Protein structure and modelling

● Orientation● Protein structure● Protein modelling

Andreas HegerUniversity of HelsinkiBioinformatics Group

Slides will be available at: ekhidna.biocenter.helsinki.fi:8080/downloads/teaching/hut2004/

Proteins

● Proteins are involved in all processes inside a cell– Gene regulation– Metabolism– Signalling– Development– Structure

http://www.websters-online-dictionary.org/definition/english/ce/cell.html

Chemistry

● Proteins are linear hetero-polymers of amino acids– twenty different amino acids (building blocks)

ARG LYS VAL ILE PRO ARG GLU LYS

R K V I P R E K

3-letter code

1-letter code

Peptide bond

http://www.imb-jena.de/~rake/Bioinformatics_WEB/basics_peptide_bond.html

The peptide bond is planar

2 angles freely rotatable1 is fixed

Peptide ~ 2-10 amino acidsPolypeptide ~ 10-50 amino acidsProtein ~ 50- amino acids

Double bond character of the peptide bond

Amino acids

● Side chain properties– Size– Charge– Polarity

http://www.ch.cam.ac.uk/SGTL/Structures/amino/

Proteins are very special polymers:● A given protein has always the same amino acid

sequence– Protein sequence is determined by DNA sequence

● A given protein has always a unique three- dimensional structure.– Protein structure is determined by protein sequence.

always = biological always (there are exceptions)

Protein evolutionSequence – Structure - Function

DNA sequence

Protein sequence Protein structure

Protein functionSelection

Summary

● Protein structure is the key to understanding protein function

● Topics in protein structure

1.Protein structure determination

2.Protein architecture

3.Protein function

4.Protein folding● Protein modelling and computational methods

Protein structure determination

● Protein expression– membrane proteins– aggregation

● X-Ray crystallography● NMR (nuclear magnetic resonance)● Cryo-EM (electron microscopy)

Structures by X-ray crystallography

➔ Crystallize protein● Collect diffraction patterns● Improve iteratively:

– Calculate electron density map● Phase problem

– Fit amino acid trace through map

X-ray crystallography

● Crystallization

● “An art as much as a science”Charges

http://crystal.uah.edu/~carter/protein/crystal.htm

Diffraction and electron density maps

Diffraction pattern

X-ray source Crystal

Intensities

Iterative refinement

http://www.sci.sdsu.edu/TFrey/Bio750/Bio750X-Ray.html

Higher resolution =more accurate positioning of atoms

Resolution

NMR

● Create highly concentrated protein solution● Record spectra● Assign peaks to residues● Calculate constraints● Compute structure

NMR spectra

1D 2D

http://www.cryst.bbk.ac.uk/PPS2/projects/schirra/html/2dnmr.htm

Distance constraints from NMR

● From the sequence– Topology– Bond angles– Bond lengths

● From the NMR experiment– Torsion angles– Distance constraints

HαR

CO

H

CO

Torsion angle

Ensemble of structures

SH3-domain

1aey

What is the true protein structure?

● X-Ray– “frozen” state of a protein

● crystal contacts✔ large protein structure

● NMR✔ protein in solution– limited in size

Molecular complexesvia X-ray

1fjg

30 S subunit of the ribosome

Protein

RNA

Cryo-EMSingle particle image reconstruction

Koning et al. (2003)

Bacteriophage MS2

Fitting X-Ray structures into density maps

GroEL-complex

1gr6

Hemoglobin

Protein structure databases

http://www.wwpdb.org/index.html

Protein architecture

● Protein structure is the key to understanding protein function

● Topics in protein structure

1.Protein structure determination

2.Protein architecture

3.Protein function

4.Protein folding● Protein modelling and computational methods

Topics in protein architecture

● Principles of protein architecture– Secondary structure– Supersecondary structure– Tertiary structure– Quarternary structure

● Classification of protein structures

The big surprise

DNA is a regular structure Watson & Crick (1953)

Myoglobin

Kendrew and Perutz1957

1mbn

Secondary structure● backbone

– no amino acid side chains● regular patterns

– of hydrogen-bonds– backbone torsion angles

● types of secondary structure

– α-helix– β-sheet– ...

