterias sobre una serie muestras pictóricas sometidas. El estudio de las alteraciones causadas por el biodeterioro es complicado por el hecho de que la acción de los microorganismos puede afectar tanto al pigmento como al medio aglutinante. Para esto, se prepararon una serie de muestras de pinturas al temple y emulsión que fueron inoculadas con los hongos Acremonium chrysogenum, Aspergillus niger, Mucor rouxii, Penicillium chrysogenum, y Trichoderma pseudokoningii, y las bacterias Arthrobacter oxydans, Bacillus amyloliquefaciens y Streptomyces cellulofans. El estudio voltamperometrico se realizó utilizando electrodos de grafito modificados con las muestras inmersos en un electrolito acuoso. Las conclusiones obtenidas de manera general, apuntan a que las proteínas presentes en el huevo cambian su estructura secundaria al adherirse a los granos de pigmento. La información química, morfológica y mecánica obtenida por las diferentes técnicas de análisis instrumental es consistente. Finalmente, como resultado del cruce de los datos VMP con los resultados obtenidos mediante FTIR, FESEM y AFM-nanoindentación, las señales voltamperometricas obtenidas se asociaron a la reducción electroquímica de los pigmentos y a los complejos formados con el medio aglutinante. Estos resultados fueron particularmente relevantes en el estudio del biodeterioro de las películas pictóricas inoculadas, para permitir la monitorización electroquímica del ataque microbiológico.L'ou (sencer, rovell o clara) és un producte natural utilitzat des de l'antiguitat com a mitjà aglutinant en la pintura al tremp, principalment a Europa i els països de la conca mediterrània. A més, l'ou és un complex sistema multicomponent MICROESTRUCTURAT susceptible de ser alterat pels pigments que componen les pintures, així com a font de nutrients susceptible de biodeterioració. L'efecte dels pigments sobre el medi aglutinant, així com el BIODETERIORI microbià són responsables de canvis en l'estructura i composició del medi aglutinant i, per tant, en les propietats fisicoquímiques de la pintura. És per això que, es van utilitzar tècniques analítiques com l'Espectroscòpia Infraroja per Transformada de Fourier en mode Reflexió Total Atenuada (FTIR-ATR), per a la caracterització química dels processos de deteriorament resultants de les interaccions pigment-aglutinant en la pintura al tremp. Així mateix, es va utilitzar Microscòpia Electrònica d'emissió de Rastreig (FESEM) per a l'estudi morfològic de les mostres, i per a l'estudi de les propietats mecàniques Microscòpia de Força Atòmica en mode Nanoindentació (AFM-nanoindentació). D'altra banda, la present investigació proposa l'ús de la Voltamperometría de Micropartícules (VMP), en conjunt amb altres tècniques d'anàlisi, com FTIR-ATR, FESEM i AFM-nanoindentació per a l'estudi de l'biodeterioració produït per fongs i bacteris sobre una sèrie de mostres pictòriques sotmeses. L'estudi de les alteracions causades pel biodeteriori és complicat pel fet que l'acció dels microorganismes pot afectar tant el pigment com al medi aglutinant. Per això, es van preparar una sèrie de mostres de pintures al tremp i emulsió que van ser inoculades amb els fongs Acremonium chrysogenum, Aspergillus niger, Mucor rouxii, Penicillium chrysogenum, i Trichoderma pseudokoningii i els bacteris Arthrobacter oxydans, Bacillus amyloliquefaciens i Streptomyces cellulofans. L'estudi voltamperomètric es va realitzar utilitzant electrodes de grafit modificats amb les mostres immersos en un electròlit aquós. Les conclusions obtingudes de manera general, apunten que les proteïnes presents en l'ou canvien la seva estructura secundària al adherir-se als grans de pigment. La informació química, morfològica i mecànica obtinguda per les diferents tècniques d'anàlisi instrumental és consistent. Finalment, com a resultat de l'encreuament de les dades VMP amb els resultats obtinguts mitjançant FTIR, FESEM i AFM-nanoindentació, els senyals voltamperomètrics obtinguts es van associar a la reducció electroquímica dels pigments i als complexos formats amb el medi aglutinant. Aquests resultats van ser particularment rellevants en l'estudi del biodeteriori de les pel·lícules pictòriques inoculades, per tal de permetre la monitorització electroquímica de l'atac microbiològic.Ortiz Miranda, A. (2017). Development of analytical methods for the characterization of tempera paintings at micro- and nano-scale and their deterioration and biodeterioration processes [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/90571TESI

pSM19035: dissection of the plasmid partitioning machinery

Tesis doctoral inédita leída en la Universidad Autónoma de Madrid, Facultad de Ciencias, Departamento de Biología Molecular. Fecha de lectura: 09-11-201

Annotated Cell and Molecular Biology 5e: What We Know and How We Found Out

https://dc.uwm.edu/biosci_facbooks_bergtrom/1013/thumbnail.jp

Basic Cell and Molecular Biology 5e: What We Know and How We Find Out

https://dc.uwm.edu/biosci_facbooks_bergtrom/1014/thumbnail.jp