Protein structure and modelling

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Protein structure and modelling
Andreas Heger University of Helsinki Bioinformatic
s Group

• Orientation
• Protein structure
• Protein modelling

Slides will be available at ekhidna.biocenter.he
lsinki.fi8080/downloads/teaching/hut2004/
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Proteins

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

http//www.websters-online-dictionary.org/definiti
on/english/ce/cell.html
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Chemistry

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

3-letter code
ARG LYS VAL ILE PRO ARG GLU LYS
1-letter code
R K V I P R E K
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Peptide bond
Double bond character of the peptide bond
The peptide bond is planar
Peptide 2-10 amino acids Polypeptide 10-50
amino acids Protein 50- amino acids
2 angles freely rotatable 1 is fixed
http//www.imb-jena.de/rake/Bioinformatics_WEB/ba
sics_peptide_bond.html
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Amino acids

• Side chain properties
• Size
• Charge
• Polarity

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

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Protein evolutionSequence Structure - Function
Selection
DNA sequence
Protein function
Protein sequence
Protein structure
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Summary

• Protein structure is the key to understanding
  protein function
• Topics in protein structure
• Protein structure determination
• Protein architecture
• Protein function
• Protein folding
• Protein modelling and computational methods

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Protein structure determination

• Protein expression
• membrane proteins
• aggregation
• X-Ray crystallography
• NMR (nuclear magnetic resonance)
• Cryo-EM (electron microscopy)

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Structures by X-ray crystallography

• Crystallize protein
• Collect diffraction patterns
• Improve iteratively
• Calculate electron density map
• Phase problem
• Fit amino acid trace through map

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X-ray crystallography

• Crystallization
• An art as much as a science

Charges
http//crystal.uah.edu/carter/protein/crystal.htm
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Diffraction and electron density maps
Intensities
X-ray source
Crystal
Diffraction pattern
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Iterative refinement
Resolution
Higher resolution more accurate positioning of
atoms
http//www.sci.sdsu.edu/TFrey/Bio750/Bio750X-Ray.h
tml
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NMR

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

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NMR spectra
2D
1D
http//www.cryst.bbk.ac.uk/PPS2/projects/schirra/h
tml/2dnmr.htm
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Distance constraints from NMR

• From the sequence
• Topology
• Bond angles
• Bond lengths
• From the NMR experiment
• Torsion angles
• Distance constraints

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Ensemble of structures
SH3-domain
1aey
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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

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Molecular complexesvia X-ray
30 S subunit of the ribosome
Protein
RNA
1fjg
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Cryo-EMSingle particle image reconstruction
Bacteriophage MS2
Koning et al. (2003)
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Fitting X-Ray structures into density maps
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GroEL-complex
Hemoglobin
1gr6
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Protein structure databases
http//www.wwpdb.org/index.html
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Protein architecture

• Protein structure is the key to understanding
  protein function
• Topics in protein structure
• Protein structure determination
• Protein architecture
• Protein function
• Protein folding
• Protein modelling and computational methods

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Topics in protein architecture

• Principles of protein architecture
• Secondary structure
• Supersecondary structure
• Tertiary structure
• Quarternary structure
• Classification of protein structures

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The big surprise
DNA is a regular structure Watson Crick (1953)
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Myoglobin
Kendrew and Perutz 1957
1mbn
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Secondary structure

• backbone
• no amino acid side chains
• regular patterns
• of hydrogen-bonds
• backbone torsion angles
• types of secondary structure
• a-helix
• ß-sheet
• ...

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a-Helix
hydrogen bond pattern n, n4
ß-Sheet
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ß-sheet
ß-strands
view from the side
view from the top
http//broccoli.mfn.ki.se/pps_course_96
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Cartoon representation
2AAC
2TRX
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Supersecondary structures

• local arrangments of secondary structure elements

http//www.expasy.org/swissmod/course/text/chapter
2.htm
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Tertiary structure
1coh
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Quaternary structure
1coh
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Protein structure

• Primary structure
• Secondary structure
• Super-secondary structure
• Tertiary structure
• Quaternary structure

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Protein domains/modules

• globular
• independently foldable
• occur in different contexts

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Domains via the contact matrix
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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.biocent
  er.helsinki.fi8080/dali/index.html

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Hierachical description of protein architecture
CATH
SCOP

• Class
• a, ß, a/ß, aß
• Fold
• Structural similarity
• Superfamily
• Evolutionary relationship
• Family
• Sequence similarity

• Class
• a, ß, aß
• Architecture
• SS Spatial arrangement
• Topology
• SS Topology
• Homology
• structural/sequence similarity

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CATH
Class
Architecture
Topology
http//www.biochem.ucl.ac.uk/bsm/cath/cath_info.ht
ml
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Dali Domain Dictionary

• Fold space attractor region
• Secondary structure composition and
  supersecondary structural motifs
• Globular folding topology
• Structural comparison
• Functional family
• Neural network
• Sequence family
• Sequence comparison

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(No Transcript)
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Deviation from globularity

• Domain swapping
• Repetitive structures
• Open/closed conformations

5rsa
1bsr
1d0b
1amy
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Protein function

• Protein structure is the key to understanding
  protein function
• Topics in protein structure
• Protein structure determination
• Protein architecture
• Protein function
• Protein folding
• Protein modelling and computational methods

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Topics in protein function

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

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Structural proteins

• Collagen

1K6F
http//www.aw-bc.com/mathews/ch06/fi6p13ad.htm
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Actin and muscles
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Enzymes

• Catalytic triad Asp, Ser, His

1CHO
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Mechanism

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

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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
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Substrate specificity
Perona Craik (1997)
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Transcription factors
Ligand
DNA
1L3L
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Hydrogen bonding pattern
Vannini (2002)
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Protein folding

• Protein structure is the key to understanding
  protein function
• Topics in protein structure
• Protein structure determination
• Protein architecture
• Protein function
• Protein folding
• Protein modelling and computational methods

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Protein denaturation

• Denatured state unfolded state
• Native state folded state
• Denaturation heat, urea, salts

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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

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Hydrophobic core of lysozyme
Hydrophilic amino acid
Hydrophobic amino acid
1HEL
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Protein folding

• Folding Funnel
• Energy landscape guides protein towards native
  structure

C total contacts
Q native contacts
Dobson (2004)
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Energy landscape for the folding of lysozyme
Fast track
Slow track
Dobson (2004)
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Misfolded proteins

• Disulfid-isomerases, Prolin-isomerases
• Chaperones unfold misfolded proteins
• Protein folding diseases
• BSE
• Alzheimer's disease
• Parkinson's disease
• ...

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GroEL a chaperone
1gr6
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GroEL mechanism
Wang Weissmann (1999)
Roseman et al. (1996)
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Protein structure

• Protein structure is the key to understanding
  protein function
• Topics in protein structure
• Protein structure determination
• Protein architecture
• Protein function
• Protein folding
• Protein modelling and computational methods