α-Helix

β-Sheethydrogen bond pattern: n, n+4

β-sheet

http://broccoli.mfn.ki.se/pps_course_96

view from the top view from the side

β-strands

Cartoon representation

2TRX 2AAC

Supersecondary structures

● local arrangments of secondary structure elements

http://www.expasy.org/swissmod/course/text/chapter2.htm

Tertiary structure

1coh

Quaternary structure

1coh

Protein structure

● Primary structure

● Secondary structure

● Super-secondary structure

● Tertiary structure

● Quaternary structure

Protein domains/modules

● globular● independently foldable● occur in different contexts

Domains via the contact matrix

Structure classification

● 24908 structures in the Protein Databank (PDB)● major classifications of proteins:

– SCOPhttp://scop.mrc-lmb.cam.ac.uk/scop/

– CATHhttp://www.biochem.ucl.ac.uk/bsm/cath/

– DALI DOMAIN DICTIONARY/FSSPhttp://ekhidna.biocenter.helsinki.fi:8080/dali/index.html

Hierachical description of protein architecture

1.Class:

α, β, α/β, α+β

2.FoldStructural similarity

3.SuperfamilyEvolutionary relationship

4.FamilySequence similarity

1.Class

α, β, α&β

2.ArchitectureSS: Spatial arrangement

3.TopologySS: Topology

4.Homologystructural/sequence similarity

SCOP CATH

CATH

http://www.biochem.ucl.ac.uk/bsm/cath/cath_info.html

Class

Architecture

Topology

Dali Domain Dictionary

1.Fold space attractor region

Secondary structure composition and supersecondary structural motifs

2.Globular folding topology

Structural comparison

3.Functional family

Neural network

4.Sequence family

Sequence comparison

Deviation from globularity

● Domain swapping● Repetitive structures● Open/closed conformations

1bsr

5rsa

1amy

1d0b

Protein function

● Protein structure is the key to understanding protein function

● Topics in protein structure

1.Protein structure determination

2.Protein architecture

3.Protein function

4.Protein folding● Protein modelling and computational methods

Topics in protein function

● How does structure determine function?– Structural proteins– Enzymes– Transcription factors– ...

Structural proteins

● Collagen

1K6F http://www.aw-bc.com/mathews/ch06/fi6p13ad.htm

Actin and muscles

Enzymes

● Catalytic triad: Asp, Ser, His

1CHO

Mechanism

● Enzymes speed up chemical reactions● Enzymes are not consumed by the reaction● Stabilization of the transition state● Charge-relay cascade

Convergent evolution in serine proteases

● same reaction● same mechanism● same orientation of

catalytic residues● different structures

– Chymotrypsin:● His-57, Asp-102, Ser-195

– Subtilisin:● Asp-32, His-64, Ser-221

1cho / 1sib

Substrate specificity

Perona & Craik (1997)

Transcription factors

1L3L

Ligand

DNA

Hydrogen bonding pattern

Vannini (2002)

Protein folding

● Protein structure is the key to understanding protein function

● Topics in protein structure

1.Protein structure determination

2.Protein architecture

3.Protein function

4.Protein folding● Protein modelling and computational methods

Protein denaturation

● Denatured state = unfolded state● Native state = folded state● Denaturation = heat, urea, salts

Reaction coordinate

Energy

FoldedUnfolded

Reaction coordinate

Energy

FoldedUnfolded

Protein stability

● Native state only marginally more stable than denatured state

● Contributions to protein stability– hydrophobic effect: entropic effect– hydrogen bonds: net effect = 0– others

● salt bridges● disulphide bonds● aromatic-aromatic interactions● metal binding

Hydrophobic core of lysozyme

1HELHydrophobic amino acid

Hydrophilic amino acid

Protein folding

● Folding Funnel● Energy landscape

guides protein towards native structure

Dobson (2004)

C: total contacts

Q: native contacts

Energy landscape for the folding of lysozyme

Fast trackSlow track

Dobson (2004)

Misfolded proteins

● Disulfid-isomerases, Prolin-isomerases● Chaperones: unfold misfolded proteins● Protein folding diseases

– BSE– Alzheimer's disease– Parkinson's disease– ...

GroEL – a chaperone

1gr6

Wang & Weissmann (1999)

Roseman et al. (1996)

GroEL mechanism

Protein structure

● Protein structure is the key to understanding protein function

● Topics in protein structure

1.Protein structure determination

2.Protein architecture

3.Protein function

4.Protein folding● Protein modelling and computational methods