second genetic codeclasses.biology.ucsd.edu/bibc100.fa16/documents... · • protein engineering...
TRANSCRIPT
![Page 1: Second Genetic Codeclasses.biology.ucsd.edu/bibc100.FA16/documents... · • Protein engineering (mutagenesis) 1. S-S bridges a. -CH2-S-S-CH2-b. Analysis of all possibilities (many)](https://reader035.vdocuments.site/reader035/viewer/2022081407/5f1fce5329b4412d2a6360e3/html5/thumbnails/1.jpg)
Second Genetic Code:
Sequence StructureFolding
Design(reverse folding)
Computer Algorithm
Input Output
Folding Sequence Structure
Design Structure Sequence
![Page 2: Second Genetic Codeclasses.biology.ucsd.edu/bibc100.FA16/documents... · • Protein engineering (mutagenesis) 1. S-S bridges a. -CH2-S-S-CH2-b. Analysis of all possibilities (many)](https://reader035.vdocuments.site/reader035/viewer/2022081407/5f1fce5329b4412d2a6360e3/html5/thumbnails/2.jpg)
Protein Stability (thermal)• Protein engineering (mutagenesis)1. S-S bridges
a. -CH2-S-S-CH2-b. Analysis of all possibilities (many)c. Energy minimization to reduce to a few plausible candidatesd. Site-selective mutationse. Protein synthesisf. Assay:
example – T4 lysozyme (x-ray structure known)Reducing degrees of freedom (entropy) increases protein stability
![Page 3: Second Genetic Codeclasses.biology.ucsd.edu/bibc100.FA16/documents... · • Protein engineering (mutagenesis) 1. S-S bridges a. -CH2-S-S-CH2-b. Analysis of all possibilities (many)](https://reader035.vdocuments.site/reader035/viewer/2022081407/5f1fce5329b4412d2a6360e3/html5/thumbnails/3.jpg)
![Page 4: Second Genetic Codeclasses.biology.ucsd.edu/bibc100.FA16/documents... · • Protein engineering (mutagenesis) 1. S-S bridges a. -CH2-S-S-CH2-b. Analysis of all possibilities (many)](https://reader035.vdocuments.site/reader035/viewer/2022081407/5f1fce5329b4412d2a6360e3/html5/thumbnails/4.jpg)
![Page 5: Second Genetic Codeclasses.biology.ucsd.edu/bibc100.FA16/documents... · • Protein engineering (mutagenesis) 1. S-S bridges a. -CH2-S-S-CH2-b. Analysis of all possibilities (many)](https://reader035.vdocuments.site/reader035/viewer/2022081407/5f1fce5329b4412d2a6360e3/html5/thumbnails/5.jpg)
Protein Stability Cont…
2. Gly and Pro-Gly freedom-Pro Constraints (side chain is fixed by covalent bond to main chain- Gly Pro has propensity to increase stability (more delicate)- GlyAla usually increase- ProAla usually decrease
![Page 6: Second Genetic Codeclasses.biology.ucsd.edu/bibc100.FA16/documents... · • Protein engineering (mutagenesis) 1. S-S bridges a. -CH2-S-S-CH2-b. Analysis of all possibilities (many)](https://reader035.vdocuments.site/reader035/viewer/2022081407/5f1fce5329b4412d2a6360e3/html5/thumbnails/6.jpg)
