Studying the Effects of ACE2 Mutations on the Stability, Dynamics, and Dissociation Process of SARS-CoV-2 S1/hACE2 Complexes

被引:16
作者
Hadi-Alijanvand, Hamid [1 ]
Rouhani, Maryam [1 ]
机构
[1] Inst Adv Studies Basic Sci IASBS, Dept Biol Sci, Zanjan 4513766731, Iran
关键词
SARS-CoV-2; ACE2; polymorphism; Iranian ethnic groups; adaptive biasing force; ACE2 closed state; binding affinity; ANGIOTENSIN-CONVERTING ENZYME; RESPIRATORY-SYNDROME-CORONAVIRUS; SPIKE PROTEIN; SARS-CORONAVIRUS; FUNCTIONAL RECEPTOR; MOLECULAR-DYNAMICS; WEB SERVER; HOST-RANGE; BINDING; GLYCOPROTEIN;
D O I
10.1021/acs.jproteome.0c00348
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
A highly infectious coronavirus, SARS-CoV-2, has spread in many countries. This virus recognizes its receptor, angiotensin-converting enzyme 2 (ACE2), using the receptor binding domain of its spike protein subunit S1. Many missense mutations are reported in various human populations for the ACE2 gene. In the current study, we predict the affinity of many ACE2 variants for binding to S1 protein using different computational approaches. The dissociation process of S1 from some variants of ACE2 is studied in the current work by molecular dynamics approaches. We study the relation between structural dynamics of ACE2 in closed and open states and its affinity for S1 protein of SARS-CoV-2.
引用
收藏
页码:4609 / 4623
页数:15
相关论文
共 83 条
[51]   Retroviruses pseudotyped with the severe acute respiratory syndrome coronavirus spike protein efficiently infect cells expressing angiotensin-converting enzyme 2 [J].
Moore, MJ ;
Dorfman, T ;
Li, WH ;
Wong, SK ;
Li, YH ;
Kuhn, JH ;
Coderre, J ;
Vasilieva, N ;
Han, ZC ;
Greenough, TC ;
Farzan, M ;
Choe, H .
JOURNAL OF VIROLOGY, 2004, 78 (19) :10628-10635
[52]   Interaction of the spike protein RBD from SARS-CoV-2 with ACE2: Similarity with SARS-CoV, hot-spot analysis and effect of the receptor polymorphism [J].
Othman, Houcemeddine ;
Bouslama, Zied ;
Brandenburg, Jean-Tristan ;
da Rocha, Jorge ;
Hamdi, Yosr ;
Ghedira, Kais ;
Srairi-Abid, Najet ;
Hazelhurst, Scott .
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 2020, 527 (03) :702-708
[53]   SAAMBE-3D: Predicting Effect of Mutations on Protein-Protein Interactions [J].
Pahari, Swagata ;
Li, Gen ;
Murthy, Adithya Krishna ;
Liang, Siqi ;
Fragoza, Robert ;
Yu, Haiyuan ;
Alexov, Emil .
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 2020, 21 (07)
[54]   Coronaviruses post-SARS: update on replication and pathogenesis [J].
Perlman, Stanley ;
Netland, Jason .
NATURE REVIEWS MICROBIOLOGY, 2009, 7 (06) :439-450
[55]   Severe respiratory SARS-CoV2 infection: Does ACE2 receptor matter? [J].
Perrotta, Fabio ;
Matera, Maria Gabriella ;
Cazzola, Mario ;
Bianco, Andrea .
RESPIRATORY MEDICINE, 2020, 168
[56]   Scalable molecular dynamics with NAMD [J].
Phillips, JC ;
Braun, R ;
Wang, W ;
Gumbart, J ;
Tajkhorshid, E ;
Villa, E ;
Chipot, C ;
Skeel, RD ;
Kalé, L ;
Schulten, K .
JOURNAL OF COMPUTATIONAL CHEMISTRY, 2005, 26 (16) :1781-1802
[57]  
Procko E., 2020, bioRxiv, DOI DOI 10.1101/2020.03.16.994236
[58]   Identification of two critical amino acid residues of the severe acute respiratory syndrome coronavirus spike protein for its variation in zoonotic tropism transition via a double substitution strategy [J].
Qu, XX ;
Hao, P ;
Song, XJ ;
Jiang, SM ;
Liu, YX ;
Wang, PG ;
Rao, X ;
Song, HD ;
Wang, SY ;
Zuo, Y ;
Zheng, AH ;
Luo, M ;
Wang, HL ;
Deng, F ;
Wang, HZ ;
Hu, ZH ;
Ding, MX ;
Zhao, GP ;
Deng, HK .
JOURNAL OF BIOLOGICAL CHEMISTRY, 2005, 280 (33) :29588-29595
[59]   Assessing the efficiency of free energy calculation methods [J].
Rodriguez-Gomez, D ;
Darve, E ;
Pohorille, A .
JOURNAL OF CHEMICAL PHYSICS, 2004, 120 (08) :3563-3578
[60]   The N-terminal region of the murine coronavirus spike glycoprotein is associated with the extended host range of viruses from persistently infected murine cells [J].
Schickli, JH ;
Thackray, LB ;
Sawicki, SG ;
Holmes, KV .
JOURNAL OF VIROLOGY, 2004, 78 (17) :9073-9083