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Protein Properties

Explore the properties, functions, and structures of proteins, including residue features and targeting mechanisms for post-translational modifications. Learn about reading methods and tools such as NCBI CDD and Interpro, protein composition analysis, isoelectric point determination, and cleavage patterns. Gain insights from simple analyses like CDD domains in specific proteins like the Insulin-Like Growth Factor Receptor.

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Protein Properties

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  1. Protein Properties Function, structure Residue features Targeting Post-trans modifications Reading: Chapter 11.1-3, 11.7, 12.1, Ch 14 BIO520 Bioinformatics Jim Lund

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

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

  4. CDD domains in Insulin-Like Growth Factor Receptor

  5. 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

  6. Cleave polypeptide with proteases, reagents Predict HPLC properties of peptide fragments PeptideMapPeptideSort

  7. Secondary Structure Prediction Hydrophobicity/membrane insertion Antigenicity Surface Accessibility Protein Analyses Baylor Search Launcher: http://searchlauncher.bcm.tmc.edu/seq-search/struc-predict.html ExPASy: http://www.expasy.ch/tools/

  8. Amino acid preferences Local aa interactions Non-local interactions Homology/Multiple alignments Secondary Structure Prediction

  9. 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

  10. Hydropathy, Hydophobicity Gtransfer (water-vapor) % sidechains buried (100% or 95%) Identify membrane-associated regions Identify membrane-spanning regions (>16 aa, ~80 Å helix) Membrane Association ~10% proteins membrane bound

  11. 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 HydrophobicityMembrane Topology

  12. SOAP (Kyte-Doolittle) Plots Membrane-spanning

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

  14. 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 Localization

  15. 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 Surface Accessibility

  16. 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 Antigenicity

  17. Hydrophobicity Membrane association/topology Programs PHDhtm TopPred TMHMM Transmembrane segment prediction

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