VMD as a Platform for Interactive Small Molecule Preparation and Visualization in Quantum and Classical Simulations

Spivak, Mariano; Stone, John E.; Ribeiro, J. F.; Saam, Jan; Freddolino, Peter L.; Bernardi, Rafael C.; Tajkhorshid, Emad

doi:10.1021/acs.jcim.3c00658

Cited by 17 publications

(9 citation statements)

References 46 publications

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“…Statistical analyses were performed using GraphPad Prism software 8.3 and Microsoft Excel. The 3D structure of the location of the nanobody epitope binding on the spike protein (PDB ID code: 6VXX and 6M0J) was visualized using Visual Molecular Dynamics (VMD) 1.9.3 . The nanobody sequences were first aligned and numbered according to the Kabat Numbering Scheme .…”

Section: Methodsmentioning

confidence: 99%

Proteomics Platform Reveals Broad-Spectrum Nanobodies for SARS-CoV-2 Variant Neutralization

Zhang,

Huang,

Zhang

et al. 2024

J. Proteome Res.

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The ongoing evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to the emergence of different variants of concerns with immune evasion that have been prevalent over the past three years. Nanobodies, the functional variable regions of camelid heavy-chain-only antibodies, have garnered interest in developing neutralizing antibodies due to their smaller size, structural stability, ease of production, high affinity, and low immunogenicity, among other characteristics. In this work, we describe an integrated proteomics platform for the high-throughput screening of nanobodies against different SARS-CoV-2 spike variants. To demonstrate this platform, we immunized a camel with subunit 1 (S1) of the wild-type spike protein and constructed a nanobody phage library. The binding and neutralizing activities of the nanobodies against 72 spike variants were then measured, resulting in the identification of two nanobodies (C-282 and C-39) with broad neutralizing activity against six non-Omicron variants (D614G, Alpha, Beta, Gamma, Delta, Kappa) and five Omicron variants (BA.1−5). Their neutralizing capability was validated using in vitro pseudovirus-based neutralization assays. All these results demonstrate the utility of our proteomics platform to identify new nanobodies with broad neutralizing capability and to develop a treatment for patients with SARS-CoV-2 variant infection in the future.

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Section: Methodsmentioning

confidence: 99%

Proteomics Platform Reveals Broad-Spectrum Nanobodies for SARS-CoV-2 Variant Neutralization

Zhang,

Huang,

Zhang

et al. 2024

J. Proteome Res.

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“…The final complex was further refined using a molecular dynamic simulation in explicit solvent with NAMD (Phillips et al 2020). This step was performed using periodic boundary conditions in a water box with a 10 Å padding, 0.15 M NaCl, and a temperature of 298 K (Spivak et al 2023). Docking of RHD1 and the VPg protein was performed using a global docking protocol using the AlphaFold RHD1 model available at Uniprot (Jumper et al 2021).…”

Section: Methodsmentioning

confidence: 99%

Adaptation of turnip mosaic virus toArabidopsis thalianainvolves rewiring of VPg - host proteome interactions

Carrasco,

Ambrós,

Gutiérrez

et al. 2024

Preprint

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The outcome of a viral infection depends on a complex interplay between the host physiology and the virus, mediated through numerous protein-protein interactions. In a previous study we used high-throughput yeast two-hybrid (HT-Y2H) to identify proteins inArabidopsis thalianathat bind to the proteins encoded by the turnip mosaic virus (TuMV) genome. Furthermore, after experimental evolution of TuMV lineages in plants with mutations in defense-related or proviral genes, most mutations observed in the evolved viruses affected the VPg cistron. Among these mutations, D113G was a convergent mutation selected in many lineages across different plant genotypes. In contrast, mutation R118H specifically emerged in thejin1mutant with affected jasmonate signaling. Using the HT-Y2H system, we analyzed the impact of these two mutations on VPg’s interaction with plant proteins. Interestingly, both mutations severely compromised the interaction of VPg with the translation initiation factor eIF(iso)4E, a crucial interactor for potyvirus infection. Moreover, mutation D113G, but not R118H, adversely affected the interaction with RHD1, a zinc-finger homeodomain transcription factor involved in regulating DNA demethylation. Our results suggest that RHD1 enhances plant tolerance to TuMV infection.

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“…The solvent was uniformly selected as acetone mentioned in the literature. 25 The data processing and molecular visualization were performed by Multiwfn (version: dev 3.8) 26 and VMD (version: 1.9.3), 27 respectively.…”

Section: Characterizationmentioning

confidence: 99%

Design and Mechanism Study of High-Safety and Long-Life Electrolyte for High-Energy-Density Lithium-Ion Batteries

Chang,

Ma,

Wang

et al. 2024

ACS Appl. Mater. Interfaces

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Although nonflammable electrolytes are beneficial for battery safety, they often adversely affect the electrochemical performance of lithium-ion batteries due to their poor compatibility with electrodes. Herein, we design a nonflammable electrolyte consisting of cyclic carbonate and 2,2-difluoroethyl acetate (DFEA) solvents paired with several surface-film-forming additives, significantly improving the safety and cycling performance of NMC811||SiO x / graphite pouch cells. The DFEA solvent exhibits not only good flame retardancy but also lower lowest unoccupied molecular orbital (LUMO) energy, promoting the formation of a robust inorganicrich and gradient-architecture hybrid interface between the SiO x / graphite anode and electrolyte. The double insurance of good flame retardancy of the DFEA solvent and decreased exothermic effects of both bulk electrolyte and DFEA-derived solid electrolyte interphase (SEI) can ensure the high safety of the pouch cell. Moreover, the highly robust SEI can prevent the excessive reduction decomposition of the electrolyte and alleviate the structural decay of the anode, which can restrain the formation of lithium deposition on the anode surface and further suppress the structural decay of NMC materials. This contributes to the unprecedented cycling performance of the NMC811||SiO x /graphite pouch cells with a capacity retention of 80% after 1000 cycles at a 0.33C rate.

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VMD as a Platform for Interactive Small Molecule Preparation and Visualization in Quantum and Classical Simulations

Cited by 17 publications

References 46 publications

Proteomics Platform Reveals Broad-Spectrum Nanobodies for SARS-CoV-2 Variant Neutralization

Proteomics Platform Reveals Broad-Spectrum Nanobodies for SARS-CoV-2 Variant Neutralization

Adaptation of turnip mosaic virus toArabidopsis thalianainvolves rewiring of VPg - host proteome interactions

Design and Mechanism Study of High-Safety and Long-Life Electrolyte for High-Energy-Density Lithium-Ion Batteries

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