protein contact networks
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Biophysica ◽  
2021 ◽  
Vol 1 (2) ◽  
pp. 157-167
Author(s):  
Christos T. Chasapis ◽  
Alexios Vlamis-Gardikas

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).



Author(s):  
Luisa Di Paola ◽  
Giampiero Mei ◽  
Almerinda Di Venere ◽  
Alessandro Giuliani


2017 ◽  
Vol 471 ◽  
pp. 804-817 ◽  
Author(s):  
Enrico Maiorino ◽  
Antonello Rizzi ◽  
Alireza Sadeghian ◽  
Alessandro Giuliani


2016 ◽  
Vol 92 (4-5) ◽  
pp. 401-410 ◽  
Author(s):  
Sara Cimini ◽  
Luisa Di Paola ◽  
Alessandro Giuliani ◽  
Alessandra Ridolfi ◽  
Laura De Gara


2016 ◽  
Vol 34 (7) ◽  
pp. 1441-1454 ◽  
Author(s):  
Lorenzo Livi ◽  
Enrico Maiorino ◽  
Alessandro Giuliani ◽  
Antonello Rizzi ◽  
Alireza Sadeghian




2015 ◽  
Vol 428 ◽  
pp. 302-313 ◽  
Author(s):  
Enrico Maiorino ◽  
Lorenzo Livi ◽  
Alessandro Giuliani ◽  
Alireza Sadeghian ◽  
Antonello Rizzi


2012 ◽  
Vol 113 (3) ◽  
pp. 1598-1613 ◽  
Author(s):  
L. Di Paola ◽  
M. De Ruvo ◽  
P. Paci ◽  
D. Santoni ◽  
A. Giuliani


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