Deciphering the free energy landscapes of SARS-CoV-2 wild type and Omicron variant interacting with human ACE2

被引：2

作者：

Lan, Pham Dang ^{[1
,2
]}

Nissley, Daniel A. ^{[3
]}

O'Brien, Edward P. ^{[4
,5
,6
]}

Nguyen, Toan T. ^{[7
,8
]}

Li, Mai Suan ^{[9
]}

机构：

[1] Quang Trung Software City, Tan Chanh Hiep Ward, Inst Computat Sci & Technol, Life Sci Lab, Dist 12, Ho Chi Minh City 729110, Vietnam

[2] Univ Sci, Fac Phys & Engn Phys, VNUHCM, 227 Nguyen Van Cu St,Dist 5, Ho Chi Minh City 749000, Vietnam

[3] Univ Oxford, Dept Stat, Oxford Prot Bioinformat Grp, Oxford OX1 2JD, England

[4] Penn State Univ, Dept Chem, University Pk, PA 16802 USA

[5] Penn State Univ, Huck Inst Life Sci, Bioinformat & Genom Grad Program, University Pk, PA 16802 USA

[6] Penn State Univ, Inst Computat & Data Sci, University Pk, PA 16802 USA

[7] Vietnam Natl Univ Hanoi, Univ Sci, Fac Phys, Key Lab Multiscale Simulat Complex Syst, 334 Nguyen Trai St, Hanoi 11400, Vietnam

[8] Vietnam Natl Univ Hanoi, Univ Sci, Fac Phys, Dept Theoret Phys, 334 Nguyen Trai St, Hanoi 11400, Vietnam

[9] Polish Acad Sci, Inst Phys, Al Lotnikow 32-46, PL-02668 Warsaw, Poland

来源：

JOURNAL OF CHEMICAL PHYSICS | 2024年 / 160卷 / 05期

关键词：

RECEPTOR-BINDING DOMAIN; ANTIBODY EVASION; PROTEIN; SPIKE; DYNAMICS; TRANSITION; ADHESION; MODELS; STATES; CELLS;

D O I：

10.1063/5.0188053

中图分类号：

O64 [物理化学（理论化学）、化学物理学];

学科分类号：

070304 ; 081704 ;

摘要：

The binding of the receptor binding domain (RBD) of the SARS-CoV-2 spike protein to the host cell receptor angiotensin-converting enzyme 2 (ACE2) is the first step in human viral infection. Therefore, understanding the mechanism of interaction between RBD and ACE2 at the molecular level is critical for the prevention of COVID-19, as more variants of concern, such as Omicron, appear. Recently, atomic force microscopy has been applied to characterize the free energy landscape of the RBD-ACE2 complex, including estimation of the distance between the transition state and the bound state, x(u). Here, using a coarse-grained model and replica-exchange umbrella sampling, we studied the free energy landscape of both the wild type and Omicron subvariants BA.1 and XBB.1.5 interacting with ACE2. In agreement with experiment, we find that the wild type and Omicron subvariants have similar xu values, but Omicron binds ACE2 more strongly than the wild type, having a lower dissociation constant K-D.

引用

页数：10

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