Loops, Turns, Motifs - Sept 27th

Outcomes

  • Role of turns in protein structure and function
  • Nuaanced understanding of the types of turns and how they are categorized
  • Be able to resources (PDB file, Ramachandran Plot, phi and psi, and PDB sum) to determine the type of turn in a protein
  • Know definition of super secondary structure, domains, and fold and common types of each (Primarily Voet reading)
  • Understand the relationship between fold and the topological diagram

Reading (to be completed before class!)

Reading on Loops and Turns

  • 1) Whitford This first reading is very short but provides a nice introduction to the topic.
  • 2) Chou Analytical Biochemistry 2000
    • Read just through beta-turns
      • Note there is a mistake in the phi and psi angles for residue i+1 in the type II' turn in table I. They should be phi = 60o psi = -120o
  • 3) From EXPASY text Chp 1- The image of type I and II turns nicely compliment table I of Chou
    • 1.6.1 beta-turns (reverse turns)

Reading on Super Secondary Structure, Motifs, and Folds

  • 5) Voet  (B. Tertiary Structure, p249-p256
    • Focus of this reading is on
      • Motifs (supersecondary structure) 
      • Domains
      • Folds

6) Loops and Turns Pre-Assignment Worksheet

In Class Activities

  • Discussion of Chou and Voet readings
  • Turns and loops as secondary structure analyzed - using molecular modeling software get worksheet
    • Inspect the structures of 1HEW, 1TNF, or 1RCP
      • Identify two β-turns (according to the nomenclature of Chou), identify the residues in the turn, and discuss an stabilizing interactions in the turn.
  • Slideshow

Problems

  1. Topology and Turns (See Worksheet) - Due Wednesday next week (see assignment in Worksheet)

You can practice looking at turns and loops using the identified structures from this paper
Protein Structure 1973 Lewis
Go to table II. Find some of the identified β-turns and then confirm in DeepView using the PDB structures of those enzymes

Use PDBsum. Please try out this tool and compare to the answers you assigned for 4CHA and other proteins. Help with the Codes in PDBsum, ProMotif