Toward Atomistic Models of Intact SARS-CoV-2 via Martini Coarse-Grained Molecular Dynamics Simulations

Wang, Dali; Li, Jiaxuan; Wang, Lei; Cao, Yipeng; Li, Sai; Song, Chen

doi:10.1101/2022.01.31.478415

Cited by 5 publications

(3 citation statements)

References 87 publications

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“…However, a relatively small virus particle was simulated with a stoichiometry incompatible with current experimental data. Another Martini-based model was put forward by the group of Song (27). The model features N-bound RNA segments, and was back-mapped to full atomistic resolution.…”

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confidence: 99%

Molecular architecture and dynamics of SARS-CoV-2 envelope by integrative modeling

Pezeshkian

Grünewald

Narykov

et al. 2021

Preprint

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Despite tremendous efforts by research community during the COVID-19 pandemic, the exact structure of SARS-CoV-2 and related betacoronaviruses remains elusive. Here, we developed and applied an integrative multi-scale computational approach to model the envelope structure of SARS-CoV-2, focusing on studying the dynamic nature and molecular interactions of its most abundant, but largely understudied, M (membrane) protein. The molecular dynamics simulations allowed us to test the envelop stability under different configurations and revealed that M dimers agglomerated into large, filament-like, macromolecular assemblies with distinct molecular patterns formed by M's transmembrane and intra-virion (endo) domains. These results were in agreement with the experimental data, demonstrating a generic and versatile integrative approach to model the structure of a virus de novo, providing insights into critical roles of structural proteins in the viral assembly and integration, and proposing new targets for the antiviral therapies.

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confidence: 99%

Molecular architecture and dynamics of SARS-CoV-2 envelope by integrative modeling

Pezeshkian

Grünewald

Narykov

et al. 2021

Preprint

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“…Moreover, the correlations between Nc/Pc and Kc/Pc and yield were highest at the FB, indicating that maintaining high Pc at late growth stages promotes cotton yield. Therefore, P fertilizer could be shifted back to actual fertilizer management, similar to the study stating that increased application of P fertilizers during late growth could increase yield and efficiency in cotton [56,57]. However, this study analyzed all sources of N, P, K in cotton and neglected the different sources of N, P, K, not only from fertilizer but also from the soil.…”

Section: Discussionmentioning

confidence: 91%

Variation of Nitrogen, Phosphorus, and Potassium Contents in Drip-Irrigated Cotton at Different Yield Levels under Combined Effects of Nitrogen, Phosphorus and Potassium

Chen,

Wen,

et al. 2024

Agronomy

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To elucidate the variation characteristics of nitrogen (N), phosphorus (P), and potassium (K) content and accumulation in cotton at different yield levels, a two-year experiment was conducted using cotton variety Lumianyan 24 under four N treatments (506, 402.5, 299, and 195.5 kg ha−1, designated as N1, N2, N3, and N4, respectively). The four P and K fertilization ratios were (PK-M1, 25% P and K applied at squaring stage (SS) and 75% at the bloom-bolling stages (BS)), 50%:50% (PK-M2, 50% P and K applied at each stage), 75%:25% (PK-M3, 75% P and K applied at SS and 25% at the BS) and 100%:0% (PK-M4, total P and K applied at SS). The results showed that the N content (Nc), P content (Pc), and K content (Kc) of cotton plants at high yield levels were 23.3%, 44.2%, and 31.6% higher than those at low yield levels. In addition, the reproductive organs maintained higher Pc and Kc at high yield levels, and the Nc, Pc, and Kc exhibited positive linear correlations with yield, while Nc/Pc, Nc/Kc, and Kc/Pc had significant negative correlations with yield. In conclusion, seed cotton yield was mainly limited by Nc at low yield levels and affected by Pc and Kc at high yield levels. Then, when 0.85 < Nc/Kc < 1.0 at the full squaring stage (FS), 0.8 < Nc/Kc < 1.0 at the full flowering stage (FF), 4.3 < Nc/Pc < 6.7 at the early-full bolling stage (EFB) and 4.9 < Nc/Pc < 7.1 at the late-full bolling stage (LFB), there is a high yield potential of 7000–9000 kg ha−1. Furthermore, yields can be improved by reducing the application of N during the growing period and increasing the application of P fertilizer during the later growth period.

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“…A 5.8 MDa mitochondrial respiratory complex has also been simulated using Martini, showcasing how it impacts the curvature of the surrounding membrane region (Figure , d). Additionally, Martini has been applied to model the SARS-CoV and SARS-CoV-2 − envelope structures. In one of these studies, Pezeshkian et al studied 100 nm diameter SARS-CoV-2 envelope structures containing over 2000 proteins for 4 μs, allowing the observation of significant molecular rearrangements.…”

Section: Main Cg Protein Model Applicationsmentioning

confidence: 99%

Pragmatic Coarse-Graining of Proteins: Models and Applications

Borges-Araújo,

Patmanidis,

Singh

et al. 2023

J. Chem. Theory Comput.

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The molecular details involved in the folding, dynamics, organization, and interaction of proteins with other molecules are often difficult to assess by experimental techniques. Consequently, computational models play an ever-increasing role in the field. However, biological processes involving large-scale protein assemblies or long time scale dynamics are still computationally expensive to study in atomistic detail. For these applications, employing coarse-grained (CG) modeling approaches has become a key strategy. In this Review, we provide an overview of what we call pragmatic CG protein models, which are strategies combining, at least in part, a physics-based implementation and a top-down experimental approach to their parametrization. In particular, we focus on CG models in which most protein residues are represented by at least two beads, allowing these models to retain some degree of chemical specificity. A description of the main modern pragmatic protein CG models is provided, including a review of the most recent applications and an outlook on future perspectives in the field.

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Toward Atomistic Models of Intact SARS-CoV-2 via Martini Coarse-Grained Molecular Dynamics Simulations

Cited by 5 publications

References 87 publications

Molecular architecture and dynamics of SARS-CoV-2 envelope by integrative modeling

Molecular architecture and dynamics of SARS-CoV-2 envelope by integrative modeling

Variation of Nitrogen, Phosphorus, and Potassium Contents in Drip-Irrigated Cotton at Different Yield Levels under Combined Effects of Nitrogen, Phosphorus and Potassium

Pragmatic Coarse-Graining of Proteins: Models and Applications

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