3d structure prediction
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H-INDEX

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(FIVE YEARS 4)

2021 ◽  
pp. 21-56
Author(s):  
Sheikh Arslan Sehgal ◽  
Rana Adnan Tahir ◽  
Muhammad Waqas

2021 ◽  
Vol 22 (18) ◽  
pp. 9771
Author(s):  
Akhila Melarkode Vattekatte ◽  
Frédéric Cadet ◽  
Jean-Christophe Gelly ◽  
Alexandre G. de Brevern

In the particular case of the Camelidae family, immunoglobulin proteins have evolved into a unique and more simplified architecture with only heavy chains. The variable domains of these chains, named VHHs, have a number of Complementary Determining Regions (CDRs) reduced by half, and can function as single domains making them good candidates for molecular tools. 3D structure prediction of these domains is a beneficial and advantageous step to advance their developability as molecular tools. Nonetheless, the conformations of CDRs loops in these domains remain difficult to predict due to their higher conformational diversity. In addition to CDRs loop diversity, our earlier study has established that Framework Regions (FRs) are also not entirely conformationally conserved which establishes a need for more rigorous analyses of these regions that could assist in template selection. In the current study, VHHs models using different template selection strategies for comparative modeling using Modeller have been extensively assessed. This study analyses the conformational changes in both CDRs and FRs using an original strategy of conformational discretization based on a structural alphabet. Conformational sampling in selected cases is precisely reported. Some interesting outcomes of the structural analyses of models also draw attention towards the distinct difficulty in 3D structure prediction of VHH domains.


Ribozymes ◽  
2021 ◽  
pp. 861-881
Author(s):  
Pritha Ghosh ◽  
Chandran Nithin ◽  
Astha Joshi ◽  
Filip Stefaniak ◽  
Tomasz K. Wirecki ◽  
...  

2021 ◽  
Author(s):  
Li Yuan ◽  
Zhi-Hao Guo ◽  
Wen-Jie Cao ◽  
Yong Luo ◽  
Ya-Zhou Shi

Toxins ◽  
2020 ◽  
Vol 12 (9) ◽  
pp. 538
Author(s):  
Rosario Iglesias ◽  
Letizia Polito ◽  
Massimo Bortolotti ◽  
Manuela Pedrazzi ◽  
Lucía Citores ◽  
...  

Stenodactylin is one of the most potent type 2 ribosome-inactivating proteins (RIPs); its high toxicity has been demonstrated in several models both in vitro and in vivo. Due to its peculiarities, stenodactylin could have several medical and biotechnological applications in neuroscience and cancer treatment. In this work, we report the complete amino acid sequence of stenodactylin and 3D structure prediction. The comparison between the primary sequence of stenodactylin and other RIPs allowed us to identify homologies/differences and the amino acids involved in RIP toxic activity. Stenodactylin RNA was isolated from plant caudex, reverse transcribed through PCR and the cDNA was amplificated and cloned into a plasmid vector and further analyzed by sequencing. Nucleotide sequence analysis showed that stenodactylin A and B chains contain 251 and 258 amino acids, respectively. The key amino acids of the active site described for ricin and most other RIPs are also conserved in the stenodactylin A chain. Stenodactylin amino acid sequence shows a high identity degree with volkensin (81.7% for A chain, 90.3% for B chain), whilst when compared with other type 2 RIPs the identity degree ranges from 27.7 to 33.0% for the A chain and from 42.1 to 47.7% for the B chain.


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