11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont.1 11/9/05 Protein Structure Databases (continued) Prediction & Modeling

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 Atanasoff

Computational EpidemiologyArmin 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 Seminars

CORRECTION:

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 Protein structure analysis &

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

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 310:638 Progress 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 C


Peptide bond is rigid and planar


Hydrophobic Amino Acids


Charged Amino Acids


Polar Amino Acids


Certain side-chain configurations are energetically favored (rotamers)

Ramachandran plot: "Allowable" psi & phi angles


Glycine is smallest amino acidR group = H atom

• Glycine residues increase backbone flexibility because they have no R group


Proline is cyclic• Proline residues reduce flexibility of polypeptide chain

• Proline cis-trans isomerization is often a rate-limiting step in protein folding • Recent work suggests it also may also regulate ligand binding in native proteins -Andreotti


Cysteines can form disulfide bonds

• Disulfide bonds (covalent) stabilize 3-D structures

• In eukaryotes, disulfide bonds are found only in secreted proteins or extracellular domains


Globular proteins have a compact hydrophobic core

Packing of hydrophobic side chains into interior is main driving force for folding

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

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


Exterior surface of globular proteins is generally hydrophilic

Hydrophobic core formed by packed secondary structural elements provides compact, stable core

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

Hydrophobic "patches" on protein surface are often involved in protein-protein interactions


Protein Secondary Structures

HelicesSheetsLoopsCoils


helix: stabilized by H-bonds between every ~ 4th residue in

backbone

C = blackO = redN = blue


Certain amino acids are "preferred" & others are rare in 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


-sheets - also stabilized by H-bonds between 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 not helices, sheets, or recognizable turns

• Intrinsically disordered regions appear to play important functional roles


Globular proteins are built from recurring 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 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


-domain structures: 4-helix bundles


-sheets: up-and-down sheets & barrels


-domains: leucine-rich motifs can form horseshoes


New today:

Protein Structure

DatabasesClassificationVisualization

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 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


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


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 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

• Cn3D http://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 site http://pdbbeta.rcsb.org/pdb/Welcome.do


RCSB PDB - New Tutorial http://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 Alignment Search 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)

QuickTime™ and aTIFF (LZW) decompressor

are needed to see this picture.


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) & structure prediction


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 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

Documents

11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont.1 11/9/05 Protein Structure Databases (continued) Prediction & Modeling