protein feature analysis Flashcards

1
Q

membrane proteins

A
  • single spanning segments or entire protein domains
  • membrane region is in a hydrophobic environment
  • side-chains tend to be hydrophobic
  • main chains cna’t have NH/CO groups that don’t form hydrogen bonds
  • single spanning must be alpha helical
  • most are alpha helical
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2
Q

transmembrane helices

A
  • hydrophobic section ~35-50A wide
  • often positive charges in the section abutting the membrane
  • each residue in helix advances structure by 1.8A
  • usually 20-30 residues long
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3
Q

methods to identify TM regions

A
  • early methods
    • search for runs of hydrophobic residues
    • scale of hydrophobicity
      • Hopp & Woods
      • Kyte & Doolittle
    • hydrophobic plots
  • current methods
    • machine learning based
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4
Q

hydrophobic plots

A
  • moving window of 11 residues
  • count hydrophobicity according to scale
  • above a cutoff indicates TM region
  • originally few sequences known
    • improved by sequence availability
    • build up to create HMM for ML
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5
Q

mahcine learning methods of TM identification

A
  • HMMs, neural networks or SVM
  • OCTOPUS, PHOBIUS
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6
Q

homology searching with TM regions

A
  • many TM regions have similar hydrophobic residues
  • easy to find false matches for your protein that seem significant
  • conservative cutoffs needed
  • can be better if only intracellular/extracellular parts of sequence put in to e.g. PSI-BLAST
    • reduce false matches
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7
Q

signal peptides

A
  • 15-60 residues at start of protein
  • directs to correct cellular location
  • generally cleaved
  • often hydrophobic region followed by pattern (cleavage site)
  • SignalP:
    • HMMs and neural networks to rpedict location
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8
Q

low complexity regions

A
  • composition biased strongly to a small number of amino acids
  • in many proteins
  • distorts statistical significance of alignments
  • SEG
    • replaces low complexity with lower case letters in blast
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9
Q

coiled coils

A
  • 2/3 intertwined alpha helices
    • often hydrophobic where wthey pack together
  • short (20 res) or much longer
  • identify with COILS
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10
Q

disordered proteins

A
  • small disordered regions that can’t be identified experimentally with px/NMR
    • often C/N term, or long loop
  • or fleixble proteins that adopts multiple structures
    • may be structured upon binding
  • often lower fraction of hydrophobic residues than folded protein with hydrophobic core
  • use neural networks or SVM
    • DISOPRED2
    • IUPRED
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