Protein Properties

1
Protein Properties

• Function, structure
• Residue features
• Targeting
• Post-trans modifications

BIO520 Bioinformatics Jim Lund
2
Protein function, structure

• Homology to known proteins through protein search
  and alignment
• Functional domains
• NCBI CDD (conserved domain database)
• Interpro (PROSITE, Pfam, SMART, etc.)

3
Simple Analyses

• Composition (s of each aa)
• Isoelectric point
• Extinction co-efficient
• Peptide cleavage
• Repetitive regions
• ExPASy, BCM Search Launcher, other sites.

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CDD domains in Insulin-Like Growth Factor Receptor
5
Composition
(Peptide) COMPOSITION of (Human
glyceraldehyde-3-phosphate dehydrogenase) .pep
Check 5354 from 1 to 334 October 6, 1998
1318 A
33 C 3 D 23 E
16 F 15 G 34 H 10
I 21 K 27 L 20
M 9 N 13 P 11 Q 4
R 10 S 20 T 21
V 32 W 3 Y 9
Other 0
Total 334
6
Isoelectric Point(pI)
Number of Hydrogen Ions Bound
--------------------------------------------------
-------- Net pH Arg Lys His Tyr
Cys Glu Asp NH2 COOH Total Charge ..
1.00 10.00 27.00 10.00 9.00 3.00 15.99 22.97
1.00 1.00 99.96 47.96 1.50 10.00 27.00
10.00 9.00 3.00 15.97 22.91 1.00 0.99 99.87
47.87 2.00 10.00 27.00 10.00 9.00 3.00
15.91 22.72 1.00 0.97 99.60 47.60 2.50
10.00 27.00 10.00 9.00 3.00 15.72 22.14 1.00
0.92 98.78 46.78 3.00 10.00 27.00 10.00
9.00 3.00 15.15 20.48 1.00 0.78 96.41
44.41 3.50 10.00 27.00 9.99 9.00 3.00 13.58
16.56 1.00 0.53 90.67 38.67 4.00 10.00
27.00 9.97 9.00 3.00 10.24 10.31 1.00 0.27
80.79 28.79 4.50 10.00 27.00 9.90 9.00
3.00 5.76 4.70 1.00 0.10 70.47 18.47
5.00 10.00 27.00 9.69 9.00 3.00 2.42 1.73
1.00 0.04 63.87 11.87 5.50 10.00 27.00
9.09 9.00 3.00 0.85 0.58 1.00 0.01 60.52
8.52 6.00 10.00 27.00 7.60 9.00 2.99 0.28
0.19 1.00 0.00 58.05 6.05 6.50 10.00
27.00 5.00 9.00 2.95 0.09 0.06 0.99 0.00
55.09 3.09 7.00 10.00 27.00 2.40 9.00
2.86 0.03 0.02 0.97 0.00 52.27 0.27
7.50 10.00 26.99 0.91 9.00 2.59 0.01 0.01
0.92 0.00 50.42 -1.58 8.00 10.00 26.96
0.31 8.99 2.00 0.00 0.00 0.78 0.00 49.04
-2.96 8.50 10.00 26.86 0.10 8.97 1.16 0.00
0.00 0.53 0.00 47.63 -4.37 9.00 10.00
26.57 0.03 8.90 0.50 0.00 0.00 0.27 0.00
46.26 -5.74 9.50 9.99 25.68 0.01 8.69
0.18 0.00 0.00 0.10 0.00 44.66
-7.34 10.00 9.97 23.23 0.00 8.09 0.06 0.00
0.00 0.04 0.00 41.39 -10.61 10.50 9.90
17.85 0.00 6.64 0.02 0.00 0.00 0.01 0.00
34.42 -17.58 11.00 9.69 10.30 0.00 4.24
0.01 0.00 0.00 0.00 0.00 24.24
-27.76 11.50 9.09 4.41 0.00 1.98 0.00 0.00
0.00 0.00 0.00 15.48 -36.52
7
Extinction co-efficient
SH
S-S
1?g/ml

• Used for determining protein concentration.
• Based on number C, Y, and W residues.

8
PeptideMapPeptideSort

• Cleave polypeptide with proteases, reagents
• Predict HPLC properties of peptide fragments

9
Protein Analyses

• Secondary Structure Prediction
• Hydrophobicity/membrane insertion
• Antigenicity
• Surface Accessibility

http//searchlauncher.bcm.tmc.edu/seq-search/stru
c-predict.html http//www.expasy.ch/tools/
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Secondary Structure Prediction

• Amino acid preferences
• Local aa interactions
• Non-local interactions
• Homology/Multiple alignments

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Secondary Structure Prediction

• Predict H, E, L (Helix, B-strand, Loop)
• 75 aa accuracy
• Programs
• APSSP
• Jpred
• PHDsec
• SAM-T99
• PredictProtein
• Web sites
• BCM Search Launcher
• ExPASy Tools

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Membrane Association

• Hydropathy, Hydophobicity
• ?Gtransfer (water-vapor)
• sidechains buried (100 or 95)
• Identify membrane-associated regions
• Identify membrane-spanning regions (gt16 aa, 80 Å
  helix)

10 proteins membrane bound
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HydrophobicityMembrane Topology

• Original paper
• Kyte-Doolittle
• J. Mol. Biol. (1978) 157105-132
• Further refinements
• Hopp-Woods
• Proc Natl Acad Sci U S A (1981) 783824

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SOAP (Kyte-Doolittle) Plots
Membrane-spanning
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Membrane Topology

• Hydrophobic helices
• Dipoles aligned
• Charges?
• What is the overall structure?
• External and internal domains?

16
Localization

• Signal sequences direct proteins
• Usually N or C terminal signal sequences
• Targeted to membrane, secretion, nucleus,
  mitochondria, chloroplast, lysosome, peroxisome,
  periplasm
• Program criteria N-term motifs, aa composition,
  protein domains specific to locations, homology
  to proteins with experimentally determined
  locations.
• Accuracy varies with type of prediction, 50-80
• Programs
• WoLF PSORT (eukaryotic), PSORTb (bacterial),
  PSORT (plant)
• SUBLOC
• TargetP

17
Surface Accessibility

• Emini et al (1985) 55836
• Can also calculate (for real) on a PDB structure
  via WWW
• http//www.bork.embl-heidelberg.de/ASC/scr1-form.h
  tml

18
Antigenicity

• Jameson and Wolf (CABIOS 4181)
• Sums secondary structure indices, surface
  accessibility, backbone flexibility
• Many epitopes linear, surface loops
• Used when picking antigenic peptides

19
Transmembrane segment prediction

• Hydrophobicity
• Membrane association/topology
• Programs
• PHDhtm
• TopPred
• TMHMM