Bioinformatics Practical for Biochemists
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1 Bioinformatics Practical for Biochemists Andrei Lupas, Birte Höcker, Steffen Schmidt WS 2013/ Sequence Features
2 Targeting proteins signal peptide targets proteins to the secretory pathway N-terminal sequence recognized while peptide is still synthesized on the ribosome Günter Blobel, 1999, nobelprize.org
3 Signal Peptide Prediction Sequence Logo of eukaryotic signal peptides Nielsen et al. (2007)
4 Signal Peptide Prediction - SignalP
5 Transmembrane Helices unusually long stretch of hydrophobic residues >18 hydrophobic amino acids hydrophobic interaction with lipids in membrane orientation of helix / topology of the protein looking at the loops : R & K mainly found on cytoplasmic side positive inside rule TGRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGL N C PDB-id: 1c3w
6 Transmembrane Helices TMHMM Accuracy of predicting TM helices high > 90% Accuracy of predicting the topology prediction > 75% Sonnhammer et al. (1998)
7 Transmembrane Helices TMHMM
8 Secondary Structure amino acid preferences -helix" β-strand" β-turn " Glu" 1.59" 0.52" 1.01" Ala" 1.41" 0.72" 0.92" Leu" 1.34" 1.22" 0.57" Met" 1.3" 1.14" 0.52" Gln" 1.27" 0.98" 0.84" Lys" 1.23" 0.69" 1.07" Arg" 1.21" 0.84" 0.9" His" 1.05" 0.8" 0.81" Val" 0.9" 1.87" 0.41" Ile" 1.09" 1.67" 0.47" Tyr" 0.74" 1.45" 0.76" Cys" 0.66" 1.4" 0.54" Trp" 1.02" 1.35" 0.65" Phe" 1.16" 1.33" 0.59" Thr" 0.76" 1.17" 0.9" Gly" 0.43" 0.58" 1.77" Asn" 0.76" 0.48" 1.34" Pro" 0.34" 0.31" 1.32" Ser" 0.57" 0.96" 1.22" Asp" 0.99" 0.39" 1.24" William (1987) Biochim Biophys Acta
9 Secondary Structure buried ß-sheet PDB: 1kgs, Buckler et al. (2002), Structure
10 Secondary Structure amphiphilic partially buried -helix PDB: 1kgs, Buckler et al. (2002), Structure
11 Secondary Structure amphiphilic ß-strand PDB: 1jat, VanDenmark et al. (2001), Cell
12 Secondary Structure collagen
13 Secondary Structure Prediction Toolkit Quick2D
14 Secondary Structure Prediction Toolkit Ali2D
15 Disordered Regions Today, programs predict that about 40% of all human proteins contain at least one intrinsically disordered segment of 30 amino acids or more, and that some 25% are likely to be disordered from beginning to end. lack of hydrophobic residues often with overrepresentation of a few amino acids
16 Secondary Structure Prediction Toolkit - Ali2D
17 Disorder Prediction IUPRED -
18 Short Linear Motifs Eukaryotic Linear Motifs (ELM) / Short Linear Motifs (SLiM) Hunt T (1990) These motifs are linear, in the sense that three- dimensional organization is not required to bring distant segments of the molecule together to make the recognizable unit. The conservation of these motifs varies: some are highly conserved while others allow substitutions that retain only a certain pattern of charge across the motif.
19 Short Linear Motifs Characteristics 3-11 amino acids long poorly conserved / evolve fast 1-3 amino acids in the motifs are hot spots ~ 80% in disordered regions relatively low affinity to interacting partner (1-150µM) interaction via induced fit
20 Short Linear Motifs Function protein-protein interactions post-translational modifications e.g. Phosphorylation proteolytic cleavage/processing sites KEN / D box in cell cycle - degradation signals subcellular targeting sites NES - nuclear export signal modulation of interactions - fine tuning
21 Short Linear Motifs Nuclear Localization Signal (NLS) Impor'n- beta (1qgk; blue) recognizes nuclear pores and moves through them. It wraps around the end of importin-alpha (1ee5; green), an adaptor molecule that connects importin-beta with the cargo, here nucleoplasmin(1k5j; yellow), a chaperone important in nucleosome assembly. All interactions are mediated by linear motifs in unstructured segments (bipartite nuclear localization signals). David Goodsell,
22 ELM Resources elm.eu.org NUPL_XENLA
23 NLS in nucleoplasmin Quick 2D secondary structure prediction for nucleoplasmin, showing the unstructured C-terminal tail and the bipartite nuclear localization motif !! MASTVSNTSKLEKPVSLIWGCELNEQNKTFEFKVEDDEEKCEHQLALRTVCLGDKAKDEFHIVEIVTQEEGAEKSVPIATLKPSILPMATMVGIELTPPVTFRLKAGSG! SS PSIPRED EEEEEEEE EEEE EEEEEEEEE EEEEEE EEEEEEEE EEE EE EEEEEE! SS JNET EEEEEEE EEE HHHHHHHHHHHH EEEEEEEE EEEEEE EEEEEE! DO DISOPRED2 DDDDDDDDDDDDDDDDD! DO IUPRED DDD D DDDD DDD D D DDD DDDDDDD DDDD D DDDD DDDD! SO Prof (Rost) B B B BBBBB B B B B B BBB BBB BBBB BB B BB B BB BB BBBB B B B B! SO JNET B BBBBBBBB B B B B B BBBBBBBBBBB B BBBBBBB B BBBBBB B B BBBB B B B BBB B B!! 150!! PLYISGQHVAMEEDYSWAEEEDEGEAEGEEEEEEEEDQESPPKAVKRPAATKKAGQAKKKKLDKEDESSEEDSPTKKGKGAGRGRKPAAKK! SS PSIPRED EEEEEEEEEE HH! SS JNET EEE E! DO DISOPRED2 DDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD! DO IUPRED DDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD! SO Prof (Rost) BBB BBB B B B B B! SO JNET BBBBBBBBBB!! SS = Alpha-Helix Beta-Sheet Secondary Structure! DO = Disorder! SO = Solvent accessibility (A burried residue has at most 25% of its surface exposed to the solvent.)!
24 DDX6 & Scd6 / EDC3 Interaction EDC3 LSM FDF FDK YjeF DDX6/Me31B DEAD-box helicase Scd6/Tral LSM FDF
25 DDX6 & Scd6 / EDC3 Interaction
26 DDX6 & Scd6 / EDC3 Interaction PDB: 2wax, Tritschler et al. (2009), Mol Cell
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