Protein Stability Cont…
3. Dipolar stabilityN-end (-a.a.)
C-end (+a.a.)increase stability by mutating residues at N-
end of helices from polar to negative (e.g. ASNASP, SERASP)
Helix:
![Page 7: Second Genetic Codeclasses.biology.ucsd.edu/bibc100.FA16/documents... · • Protein engineering (mutagenesis) 1. S-S bridges a. -CH2-S-S-CH2-b. Analysis of all possibilities (many)](https://reader035.vdocuments.site/reader035/viewer/2022081407/5f1fce5329b4412d2a6360e3/html5/thumbnails/7.jpg)
![Page 8: Second Genetic Codeclasses.biology.ucsd.edu/bibc100.FA16/documents... · • Protein engineering (mutagenesis) 1. S-S bridges a. -CH2-S-S-CH2-b. Analysis of all possibilities (many)](https://reader035.vdocuments.site/reader035/viewer/2022081407/5f1fce5329b4412d2a6360e3/html5/thumbnails/8.jpg)
Protein Stability4. Hydrophobicity in the core (cavity)
-Barnase (bacterial RNAse-110 a.a.)-structure by both x-ray and NMR
-introducing cavities in the core by mutations such as IleVal or PheLeu
Cavity for a CH2
Stability by 1kcal/mol
-More delicate design-Needs structure
![Page 9: Second Genetic Codeclasses.biology.ucsd.edu/bibc100.FA16/documents... · • Protein engineering (mutagenesis) 1. S-S bridges a. -CH2-S-S-CH2-b. Analysis of all possibilities (many)](https://reader035.vdocuments.site/reader035/viewer/2022081407/5f1fce5329b4412d2a6360e3/html5/thumbnails/9.jpg)
Agonist of the erythropoietin receptor identified from peptide libraries
![Page 10: Second Genetic Codeclasses.biology.ucsd.edu/bibc100.FA16/documents... · • Protein engineering (mutagenesis) 1. S-S bridges a. -CH2-S-S-CH2-b. Analysis of all possibilities (many)](https://reader035.vdocuments.site/reader035/viewer/2022081407/5f1fce5329b4412d2a6360e3/html5/thumbnails/10.jpg)
Prediction of Structure From Sequence
• Empirical – in progress• ~75% successful-at best (62-65%). For the membrane-
embedded domains of membrane proteins up to 90%• Essence: Pattern Recognition• Key: Evolutionary Information
– Sequence homology implies similarity in structure and function– By inference/By Anaysis
• Data bases (2007 >500,000 seq., 2015 >107,000 Structures
• Information: Prediction• Example: Homologous proteins
Conserved Core Variable Loop
![Page 11: Second Genetic Codeclasses.biology.ucsd.edu/bibc100.FA16/documents... · • Protein engineering (mutagenesis) 1. S-S bridges a. -CH2-S-S-CH2-b. Analysis of all possibilities (many)](https://reader035.vdocuments.site/reader035/viewer/2022081407/5f1fce5329b4412d2a6360e3/html5/thumbnails/11.jpg)
Secondary Structure Prediction for 3-Model
• Predict: α, β, loop, β-turn• Predict: membrane-spanning α-helix• Predict: Amphipatic structures
α β• Prediction of the folded structure of
tryptophan synthetase, and• the catalytic subunit of c-AMP dependent
protein kinase
![Page 12: Second Genetic Codeclasses.biology.ucsd.edu/bibc100.FA16/documents... · • Protein engineering (mutagenesis) 1. S-S bridges a. -CH2-S-S-CH2-b. Analysis of all possibilities (many)](https://reader035.vdocuments.site/reader035/viewer/2022081407/5f1fce5329b4412d2a6360e3/html5/thumbnails/12.jpg)
Chou & Fassman (1974)• Frequency of occurrence of a given a.a. in α, β,
and loops in all protein structures in the database (statistical)
• Nearest neighbors• output: probability for each residue to be in α,
β, or Loop• Artificial intelligence/neural networks
– Train a computer to recognize patterns – the more information and the “more practice” the higher the accuracy (in progress)
![Page 13: Second Genetic Codeclasses.biology.ucsd.edu/bibc100.FA16/documents... · • Protein engineering (mutagenesis) 1. S-S bridges a. -CH2-S-S-CH2-b. Analysis of all possibilities (many)](https://reader035.vdocuments.site/reader035/viewer/2022081407/5f1fce5329b4412d2a6360e3/html5/thumbnails/13.jpg)
![Page 14: Second Genetic Codeclasses.biology.ucsd.edu/bibc100.FA16/documents... · • Protein engineering (mutagenesis) 1. S-S bridges a. -CH2-S-S-CH2-b. Analysis of all possibilities (many)](https://reader035.vdocuments.site/reader035/viewer/2022081407/5f1fce5329b4412d2a6360e3/html5/thumbnails/14.jpg)
