scholarly journals AdoMet radical proteins--from structure to evolution--alignment of divergent protein sequences reveals strong secondary structure element conservation

2004 ◽  
Vol 32 (13) ◽  
pp. 4015-4025 ◽  
Author(s):  
Y. Nicolet
Keyword(s):  
Secondary Structure ◽  
Protein Sequences ◽  
Secondary Structure Element

scholarly journals Extension of a de novo TIM barrel with a rationally designed secondary structure element

2021 ◽  
Vol 30 (5) ◽  
pp. 982-989
Author(s):  
Jonas Gregor Wiese ◽  
Sooruban Shanmugaratnam ◽  
Birte Höcker
Keyword(s):  
Secondary Structure ◽  
De Novo ◽  
Secondary Structure Element ◽  
Tim Barrel

scholarly journals Aligning Protein Sequences with Predicted Secondary Structure

2010 ◽  
Vol 17 (3) ◽  
pp. 561-580 ◽  
Author(s):  
John Kececioglu ◽  
Eagu Kim ◽  
Travis Wheeler
Keyword(s):  
Secondary Structure ◽  
Protein Sequences

УРОВНИ ИЕРАРХИЧЕСКОЙ ОРГАНИЗАЦИИ БЕЛКОВЫХ ПОСЛЕДОВАТЕЛЬНОСТЕЙ. АНАЛИЗ ЭНТРОПИЙНЫХ ХАРАКТЕРИСТИК

2020 ◽  
Vol 65 (6) ◽  
pp. 1065-1071
Author(s):  
А.Н. Некрасов ◽  
◽  
Ю.П. Козмин ◽  
С.В. Козырев ◽  
Н.Г. Есипова ◽  
...  
Keyword(s):  
Mathematical Method ◽  
Amino Acid ◽  
Secondary Structure ◽  
Protein Sequences ◽  
Amino Acid Residues ◽  
Homologous Protein ◽  
Levels Of Organization

This research investigates 24 647 non-homologous protein sequences. The occurrence profile of peptapeptides was constructed for every sequence and hierarchically organized elements of various sizes were revealed by a special mathematical method in each profile. The correlations between these hierarchical elements were analyzed and it was shown that in a tested set of protein sequences there are 11 levels of protein organization with elements ranging in length from 7 to 56 amino acid residues. It was suggested that the identified levels of organization correspond to elements of a super-secondary structure with different topology.

scholarly journals Evolution and conservation in human parechovirus genomes

2009 ◽  
Vol 90 (7) ◽  
pp. 1702-1712 ◽  
Author(s):  
Çiğdem H. Williams ◽  
Maria Panayiotou ◽  
Gareth D. Girling ◽  
Curtis I. Peard ◽  
Sami Oikarinen ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Detailed Analysis ◽  
Clinical Isolate ◽  
Complete Genome ◽  
Rna Secondary Structure ◽  
Protein Sequences ◽  
Human Parechovirus ◽  
Coding Regions ◽  
Structure Domain

Human parechoviruses (HPeVs) are frequent pathogens with a seroprevalance of over 90 % in adults. Recent studies on these viruses have increased the number of HPeV types to eight. Here we analyse the complete genome of one clinical isolate, PicoBank/HPeV1/a, and VP1 and 3D protein sequences of PicoBank/HPeV6/a, isolated from the same individual 13 months later. PicoBank/HPeV1/a is closely related to other recent HPeV1 isolates but is distinct from the HPeV1 Harris prototype isolated 50 years ago. The availability of an increasing number of HPeV sequences has allowed a detailed analysis of these viruses. The results add weight to the observations that recombination plays a role in the generation of HPeV diversity. An important finding is the presence of unexpected conservation of codons utilized in part of the 3D-encoding region, some of which can be explained by the presence of a phylogenetically conserved predicted secondary structure domain. This suggests that in addition to the cis-acting replication element, RNA secondary structure domains in coding regions play a key role in picornavirus replication.

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