Molecular dynamic analyses of the interaction of SARS-CoV-1 or 2 variants with various angiotensin-converting enzyme-2 species

被引:3
作者
Aloufi, Abeer S. [1 ]
El-Arabey, Amr Ahmed [2 ]
Eltayb, Wafa Ali [3 ]
Elsayim, Rasha [4 ]
Marenga, Hanin S. [5 ]
Modafer, Yosra [6 ]
Awadalla, Maaweya E. [7 ]
Mohapatra, Pranab K. [8 ]
Mohapatra, Ranjan K. [9 ]
Abdalla, Mohnad [10 ]
机构
[1] Princess Nourah Bint Abdulrahman Univ, Coll Sci, Dept Biol, Riyadh, Saudi Arabia
[2] Al Azhar Univ, Fac Pharm, Dept Pharmacol & Toxicol, Cairo, Egypt
[3] Shendi Univ, Fac Sci & Technol, Biotechnol Dept, Shendi, Nher Anile, Sudan
[4] King Saud Univ, Coll Sci, Dept Bot & Microbiol, Riyadh, Saudi Arabia
[5] King Saud Univ, Coll Pharm, Dept Pharmaceut Chem, Riyadh, Saudi Arabia
[6] Jazan Univ, Fac Sci, Dept Biol, Jazan, Saudi Arabia
[7] King Fahad Med City, Res Ctr, Riyadh, Saudi Arabia
[8] CV Raman Global Univ, Dept Chem, Bhubaneswar, Odisha, India
[9] Govt Coll Engn, Dept Chem, Keonjhar 758002, Odisha, India
[10] Shandong Univ, Childrens Hosp, Pediat Res Inst, Jinan 250022, Peoples R China
关键词
ACE2; SARS-CoV-2; molecular dynamics simulation; RBD; ACCESSIBLE SURFACE-AREA; RECEPTOR; PROTEIN; BINDING;
D O I
10.1080/07391102.2024.2314745
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
The transmembrane glycoprotein angiotensin-converting enzyme 2 (ACE2) is a key component of the renin-angiotensin system (RAS). It was shown to be the receptor of severe acute respiratory syndrome coronavirus 2 in the COVID-19 outbreak (SARS-COV-2). Furthermore, ACE2 aids in the transport of amino acids across the membrane. ACE2 is lost from the membrane, resulting in soluble ACE2 (sACE2). We aim to examine the structural conformation alterations between SARS-CoV-1 or 2 variants at various periods with ACE2 from various sources, particularly in the area where it interacts with the viral protein and the receptor. It is important to study the molecular dynamics of ACE2/SARS-COV RBD when the structure is available on the database. Here we analyzed the crystal structure of ACE2 from Human, Dog, Mus, Cat, and Bat ACE2 in complex with RBD from SARS-COV-1 and SARS-COV-2. The result shows, there is a variation in the type of residues, number of contact atoms and hydrogen bonds in ACE2 and RBD during the interaction interfaces. By using molecular dynamics simulation, we can measure RMSD, RMSF, SASA, Rg and the difference in the percentage of alpha helix and beta strand. As bat ACE2 & SARS-CoV-2 RBD found to have a high amount of beta strand compared to another structure complex, while hACE2 & SARS-CoV-1 RBD has fewer amounts of beta strand. Our study provides a deep view of the structure which is available and a summary of many works around ACE2/SARS-CoV RBD interaction.Communicated by Ramaswamy H. Sarma
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页数:10
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