scholarly journals Identification of Secondary Structure of Extracellular Signal Regulated Kinase (ERK) Interacting Proteins and Their Domain: An in Silico Study

2021 ◽  
Vol 11 (01) ◽  
pp. 67-89
Author(s):  
Kurrey Khuleshwari ◽  
Paramanik Vijay
Keyword(s):  
Secondary Structure ◽  
In Silico ◽  
Interacting Proteins ◽  
Extracellular Signal Regulated Kinase ◽  
Extracellular Signal ◽  
In Silico Study

scholarly journals Nested plant LTR retrotransposons target specific regions of other elements, while all LTR retrotransposons often target palindromes and nucleosome-occupied regions: in silico study

Mobile DNA ◽  
2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Pavel Jedlicka ◽  
Matej Lexa ◽  
Ivan Vanat ◽  
Roman Hobza ◽  
Eduard Kejnovsky
Keyword(s):  
Secondary Structure ◽  
In Silico ◽  
Negative Impact ◽  
Nucleosome Occupancy ◽  
Ltr Retrotransposons ◽  
Sequence Composition ◽  
Plant Genomes ◽  
Weak Preference ◽  
In Silico Study ◽  
Impact On Family

Abstract Background Nesting is common in LTR retrotransposons, especially in large genomes containing a high number of elements. Results We analyzed 12 plant genomes and obtained 1491 pairs of nested and original (pre-existing) LTR retrotransposons. We systematically analyzed mutual nesting of individual LTR retrotransposons and found that certain families, more often belonging to the Ty3/gypsy than Ty1/copia superfamilies, showed a higher nesting frequency as well as a higher preference for older copies of the same family (“autoinsertions”). Nested LTR retrotransposons were preferentially located in the 3’UTR of other LTR retrotransposons, while coding and regulatory regions (LTRs) are not commonly targeted. Insertions displayed a weak preference for palindromes and were associated with a strong positional pattern of higher predicted nucleosome occupancy. Deviation from randomness in target site choice was also found in 13,983 non-nested plant LTR retrotransposons. Conclusions We reveal that nesting of LTR retrotransposons is not random. Integration is correlated with sequence composition, secondary structure and the chromatin environment. Insertion into retrotransposon positions with a low negative impact on family fitness supports the concept of the genome being viewed as an ecosystem of various elements.

In Silico Study of Structural and Geometrical Requirements of Natural Sesquiterpene Lactones with Trypanocidal Activity

2013 ◽  
Vol 13 (10) ◽  
pp. 1407-1414 ◽  
Author(s):  
L. Fabian ◽  
V. Sulsen ◽  
F. Frank ◽  
S. Cazorla ◽  
E. Malchiodi ◽  
...  
Keyword(s):  
In Silico ◽  
Sesquiterpene Lactones ◽  
Trypanocidal Activity ◽  
In Silico Study
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