Homology Modeling

1
Homology Modeling

• comparative modeling vs. ab initio folding
• alignment (check gaps)
• threading
• loop building
• re-packing side-chains in core, DEE, SCWRL
• fold evaluation/scoring
• statistical potentials (pot. of mean force) -
  DFIRE
• minimization
• servers Swiss-model

2

• ab initio folding
• Rosetta (Baker)
• MONSSTER (Skolnick)
• I-TASSER (Zhang)

3
Sequence Alignment

• critical step
• gaps should be in loops (check in final model)
• dynamic programming (Smith-Waterman)
• LALIGN http//www.ch.embnet.org/software/LALIGN_f
  orm.html
• adjust gap parameters gap-open
  penaltygtx? gap-extension penaltyltx? xaverage
  match score
• could also adjust substitution matrix (PAM250,
  BLOSUM62)
• use PSI-Blast to include info from homologs
• iterative retrieves homologs, refines search...
• use HMM to align to family

4
Threading

• use info about 3D structure to improve alignment
• local secondary structure, solvent-accessibility
• 3D profiles (Eisenberg)
• 3D-PSSM/Phyre (Sternberg, Lawrence Kelley)
• THREADER
• RAPTOR

5
MODELLER (Sali)

• references
• A. Šali and T. L. Blundell. Comparative protein
  modelling by satisfaction of spatial restraints.
  J. Mol. Biol. 234, 779-815, 1993.
• A. Fiser, R. K. G. Do and A. Š ali. Modeling of
  loops in protein structures. Protein Science 9,
  1753-1773, 2000.
• Fiser A, Sali A. (2003). Modeller generation and
  refinement of homology-based protein structure
  models. Methods Enz. 374461-91.
• loop-modeling via dynamics
• evaluation
• gt30 identity?
• stereochemistry Procheck
• contacts/exposure ProSA (Sippl, 1993)
  distance-based pair potentials

6
Side-chain re-packing

• mutations cause steric conflicts (and voids)
• changing rotamers can relieve conflicts
• adjacent side-chains are coupled
• multiple changes might be required
• combinatorial search exhaustive versus Monte
  Carlo (Holm Sander, 1992)
• DEE (Dead-End Elimination)
• pruning method
• pre-processing, singles, pairs
• Desmet, Mayo
• reduction in branching factor?

• rigid backbone assumption
• how important is backbone flexibility?
• also sample alternative backbone conformations at
  each site
• (Georgiev and Donald, 2007)

• interesting application use DEE to
• determine rotamer populations for
• tryptophans use to predict fluorescence
• quenching times (Hellings 2003, BiophysJ)

7
SCWRL 3.0

• Canutescu et al. (2003)
• Dunbrack BBdep rotamer library
• de-couple interaction graph into
  bi-connected components representing
  local dependencies
• TreePack (Xu and Berger, JACM 2006)
• geometric neighborhood graph decomposition up to
  90x faster

side-chain interactions
energy of configuration
8
Loop Modeling

• two approaches
• 1. MD/conformational sampling
• 2. templates from loop library
• accuracy depends on length 2-4 (turns), 4-8,
  gt8 (ab initio)
• importance in immunoglobulins (hyper-variable
  loops in antigen-binding region)

9

• modeling loops via molecular dynamics
• Monte Carlo conformational search using a
  FF/energy function, high temp MD 800K
  (Bruccoleri Karplus, 1990)
• Does Conformational Free Energy Distinguish Loop
  Conformations in Proteins?
• templates from loop library (examples from
  existing structures)
• amino acid similarities
• fit to stems
• Ca distance, vectors (i-1i,j,j1), carbonyls?,
  f/y angles

10
Scoring

• statistical potentials
• knowledge-based poten (Sippl, 1990)
• potential of mean force
• residue-based potentials (e.g. Cb-Cb contact
  distance, or centers-of-mass)
• atomic pairwise potentials
• (Lu Skolnick, 2001)
• capture side-chain interactions better
• discriminate correct folds better
• z-score of true fold vs. decoys (gapless
  threading)

11
DFIRE (Yaoqi Zhou)

• Distance-scaled Finite Ideal-gas REference state
• Zhou and Zhou (Prot. Sci, 2002)
• all-atom potential
• Nexp(i,j,r) will not increase in r2 as in an
  infinite system
• a1.57 gives best correlation with density in
  radial shells
• improves ability to recognize correct fold versus
  decoys
• see also
• RAPDF (Samudrala and Moult, 1998)
• DOPE (Shen and Sali, 2006)

instead, assume
fair???
12
Minimization

• a logical step, however...
• one of the conclusions from CASP4 (Baker)
• minimization generally made models worse (took
  predicted structures farther from native)
• threshold
• minimization works if rmsdlt2Å,
• but ab initio models are often 4-6Å rmsd
• backbone adjustments required?