Protein Structure Databases, cont. 11/09/05web.cs.iastate.edu/~cs544/Lectures/1109ProteinStructure.pdfProtein Structure Databases, cont. 11/09/05 D Dobbs ISU - BCB 444/544X 3 11/09/05

Protein Structure Databases, cont. 11/09/05

D Dobbs ISU - BCB 444/544X 1

11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont. 1

11/9/05

Protein Structure Databases(continued)

Prediction & Modeling


Bioinformatics Seminars

Nov 10 Thurs 3:40 Com S Seminar in 223 AtanasoffComputational Epidemiology

Armin R. Mikler, Univ. North Texashttp://www.cs.iastate.edu/~colloq/#t3

Nov 10 Thurs 4:10 EEOB Seminar in 210 BesseyDiversity and Evolution of Plant Immunity Genes: Insights from Molecular Population Genetics

Peter Tiffin, Univ. of Minnesotahttp://www.cbs.umn.edu/tiffin/index.html


Bioinformatics SeminarsCORRECTION:

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 KansasModeling 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 Protein structure analysis & prediction

Fri Protein structure prediction Protein-nucleic acid interactions


Reading Assignment (for Mon-Fri)Mount Bioinformatics

• Chp 10 Protein classification & structure predictionhttp://www.bioinformaticsonline.org/ch/ch10/index.html

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

Additional reading assignments for BCB 544:• Gene Prediction: Burge & Karlin 1997 JMB 268:78

Prediction of complete gene structures in human genomic DNA

• Structure Prediction: Schueler-Furman…Baker, Science 310:638Progress in modeling of protein structures and interactions


Review last lecture:

Protein Structure: Basics




Protein Structure & Function

• Amino acids characteristics• Structural classes & motifs• Protein functions & functional families

(not much - more on this later)

• Classification• Databases• Visualization


Amino Acids

Each of 20 different amino acids has different"R-Group," side chain attached to Cα


Peptide bond is rigid and planar


Hydrophobic Amino Acids


Charged Amino Acids


Polar Amino Acids




Certain side-chain configurations areenergetically favored (rotamers)

Ramachandran plot:"Allowable" psi & phi angles


Glycine is smallest amino acidR group = H atom

• Glycine residues increasebackbone flexibility becausethey have no R group


Proline is cyclic• Proline residuesreduce flexibility ofpolypeptide chain

• Proline cis-transisomerization is oftena rate-limiting step inprotein folding• Recent worksuggests it also mayalso regulate ligandbinding in nativeproteins -Andreotti


Cysteines can form disulfide bonds

• Disulfide bonds(covalent) stabilize3-D structures

• In eukaryotes,disulfide bonds arefound only in secretedproteins orextracellular domains


Globular proteins have a compacthydrophobic core

Packing of hydrophobic side chains into interior is maindriving force for folding

Problem? Polypeptide backbone is highly polar(hydrophilic) due to polar -NH and C=O in eachpeptide unit; these polar groups must be neutralized

Solution? Form regular secondary structures,e.g., α-helix, β-sheet, stabilized by H-bonds


Exterior surface of globular proteinsis generally hydrophilic

Hydrophobic core formed by packed secondarystructural elements provides compact, stable core

"Functional groups" of protein are attached to thisframework; exterior has more flexible regions(loops) and polar/charged residues

Hydrophobic "patches" on protein surface are ofteninvolved in protein-protein interactions




Protein Secondary Structures

α−Helicesβ−SheetsLoopsCoils


α−helix: stabilized by H-bonds betweenevery ~ 4th residue in backbone

C = blackO = redN = blue


Certain amino acids are "preferred" &others are rare in α−helices

• Ala, Glu, Leu, Met = good helix formers• Pro, Gly Tyr, Ser = very poor• Amino acid composition & distribution varies, depending

on on location of helix in 3-D structure


β-sheets - also stabilized by H-bondsbetween back bone atoms

Anti-parallel Parallel


Loops• Connect helices and sheets• Vary in length and 3-D

configurations• Are located on surface of

structure• Are more "tolerant" of mutations• Are more flexible and can adopt

multiple conformations• Tend to have charged and polar

amino acids• Are frequently components of

active sites• Some fall into distinct

structural families (e.g.,hairpin loops, reverse turns)


Coils

• Regions of 2' structure that are nothelices, sheets, or recognizable turns

• Intrinsically disordered regions appear toplay important functional roles




Globular proteins are built fromrecurring structural patterns

Motifs or supersecondary structures =combinations of 2' structural elements

Domains = combinations of motifs• Independently folding unit (foldon)• Functional unit


Simple motifs combine to form domains


6 main classes of protein structure1) α Domains

• Bundles of helices connected by loops

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

sandwich

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

mixed sheets

4) α+β Domains• Mainly segregated helices and sheets

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

6) Membrane & cell-surface proteins


α-domain structures: 4-helix bundles


β-sheets: up-and-down sheets & barrels


α/β-domains: leucine-rich motifs canform horseshoes




New today:

Protein StructureDatabasesClassificationVisualization

Protein Structure PredictionSecondary structure Tertiary structure


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


Protein sequence & structure: analysis• Diamond STING Millennium - many useful structure

analysis tools, including Protein Dossierhttp://trantor.bioc.columbia.edu/SMS/

• SwissProt (UniProt)protein knowledgebasehttp://us.expasy.org/sprot

• InterPROsequence analysis toolshttp://www.ebi.ac.uk/interpro


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/msdEspecially good for interactions, binding sites


Protein structure classification• SCOP = Structural Classification of Proteins

Levels reflect both evolutionary and structural relationshipshttp://scop.mrc-lmb.cam.ac.uk/scop

• CATH = Classification by Class, Architecture, Topology & Homologyhttp://cathwww.biochem.ucl.ac.uk/latest/

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

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

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• CHIME

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

• Cn3Dhttp://www.biosino.org/mirror/www.ncbi.nlm.nih.gov/Structure/cn3d/

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




PDB (RCSB)http://www.rcsb.org/pdb


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


RCSB PDB - New Tutorialhttp://core1.rcsb.org/tutorial


NCBI Structurehttp://www.ncbi.nlm.nih.gov/Structure


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


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




MMDB: MMolecular MModeling Data Base

Derived PDB structure recordsValue added to PDB records including:

• Integration with other ENTREZ databases & tools• Conversion to parseable ASN.1 data description language• Correction of numbering discrepancies in structure vs sequence• Validation• Addition of explicit chemical graph information

Structure neighbors determined by Vector AlignmentSearch Tool (VAST)


Searching MMDB

1CET


MMDB Structure Summary

Cn3D viewer

VAST neighbors

BLAST neighbors


Cn3D : Displaying 2' Structures

Chloroquine


Cn3D : Displaying 3' Structures

Chloroquine


Cn3D: Structural Alignments

Chloroquine

NADH




Protein Explorer (RasMol/Chime)


Protein Explorer


SCOP - Structure Classification


CATH - Structure Classification


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) & structureprediction


Structural Genomics Projects

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

Protein Structure Prediction?




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 Folding1- "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

Documents

Protein Structure Databases, cont. 11/09/05web.cs.iastate.edu/~cs544/Lectures/1109ProteinStructure.pdfProtein Structure Databases, cont. 11/09/05 D Dobbs ISU - BCB 444/544X 3 11/09/05