Serum C-reactive protein (CRP) is used as a marker of inflammation in several diseases including autoimmune disease and cardiovascular disease. CRP, a member of the pentraxin family, is comprised of five identical subunits. CRP has diverse ligand-binding properties which depend upon different structural states of CRP. However, little is known about the molecular dynamics and interaction properties of CRP. In this study, we used SAPS, SCRATCH protein predictor, PDBsum, ConSurf, ProtScale, Drawhca, ASAView, SCide and SRide server and performed comprehensive analyses of molecular dynamics, protein-protein and residue-residue interactions of CRP. We used 1GNH.pdb file for the crystal structure of human CRP which generated two pentamers (ABCDE and FGHIJ). The number of residues involved in residue-residue interactions between A-B, B-C, C-D, D-E, F-G, G-H, H-I, I-J, A-E and F-J subunits were 12, 11, 10, 11, 12, 11, 10, 11, 10 and 10, respectively. Fifteen antiparallel β sheets were involved in β-sheet topology, and five β hairpins were involved in forming the secondary structure. Analysis of hydrophobic segment distribution revealed deviations in surface hydrophobicity at different cavities present in CRP. Approximately 33 % of all residues were involved in the stabilization centers. We show that the bioinformatics tools can provide a rapid method to predict molecular dynamics and interaction properties of CRP. Our prediction of molecular dynamics and interaction properties of CRP combined with the modeling data based on the known 3D structure of CRP is helpful in designing stable forms of CRP mutants for structure-function studies of CRP and may facilitate in silico drug design for therapeutic targeting of CRP.

Serum C-reactive protein (CRP) is used as a marker of inflammation in several diseases including autoimmune disease and cardiovascular disease. CRP, a member of the pentraxin family, is comprised of five identical subunits. CRP has diverse ligand-binding properties which depend upon different structural states of CRP. However, little is known about the molecular dynamics and interaction properties of CRP. In this study, we used SAPS, SCRATCH protein predictor, PDBsum, ConSurf, ProtScale, Drawhca, ASAView, SCide and SRide server and performed comprehensive analyses of molecular dynamics, protein-protein and residue-residue interactions of CRP. We used 1GNH.pdb file for the crystal structure of human CRP which generated two pentamers (ABCDE and FGHIJ). The number of residues involved in residue-residue interactions between A-B, B-C, C-D, D-E, F-G, G-H, H-I, I-J, A-E and F-J subunits were 12, 11, 10, 11, 12, 11, 10, 11, 10 and 10, respectively. Fifteen antiparallel β sheets were involved in β-sheet topology, and five β hairpins were involved in forming the secondary structure. Analysis of hydrophobic segment distribution revealed deviations in surface hydrophobicity at different cavities present in CRP. Approximately 33 % of all residues were involved in the stabilization centers. We show that the bioinformatics tools can provide a rapid method to predict molecular dynamics and interaction properties of CRP. Our prediction of molecular dynamics and interaction properties of CRP combined with the modeling data based on the known 3D structure of CRP is helpful in designing stable forms of CRP mutants for structure-function studies of CRP and may facilitate in silico drug design for therapeutic targeting of CRP.

Submitted by Eunice Novais (enovais@uepg.br) on 2018-06-28T19:18:21Z No. of bitstreams: 2 license_rdf: 811 bytes, checksum: e39d27027a6cc9cb039ad269a5db8e34 (MD5) Talita Rosas Ferreira.pdf: 3918159 bytes, checksum: 3af8401f079b1540a49f10a3f6fd3b2d (MD5) / Made available in DSpace on 2018-06-28T19:18:21Z (GMT). No. of bitstreams: 2 license_rdf: 811 bytes, checksum: e39d27027a6cc9cb039ad269a5db8e34 (MD5) Talita Rosas Ferreira.pdf: 3918159 bytes, checksum: 3af8401f079b1540a49f10a3f6fd3b2d (MD5) Previous issue date: 2018-04-23 / No presente estudo, foram investigados os efeitos da calagem superficial sobre: os atributos químicos, as propriedades de interação com a radiação e a estrutura (sistema poroso) de um Cambissolo Háplico alumínico. A estrutura do solo foi analisada em escala micrométrica, considerando monólitos (8×8×8 cm) e pequenos agregados do solo (2-4 e 1-2 mm de diâmetro). O experimento consistia de cinco faixas, uma delas em área de pasto, considerada como referência (REF) e representando as condições do solo antes da implementação do sistema de plantio direto (SPD), e as demais, sob SPD, receberam as seguintes doses de calcário: 0 (C0), 10 (C10), 15 (C15) e 20 (C20) t ha-1 aplicadas na superfície do solo. A coleta das amostras se deu aos trinta meses após o procedimento de calagem, nas camadas 0-10 cm (A) e 10-20 cm (B). Os atributos químicos do solo foram caracterizados de acordo com procedimentos experimentais padrões e a composição de óxidos do solo, obtida por meio de análise de espectroscopia de fluorescência de raios X (FRX), foi usada para o cálculo do coeficiente de atenuação de massa do solo (μm), por meio do código computacional XCOM, para as energias de ≈ 60 keV (241Am) e ≈ 662 keV (137Cs). Os valores de μm foram utilizados para calcular as demais propriedades de interação da radiação com o solo e para simular as variações causadas na densidade (D) e porosidade total (Pt) do solo. Para a análise da estrutura do solo, foram utilizadas imagens 3D de microtomografia computadorizada de raios X (μTC), com resolução espacial de 60 μm (monólitos), e de μTC utilizando radiação síncrotron (μTC-RS), com resolução espacial de 1,64 μm (agregados). A visualização, processamento e análise das imagens foram realizadas com o software Avizo Fire. Foram determinadas as seguintes