4. Threading: From Sequence to 3D Fold

4.1 Threading: Principles

It has been estimated that the total number of possible protein folds is about 1,000. Hence, once the 3D structure of all the folds is known, it should be possible to deduce the fold of any given amino acid sequence. To address this question the sequence is simply aligned in 3D on each of the folds, each of the fits is scored, and the best score indicates the correct fold. This process has been coined threading.

Though the details differ between different threading methods all have the following components:

• Creation of a fold database
  SCOP Feb 2000 has 548 folds
• Representation of the protein
  coordinates of all atoms, backbone atoms, or only CB carbon atoms?
• Scoring function
  substitution matrices or residue versus environment matrices?
  Examples of pair potentials:
• Short-range:Ala...Ala CB...CB in AXXXA arrangement
  exhibits an energy minimum at 6 Å (alpha helix) and 9 Å (beta sheet)
• Long-range:Cys...Cys CB...CB separated by more than 30 residues
  exhibits an energy minimum at 4 Å (disulphide bridge)
• Solvation potential for Leu:prefers to be buried
• Solvation potential for Glu:prefers to be exposed on the surface
• Optimal alignment
  dynamic programming or Monte Carlo?
• Statistical significance of the score
  raw or normalized scores? Z-scores (number of standard deviations from the mean)?

CAVEAT: Frequently threading identifies the correct fold but has the detailed sequence alignment wrong. Always try to improve the alignment!

For more info:

• D.J. Jones, W.R. Taylor & J.M. Thornton (1992). A new approach to protein fold recognition, Nature 358, 86-89.
• S.H. Bryant & S.F. Altshul (1995). Statistics of sequence-structure threading, Curr. Op. Struct. Biol. 5, 236-244.
• T. Madej, M.S. Boguski & S.H. Bryant (1995). Threading analysis suggests that the obese gene product may be a helical cytokine, FEBS Lett. 373, 13-18.
• C.M.R. Lemer, M.J. Rooman & S.J. Wodak (1995). Protein Structure Prediction by Threading Methods: Evaluation of Current Techniques, Proteins 23, 337-355.

4.2 Threading: Servers and Freeware