hydrophobic clustering
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eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Jennifer E James ◽  
Sara M Willis ◽  
Paul G Nelson ◽  
Catherine Weibel ◽  
Luke J Kosinski ◽  
...  

Extant protein-coding sequences span a huge range of ages, from those that emerged only recently, to those present in the last universal common ancestor. Because evolution has had less time to act on young sequences, there might be 'phylostratigraphy' trends in any properties that evolve slowly with age. A long-term reduction in hydrophobicity and hydrophobic clustering was found in previous, taxonomically restricted studies. Here we perform integrated phylostratigraphy across 435 fully sequenced species, using sensitive HMM methods to detect protein domain homology. We find that the reduction in hydrophobic clustering is universal across lineages. However, only young animal domains have a tendency to have higher structural disorder. Among ancient domains, trends in amino acid composition reflect the order of recruitment into the genetic code, suggesting that the composition of the contemporary descendants of ancient sequences reflects amino acid availability during the earliest stages of life, when these sequences first emerged.


Author(s):  
Jennifer E James ◽  
Sara M Willis ◽  
Paul G Nelson ◽  
Catherine Weibel ◽  
Luke J Kosinski ◽  
...  

AbstractExtant protein-coding sequences span a huge range of ages, from those that emerged only recently in particular lineages, to those present in the last universal common ancestor. Because evolution has had less time to act on young sequences, there might be “phylostratigraphy” trends in any properties that evolve slowly with age. Indeed, a long-term reduction in hydrophobicity and in hydrophobic clustering has been found in previous, taxonomically restricted studies. Here we perform integrated phylostratigraphy across 435 fully sequenced and dated eukaryotic species, using sensitive HMM methods to detect homology of protein domains (which may vary in age within the same gene), and applying a variety of quality filters. We find that the reduction in hydrophobic clustering is universal across diverse lineages, showing limited sign of saturation. But the tendency for young domains to have higher protein structural disorder, driven primarily by more hydrophilic amino acids, is found only among young animal domains, and not young plant domains, nor ancient domains predating the existence of the last eukaryotic common ancestor. Among ancient domains, trends in amino acid composition reflect the order of recruitment into the genetic code, suggesting that events during the earliest stages of life on earth continue to have an impact on the composition of ancient sequences.


2018 ◽  
Vol 8 (1) ◽  
Author(s):  
Jaesung Kim ◽  
Se Pyeong Im ◽  
Jung Seok Lee ◽  
Jassy Mary S. Lazarte ◽  
Si Won Kim ◽  
...  

2016 ◽  
Vol 55 (23) ◽  
pp. 6563-6563
Author(s):  
Somenath Garai ◽  
Hartmut Bögge ◽  
Alice Merca ◽  
Olga A. Petina ◽  
Alina Grego ◽  
...  

2016 ◽  
Vol 128 (23) ◽  
pp. 6673-6673
Author(s):  
Somenath Garai ◽  
Hartmut Bögge ◽  
Alice Merca ◽  
Olga A. Petina ◽  
Alina Grego ◽  
...  

2016 ◽  
Vol 128 (23) ◽  
pp. 6746-6749 ◽  
Author(s):  
Somenath Garai ◽  
Hartmut Bögge ◽  
Alice Merca ◽  
Olga A. Petina ◽  
Alina Grego ◽  
...  

2016 ◽  
Vol 55 (23) ◽  
pp. 6634-6637 ◽  
Author(s):  
Somenath Garai ◽  
Hartmut Bögge ◽  
Alice Merca ◽  
Olga A. Petina ◽  
Alina Grego ◽  
...  

2013 ◽  
Vol 32 (6) ◽  
pp. 899-915 ◽  
Author(s):  
Biswa Ranjan Meher ◽  
Mattaparthi Venkata Satish Kumar ◽  
Pradipta Bandyopadhyay

Biochemistry ◽  
2003 ◽  
Vol 42 (29) ◽  
pp. 8687-8695 ◽  
Author(s):  
Karin A. Crowhurst ◽  
Julie D. Forman-Kay

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