A computational protein design protocol for optimization of the SARS-CoV-2 receptor-binding-motif affinity for human ACE2

Autor: Savvas Polydorides, Georgios Archontis

Publikováno v: STAR Protocols, Vol 3, Iss 2, Pp 101254- (2022)

Summary: The present protocol describes the computational design of the SARS-CoV-2 receptor binding motif (RBD) to identify mutations that can potentially improve binding affinity for the human ACE2 (hACE2) receptor. We focus on four positions locate

Externí odkaz: https://doaj.org/article/d46b855f790f4a49acd2c25f8e80c3c1

Computational Design of Peptides with Improved Recognition of the Focal Adhesion Kinase FAT Domain

Autor: Eleni, Michael, Savvas, Polydorides, Georgios, Archontis

Publikováno v: Methods in molecular biology (Clifton, N.J.). 2405

We describe a two-stage computational protein design (CPD) methodology for the design of peptides binding to the FAT domain of the protein focal adhesion kinase. The first stage involves high-throughput CPD calculations with the Proteus software. The

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=pmid________::28d25253ee8136bb37952d1e74e6c85b
https://pubmed.ncbi.nlm.nih.gov/35298823

Physics-Based Computational Protein Design: An Update

Autor: David Mignon, Georgios Archontis, Vaitea Opuu, Nicolas Panel, Karen Druart, Francesco Villa, Thomas Gaillard, Thomas Simonson, Eleni Michael, Savvas Polydorides

Publikováno v: Journal of Physical Chemistry A
Journal of Physical Chemistry A, American Chemical Society, 2020, 124 (51), pp.10637-10648. ⟨10.1021/acs.jpca.0c07605⟩

We describe methods for physics-based protein design and some recent applications from our work. We present the physical interpretation of a MC simulation in sequence space and show that sequences and conformations form a well-defined statistical ens

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c3bc7d58ed993f5160ffa45936a019bc
https://pubmed.ncbi.nlm.nih.gov/33170681

Recognition of LD motifs by the focal adhesion targeting domains of focal adhesion kinase and proline-rich tyrosine kinase 2-beta: Insights from molecular dynamics simulations

Autor: Vasilis J. Promponas, Georgios Archontis, Savvas Polydorides, Paris A. Skourides, Eleni Michael

Publikováno v: ProteinsREFERENCES.

The focal adhesion kinase (FAK) and the proline-rich tyrosine kinase 2-beta (PYK2) are implicated in cancer progression and metastasis and represent promising biomarkers and targets for cancer therapy. FAK and PYK2 are recruited to focal adhesions (F

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::95a4a0a6067fb2abbbe97bc22a4e10bf
https://pubmed.ncbi.nlm.nih.gov/32776636

Hybrid MC/MD for protein design

Autor: Thomas Simonson, Eleni Michael, Savvas Polydorides, Georgios Archontis

Publikováno v: The Journal of Chemical Physics. 153:054113

Computational protein design relies on simulations of a protein structure, where selected amino acids can mutate randomly, and mutations are selected to enhance a target property, such as stability. Often, the protein backbone is held fixed and its d

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::20c8598c2e0d97b8cc44b6e448ec5479
https://doi.org/10.1063/5.0013320