The Mechanism and Consequences of SARS-CoV-2 Spike-Mediated Fusion and Syncytia Formation.

Neurotransmitter release is accomplished by a multi-component machinery including the membrane-fusing SNARE proteins and Ca2+-sensing Synaptotagmin molecules. However, the Ca2+ sensitivity of release was found to increase or decrease with more or fewer SNARE complexes at the release site, respectively, while the cooperativity is unaffected (Acuna et al., 2014; Arancillo et al., 2013), suggesting that there is no simple division of labor between these two components. To examine the mechanisms underlying these findings, we developed molecular dynamics simulations of the neurotransmitter release machinery, with variable numbers of Synaptotagmin molecules and assembled SNARE complexes at the release site. Ca2+ uncaging simulations showed that increasing the number of SNARE complexes at fixed stoichiometric ratio of Synaptotagmin to SNAREs increased the Ca2+ sensitivity without affecting the cooperativity. The physiological cooperativity of ~4-5 was reproduced with 2-3 Synaptotagmin molecules per SNARE complex, suggesting that Synaptotagmin and SNAREs cooperate in fixed stoichiometry modules. In simulations of action potential-evoked release, increased numbers of Synaptotagmin-SNARE modules increased release probability, consistent with experiment. Our simulations suggest that the final membrane fusion step is driven by SNARE complex-mediated entropic forces, and by vesicle-tethering forces mediated by the long Synaptotagmin linker domains. In consequence, release rates are increased when more SNARE complexes and Synaptotagmin monomers are present at the fusion site.

/pdf/snares-and-synaptotagmin-cooperatively-determine-the-ca2-re8v1e3evn.pdf

SNAREs and Synaptotagmin cooperatively determine the Ca2+ sensitivity of neurotransmitter release in fixed stoichiometry modules

As emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants (Omicron) continue to outpace and negate combinatorial vaccines and monoclonal antibody therapies targeting the spike protein (S) receptor binding domain (RBD), the appetite for developing similar COVID-19 treatments has significantly diminished, with the attention of the scientific community switching to long COVID treatments. However, treatments that reduce the risk of “post-COVID-19 syndrome” and associated sequelae remain in their infancy, particularly as no established criteria for diagnosis currently exist. Thus, alternative therapies that reduce infection and prevent the broad range of symptoms associated with ‘post-COVID-19 syndrome’ require investigation. This review begins with an overview of the parasitic–diarylamidine connection, followed by the renin-angiotensin system (RAS) and associated angiotensin-converting enzyme 2 (ACE2) and transmembrane serine protease 2 (TMPRSSR2) involved in SARS-CoV-2 infection. Subsequently, the ability of diarylamidines to inhibit S-protein binding and various membrane serine proteases associated with SARS-CoV-2 and parasitic infections are discussed. Finally, the roles of diarylamidines (primarily DIZE) in vaccine efficacy, epigenetics, and the potential amelioration of long COVID sequelae are highlighted.

/pdf/covid-19-and-diarylamidines-the-parasitic-connection-1xhojt19.pdf

COVID-19 and Diarylamidines: The Parasitic Connection

/pdf/the-constellation-of-cholesterol-dependent-processes-rduqk854.pdf

The constellation of cholesterol-dependent processes associated with SARS-CoV-2 infection

Current trends in molecular modelling are geared towards increasingly realistic representations of the modelled systems. This is reflected in larger, more complex systems, which are difficult to build and would ideally rely on a software that converts user-provided descriptors into system coordinates. This is not a trivial task, as the building algorithms use simplifications that can introduce inaccuracies in the system properties that do not correspond to the requested values. We created COBY, a coarse-grained system builder that can create a large variety of systems in a single command call using Martini molecule models. We improved the accuracy of the complex membrane and solvent building procedures, introduced a variety of arguments that can be used to build diverse systems, and implemented features intended for force field development. COBY can be used to build flat membranes of any degree of complexity, handle protein and solvent insertion, solute flooding, stacked membranes, membrane patches and pores, and includes advanced functionalities such as molecule import, lipid building from fragments, handling of multiple parameter libraries, and several choices of algorithms for interpreting user-provided system descriptors. COBY is an open-source software written in Python 3, and the code, documentation, and tutorials are hosted at github.com/MikkelDA/COBY. 