![Page 15: Second Genetic Codeclasses.biology.ucsd.edu/bibc100.FA16/documents... · • Protein engineering (mutagenesis) 1. S-S bridges a. -CH2-S-S-CH2-b. Analysis of all possibilities (many)](https://reader035.vdocuments.site/reader035/viewer/2022081407/5f1fce5329b4412d2a6360e3/html5/thumbnails/15.jpg)
![Page 16: Second Genetic Codeclasses.biology.ucsd.edu/bibc100.FA16/documents... · • Protein engineering (mutagenesis) 1. S-S bridges a. -CH2-S-S-CH2-b. Analysis of all possibilities (many)](https://reader035.vdocuments.site/reader035/viewer/2022081407/5f1fce5329b4412d2a6360e3/html5/thumbnails/16.jpg)
Bacterial Photosynthetic Reaction Center
![Page 17: Second Genetic Codeclasses.biology.ucsd.edu/bibc100.FA16/documents... · • Protein engineering (mutagenesis) 1. S-S bridges a. -CH2-S-S-CH2-b. Analysis of all possibilities (many)](https://reader035.vdocuments.site/reader035/viewer/2022081407/5f1fce5329b4412d2a6360e3/html5/thumbnails/17.jpg)
![Page 18: Second Genetic Codeclasses.biology.ucsd.edu/bibc100.FA16/documents... · • Protein engineering (mutagenesis) 1. S-S bridges a. -CH2-S-S-CH2-b. Analysis of all possibilities (many)](https://reader035.vdocuments.site/reader035/viewer/2022081407/5f1fce5329b4412d2a6360e3/html5/thumbnails/18.jpg)
![Page 19: Second Genetic Codeclasses.biology.ucsd.edu/bibc100.FA16/documents... · • Protein engineering (mutagenesis) 1. S-S bridges a. -CH2-S-S-CH2-b. Analysis of all possibilities (many)](https://reader035.vdocuments.site/reader035/viewer/2022081407/5f1fce5329b4412d2a6360e3/html5/thumbnails/19.jpg)
Bacterial Photosynthetic Reaction Center
![Page 20: Second Genetic Codeclasses.biology.ucsd.edu/bibc100.FA16/documents... · • Protein engineering (mutagenesis) 1. S-S bridges a. -CH2-S-S-CH2-b. Analysis of all possibilities (many)](https://reader035.vdocuments.site/reader035/viewer/2022081407/5f1fce5329b4412d2a6360e3/html5/thumbnails/20.jpg)
Protein Codesaa Sequence, 1D
Structure, 3D
REVERSE FOLDING(design)
FOLDING
http://www.npaci.edu/enVision/v15.4/images/proteinfolding1.jp
![Page 21: Second Genetic Codeclasses.biology.ucsd.edu/bibc100.FA16/documents... · • Protein engineering (mutagenesis) 1. S-S bridges a. -CH2-S-S-CH2-b. Analysis of all possibilities (many)](https://reader035.vdocuments.site/reader035/viewer/2022081407/5f1fce5329b4412d2a6360e3/html5/thumbnails/21.jpg)
Design
• Minibody• Chymohelizyme• Calcium sensor• Acetylcholine Receptor Channel
![Page 22: Second Genetic Codeclasses.biology.ucsd.edu/bibc100.FA16/documents... · • Protein engineering (mutagenesis) 1. S-S bridges a. -CH2-S-S-CH2-b. Analysis of all possibilities (many)](https://reader035.vdocuments.site/reader035/viewer/2022081407/5f1fce5329b4412d2a6360e3/html5/thumbnails/22.jpg)
Minibody
• 61 residue synthetic peptide• All • Template: Heavy chain variable domain of
the immunoglobulin• Hypervariable loops• Binding site: Histidines in each
hypervariable loop• The protein folds and binds Zn2+
• Nature 362: March 25, 1993
![Page 23: Second Genetic Codeclasses.biology.ucsd.edu/bibc100.FA16/documents... · • Protein engineering (mutagenesis) 1. S-S bridges a. -CH2-S-S-CH2-b. Analysis of all possibilities (many)](https://reader035.vdocuments.site/reader035/viewer/2022081407/5f1fce5329b4412d2a6360e3/html5/thumbnails/23.jpg)
Chymohelizyme• Design: Computer-assisted protein design• Four helix bundle – parallel, amphipathic• Serine protease catalytic triad –Ser, His, Asp at
the N-end of the four-helix bundle in the same spatial arrangement as chymotrypsin
• Oxyanion hole and substrate binding pocket for acetyltyrosineethylester, a classical substrate of CT were included in the design
• Synthetic enzyme folds, is catalytically active and sensitive to a specific inhibitor
• Science 248:1544, 1990)
![Page 24: Second Genetic Codeclasses.biology.ucsd.edu/bibc100.FA16/documents... · • Protein engineering (mutagenesis) 1. S-S bridges a. -CH2-S-S-CH2-b. Analysis of all possibilities (many)](https://reader035.vdocuments.site/reader035/viewer/2022081407/5f1fce5329b4412d2a6360e3/html5/thumbnails/24.jpg)
Channel Design
REVERSE FOLDINGDesign
Sequence?
