Protein Properties

Function, structure

Residue features

Targeting

Post-trans modifications

BIO520 Bioinformatics Jim Lund

Reading: Chapter 11.1-3, 11.7, 12.1, Ch 14

Protein function, structure

• Homology to known proteins through protein search and alignment

• Functional domains– NCBI CDD (conserved domain database)

– Interpro (PROSITE, Pfam, SMART, etc.)

Simple Analyses

• Composition (#’s of each aa)• Isoelectric point• Extinction co-efficient• Peptide cleavage• Repetitive regions

ExPASy, BCM Search Launcher, other sites.

CDD domains in Insulin-Like Growth Factor Receptor

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 -7.3410.00 9.97 23.23 0.00 8.09 0.06 0.00 0.00 0.04 0.00 41.39 -10.6110.50 9.90 17.85 0.00 6.64 0.02 0.00 0.00 0.01 0.00 34.42 -17.5811.00 9.69 10.30 0.00 4.24 0.01 0.00 0.00 0.00 0.00 24.24 -27.7611.50 9.09 4.41 0.00 1.98 0.00 0.00 0.00 0.00 0.00 15.48 -36.52

PeptideMapPeptideSort

• Cleave polypeptide with proteases, reagents

• Predict HPLC properties of peptide fragments

Protein Analyses

• Secondary Structure Prediction

• Hydrophobicity/membrane insertion

• Antigenicity

• Surface AccessibilityBaylor Search Launcher: http://searchlauncher.bcm.tmc.edu/seq-search/struc-predict.htmlExPASy: http://www.expasy.ch/tools/

Secondary Structure Prediction

• Amino acid preferences

• Local aa interactions

• Non-local interactions

• Homology/Multiple alignments

• 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

Secondary Structure Prediction

Membrane Association

• Hydropathy, Hydophobicity Gtransfer (water-vapor)

– % sidechains buried (100% or 95%)

• Identify membrane-associated regions

• Identify membrane-spanning regions (>16 aa, ~80 Å helix)

HydrophobicityMembrane Topology

Original paper:• Kyte-Doolittle

– J. Mol. Biol. (1978) 157:105-132

Further refinements:• Hopp-Woods

– Proc Natl Acad Sci U S A (1981) 78:3824

• Gunnar von Heijne• GES-scale (Goldman, Engelman, Steitz)

– Engelman et al, 1982

SOAP (Kyte-Doolittle) Plots

Membrane Topology

• Hydrophobic helices• Dipoles aligned• Charges?

• What is the overall structure?

• External and internal domains?

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

Surface Accessibility

• Emini et al (1985) 55:836

• Can also calculate (for real) on a PDB structure via WWW

http://www.bork.embl-heidelberg.de/ASC/scr1-form.html

Antigenicity

• Jameson and Wolf (CABIOS 4:181)– Sums secondary structure indices, surface

accessibility, backbone flexibility

– Many good epitopes are linear, surface loops

• Used when “picking” antigenic peptides

Transmembrane segment prediction

• Hydrophobicity

• Membrane association/topology

• Programs– PHDhtm

– TopPred

– TMHMM