Molecular architecture and dynamics of SARS-CoV-2 envelope by integrative modeling
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Molecular architecture and dynamics of SARS-CoV-2 envelope by integrative modeling. / Pezeshkian, Weria; Grunewald, Fabian; Narykov, Oleksandr; Lu, Senbao; Arkhipova, Valeria; Solodovnikov, Alexey; Wassenaar, Tsjerk A.; Marrink, Siewert J.; Korkin, Dmitry.
I: Structure, Bind 31, Nr. 4, 06.04.2023, s. 492-50.Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › fagfællebedømt
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TY - JOUR
T1 - Molecular architecture and dynamics of SARS-CoV-2 envelope by integrative modeling
AU - Pezeshkian, Weria
AU - Grunewald, Fabian
AU - Narykov, Oleksandr
AU - Lu, Senbao
AU - Arkhipova, Valeria
AU - Solodovnikov, Alexey
AU - Wassenaar, Tsjerk A.
AU - Marrink, Siewert J.
AU - Korkin, Dmitry
PY - 2023/4/6
Y1 - 2023/4/6
N2 - Despite tremendous efforts, the exact structure of SARS-CoV-2 and related betacoronaviruses remains elusive. SARS-CoV-2 envelope is a key structural component of the virion that encapsulates viral RNA. It is composed of three structural proteins, spike, membrane (M), and envelope, which interact with each other and with the lipids acquired from the host membranes. Here, we developed and applied an integrative multi -scale computational approach to model the envelope structure of SARS-CoV-2 with near atomistic detail, focusing on studying the dynamic nature and molecular interactions of its most abundant, but largely under-studied, M protein. The molecular dynamics simulations allowed us to test the envelope stability under different configurations and revealed that the M dimers agglomerated into large, filament-like, macromolec-ular assemblies with distinct molecular patterns. These results are in good agreement with current experi-mental data, demonstrating a generic and versatile approach to model the structure of a virus de novo.
AB - Despite tremendous efforts, the exact structure of SARS-CoV-2 and related betacoronaviruses remains elusive. SARS-CoV-2 envelope is a key structural component of the virion that encapsulates viral RNA. It is composed of three structural proteins, spike, membrane (M), and envelope, which interact with each other and with the lipids acquired from the host membranes. Here, we developed and applied an integrative multi -scale computational approach to model the envelope structure of SARS-CoV-2 with near atomistic detail, focusing on studying the dynamic nature and molecular interactions of its most abundant, but largely under-studied, M protein. The molecular dynamics simulations allowed us to test the envelope stability under different configurations and revealed that the M dimers agglomerated into large, filament-like, macromolec-ular assemblies with distinct molecular patterns. These results are in good agreement with current experi-mental data, demonstrating a generic and versatile approach to model the structure of a virus de novo.
KW - RESPIRATORY SYNDROME CORONAVIRUS
KW - PROTEIN-STRUCTURE PREDICTION
KW - COARSE-GRAINED MODEL
KW - FORCE-FIELD
KW - STRUCTURE VALIDATION
KW - SIMULATIONS
KW - MEMBRANE
KW - MOLPROBITY
KW - INSIGHTS
KW - SERVER
U2 - 10.1016/j.str.2023.02.006
DO - 10.1016/j.str.2023.02.006
M3 - Journal article
C2 - 36870335
VL - 31
SP - 492
EP - 450
JO - Structure
JF - Structure
SN - 0969-2126
IS - 4
ER -
ID: 347302501