![Page 25: Second Genetic Codeclasses.biology.ucsd.edu/bibc100.FA16/documents... · • Protein engineering (mutagenesis) 1. S-S bridges a. -CH2-S-S-CH2-b. Analysis of all possibilities (many)](https://reader035.vdocuments.site/reader035/viewer/2022081407/5f1fce5329b4412d2a6360e3/html5/thumbnails/25.jpg)
The Acetylcholine Receptor• Nicotinic acetylcholine receptor: A pentamer
– Ion channel for influx of Na+, Ca2+– Gate opened by acetylcholine
![Page 26: Second Genetic Codeclasses.biology.ucsd.edu/bibc100.FA16/documents... · • Protein engineering (mutagenesis) 1. S-S bridges a. -CH2-S-S-CH2-b. Analysis of all possibilities (many)](https://reader035.vdocuments.site/reader035/viewer/2022081407/5f1fce5329b4412d2a6360e3/html5/thumbnails/26.jpg)
Channel Design
REVERSE FOLDING
EKMSTAISVLLAQAVFLLLTSQR ?
design
![Page 27: Second Genetic Codeclasses.biology.ucsd.edu/bibc100.FA16/documents... · • Protein engineering (mutagenesis) 1. S-S bridges a. -CH2-S-S-CH2-b. Analysis of all possibilities (many)](https://reader035.vdocuments.site/reader035/viewer/2022081407/5f1fce5329b4412d2a6360e3/html5/thumbnails/27.jpg)
The Acetylcholine Receptor: Pentamer
M2 HELICES
![Page 28: Second Genetic Codeclasses.biology.ucsd.edu/bibc100.FA16/documents... · • Protein engineering (mutagenesis) 1. S-S bridges a. -CH2-S-S-CH2-b. Analysis of all possibilities (many)](https://reader035.vdocuments.site/reader035/viewer/2022081407/5f1fce5329b4412d2a6360e3/html5/thumbnails/28.jpg)
Channel Design
REVERSE FOLDING
EKMSTAISVLLAQAVFLLLTSQR ?
design
![Page 29: Second Genetic Codeclasses.biology.ucsd.edu/bibc100.FA16/documents... · • Protein engineering (mutagenesis) 1. S-S bridges a. -CH2-S-S-CH2-b. Analysis of all possibilities (many)](https://reader035.vdocuments.site/reader035/viewer/2022081407/5f1fce5329b4412d2a6360e3/html5/thumbnails/29.jpg)
M2 Channels:Pentamer (T5M2)
K*AK*KK*PEK*EK*G
* = M2 = EKMSTAISVLLAQAVFLLLTSQR
Montal et al. Design, synthesis and functional characterization of a pentameric channel protein that mimics the presumed pore structure of the nicotinic cholinergic receptor. FEBS Lett. 1993, 209(3): p. 261-266.
