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Comp Structural Bioinfo

by: Ashleigh Dare

Comp Structural Bioinfo ECS 229

Ashleigh Dare
GPA 3.75


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Class Notes
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This 26 page Class Notes was uploaded by Ashleigh Dare on Tuesday September 8, 2015. The Class Notes belongs to ECS 229 at University of California - Davis taught by Staff in Fall. Since its upload, it has received 44 views. For similar materials see /class/191703/ecs-229-university-of-california-davis in Engineering Computer Science at University of California - Davis.

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Date Created: 09/08/15
Protein Tertiary Structure Protein Tertiary Structure Packing helixhelix packing sheetsheet packing helixsheet packing 0 Protein Structural Classes All Alpha All Beta Alpha and Beta Helix Helix Packing The RidgeGroove model Pairs of helices Q angle between the 2 axes D distance between the two axes Two types of ridges in helices Ridge 4n Ridge 3n Ridge groove model for helixhelix packing Helix 1 Helix 2 Orientation Comment 4n 4n 9 12A Common favorable sidechain interactions 4n 4n 140 9 12A Common favorable sidechain interactions 4n 3n 20 9 12A Common favorable sidechain interactions 4n 3n 547474 l60 9 12A Rare Example Helix B and G in myoglobin Example Helix B and G in myoglobin Backbone only Backbone Sidech ain SheetSheet Packing Parallel sheets tend to be covered by helices on both sides Antiparallel sheets tend to have one side covered by a sheet sandwichtype structure Two types of packing aligned or orthogonal Aligned sheetsheet packing Approx 20 degrees between the directions ofthe sheets Sidechains are well packed Orthogonal SheetSheet Packing HelixSheet Packing Because the periodicities 0f helices and strands are different there is not regular packing patterns Helices tend to be on both sides of parallel beta sheets Protein Architectures A1106 proteins All 3 proteins Alpha and beta proteins ocB proteins alternating 06 and B 06 3 proteins AllAlpha topologies The lone helix Glucagon hormone involved PDB code IGCN The helixturn helix motif ROP RNAbinding v Protein 6 PDB code IROP 171 e 2 helices a are twisted AllAlpha topologies 2 The four helix bundle hydrophobic hydrophilic Four helix bundle topologies Myohemelythrin PDB code 2mhr All Beta Topology Beta sandwich es Fatty acid binding protein PDB code IIFB The Greek Key Topology Folds including the Greek key topology include 5 to 13 strands The Greek Key Topology The Jellyroll Topology A Greek key with an 1 extra swirl The Beta Propellor Sevenplatedpropellor Each plate is afour stranded antiparallel sheet PDB code 1ERJ The Beta Helix PDB code IEZG Antifreeze protein from Tenebrio Moiz or beetle The Rossman Fold Alternate beta alpha motif Always right handed The Horseshoe PDB code ZBNH a 3 m i V a 4 quotQ 4 0 h g 9 h quot kw l 9quot g i a The alphabeta barrel In a succession of alphabeta motifs ifthe rst strand Hydrogen bonds to the last then the structure resemble a Barrel PDB code 1 TIM Summary Stacking of helices is best described using the ridgegroove model Antiparallel sheets tend to have one side covered by a shee 39 sandwichtype structure Two types of packing aligned or orthogonal Helices tend to be on both sides of parallel beta sheets There are three main classes of proteins all Alpha all Beta and Alpha Beta Sometimes the latter is divided in two considering the alternating alphabeta proteins as defining their own class Bundles are common alphaproteins Common beta folds include the greek key the jellyroll and sandwiches More unusual beta structures include the beta propeller and the beta helix The Rossman fold alternating alphabeta is a common motif in proteins It is found in the horseshoe as well as in the TIM fold


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