structures
Protein structures
Protein denaturation & folding
Protein structure prediction, engineering, design
Proteins in action
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Introduction & overview презентация
Содержание
- 1. Introduction & overview
- 2. Олег Борисович Птицын (1929-1999)
- 3. PROTEIN PHYSICS LECTURE 1 Introduction & overview
- 4. Globular proteins Fibrous proteins H-bonds (NH:::OC) & hydrophobic forces Membrane proteins
- 5. Protein chain (gene-encoded sequence)
- 6. Secondary structures (α-helices, β-strands) are most
- 9. Globular proteins Fibrous proteins H-bonds (NH:::OC)
- 10. Globular domains C A T H
- 11. PROTEIN CHAIN CAN FORM ITS UNIQUE 3D STRUCTURE SPONTANEOUSLY IN VITRO
- 12. phase separation
- 13. BIND ? TRANSFORM ? RELEASE: ENZYMES (chymotrypsin) Note small active site
- 14. POST-TRANSLATIONAL MODIFICATIONS Sometimes, CHAIN CUT-INDUCED DEFORMATION MAKES
- 15. POST-TRANSLATIONAL MODIFICATIONS: (especially in eukaryotes): PROTEIN
- 16. Sometimes: Different folds with the same active site: the same biochemical function
- 17. Sometimes: Similar folds with different active
- 18. Standard positions of active sites in protein folds
- 19. Natively disordered protein: X-ray + SAXS + NMR + MD simulations
- 20. Chaperone GroEL
- 21. ______ NMR
- 22. Protein engineering Wanted: new protein with additional
- 23. PROTEIN PHYSICS LECTURE 2 Elementary interactions: covalent
- 24. Protein chain: regular backbone & gene-encoded sequence of side chains
- 25. Protein chain Covalent bond lengths: 0.9 –
- 26. Side chains
- 27. Main-chain: peptide group: flat & rigid
- 28. Ala _L Gly Thr Ile
- 29. ~ V = ±|V| ≅ semi-classical approximation
- 30. Werner Karl Heisenberg (1901-76) — Nobel Prize 1932 Wolfgang Ernst Pauli ) (1900-58) — Nobel Prize 1945
- 31. Peptide group: flat & rigid sp2
- 32. Main-chain: φ (N-Cα) , ψ (Cα-C’),
- 33. Counting angles: _____________________________________________ 0o 180o 120o
- 34. sp2 - sp2 (ω) ω =
- 35. Potentials: from IR spectra of vibrations
- 36. Harold Abraham Scheraga (1921) Paul
- 37. The Nobel Prize in Chemistry 2013
Олег Борисович Птицын (1929-1999)
Слайд 1
PROTEIN PHYSICS
Introduction & overview
Structure elements & elementary interactions
Transitions: thermodynamics & kinetics
Secondary
Слайд 6Secondary structures (α-helices, β-strands)
are most conserved structural elements.
They form
a basis of protein classification
One protein - various
crystallization, NMR
Homologous
(closely related)
proteins
PROTEIN HAS DEFINITE 3D STRUCTURE
Слайд 9
Globular proteins
Fibrous proteins
H-bonds (NH:::OC) & hydrophobic forces
Membrane
proteins
Sequence
&
Structure
Слайд 14POST-TRANSLATIONAL MODIFICATIONS
Sometimes,
CHAIN CUT-INDUCED DEFORMATION MAKES ENZYME ACTIVE
Chymotripsin
Chymotripsinogen
active cat. site
non-active cat. site
Слайд 15POST-TRANSLATIONAL MODIFICATIONS: (especially in eukaryotes): PROTEIN CHAIN CUTS (proteolysis),
- SPLICING (inteins)
- CYCLIZATION
- INTERNAL CHEM. TRANSFORMATION
GLYCOSYLATION, etc.
MODIFICATION OF ENDS (acetylation, etc.)
MODIFICATION OF SIDE CHAINS (S-S bonding,
phosphorilation, etc.)
COFACTORS …
Слайд 17Sometimes:
Similar folds with different active sites: different biochemical function
4-helix bundle
COFACTORS:
HEME, 2Fe, RNA, …
Слайд 25Protein chain
Covalent bond lengths:
0.9 – 1.8 Å
Covalent bond angles:
109o – 120o
Atom
radii:
1 – 2 Å
1 – 2 Å
Слайд 27Main-chain:
peptide group:
flat & rigid
Side chains: L
amino acids
___
______
______
Protein chain
Слайд 28Ala _L
Gly
Thr
Ile
Two
asymmetric
side
chains:
Symmetric
Asymmetric
backbone-to-
side_chain:
Stereo images
Слайд 30
Werner Karl Heisenberg (1901-76)
— Nobel Prize 1932
Wolfgang Ernst Pauli ) (1900-58)
— Nobel Prize 1945
Слайд 31Peptide group:
flat & rigid
sp2 + p sp2
+ p
Covalent bonding in peptide group:
=
Pauling resonance
theory of = bonds:
O=C-N ↔ O-C=N
Linus Carl Pauling
(1901-94)
— Nobel Prizes:
1954, 62
O
O
↓
O C N
Слайд 35Potentials: from IR spectra of vibrations
sp2 - sp2 (ω)
sp3
– sp3 (χ)
sp2 – sp3 (φ, ψ)
_____________________________________________
classical
Pro
All,
except Pro
H3C-CH3
H3C-C6H5
Слайд 36
Harold
Abraham
Scheraga
(1921)
Paul John Flory (1910-85)
— Nobel Prize 1974
Александр
Исаакович
Китайгородский
(1914–1985)
Михаил Владимирович
Волькенштейн (1912-92)
Олег Борисович
Птицын
(1929-99)
Поворотно-изомерная теория полимеров
Конформационный анализ
Слайд 37
The Nobel Prize in Chemistry 2013
Martin Karplus
Michael Levitt Arieh Warshel
"for the development of multiscale models
for complex chemical systems"
(conformational & quantum-mechanical methods)
