Protein Tertiary Structure PredictionStructural Bioinformatics

Primary: amino acid linear sequence.Secondary: -helices, -sheets and loops.

Tertiary: the 3D shape of the fully folded polypeptide chainThe Different levels of Protein Structure

How can we view the protein structure ?Download the coordinates of the structure from the PDB http://www.rcsb.org/pdb/

Launch a 3D viewer program For example we will use the program Pymol The program can be downloaded freely from the Pymol homepage http://pymol.sourceforge.net/

Upload the coordinates to the viewer

Pymol exampleLaunch PymolOpen file 1aqb (PDB coordinate file)Display sequenceHide everythingShow main chain / hide main chainShow cartoon Color by ssColor redColor green, resi 1:40

Help http://pymol.sourceforge.net/newman/user/toc.html

Predicting 3D Structure

Comparative modeling (homology)

Based on structural homology

Fold recognition (threading)Outstanding difficult problemBased on sequence homology

Comparative ModelingSimilar sequences suggests similar structure

Sequence and Structure alignments of two Retinol Binding Protein

Structure AlignmentsThe outputs of a structural alignment are a superposition of the atomic coordinates and a minimal Root Mean Square Distance (RMSD) between the structures. The RMSD of two aligned structures indicates their divergence from one another. Low values of RMSD mean similar structuresThere are many different algorithms for structural Alignment.

Dali (Distance mAtrix aLIgnment)DALI offers pairwise alignments of protein structures. The algorithm uses the three-dimensional coordinates of each protein to calculate distance matrices comparing residues.

See Holm L and Sander C (1993) J. Mol. Biol. 233:123-138.SALIGN http://salilab.org/DBALI/?page=tools

Fold classification based on structure-structurealignment of proteins (FSSP)Page 293FSSP is based on a comprehensive comparison ofPDB proteins (greater than 30 amino acids in length) using DALI. Representative sets exclude sequence homologs sharing > 25% amino acid identity.

http://www.ebi.ac.uk/dali/fssp

Comparative ModelingComparative structure predictionproduces an all atom model of asequence, based on its alignment to oneor more related protein structures in thedatabase

Similar sequence suggests similar structure

Comparative ModelingAccuracy of the comparative model is related to the sequence identity on which it is based >50% sequence identity = high accuracy 30%-50% sequence identity= 90% modeled

Homology Threshold for Different Alignment Lengths

Alignment length (L) Homology Threshold (t)A sequence alignment between two proteins is considered to imply structural homology if the sequence identity is equal to or above the homology threshold t in a sequence region of a given length L. The threshold values t(L) are derived from PDB

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Comparative ModelingSimilarity particularly high in coreAlpha helices and beta sheets preservedEven near-identical sequences vary in loops

Comparative Modeling MethodsMODELLER (Sali Rockefeller/UCSF)SCWRL (Dunbrack- UCSF )SWISS-MODEL http://swissmodel.expasy.org//SWISS-MODEL.html

Comparative ModelingModeling of a sequence based on known structuresConsist of four major steps :Finding a known structure(s) related to the sequence to be modeled (template), using sequence comparison methods such as PSI-BLAST2. Aligning sequence with the templates3. Building a model4. Assessing the model

Fold Recognition

Protein FoldsA combination of secondary structural unitsForms basic level of classificationEach protein family belongs to a foldDifferent sequences can share similar folds

HemoglobinTIMProtein Folds: sequential and spatial arrangement of secondary structures

Protein FoldsA combination of secondary structural unitsForms basic level of classificationEach protein family belongs to a foldDifferent sequences can share similar folds

Similar folds usually mean similar functionHomeodomain

Transcriptionfactors

Protein FoldsA combination of secondary structural unitsForms basic level of classificationEach protein family belongs to a foldDifferent sequences can share similar folds

The same fold can have multiple functionsRossmannTIM barrel12 functions31 functions

Fold classification:

Class:All alphaAll betaAlpha/betaAlpha+betaFoldSuperfamilyFamilySCOP Structure Classification Of Proteins

Retinol Binding Protein

Fold RecognitionMethods of protein fold recognition attempt to detect similarities between protein 3D structure that have no significant sequence similarity.

Search for folds that are compatible with a particular sequence.

"the turn the protein folding problem on it's head rather than predicting how a sequence will fold, they predict how well a fold will fit a sequence

Basic steps in Fold Recognition :Compare sequence against a Library of all known Protein Folds (finite number)Query sequence MTYGFRIPLNCERWGHKLSTVILKRP...Goal: find to what folding template the sequence fits bestThere are different ways to evaluate sequence-structure fit

MAHFPGFGQSLLFGYPVYVFGD... ... 1) ... 56) ... n) ... -10 ... -123 ... 20.5 There are different ways to evaluate sequence-structure fit

Programs for fold recognitionTOPITS (Rost 1995)GenTHREADER (Jones 1999)SAMT02 (UCSC HMM)3D-PSSM http://www.sbg.bio.ic.ac.uk/~3dpssm/

Ab Initio ModelingCompute molecular structure from laws of physics and chemistry alone Theoretically Ideal solution Practically nearly impossibleWHY ?Exceptionally complex calculationsBiophysics understanding incomplete

Ab Initio MethodsRosetta (Bakers lab, Seattle)

Undertaker (Karplus, UCSC)

CASP - Critical Assessment of Structure PredictionCompetition among different groups for resolving the 3D structure of proteins that are about to be solved experimentally.Current state -ab-initio - the worst, but greatly improved in the last years. Modeling - performs very well when homologous sequences with known structures exist.Fold recognition - performs well.

Whats NextPredicting function from structure

Structural Genomics : a large scale structure determination project designed to cover all representative protein structures

Zarembinski, et al., Proc.Nat.Acad.Sci.USA, 99:15189 (1998)ATP binding domain of protein MJ0577

~300unique foldsin PDB

Currently ~800 unique folds

~1000- 3000unique folds in structure spaceEstimated

Structure Genomics expectations ~ 5 proteins to characterize thesequence space

corresponding to 1 fold~10000-15000new structuresexpected

As a result of the Structure Genomic initiative many structures of proteins with unknown function will be solved

Approaches for predicting function from structure ConSurf - Mapping the evolution conservation on the protein structure http://consurf.tau.ac.il/

Approaches for predicting function from structure PHPlus Identifying positive electrostatic patches on the protein structure http://pfp.technion.ac.il/

Approaches for predicting function from structure SHARP2 Identifying positive electrostatic patches on the protein structure http://www.bioinformatics.sussex.ac.uk/SHARP2

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