Looking at structure, stability, and evolution of proteins through the principal eigenvector of contact matrices and hydrophobicity profiles
| dc.creator | Bastolla, Ugo | |
| dc.creator | Porto, Markus | |
| dc.creator | Roman, H. Eduardo | |
| dc.creator | Vendruscolo, Michele | |
| dc.date | 2004-12-02 | |
| dc.date.accessioned | 2026-07-07T05:58:47Z | |
| dc.date.available | 2026-07-07T05:58:47Z | |
| dc.description | We review and further develop an analytical model that describes how thermodynamic constraints on the stability of the native state influence protein evolution in a site-specific manner. To this end, we represent both protein sequences and protein structures as vectors: Structures are represented by the principal eigenvector (PE) of the protein contact matrix, a quantity that resembles closely the effective connectivity of each site; Sequences are represented through the ``interactivity'' of each amino acid type, using novel parameters that are correlated with hydropathy scales. These interactivity parameters are more strongly correlated than the other hydropathy scales that we examine with: (1) The change upon mutations of the unfolding free energy of proteins with two-states thermodynamics; (2) Genomic properties as the genome-size and the genome-wide GC content; (3) The main eigenvectors of the substitution matrices. The evolutionary average of the interactivity vector correlates very strongly with the PE of a protein structure. Using this result, we derive an analytic expression for site-specific distributions of amino acids across protein families in the form of Boltzmann distributions whose ``inverse temperature'' is a function of the PE component. We show that our predictions are in agreement with site-specific amino acid distributions obtained from the Protein Data Bank, and we determine the mutational model that best fits the observed site-specific amino acid distributions. Interestingly, the optimal model almost minimizes the rate at which deleterious mutations are eliminated by natural selection. | |
| dc.description | 11 pages, 5 figures | |
| dc.identifier | https://arxiv.org/abs/q-bio/0412004 | |
| dc.identifier | http://arxiv.org/abs/q-bio/0412004 | |
| dc.identifier | Gene 347, 219 (2005) | |
| dc.identifier.uri | http://salesiana.dossiersoluciones.com/handle/123456789/88489 | |
| dc.subject | Biomolecules | |
| dc.subject | Populations and Evolution | |
| dc.title | Looking at structure, stability, and evolution of proteins through the principal eigenvector of contact matrices and hydrophobicity profiles | |
| dc.type | text |