propriedades micromorfológicas e geométricas: porosidade baseada na imagem (P’), número de poros (NP), distribuições de P’ e NP em função de intervalos de volume, comprimento, alongamento, formato, conectividade e tortuosidade dos poros (monólitos); e: P’, distribuições de P’ e NP em função de intervalos de volume, conectividade, tortuosidade e dimensão fractal (agregados). Complementarmente, a composição elementar dos agregados do solo foi avaliada por meio de medidas de FRX. Na maioria dos casos, os efeitos da calagem concentraram-se na camada A, onde houve melhora nos atributos químicos e, portanto, no grau de acidez do solo, bem como houve aumento nas propriedades de interação da radiação em função das doses de calcário. O aumento nas propriedades de interação da radiação foi mais acentuado para a energia de ≈ 60 keV em relação a ≈ 662 keV e, no primeiro caso, as mudanças causadas em μm promoveram variação considerável na D e Pt do solo, demonstrando a relevância do estudo. A exemplo dos efeitos da calagem sobre o sistema poroso de monólitos do solo, na camada A, ressalta-se o aumento de P’ e do número de poros em que o poro principal foi separado, os quais foram identificados como sendo mais alongados e mais conectados devido à calagem. A calagem promoveu ainda alterações no arranjo dos poros separados, em ambas as camadas, com a formação de poros cilíndricos na direção horizontal, o que pode ser atribuído ao estímulo da atividade da fauna do solo. Para os agregados de solo, na camada A, a porcentagem de cálcio foi elevada a um valor mais alto em agregados de 1-2 mm em comparação com aqueles de 2-4 mm, em função das doses de calcário. A calagem afetou negativamente a estrutura de pequenos agregados do solo, diminuindo a P’ e aumentando a tortuosidade de poros para agregados de 1-2 mm. Além disso, a calagem reduziu a dimensão fractal em agregados de ambas as classes de tamanhos, em acordo com o fato de que, com a calagem, poros maiores foram substituídos por poros menores em agregados de 1-2 mm, conforme análises de natureza quantitativa e qualitativa. / In the present study, effects of surface liming on: chemical attributes, soil-radiation interaction properties and the structure (porous system) of a Dystrudept soil were investigated. The soil structure was analyzed in micrometric scale, considering monoliths (8×8×8 cm) and tiny aggregates (2-4 and 1-2 mm in diameter). The trial consisted of five stripes, one of them under pasture, considered here as reference (REF), representing the soil conditions before the no-till system (NTS) implementation, and the remaining, under NTS, received the following lime rates: 0 (C0), 10 (C10), 15 (C15) and 20 (C20) t ha-1 on the soil surface. Samples were collected thirty months after the liming procedure, at the 0-10 cm (A) and 10-20 cm (B) soil layers. The soil chemical attributes were characterized according to standard experimental procedures and the soil oxide composition, obtained by X-ray fluorescence spectroscopy (XRF), was used for the calculation of the soil mass attenuation coefficient (μm), by means of the computer code XCOM, for the energies of ≈ 60 keV (241Am) amd ≈ 662 keV (137Cs). The μm values were used to calculate the remaining soil-radiation interaction properties and to simulate variations caused on soil density (D) and total porosity (Pt). For the soil structure analysis, 3D images of X-ray computed microtomography (μCT), with spatial resolution of 60 μm (monoliths), and 3D images of synchrotron radiation based X-ray computed microtomography (SR-μCT), with spatial resolution of 1,64 μm (aggregates) were used. The image visualization, processing and analysis were performed in the Avizo Fire software. The following micromorphological and geometrical properties were determined: image-based porosity (P’), number of pores (NP), distributions of P’ and NP as function of volume intervals, length, elongation, shape, connectivity, and tortuosity of pores (monoliths); and: P’, distributions of P’ and NP as function of volume intervals, connectivity, tortuosity, and fractal dimension (aggregates). Additionally, the elemental composition of the soil aggregates was evaluated by XRF. In the majority of cases, liming effects were concentrated at layer A, where there was an improvement of soil chemical attributes and, therefore, of soil acidity level, as well as there was an increase in the soil-radiation interaction properties as function of lime rates. The increase in soil-radiation interaction properties was more accentuated for the energy of ≈ 60 keV in relation to ≈ 662 keV and, in the former case, the μm variation promoted considerable variation in D and Pt, demonstrating the relevance of the study. Highlighted instances of liming effects on the porous system of the soil monoliths, at layer A, were an increase in P’ and in the number of pores into which the main soil pore was separated, which were identified as being longer and more connected due to liming. Moreover, liming promoted changes in the arrangement of the separated pores, at both soil layers, with the formation of cylindrical pores in the horizontal orientation, which can be attributed to stimulation of the soil fauna activity. Regarding the soil aggregates, at layer A, calcium was raised to a higher percentage in aggregates of 1-2 mm when compared to those of 2-4 mm, as function of the lime rates. Liming affected negatively the structure of the soil tiny aggregates, decreasing P’ and increasing the tortuosity of pores for 1-2 mm aggregates. Besides, liming decreased the fractal dimension in aggregates from both size classes, in accord to the fact that, with liming, larger pores were replaced by smaller ones in 1-2 mm aggregates, as both quantitatively and qualitatively analyzed.