Protein threading algorithms

1. GenTHREADER Jones, D. T. JMB(1999) 287, 797-8152. Protein Fold Recognition by Prediction-based Threading Rost, B., Schneider, R. & Sander, C. JMB(1997)270,471-480

Presented by Jian Qiu

Why do we need protein threading?

To detect remote homologue Genome annotation Structures are better conserved than sequences. Remote homologues with low sequence similarity may share significant structure similarity.

To predict protein structure based on structure template Protein A shares structure similarity with protein B. We could model the structure of protein A using the structure of protein B as a starting point.

An successful example by GenTHREADER

ORF MG276 from Mycoplasma genitalium was predicted to share structure similarity with 1HGX. MG276 shares a low sequence similarity (10% sequence identity) with 1HGX.

Supporting Evidence: MG276 has an annotation of adenine phosphoribosyltransferase, based on

high sequence similarity to the Escherichia coli protein;

1HGX is a hypoxanthine-guanine-xanthine phosphoribosyltransferase

from the protozoan parasite Tritrichomonas foetus.

Four functionally important residues in 1HGX are conserved in MG276.

The secondary structure prediction for ORF MG276 agrees very well with

the observed secondary structure of 1HGX.

Structure of 1HGX

Functional residue conservation between 1HGX and MG276

GenTHREADER Protocol

Sequence alignment

For each template structure in the fold library, related sequences

were collected by using the program BLASTP.

A multiple sequence alignment of these sequences was generated with a simplified version of MULTAL.

Get the optimal alignment between the target sequence and the sequence profile of a template structure with dynamic programming.

Threading Potentials

Pairwise potential (the pairwise model family):

                                                                                                         

k: sequence separation s: distance interval mab: number of pairs ab observed with sequence separation k

weight given to each observation

fk(s): frequency of occurrence of all residue pairs

fkab(s): frequency of occurrence of residue pair ab

Solvation potential (the profile model family):

                                                           

r: the degree of residue burial the number of other C atoms located within 10 Å of the residue's C

atom

fa(r): frequency of occurrence of residue a with burial r

f (r): frequency of occurrence of all residues with burial r

Variables considered to predict the relationship

Pairwise energy score

Solvation energy score

Sequence alignment score

Sequence alignment length

Length of the structure

Length of the target sequence

Artificial Neural Network

A node

Neural network architecture in GenTHREADER

The effects of sequence alignment score and pairwise potential on the Network output

Confidence level with different network scores

Low Medium(80%) High(99%)

Certain(100%)

Genome analysis of Mycoplasma genitalium

All the 468 ORFs were analyzed within one day.

Distribution of protein folds in M. genitalium

PHD: Predict 1D structure from sequence

MaxHom

Sequence

Multiple Sequence Alignment

PHDsec PHDacc

Secondary structure:H(helix), E(strand),L(rest)

Solvent accessibility:Buried(<15%), Exposed(>=15%)

Threading Protocol

Similarity matrix in dynamic programming

Purely structure similarity matrix: six states (combination of three secondary structure states and two solvent accessibility states)

Purely sequence similarity matrix: McLachlan or Blosum62

Combination of strcture and sequence similarity matrix: Mij=Mij

1D structure + (100-)Mijsequence

sequence alignment only1Dstructure alignment only

Performance of the algorithm

Results on the 11 targets of CASP1

Correctly detected the remote homologues at first rank in four cases; Average percentage of correctly aligned residues: 21%; Average shift: nine residues.

Best performing methods in CASP1: Expert-driven usage of THREADER by David Jones and colleagues detected five out of nine proteins correctly at first rank. Best alignments of the potential-based threading method by Manfred Sippl and colleagues were clearly better than the best ones of this algorithm.