Fehérjék 4 Simon István
Predicting protein disorder - IUPred Basic idea: If a residue is surrounded by other residues such that they cannot form enough favorable contacts, it will not adopt a well defined structureit will be disordered …..QSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAAPRVAPAPAAPTPAAPAPA….. Amino acid composition of environ- ment: A – 10% C – 0% D – 12 % E – 10 % F – 2 % etc… Estimate the interaction energy between the residue and its sequential environment Decide the probability of the residue being disordered based on this The algorithm:
Predicting protein disorder - IUPred Back to p53: A – 10% C – 0% D – 12 % E – 10 % F – 2 % stb… Amino acid composition of the residue D: The predicted interaction energy: E = Interaction energies: 1.16*0.10+(-0.82)*0+… = %, that it is disordered
Predicting binding sites - ANCHOR 3 – Interaction with globular proteins We consider the average amino acid composition of a globular dataset instead of the own environment: A – 10% C – 0% D – 12 % E – 10 % F – 2 % stb… A – 7.67% C – 2.43% D – 4.92 % E – 5.43 % F – 3.19 % stb… Composition calculated on a large globular dataset The thus gained energy: where
Predicting binding sites - ANCHOR Example: N terminal p53 Contains three binding sites: –MDM2: –RPA70N: –RNAPII: P = p1*S average + p2*E int + p3*E gain
Transzmembrán fehérjék Anyagcsere folyamatok Transzporterek Ion csatornák Hordozók Információ csere Receptorok
A transzmembrán fehérjék két formája
E. Coli klorid csatorna fehérje
Ismert szerkezetű transzmembrán fehérjék szerkezetét vizsgáló szerverek
Hidrofobicitás
Aminosav helyettesítési mátrix
Szerkezetbecslés homológia alapján
Az emberi rodopszin és a bakteriorodopszin aminosav- sorrendjeinek összehasonlítása
A DAS szerver algoritmusa
DAS profiles of a TM protein as function of residue number
H i I o O A HMMTOP algoritmus
Ismert szegmensek lokalizációja
Pfam Prosite PrintsSmart S c a n n i n g TM selection of UniProtKB TOPDOM Protein A Protein B Protein C Unknown Protein Intracellular domain Q N C N C N C N C ? ?