A simple method for the calculation of low energy packings of α-helices—A threshold approximation. I. The use of the method to estimate the effects of amino acid substitutions, deletions and insertions in globins

1984 ◽  
Vol 110 (1) ◽  
pp. 67-91 ◽  
Author(s):  
Victor V. Solovyov ◽  
Nicolay A. Kolchanov
2021 ◽  
Author(s):  
Kazutaka Katoh ◽  
Daron M. Standley

Abstract The ability to predict emerging variants of SARS-CoV-2 would be of enormous value, as it would enable proactive design of vaccines in advance of such emergence. Based on molecular evolutionary analysis of S protein, we found a significant correspondence in the location of amino acid substitutions between SARS-CoV-2 variants recently emerging and their relatives that infected bat and pangolin before the pandemic. This observation suggests that a limited number of sites in this protein are repeatedly substituted in independent lineages of this group of viruses. It follows, therefore, that the sites of future emerging mutations in SARS-CoV-2 can be predicted by analyzing their relatives (outgroups) that have infected non-human hosts. We discuss a possible evolutionary mechanism behind these substitutions and provide a list of frequently substituted sites that potentially include future emerging variants in SARS-CoV-2.


1992 ◽  
Vol 68 (06) ◽  
pp. 672-677 ◽  
Author(s):  
Hitoshi Yahara ◽  
Keiji Matsumoto ◽  
Hiroyuki Maruyama ◽  
Tetsuya Nagaoka ◽  
Yasuhiro Ikenaka ◽  
...  

SummaryTissue-type plasminogen activator (t-PA) is a fibrin-specific agent which has been used to treat acute myocardial infarction. In an attempt to clarify the determinants for its rapid clearance in vivo and high affinity for fibrin clots, we produced five variants containing amino acid substitutions in the finger domain, at amino acid residues 7–9, 10–14, 15–19, 28–33, and 37–42. All the variants had a prolonged half-life and a decreased affinity for fibrin of various degrees. The 37–42 variant demonstrated about a 6-fold longer half-life with a lower affinity for fibrin. Human plasma clot lysis assay estimated the fibrinolytic activity of the 37–42 variant to be 1.4-fold less effective than that of the wild-type rt-PA. In a rabbit jugular vein clot lysis model, doses of 1.0 and 0.15 mg/kg were required for about 70% lysis in the wild-type and 37–42 variant, respectively. Fibrinogen was degraded only when the wild-type rt-PA was administered at a dose of 1.0 mg/kg. These findings suggest that the 37–42 variant can be employed at a lower dosage and that it is a more fibrin-specific thrombolytic agent than the wild-type rt-PA.


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