11/11/05 d dobbs isu - bcb 444/544x: protein structure prediction1 11/11/05 protein structure...

11/11/05 D Dobbs ISU - BCB 444/544X: Protein Structure Prediction 1

11/11/05

Protein StructurePrediction & Modeling


Bioinformatics SeminarsNov 11 Fri 12:10 BCB Seminar in E164 Lago

Building Supertrees Using DistancesSteve Willson, Dept of Mathematicshttp://www.bcb.iastate.edu/courses/BCB691-F2005.html

Next week - Baker Center/BCB Seminars: (seminar abstracts available at above link)

Nov 14 Mon 1:10 PM Doug Brutlag, StanfordDiscovering transcription factor binding sites

Nov 15 Tues 1:10 PM Ilya Vakser, Univ Kansas Modeling protein-protein interactions both seminars will be in Howe Hall Auditorium


Protein Structure & Function:Analysis & Prediction

Mon Protein structure: basics; classification,databases,

visualization Wed Protein structure databases - cont.

Thurs Lab Protein structure databases Visualization software Secondary structure prediction

Fri Protein structure prediction Protein-nucleic acid interactions


Reading Assignment (for Mon-Fri)

Mount Bioinformatics• Chp 10 Protein classification & structure prediction

http://www.bioinformaticsonline.org/ch/ch10/index.html

• pp. 409-491 • Ck Errata: http://www.bioinformaticsonline.org/help/errata2.html


BCB 544 Additional Reading

Required:• Gene Prediction: • Burge & Karlin 1997 JMB 268:78

Prediction of complete gene structures in human genomic DNA

Optional:

• Structure Prediction: • Schueler-Furman…Baker 2005 Science 310:638

Progress in modeling of protein structures and interactions


Review last lecture:

Protein Structure: Databases, Classification &

Visualization


Protein sequence databases

• UniProt (SwissProt, PIR, EBI)http://www.pir.uniprot.org

• NCBI Protein http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Protein

More on these later: protein function prediction

http://www.pir.uniprot.org/

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Protein

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Protein


Protein sequence & structure: analysis

• Diamond STING Millennium - many useful structure analysis tools, including Protein Dossier http://trantor.bioc.columbia.edu/SMS/

• SwissProt (UniProt)protein knowledgebase

http://us.expasy.org/sprot

• InterPROsequence analysis tools

http://www.ebi.ac.uk/interpro

http://trantor.bioc.columbia.edu/SMS/








Protein structure databases

• PDB Protein Data Bank http://www.rcsb.org/pdb/ (RCSB) - THE protein structure database

• MMDB Molecular Modeling Databasehttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Structure

(NCBI Entrez) - has "added" value

• MSD Molecular Structure Database http://www.ebi.ac.uk/msd

Especially good for interactions, binding sites

http://www.rcsb.org/pdb/

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Structure

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Structure

http://www.ebi.ac.uk/msd


Protein structure classification

• SCOP = Structural Classification of ProteinsLevels reflect both evolutionary and structural relationshipshttp://scop.mrc-lmb.cam.ac.uk/scop

• CATH = Classification by Class, Architecture, Topology & Homology

http://cathwww.biochem.ucl.ac.uk/latest/

• DALI/FSSP (recently moved to EBI & reorganized)• fully automated structure alignments

• DALI serverhttp://www.ebi.ac.uk/dali/index.html• DALI Database (fold classification)

http://ekhidna.biocenter.helsinki.fi/dali/start

http://scop.mrc-lmb.cam.ac.uk/scop



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

http://ekhidna.biocenter.helsinki.fi/dali/start


Protein structure visualization

• Molecular Visualization Freeware:http://www.umass.edu/microbio/rasmol

• MolviZ.Orghttp://www.umass.edu/microbio/chime

• Protein Explorer http://www.umass.edu/microbio/chime/pe/protexpl/frntdoor.htm

• RASMOL (& many decendents: Protein Explorer,PyMol, MolMol, etc.)http://www.umass.edu/microbio/rasmol/index2.htm