Creating Coarse-Grained Systems with COBY: Towards Higher Accuracy in Membrane Complexity

Cell entry by SARS-CoV-2 is accomplished by the S2 subunit of the spike S protein on the virion surface by capture of the host cell membrane and fusion with the viral envelope. Capture and fusion require the prefusion S2 to transit to its potent, fusogenic form, the fusion intermediate (FI). However, the FI structure is unknown, detailed computational models of the FI are unavailable, and the mechanisms and timing of membrane capture and fusion are not established. Here, we constructed a full-length model of the CoV-2 FI by extrapolating from known CoV-2 pre- and postfusion structures. In atomistic and coarse-grained molecular dynamics simulations the FI was remarkably flexible and executed large bending and extensional fluctuations due to three hinges in the C-terminal base. Simulations suggested a host cell membrane capture time of ∼ 2 ms. Isolated fusion peptide simulations identified an N-terminal helix that directed and maintained binding to the membrane but grossly underestimated the binding time, showing that the fusion peptide environment is radically altered when attached to its host fusion protein. The large configurational fluctuations of the FI generated a substantial exploration volume that aided capture of the target membrane, and may set the waiting time for fluctuation-triggered refolding of the FI that draws the viral envelope and host cell membrane together for fusion. These results describe the FI as a machinery designed for efficient membrane capture and suggest novel potential drug targets.

/pdf/host-cell-membrane-capture-by-the-sars-cov-2-spike-protein-49j2iz3r0j.pdf

Host cell membrane capture by the SARS CoV-2 spike protein fusion intermediate

Cell entry of SARS-CoV-2 is accomplished by the S2 subunit of the spike S protein on the virion surface by fusion of the viral envelope and host cell membrane. Fusion requires the prefusion S2 to transit to its potent, fusogenic form, the fusion intermediate (FI). However, the FI structure is unknown, detailed computational models of the FI are unavailable, and the mechanisms of fusion and entry remain unclear. Here, we constructed a full-length model of the CoV-2 FI by extrapolating from known CoV-2 pre- and postfusion structures. Atomistic and coarse-grained simulations showed the FI is a remarkably flexible mechanical assembly executing large orientational and extensional fluctuations due to three hinges in the C-terminal base. Fluctuations generate a large fusion peptide exploration volume and may aid capture of the host cell target membrane and define the clock for fluctuation-triggered refolding and membrane fusion. This work suggests several novel potential drug targets.

https://www.biorxiv.org/content/biorxiv/early/2021/04/10/2021.04.09.439051.full.pdf

Large fluctuations of the fusion intermediate help SARS-CoV-2 capture host cell membranes

Neurotransmitter (NT) release is accomplished by a machinery that unclamps fusion in response to calcium and then fuses the synaptic vesicle and plasma membranes. These are often thought of as distinct tasks assigned to non-overlapping components. Vesicle release rates have a power law dependence on [Ca2+] with an exponent of 3-5, long taken to indicate that 3-5 Ca2+ ions bind the calcium sensor Synaptotagmin to trigger release. However, dependencies at low [Ca2+] are inconsistent with simple sequential binding to a single Ca2+ sensor followed by a final fusion step. Here we developed coarse-grained molecular dynamics simulations of the NT release machinery accounting for Synaptotagmin-mediated unclamping and SNARE-mediated fusion. Calcium-triggered unclamping and SNARE-mediated fusion emerged from simulations as contemporaneous, coupled processes. Increasing cytosolic [Ca2+], the instantaneous fusion rate increased as SNAREpins were progressively and reversibly released by dissociation of Synaptotagmin-SNAREpin complexes. Simulations reproduced the observed dependence of release rates on [Ca2+], but the power law was unrelated to the number of Ca2+ ions required. Action potential-evoked vesicle release probabilities depended on the number of transiently unclamped SNAREpins, explaining experimental dependencies of release probabilities on both unclamping and membrane-fusing machinery components. These results describe a highly cooperative NT release machinery with intrinsically inseparable unclamping and membrane-fusing functionalities.

