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The PIN can be modeled as a simple graph G = (V, E), in which a node element in node set V represents a protein and an edge element in edge set E represents an interaction between two distinct proteins.
For a given subgraph C⊆ G, let V C represent the set of proteins in C and E C denote the set of interactions between two distinct proteins in C. The density of C, denoted as den(C), is defined as the number of edges in it, divided by the number of potential edges; that is, (1) den (C ) = 2 × | E C | | V C | × (| V C | − 1 ).
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Ambroggio, X. I. & Kuhlman, B. Computational design of a single amino acid sequence that can switch between two distinct protein folds.
Interestingly, we observed statistically significant relationships between the PIWI module and two distinct protein families defined by the models "domain of unknown function" DUF3893 and Med13_C (corresponding to a conserved region in the eukaryotic Mediator complex Med13 proteins) from the Pfam database.
The two types of enzymes belong to two distinct protein families without any primary sequence similarity between them [ 16].
TCR is expressed on the surface of T cells and consists of two distinct protein chains.
Quantum mechanical analysis of electron tunneling in nine thermally fluctuating cytochrome b562 derivatives reveals two distinct protein-mediated coupling limits.
Two distinct protein types were distinguished for omega-1,2 gliadins.
Three hundred and sixteen distinct proteins have been identified in egg yolk.
Here we use theory and continuous constant pH molecular dynamics (CpHMD) simulations to provide a thermodynamic description for the coupling of proton titration and conformational exchange between two distinct states of a protein.
While an allosteric response was originally believed to result from a large structural change elicited by binding of a small molecule to a symmetric oligomeric protein, communication between two distinct binding sites on an allosteric molecule can be mediated by small structural rearrangements or a change in its dynamic properties (12, 47 51).
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