• CHIMEhttp://www.umass.edu/microbio/chime/

getchime.htm

• Cn3D http://www.biosino.org/mirror/www.ncbi.nlm.nih.gov/Structure/cn3d/

• Deep View = Swiss-PDB Viewerhttp://www.expasy.org/spdbv

http://www.umass.edu/microbio/rasmol

http://www.umass.edu/microbio/rasmol

http://www.umass.edu/microbio/chime

http://www.umass.edu/microbio/chime

http://www.umass.edu/microbio/chime/pe/protexpl/frntdoor.htm

http://www.umass.edu/microbio/chime/pe/protexpl/frntdoor.htm

http://www.umass.edu/microbio/rasmol/index2.htm

http://www.umass.edu/microbio/rasmol/index2.htm


Protein structure visualization

Superb interactive structure visualization software

by Jane & Dave Richardson, Duke University

• KINIMAGEhttp://

kinemage.biochem.duke.edu/

• Fantastic research tools for structure analysis & refinement


RCSB PDB - Beta site http://pdbbeta.rcsb.org/pdb/Welcome.do

http://pdbbeta.rcsb.org/pdb/Welcome.do


MMDBhttp://www.ncbi.nlm.nih.gov/Structure/MMDB/mmdb.shtml

http://www.ncbi.nlm.nih.gov/Structure/MMDB/mmdb.shtml

http://www.ncbi.nlm.nih.gov/Structure/MMDB/mmdb.shtml


Cn3Dhttp://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml

http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml

http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml


Cn3D : Displaying 2' Structures


Cn3D: Structural Alignments


SCOP - Structure Classification

http://scop.mrc-lmb.cam.ac.uk/scop

QuickTime™ and aTIFF (LZW) decompressor

are needed to see this picture.


6 main classes of protein structure

1) Domains • Bundles of helices connected by loops

2) Domains• Mainly antiparallel sheets, usually with 2 sheets

forming sandwich

3) Domains• Mainly parallel sheets with intervening helices, also

mixed sheets

4) Domains • Mainly segregated helices and sheets

5) Multidomain (• Containing domains from more than one class

6) Membrane & cell-surface proteins


CATH - Structure Classification


QuickTime™ and aTIFF (LZW) decompressor

are needed to see this picture.


Structural Genomics

~ 30,000 "traditional" genes in human genome

(not counting: ???)~ 3,000 proteins in a typical cell> 2 million sequences in UniProt> 33,000 protein structures in the PDB Experimental determination of protein

structure lags far behind sequence determination!

Goal: Determine structures of "all" protein folds in nature, using combination of experimental structure determination methods (X-ray crystallography, NMR, mass spectrometry) & structure prediction


Structural Genomics Projects

TargetDB: database of structural genomics targetshttp://targetdb.pdb.org

Protein Structure Prediction?

http://targetdb.pdb.org/


Protein Folding

"Major unsolved problem in molecular biology"

In cells: spontaneousassisted by enzymesassisted by chaperones

In vitro: many proteins fold spontaneously & many do not!


Steps in Protein Folding

1- "Collapse"- driving force is burial of hydrophobic aa’s

(fast - msecs)2- Molten globule - helices & sheets form, but "loose"

(slow - secs)3- "Final" native folded state - compaction, some 2'

structures rearranged

Native state? - assumed to be lowest free energy - may be an ensemble of structures


Protein Dynamics

• Protein in native state is NOT static• Function of many proteins depends on

conformational changes, sometimes large, sometimes small

• Globular proteins are inherently "unstable"(NOT evolved for maximum stability)

• Energy difference between native and denatured state is very small (5-15 kcal/mol)

(this is equivalent to 1 or 2 H-bonds!)• Folding involves changes in both entropy &

enthalpy


Protein Structure Prediction

• Structure is largely determined by sequence

BUT:• Similar sequences can assume different structures• Dissimilar sequences can assume similar structures• Many proteins are multi-functional• Protein folding:

• determination of folding pathways • prediction of tertiary structure

still largely unsolved problems


New today:

Protein Structure Prediction

Secondary structure(text focuses on this - I won't)

Tertiary structure(let's do this instead!)


Deciphering the Protein Folding Code• Protein Structure

Prediction or "Protein Folding" Problem

given the amino acid sequence of a protein, predict its 3-dimensional structure (fold)

• "Inverse Folding" Problem

given a protein fold, identify every amino acid sequence that can adopt its 3-dimensional structure


Protein Structure Determination?

High-resolution structure determination• X-ray crystallography (<1A)• Nuclear magnetic resonance (NMR) (~1-

2.5A)

Lower-resolution structure determination• Cryo-EM (electron-microscropy) ~10-15A

Theoretical Models?• Highly variable - now, some equiv to X-ray!


Tertiary Structure PredictionFold or tertiary structure prediction

problem can be formulated as a search for minimum energy conformation• search space is defined by psi/phi angles of backbone

and side-chain rotamers• search space is enormous even for small proteins!• number of local minima increases exponentially

of the number of residues

Computationally it is an exceedingly difficult problem!


Ab Initio Prediction1. Develop energy function

• bond energy• bond angle energy• dihedral angle energy• van der Waals energy• electrostatic energy

2. Calculate structure by minimizing energy function (usually Molecular Dynamics or Monte Carlo methods)

Ab initio prediction - not practical in general• Computationally? very expensive• Accuracy? Usually poor for all but short peptides

(but see Baker review!)

