Probing Conformational Dynamics by Protein Contact Networks: Comparison with NMR Relaxation Studies and Molecular Dynamics Simulations
Protein contact networks (PCNs) have been used for the study of protein structure and function for the past decade. In PCNs, each amino acid is considered as a node while the contacts among amino acids are the links/edges. We examined the possible correlation between the closeness centrality measure...
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| Format: | Article |
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MDPI AG
2021-04-01
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| Series: | Biophysica |
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| Online Access: | https://www.mdpi.com/2673-4125/1/2/12 |
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| author | Christos T. Chasapis Alexios Vlamis-Gardikas |
| author_facet | Christos T. Chasapis Alexios Vlamis-Gardikas |
| author_sort | Christos T. Chasapis |
| collection | DOAJ |
| description | Protein contact networks (PCNs) have been used for the study of protein structure and function for the past decade. In PCNs, each amino acid is considered as a node while the contacts among amino acids are the links/edges. We examined the possible correlation between the closeness centrality measure of amino acids within PCNs and their mobility as known from NMR spin relaxation experiments and molecular dynamic (MD) simulations. The pivotal observation was that plasticity within a protein stretch correlated inversely to closeness centrality. Effects on protein conformational plasticity caused by the formation of disulfide bonds or protein–protein interactions were also identified by the PCN analysis measure closeness centrality and the hereby introduced percentage of closeness centrality perturbation (% CCP). All the comparisons between PCN measures, NMR data, and MDs were performed in a set of proteins of different biological functions and structures: the core protease domain of anthrax lethal factor, the N-terminal RING domain of E3 Ub ligase Arkadia, the reduced and oxidized forms of human thioredoxin 1, and the ubiquitin molecules (Ub) of the catalytic Ub–RING–E3–E2–Ub complex of E3 ligase Ark2.The graph theory analysis of PCNs could thus provide a general method for assessing the conformational dynamics of free proteins and putative plasticity changes between different protein forms (apo/complexed or reduced/oxidized). |
| first_indexed | 2024-03-10T08:58:26Z |
| format | Article |
| id | doaj.art-68f8a81d711f4c6992c767e22196ff79 |
| institution | Directory Open Access Journal |
| issn | 2673-4125 |
| language | English |
| last_indexed | 2024-03-10T08:58:26Z |
| publishDate | 2021-04-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Biophysica |
| spelling | doaj.art-68f8a81d711f4c6992c767e22196ff792023-11-22T06:57:09ZengMDPI AGBiophysica2673-41252021-04-011215716710.3390/biophysica1020012Probing Conformational Dynamics by Protein Contact Networks: Comparison with NMR Relaxation Studies and Molecular Dynamics SimulationsChristos T. Chasapis0Alexios Vlamis-Gardikas1NMR Facility, Instrumental Analysis Laboratory, School of Natural Sciences, University of Patras, 26504 Rion, GreeceDepartment of Chemistry, University of Patras, 26504 Rion, GreeceProtein contact networks (PCNs) have been used for the study of protein structure and function for the past decade. In PCNs, each amino acid is considered as a node while the contacts among amino acids are the links/edges. We examined the possible correlation between the closeness centrality measure of amino acids within PCNs and their mobility as known from NMR spin relaxation experiments and molecular dynamic (MD) simulations. The pivotal observation was that plasticity within a protein stretch correlated inversely to closeness centrality. Effects on protein conformational plasticity caused by the formation of disulfide bonds or protein–protein interactions were also identified by the PCN analysis measure closeness centrality and the hereby introduced percentage of closeness centrality perturbation (% CCP). All the comparisons between PCN measures, NMR data, and MDs were performed in a set of proteins of different biological functions and structures: the core protease domain of anthrax lethal factor, the N-terminal RING domain of E3 Ub ligase Arkadia, the reduced and oxidized forms of human thioredoxin 1, and the ubiquitin molecules (Ub) of the catalytic Ub–RING–E3–E2–Ub complex of E3 ligase Ark2.The graph theory analysis of PCNs could thus provide a general method for assessing the conformational dynamics of free proteins and putative plasticity changes between different protein forms (apo/complexed or reduced/oxidized).https://www.mdpi.com/2673-4125/1/2/12protein contact networkcloseness centralitygraph theoryconformational dynamicsNMR spin relaxationMDs |
| spellingShingle | Christos T. Chasapis Alexios Vlamis-Gardikas Probing Conformational Dynamics by Protein Contact Networks: Comparison with NMR Relaxation Studies and Molecular Dynamics Simulations Biophysica protein contact network closeness centrality graph theory conformational dynamics NMR spin relaxation MDs |
| title | Probing Conformational Dynamics by Protein Contact Networks: Comparison with NMR Relaxation Studies and Molecular Dynamics Simulations |
| title_full | Probing Conformational Dynamics by Protein Contact Networks: Comparison with NMR Relaxation Studies and Molecular Dynamics Simulations |
| title_fullStr | Probing Conformational Dynamics by Protein Contact Networks: Comparison with NMR Relaxation Studies and Molecular Dynamics Simulations |
| title_full_unstemmed | Probing Conformational Dynamics by Protein Contact Networks: Comparison with NMR Relaxation Studies and Molecular Dynamics Simulations |
| title_short | Probing Conformational Dynamics by Protein Contact Networks: Comparison with NMR Relaxation Studies and Molecular Dynamics Simulations |
| title_sort | probing conformational dynamics by protein contact networks comparison with nmr relaxation studies and molecular dynamics simulations |
| topic | protein contact network closeness centrality graph theory conformational dynamics NMR spin relaxation MDs |
| url | https://www.mdpi.com/2673-4125/1/2/12 |
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