Predicting the Initial Steps of Salt-Stable Cowpea Chlorotic Mottle Virus Capsid Assembly with Atomistic Force Fields

Antal, Zoltan; Szoverfi, Janos; Fejer, Szilárd N.

doi:10.1021/acs.jcim.7b00078

Cited by 6 publications

(10 citation statements)

References 39 publications

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“…This fan-like motion was previously described by Globisch et al. 16 As we did not observe drastic changes on the interfaces of three types of dimers during the long simulations, we chose another, putative dimer from the docking results of our previous work 3 that had the biggest RMSD score (3.09 nm) when compared to the original T3 dimer in order to start the simulation from a dimer that is not present in the icosahedral capsid and is therefore far from any native protein-protein interface for ss-CCMV. The chains in this dimer (type X, TX) are bound together through the first 15 residues of the N-terminal tail.…”

Section: Resultsmentioning

confidence: 83%

“…This indicates that the T2 interface is less stable than T1, this being in a good agreement with our previous study. 3 Within the first 50 ns of the simulation the values quickly increase to over 0.7 nm. Interface RMSD values for the T1 dimer show a deviation from the average between 1500 and 1950 ns, afterwards returning to the average values.…”

Section: Resultsmentioning

confidence: 98%

“…Dimers of ss-CCMV capsid protein were selected according to our previous study. 3 The T1 and T2 interfaces play a significant role in the capsid formation, while T3 seemed less relevant. Type X is the dimer that had the highest RMSD compared to the original T3 dimer, selected from the 2000 docking results of two monomers.…”

Section: Studied Systemsmentioning

confidence: 98%

“…

Dynamic stability of salt stable cowpea chlorotic mottle virus capsid protein dimers and pentamers of dimersJ ános Sz öv érfi 1,2 and Szilard N. Fejer 2,3

…”

mentioning

confidence: 99%

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Dynamic stability of salt stable cowpea chlorotic mottle virus capsid protein dimers and pentamers of dimers

Fejer¹,

Szoverfi

2022

Preprint

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Parts of the self-assembly process of the salt stable cowpea chlorotic mottle virus (ss-CCMV) capsid can be modelled atomistically on realistic computational timescales only if we focus on the dissociation of protein complexes instead of their aggregation. The aim of the current study is to find and understand the conditions that lead to the separation of ss-CCMV capsid protein dimers. Our previous studies showed that among the three possible interfaces in the icosahedral capsid, two (T1 and T2) are important during capsid formation. Long timescale molecular dynamics simulations of the various dimers and the pentamer of dimers underscore the importance of large contact surfaces on stabilizing the capsid subunits within an oligomer. At higher temperature, the N-terminal tails of the protein units act as tethers, delaying dissociation for all but the most stable (T1) interfaces, therefore their flexibility likely has an important role during the self-assembling process, as tethering increases the effective concentration of the monomers and the likelihood of finding native contacts. The pentamer of dimers is also found to be stable on long timescales, with an inherent flexibility of the outer protein chains.

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Section: Resultsmentioning

confidence: 83%

Section: Resultsmentioning

confidence: 98%

Section: Studied Systemsmentioning

confidence: 98%

“…

Dynamic stability of salt stable cowpea chlorotic mottle virus capsid protein dimers and pentamers of dimersJ ános Sz öv érfi 1,2 and Szilard N. Fejer 2,3

…”

mentioning

confidence: 99%

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Dynamic stability of salt stable cowpea chlorotic mottle virus capsid protein dimers and pentamers of dimers

Fejer¹,

Szoverfi

2022

Preprint

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“…Plant virus nanoparticles can also undergo computational modeling to improve their immune response for cancer therapy [41–43]. Using computer simulations, researchers can make predictions as to the strength of plant virus coat protein interactions, and how these subunits can assemble under specific physiological conditions [44–46]. For example, Chariou et al .…”

Section: Cancer Immunotherapy Based On Mathematical and Computational Mmentioning

confidence: 99%

Future of Cancer Immunotherapy using Plant virus-based Nanoparticles

Badar

Hefferon

2019

Future Sci. OA

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Immunotherapy potentiates a patient’s immune response against some forms of cancer, including malignant tumors. In this Special Report, we have summarized the use of nanoparticles that have been designed for use in cancer immunotherapy with particular emphasis on plant viruses. Plant virus-based nanoparticles are an ideal choice for therapeutic applications, as these nanoparticles are not only capable of targeting the desired cells but also of being safely delivered to the body without posing any threat of infection. Plant viruses can be taken up by tumor cells and can be functionalized as drug delivery vehicles. This Special Report describes how the future of cancer immunotherapy could be a success through the merger of computer-based technology using plant-virus nanoparticles.

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Protein–Protein Docking in Drug Design and Discovery

Kaczor

Bartuzi

Stępniewski

et al. 2018

Methods in Molecular Biology

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Protein-protein interactions (PPIs) are responsible for a number of key physiological processes in the living cells and underlie the pathomechanism of many diseases. Nowadays, along with the concept of so-called "hot spots" in protein-protein interactions, which are well-defined interface regions responsible for most of the binding energy, these interfaces can be targeted with modulators. In order to apply structure-based design techniques to design PPIs modulators, a three-dimensional structure of protein complex has to be available. In this context in silico approaches, in particular protein-protein docking, are a valuable complement to experimental methods for elucidating 3D structure of protein complexes. Protein-protein docking is easy to use and does not require significant computer resources and time (in contrast to molecular dynamics) and it results in 3D structure of a protein complex (in contrast to sequence-based methods of predicting binding interfaces). However, protein-protein docking cannot address all the aspects of protein dynamics, in particular the global conformational changes during protein complex formation. In spite of this fact, protein-protein docking is widely used to model complexes of water-soluble proteins and less commonly to predict structures of transmembrane protein assemblies, including dimers and oligomers of G protein-coupled receptors (GPCRs). In this chapter we review the principles of protein-protein docking, available algorithms and software and discuss the recent examples, benefits, and drawbacks of protein-protein docking application to water-soluble proteins, membrane anchoring and transmembrane proteins, including GPCRs.

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Predicting the Initial Steps of Salt-Stable Cowpea Chlorotic Mottle Virus Capsid Assembly with Atomistic Force Fields

Cited by 6 publications

References 39 publications

Dynamic stability of salt stable cowpea chlorotic mottle virus capsid protein dimers and pentamers of dimers

Dynamic stability of salt stable cowpea chlorotic mottle virus capsid protein dimers and pentamers of dimers

Future of Cancer Immunotherapy using Plant virus-based Nanoparticles

Protein–Protein Docking in Drug Design and Discovery

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