Provides both folding pathway & folded structure


Comparative Modeling

Provide folded structure only

Two primary methods 1) Homology modeling2) Threading (fold recognition)

Note: both rely on availability of experimentally determined structures that are "homologous" or at least structurally very similar to target


Homology Modeling

1. Identify homologous protein sequences• PSI-BLAST • multiple sequence alignment (MSA)

2. Among those with available structures, choose closest sequence match for template

3. Build model by placing residues into corresponding positions of homologous structure models & refine by "tweaking"

Homology modeling - works "well"• Computationally? not very expensive• Accuracy? higher sequence identity better

modelRequires >30% sequence identity


Threading - Fold RecognitionIdentify “best” fit between target sequence & template structure

1. Develop energy function2. Develop template library3. Align target sequence with each template &

score4. Determine best score (1D to 3D alignment)5. Build refine structure as in homology

modeling Threading - works "sometimes"

1. Computationally? Can be expensive or cheap, depends on energy function & whether "all atom" or "backbone only" threading

2. Accuracy? in theory, should not depend on sequence identity (should depend on quality of template library & "luck")

3. But, usually higher sequence identity better model


1. Align target sequence with template structures(fold library) from the Protein Data Bank (PDB)

2. Calculate energy (score) to evaluate goodness of fit between target sequence & template structure

3. Rank models based on energy scores

Target Sequence

Structure Templates

ALKKGF…HFDTSE

Threading - a "local" example


Threading Goals & Issues

Structure database - must be complete: no decent model if no good template in library!

Sequence-structure alignment algorithm:Bad alignment Bad score!

Energy function (scoring scheme): • must distinguish correct sequence-fold alignment from

incorrect sequence-fold alignments • must distinguish “correct” fold from close decoys

Prediction reliability assessment - how determine whether predicted structure is correct (or even close?)

Find “correct” sequence-structure alignment of a target sequence with its native-like fold in PDB


Threading – Structure database

Build a template database (e.g., ASTRAL domain library derived from

PDB)

Supplement with additional decoys, e.g., generated usingab initio approach such as Rosetta (Baker)


Threading - Energy function

Two main methods (and combinations of these)

• Structural profile (environmental) physico-chemical properties of aa’s• Contact potential (statistical)

based on contact statistics from PDB (Miyazawa & Jernigan - Jernigan

now at ISU)


Protein Threading – typical energy function

MTYKLILNGKTKGETTTEAVDAATAEKVFQYANDNGVDGEWTYTE

How well does a specific residue fit structural environment?

What is "probability" that two specific residues are in contact?

Alignment gap penalty?

Total energy: E_p + E_s + E_g

Find a sequence-structure alignment that minimizing the energy function


A Rapid Threading Approach for Protein Structure Prediction

Kai-Ming Ho, Physics Haibo Cao

Yungok Ihm Zhong Gao

James MorrisCai-zhuang

Wang Drena Dobbs, GDCB

Jae-Hyung LeeMichael

TerribiliniJeff Sander


Performance Evaluation? "Blind Test"

CASP5 Competition (Critical Assessment of Protein Structure

Prediction) Given: Amino acid sequence Goal: Predict 3-D structure (before experimental results published)

Typical Results: well, actually, BEST Results: HO = #1 ranked CASP prediction for this

target

Target 174

PDB ID = 1MG7

Actual Structure

Predicted Structure

T174_1

T174_2

FR Fold Recognition

(targets manually assessed by Nick Grishin)

-----------------------------------------------------------

Rank Z-Score Ngood Npred NgNW NpNW Group-name 1 24.26 9.00 12.00 9 12 Ginalski

2 21.64 7.00 12.00 7 12 Skolnick Kolinski

3 19.55 8.00 12.50 9 14 Baker

4 16.88 6.00 10.00 6 10 BIOINFO.PL

5 15.25 7.00 7.00 7 7 Shortle

6 14.56 6.50 11.50 7 13 BAKER-ROBETTA

7 13.49 4.00 11.00 4 11 Brooks

8 11.34 3.00 6.00 3 6 Ho-Kai-Ming

9 10.45 3.00 5.50 3 6 Jones-NewFold -----------------------------------------------------------

FR NgNW - number of good predictions without weighting for multiple models

FR NpNW - number of total predictions without weighting for multiple models

Overall Performance in CASP5 Contest (M. Levitt, Stanford)

11/11/05 d dobbs isu - bcb 444/544x: protein structure prediction1 11/11/05 protein structure...

Documents

protein structure databases

ncbi protein http

protein dossier http

modeling of protein

d dobbs isu bcb

edusms http

ebi http

analysis prediction