https://www.biorxiv.org/content/biorxiv/early/2021/06/17/2021.06.16.448753.full.pdf

Coupling of Ca2+-triggered unclamping and membrane fusion during neurotransmitter release

SNARE proteins are the core components of the cellular machineries that fuse membranes for neurotransmitter or hormone release and other fundamental processes. Fusion is accomplished when SNARE proteins hosted by apposing membranes form SNARE complexes called SNAREpins, but the mechanism of fusion remains unclear. Computational simulations of SNARE-mediated membrane fusion are challenging due to the millisecond timescales of physiological membrane fusion. Here we used ultra-coarse-grained (UCG) simulations to investigate the minimal requirements for a molecular intracellular fusogen, and to elucidate the mechanisms of SNARE-mediated fusion. We find fusion by simple body forces that push vesicles together is highly inefficient. Inter-vesicle fusogens with different aspect ratios can fuse vesicles only if they are rodlike, of sufficient length to clear the fusogens from the fusion site by entropic forces. Simulations with rod-shaped SNAREpin-like fusogens fused 50-nm vesicles on ms timescales, driven by entropic forces along a reproducible fusion pathway. SNARE-SNARE and SNARE-membrane entropic forces cleared the fusion site and pressed the vesicles into an extended contact zone (ECZ), drove stalk nucleation at the high curvature ECZ boundary, and expanded the stalk into a long-lived hemifusion diaphragm in which a simple pore completed fusion. Our results provide strong support for the entropic hypothesis of SNARE-mediated membrane fusion, and implicate the rodlike structure of the SNAREpin complex as a necessity for entropic force production and fusion.

https://www.biorxiv.org/content/biorxiv/early/2021/06/24/2021.06.23.449668.full.pdf

Why are SNAREpins rod-shaped?

Handle everyday research tasks with reliable, citation-backed results

Your personal Research Agent to handle research tasks with citation-backed results

Popular Tasks used by Researchers

How can I help with your research?

Meet SciSpace

Get more enhanced response by uploading the PDFs you want me to reference.

No relevant PDFs in your library

SciSpace is the AI research assistant for academics. Run systematic literature reviews on 280M+ papers, and write papers with cited sources. Trusted by 1M+ students, PhDs & researchers.

SciSpace | AI for Research

Analyze PDFs

Code & Manuscripts

Funding & Grants

Literature & Patents

Medical & Clinical Data

Systematic Review

Visualize & Present

Web & Data

Build a Google Scholar-like website for your research.

Build a website

Create charts and images for your research

Create a Chart

Write a paper for submission to a journal

Draft a manuscript

Patent Search

Design eye-catching scientific posters in minutes.

Scientific Poster Generation

Systematic Literature Review

One task is running at the moment. Your messages will be shown right after.

Drag and drop or click here to browse

Loved by <highlight>1 million+</highlight> researchers

Extract a list of specific topics and their sources from unstructured text

Topics

Compare and analyze relevant papers that matches with your search

Papers

Get insights from PDFs and bookmarked papers from your library

My library

Recent searches

Try searching for:

Catch AI-generated content in scholarly and non-scholarly content

{ai} Detector

Ai Writer

Get PDF Summaries, highlighted text explanations 

Chat with PDF

Effortlessly create in-text citations and bibliographies in APA and 2,500 other formats

Citation generator

Get explanations, summaries, and answers on academic papers

Ease up your research workflow with {scispace}'s cohort of exciting AI tools

Elevate your academic writing skills and convey your ideas the way you want

Paraphraser

Explore our range of reading and writing tools

Your file is being prepared and should be ready in a few minutes. If it's a large file, it might take a bit longer. You can close this window, and we'll email you the file when it's done.

You have reached a maximum limit of <strong>{limit}</strong> columns in the table. Remove at least <strong>1</strong> column to add or create another one.

Jin Zeng

Author Tools

Chat about Author

Papers

Host cell membrane capture by the SARS CoV-2 spike protein fusion intermediate

Large fluctuations of the fusion intermediate help SARS-CoV-2 capture host cell membranes

Coupling of Ca2+-triggered unclamping and membrane fusion during neurotransmitter release

Why are SNAREpins rod-shaped?