Скачать презентацию PROTEIN PHYSICS LECTURES 22 -23 PROTEIN STRUCTURE PREDICTION Скачать презентацию PROTEIN PHYSICS LECTURES 22 -23 PROTEIN STRUCTURE PREDICTION

F_L_22-23.ppt

  • Количество слайдов: 29

PROTEIN PHYSICS LECTURES 22 -23 PROTEIN STRUCTURE: PREDICTION ENGINEERING DESIGN PROTEIN PHYSICS LECTURES 22 -23 PROTEIN STRUCTURE: PREDICTION ENGINEERING DESIGN

Homology -- -- -- Homology -- -- --

PREDICTION FROM HOMOLOGY SIMILAR SEQUENCES SIMILAR FOLDS ____________ SEQUENCE ALIGNMENT: _______ BIOINFORMATICS PREDICTION FROM HOMOLOGY SIMILAR SEQUENCES SIMILAR FOLDS ____________ SEQUENCE ALIGNMENT: _______ BIOINFORMATICS

N 0 TWILIGHT ======= GOOD PREDICTION ======= N 0 TWILIGHT ======= GOOD PREDICTION =======

Multiple homology PROFILE with weights V E K K I TARGET SEQUENCE. . . Multiple homology PROFILE with weights V E K K I TARGET SEQUENCE. . . A P G D E F G - - H I K K L M A A T C H A L. . .

Multiple homology PROFILE with weights V E K K I TARGET SEQUENCE. . . Multiple homology PROFILE with weights V E K K I TARGET SEQUENCE. . . A P G D E F G - - H I K K L M A A T C H A L. . .

PREDICTION FROM PHYSICS: PROTEIN CHAIN FOLDS SPONTANEOUSLY SEQUENCE HAS ALL INFO TO PREDICT: 2 PREDICTION FROM PHYSICS: PROTEIN CHAIN FOLDS SPONTANEOUSLY SEQUENCE HAS ALL INFO TO PREDICT: 2 O STRUCTURE, 3 D STRUCTURE, SIDE CHAIN ROTAMERS, S-S BONDS, etc.

“Unique” fold? Dimerization involves an isomerization of the β-sheet. monomer Structurally equivalent residues are “Unique” fold? Dimerization involves an isomerization of the β-sheet. monomer Structurally equivalent residues are few and contribute either to the Ltn 10 core (red) or to the dimeric interface of Ltn 40 (cyan). Other nonpolar residues (orange) change sides, such that the formation of the dimeric interface on one side of the βsheet destroys the hydrophobic core on the other side and vice versa. dimer

no C : coil С , 1 : , , coil С , 2 no C : coil С , 1 : , , coil С , 2 : imino: coil, turn

Pro 1, 2, 3 rot. imino: coil, turn, N P no С : coil Pro 1, 2, 3 rot. imino: coil, turn, N P no С : coil С , 1 : , , coil С , 2 :

non-polar: cor polar: surface non-polar: cor polar: surface

non_polar: in the core polar: at the surface non_polar: in the core polar: at the surface

charged : coil, _N charged +: coil, _C Half-charged: active sites charged : coil, _N charged +: coil, _C Half-charged: active sites

Pcharged + Puncharged =1 Pcharged / Puncharged = 10 (p. Ka – p. H) Pcharged + Puncharged =1 Pcharged / Puncharged = 10 (p. Ka – p. H) = 10+(p. Ka – p. H) Acids (charge ) +) p. Ka | | Bases (charge p. Ka | | Half-charged: active sites

NOT (- , +) - + - charged : coil, _N === charged +: NOT (- , +) - + - charged : coil, _N === charged +: coil, _C = = +

PREDICTION FROM PHYSICS (OR PROTEIN STATISTICS) 2 O STRUCTURES USUALLY, THIS WORKS WELL, BUT… PREDICTION FROM PHYSICS (OR PROTEIN STATISTICS) 2 O STRUCTURES USUALLY, THIS WORKS WELL, BUT…

Prediction, 1985 A B C D. ---different--- X-ray str. , 1990 Prediction, 1985 A B C D. ---different--- X-ray str. , 1990

THREADING helps, when sequence identity is low (<10 -20%) BIOINFORMATICS THREADING helps, when sequence identity is low (<10 -20%) BIOINFORMATICS

… but one still cannot reliably predict 3 D protein structure from the a. … but one still cannot reliably predict 3 D protein structure from the a. a. sequence without homologues… WHY? ? choice of one structure out of two: DOES NOT require too precise estimate of interactions GAP choice of one structure out of zillions: REQUIRES very precise estimate of interactions GAP

Predicting 3 D structures of small proteins Predicting 3 D structures of small proteins

phase separation phase separation

Protein engineering Wanted: new protein with additional salt bridge (e. g. , His+: : Protein engineering Wanted: new protein with additional salt bridge (e. g. , His+: : : Asp-)

DESIGN De. Grado, 1989 DOES NOT MELT ! MOLTEN GLOBULE… + ION BINDING SOLID DESIGN De. Grado, 1989 DOES NOT MELT ! MOLTEN GLOBULE… + ION BINDING SOLID

DESIGN Natural protein (with Zn ion) Designed without ion: Mayo, 1997 DESIGN Natural protein (with Zn ion) Designed without ion: Mayo, 1997

DESIGN Ptitsyn Dolgikh Finkelstein Fedorov Kirpichnikov 1987 -97 Albebetin; Albeferon, … (grafting functional groups) DESIGN Ptitsyn Dolgikh Finkelstein Fedorov Kirpichnikov 1987 -97 Albebetin; Albeferon, … (grafting functional groups)

DESIGN OF A “HAMELION” PROTEIN: Direct single-molecule observation of a protein living in two DESIGN OF A “HAMELION” PROTEIN: Direct single-molecule observation of a protein living in two opposed native structures Y. Gambin, A. Schug, E. A. Lemke, J. J. Lavinder, A. C. M. Ferreon, T. J. Magliery, J. N. Onuchic, A. A. Deniz PNAS, 2009 v. 106, 10153– 8

GA binds to HSA GB binds to Ig. G Fc region Protein design Wanted: GA binds to HSA GB binds to Ig. G Fc region Protein design Wanted: new protein fold Y. He, Y. Chen, P. Alexander P. N. Bryan, J. Orban. PNAS, 2008, 105, 14412 -7 NMR structures of two designed proteins with high sequence identity but different fold and function. P. A. Alexander, Y. He, Y. Chen, J. Orban, P. N. Bryan PNAS, 2007, 104, 11963 -8 The design and characterization of two proteins with 88% sequence identity but different structure and function

2008 2008

PROTEIN STRUCTURE: PREDICTION ENGINEERING DESIGN PROTEIN STRUCTURE: PREDICTION ENGINEERING DESIGN