scholarly journals Comprehensive Secondary Structure Elucidation of Four Genera of the Family Pospiviroidae

PLoS ONE ◽  
2014 ◽  
Vol 9 (6) ◽  
pp. e98655 ◽  
Author(s):  
Tamara Giguère ◽  
Charith Raj Adkar-Purushothama ◽  
Jean-Pierre Perreault
2018 ◽  
Vol 3 (02) ◽  
pp. 150-157
Author(s):  
Asad Amir ◽  
Neelesh Kapoor ◽  
Hirdesh Kumar ◽  
Mohd. Tariq ◽  
Mohd. Asif Siddiqui

Sandalwood is a commercially and culturally important plant species belonging to the family Santalaceae and the genus Santalum. In Indian sandalwood is renowned for its oil, which is highly rated for its sweet, fragrant, persistent aroma and the fixative property which is highly demanded by the perfume industry. For better production and varieties, requires to understanding the functions of proteins, their analysis and characterization of proteins sequences and their structures, their localizations in cell and their interaction with other functional partner. Due to limited number of in silico studies on sandalwood, in the present study we have performed in silico analysis by characterization of sandalwood proteins. Total 23 proteins were obtained and characterization using UniProtKB, identifying their physico-chemical parameters using ProtParam tool and prediction of their secondary structure elements using GOR of all 23 proteins.


2021 ◽  
Author(s):  
◽  
Joanna M Wojnar

<p>This study describes the isolation and structure elucidation of several known and 13 new compounds from New Zealand marine organisms. Furthermore, it describes the development of a digital mask program for the analysis of HSQC spectra of crude sponge extracts. This was used as a screening tool to identify secondary metabolite producers that warranted further analysis. As reports of metabolites from New Zealand nudibranchs are poorly represented in the literature, a study of five New Zealand nudibranch species was undertaken. These coloured and seemingly undefended nudibranchs are known to concentrate or sequester toxic metabolites from their prey, facilitating rapid isolation and structure elucidation of these metabolites. This study resulted in the isolation of a variety of metabolite classes; two new compounds, 13alpha- acetoxypukalide diol (30) and lopholide diol (31) from the nudibranch Tritonia incerta, are described. Examination of the sponge Raspailia agminata resulted in the isolation of a novel family of partially acetylated glycolipids which contain up to six glucose residues. The chromatographic separation of these compounds was a challenge due to the similarity of the congeners and their lack of a chromophore. MSguided isolation eventually led to the purification of agminosides A-E (145-149). An unidentified sponge of the order Dictyoceratida was found to contain a new isomer (186) of the known sesterterpene variabilin. As variabilin-type compounds are predominantly found from sponges of the family Irciniidae, the unidentified sponge is most likely an irciniid. In addition, the sponge contained two prenylated quinones, one of which, 189, is a new isomer of a known sponge metabolite. The sponge Darwinella oxeata contained four new nitrogenous diterpenes of the aplysulphurane (rearranged spongian) skeleton, oxeatamide A (214), isooxeatamide A (215), oxeatamide A 23-methyl ester (216) and oxeatamide B (217).</p>


Author(s):  
Felix Freire ◽  
Juan José Tarrío ◽  
Rafael Rodríguez ◽  
Berta Fernández ◽  
Emilio Quiñoá

2007 ◽  
Vol 72 (4) ◽  
pp. 1218-1225 ◽  
Author(s):  
Hirotsugu Kobayashi ◽  
Jun'ichiro Ohashi ◽  
Tsuyoshi Fujita ◽  
Takashi Iwashita ◽  
Yoichi Nakao ◽  
...  

2012 ◽  
Vol 47 (10) ◽  
pp. 1479-1487 ◽  
Author(s):  
Sanjay Kumar Singh ◽  
Santosh Kumar Singh ◽  
Vinayak Ram Tripathi ◽  
Satyendra Kumar Garg

2014 ◽  
Vol 106 (2) ◽  
pp. 384a
Author(s):  
Thomas Lane ◽  
Derek Mendez ◽  
Jongmin Sung ◽  
Daniel Ratner ◽  
Herschel Watkins ◽  
...  

2020 ◽  
Author(s):  
Adam Midlik ◽  
Veronika Navrátilová ◽  
Taraka Ramji Moturu ◽  
Jaroslav Koča ◽  
Radka Svobodová ◽  
...  

AbstractMotivationProtein structural families are groups of homologous proteins defined by the organization of secondary structure elements (SSEs). Nowadays, many families contain vast numbers of homologous structures and the SSEs can help to orient within them. Communities around specific protein families have even developed specialized SSE annotations, assigning always the same name to the equivalent SSEs in homologous proteins. A detailed analysis of the groups of equivalent SSEs and their variability provides an overview of the studied protein family and can be used to enrich the analysis of a particular protein at hand.ResultsWe developed a workflow for analysis of the secondary structure anatomy of a protein family, based on SSE annotation tool SecStrAnnotator. We applied this analysis to the model family of cytochromes P450 (CYPs) – a family of important biotransformation enzymes with a community-wide used SSE annotation. We report the occurrence, typical length and amino acid sequence for the equivalent SSE groups, as well as the conservation/variability of these properties. We also suggest a generic residue numbering scheme for the CYP family. The comparison between the bacterial and eukaryotic part of the family highlights the major differences and reveals an anomalous group of bacterial CYPs with some typically eukaryotic features. This hints at possible evolutionary and functional relationships.AvailabilityThe software and data are available at https://webchem.ncbr.muni.cz/Wiki/[email protected], [email protected]


Cells ◽  
2022 ◽  
Vol 11 (2) ◽  
pp. 230
Author(s):  
Kevin-Phil Wüsthoff ◽  
Gerhard Steger

In 1985, Keese and Symons proposed a hypothesis on the sequence and secondary structure of viroids from the family : their secondary structure can be subdivided into five structural and functional domains and “viroids have evolved by rearrangement of domains between different viroids infecting the same cell and subsequent mutations within each domain”; this article is one of the most cited in the field of viroids. Employing the pairwise alignment method used by Keese and Symons and in addition to more recent methods, we tried to reproduce the original results and extent them to further members of which were unknown in 1985. Indeed, individual members of consist of a patchwork of sequence fragments from the family but the lengths of fragments do not point to consistent points of rearrangement, which is in conflict with the original hypothesis of fixed domain borders.


2022 ◽  
Author(s):  
Felix Freire ◽  
Juan José Tarrío ◽  
Rafael Rodríguez ◽  
Berta Fernández ◽  
Emilio Quiñoá

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