![Page 30: Second Genetic Codeclasses.biology.ucsd.edu/bibc100.FA16/documents... · • Protein engineering (mutagenesis) 1. S-S bridges a. -CH2-S-S-CH2-b. Analysis of all possibilities (many)](https://reader035.vdocuments.site/reader035/viewer/2022081407/5f1fce5329b4412d2a6360e3/html5/thumbnails/30.jpg)
NMR:Structure and Orientation
Opella et al. Structures of the M2 channel-lining segments from nicotinic acetylcholine and NMDA receptors by NMR spectroscopy. Nat. Struct. Biol., 1999; 6(4): p. 374-9.
![Page 31: Second Genetic Codeclasses.biology.ucsd.edu/bibc100.FA16/documents... · • Protein engineering (mutagenesis) 1. S-S bridges a. -CH2-S-S-CH2-b. Analysis of all possibilities (many)](https://reader035.vdocuments.site/reader035/viewer/2022081407/5f1fce5329b4412d2a6360e3/html5/thumbnails/31.jpg)
NMR STRUCTURE MODEL
Opella et al. Structures of the M2 channel-lining segments from nicotinic acetylcholine and NMDA receptors by NMR spectroscopy. Nat. Struct. Biol., 1999; 6(4): p. 374-9.
![Page 32: Second Genetic Codeclasses.biology.ucsd.edu/bibc100.FA16/documents... · • Protein engineering (mutagenesis) 1. S-S bridges a. -CH2-S-S-CH2-b. Analysis of all possibilities (many)](https://reader035.vdocuments.site/reader035/viewer/2022081407/5f1fce5329b4412d2a6360e3/html5/thumbnails/32.jpg)
Moving closer?
Unwin, N. Refined Structure of the Nicotinic Acetylcholine Receptor at 4A Resolution. J. Mol. Biol., 2005; 346(4): p. 967-89.
2003 2005
![Page 33: Second Genetic Codeclasses.biology.ucsd.edu/bibc100.FA16/documents... · • Protein engineering (mutagenesis) 1. S-S bridges a. -CH2-S-S-CH2-b. Analysis of all possibilities (many)](https://reader035.vdocuments.site/reader035/viewer/2022081407/5f1fce5329b4412d2a6360e3/html5/thumbnails/33.jpg)
Acetylcholine Receptor Structure @ 4 Å in 2005
Unwin, N. Refined Structure of the Nicotinic Acetylcholine Receptor at 4A Resolution. J. Mol. Biol., 2005; 346(4): p. 967-89.
![Page 34: Second Genetic Codeclasses.biology.ucsd.edu/bibc100.FA16/documents... · • Protein engineering (mutagenesis) 1. S-S bridges a. -CH2-S-S-CH2-b. Analysis of all possibilities (many)](https://reader035.vdocuments.site/reader035/viewer/2022081407/5f1fce5329b4412d2a6360e3/html5/thumbnails/34.jpg)
Channel Design
REVERSE FOLDING
EKMSTAISVLLAQAVFLLLTSQR
FOLDING design
![Page 35: Second Genetic Codeclasses.biology.ucsd.edu/bibc100.FA16/documents... · • Protein engineering (mutagenesis) 1. S-S bridges a. -CH2-S-S-CH2-b. Analysis of all possibilities (many)](https://reader035.vdocuments.site/reader035/viewer/2022081407/5f1fce5329b4412d2a6360e3/html5/thumbnails/35.jpg)
Channel Design
REVERSE FOLDING
EKMSTAISVLLAQAVFLLLTSQR ?
design
![Page 36: Second Genetic Codeclasses.biology.ucsd.edu/bibc100.FA16/documents... · • Protein engineering (mutagenesis) 1. S-S bridges a. -CH2-S-S-CH2-b. Analysis of all possibilities (many)](https://reader035.vdocuments.site/reader035/viewer/2022081407/5f1fce5329b4412d2a6360e3/html5/thumbnails/36.jpg)
Protein Codesaa Sequence, 1D
Structure, 3D
REVERSE FOLDING(design)
FOLDING
http://www.npaci.edu/enVision/v15.4/images/proteinfolding1.jp