Networks and stability Part 5 Examples for networks

Networks and stability Part 5 – Examples for networks http: //linkgroup. hu http: //turbine. ai csermelynet@gmail. com Péter Csermely and the Turbine team

Protein structure networks • protein structure networks • residue interaction network • amino acid networks How do we construct a network from a 3 D image? Böde et al, FEBS Letters 581: 2776

Protein structure networks It is a small world but not scale-free. Why? Vendruscolo et al: Phys. Rev. E. 65: 061910 hot spots, key residues for protein folding: hubs of transition state

Key segments of protein structures Cyt-P 450 (CYP 2 B 4) Where do you find key segments besides hubs? Csermely, Ti. BS 33: 569 • anchor and latch residues • bridges, central residues, hinges, discrete-breathers: independent dynamic regions

Modules of Met-t. RNA-synthase network correspond to protein domains Szalay-Bekő et al. Bioinformatics 28: 2202 www. linkgroup. hu/modules. php

Bridges of Met-t. RNA-synthase network identify signaling amino acids Ghosh et al. PNAS 104: 15711 signaling amino acids (identified from MD cross-correlations) other amino acids Szalay-Bekő et al. Bioinformatics 28: 2202 system dynamics predicted from topology

Folding networks in the ‘reality’ Why is it good that it is a small world? 20 AA peptide nodes: conformations links: transitions JMB 342, 299

Cellular networks membrane, organelle network gene transcription network nucleus cytoskeletal network metabolic network signaling networks protein-protein interaction network