Fundamentals of Protein Structure

Outline
Protein structure
Primary Secondary Tertiary Quaternary
Fundamentals of Protein Structure

Thomas Funkhouser Princeton University CS597A, Fall 2007
Levels of Protein Structure
Outline
Protein structure
Lehninger Principles of Biochemistry (3rd edition) David L. Nelson, Michael M. Cox
Primary Structure
DNA
GGGGCTACGGGGGGTGGGGCTTCGCGCCCCGCCGGCCTAIAAGCGGGCCGCCGCGGCTCCGTGCCQTTGCCGACCTTGCCT GcCGCCGCTGCTGCTTCGCGCCCGTCGCCTCCGCCATGGCTCCCAGGAAGTTCTTCGTGGGTGGCAACTGGAAGATGAACG GCGACAAGAAGAGCTTGGGCGAGCTCATCCACACGCTGAATGGCGCCAAGCTCTCGGCCGACACCGAGGTGGTTTGCGGAG CCCCTTCAATCTACCTTGATTTTGCCCGCCAGAAGCTTGATGCAAAGATTGGAGTTGCAGCACAAAACTGTTACAACGTAC CGAAGGGTGCTTTCACAGGAGAGATCAGCCCAGCAATGATCAAAGATATTGGAGCTGCATGGGTGATCCTGGGCCACTCAG AGCGGAGGCATGTTTTTGGAGAGTCTGATGAGTTGATTGGGCAGAAGGTGGCTCATGCTCMTGCTGAAGGC .[Straus85] . .
Primary Structure
Transcription and translation (DNAProtein)
Sequence of Nucleic Acids
http://www.accessexcellence.org
Primary Structure
First Position | U(T) Second Position Third ------------------------------------ Position U(T) C A G | Phe Phe Leu Leu Leu Leu Leu Leu Ile Ile Ile Met Val Val Val Val Ser Ser Ser Ser Pro Pro Pro Pro Thr Thr Thr Thr Ala Ala Ala Ala Tyr Tyr STOP STOP His His Gln Gln Asn Asn Lys Lys Asp Asp Glu Glu Cys Cys STOP Trp Arg Arg Arg Arg Ser Ser Arg Arg Gly Gly Gly Gly U(T) C A G U(T) C A G U(T) C A G U(T) C A G
Primary Structure
Alanine Cysteine Aspartic Acid Glutamic Acid Phenylalanine Glycine Histidine Isoleucine Lysine Leucine Methionine Asparagine Proline Glutamine Arginine Serine Threonine Valine Tryptophan Tyrosine Ala Cys Asp Glu Phe Gly His Ile Lys Leu Met Asn Pro Gln Arg Ser Thr Val Trp Tyr A C D E F G H I K L M N P Q R S T V W Y
Short-hand Names for Amino Acids
Primary Structure
GGGGCTACGGGGGGTGGGGCTTCGCGCCCCGCCGGCCTAIAAGCGGGCCGCCGCGGCTCCGTGCCQTTGCCGACCTTGCCT GcCGCCGCTGCTGCTTCGCGCCCGTCGCCTCCGCCATGGCTCCCAGGAAGTTCTTCGTGGGTGGCAACTGGAAGATGAACG GCGACAAGAAGAGCTTGGGCGAGCTCATCCACACGCTGAATGGCGCCAAGCTCTCGGCCGACACCGAGGTGGTTTGCGGAG CCCCTTCAATCTACCTTGATTTTGCCCGCCAGAAGCTTGATGCAAAGATTGGAGTTGCAGCACAAAACTGTTACAACGTAC CGAAGGGTGCTTTCACAGGAGAGATCAGCCCAGCAATGATCAAAGATATTGGAGCTGCATGGGTGATCCTGGGCCACTCAG AGCGGAGGCATGTTTTTGGAGAGTCTGATGAGTTGATTGGGCAGAAGGTGGCTCATGCTCMTGCTGAAGGC . . .
Primary Structure
Sequence of Nucleic Acids
Sequence of Nucleotides
APRKFFVGGNWKMNGDKKSLGELIHTLNGAKLSADTEVVCGAPSIYLDFAR QKLDAKIGVAAQNCYKVPKGAFTGEISPAMIKDIGAAWVILGHSERRHVFGES DELIGQKVAHALAEGLGVIACIGEKLDEREAGITEKVVFEQTKAIADNVKDW SKVVLAYEPVWAIGTGKTATPQQAQEVHEKLRGWLKSHVSDAVAQSTRI IYGGSVTGGNCKELASQHDVDGFLVGGASLKPEFVDIINAKH
Sequence of Amino Acids

[Straus85]

[Straus85]
Primary Structure
Primary Structure

[Straus85]

[Straus85]
Primary Structure
Amino acid:
(Amino group) (Carboxyl group)
Primary Structure
Twenty amino acids:
(Alpha carbon)
OH
(Side chain)
[http://www.cryst.bbk.ac.uk]
Primary Structure
Amino acids are linked by peptide bonds
Primary Structure
Polypeptide chain:
Biochemistry (5th edition) Jeremy M. Berg, John L. Tymoczko, Lubert Stryer
Primary Structure
Polypeptide chain:
Backbone
Primary Structure
Polypeptide chain:
Side chain
Primary Structure
Polypeptide chain:
Side chain
Primary Structure
Polypeptide chain:
Side chain
Primary Structure
Peptide bond:
Primary Structure
Peptide bond:
omega
Most bond angles are constrained
Peptides have at most two free torsion angles (omega is 180 (trans) or 0 cis)
[http://www.cryst.bbk.ac.uk] [http://www.cryst.bbk.ac.uk]
Primary Structure
N-C and C -C bonds can rotate

Primary Structure
Ramachandran plot:
[PDBSUM]
1tim
Primary Structure
Important properties of amino acids:
Size Charge Polarity Aromaticity Hydrophobicity Conformational constraints
Primary Structure
Primary Structure
Primary Structure
Primary Structure
Primary Structure
Primary Structure
Structure
Forces affecting structure:
H-bonding Van der Waals Electrostatics Hydrophobicity Disulfide Bridges
+
H-bonds form when a hydrogen is shared by two partially negatively charged atoms
In proteins, the participating atoms are always N/N, O/O, or N/O, usually in polar residues or backbone
Structure
H-bonding Van der Waals Electrostatics Hydrophobicity Disulfide Bridges Van de Waals forces are caused by fluctuation in the positions of electrons on uncharged atoms They are repulsive or attractive, depending on the proximity of interacting atoms
Structure
http://honiglab.cpmc.columbia.edu/grasp/pictures.html
Structure
Structure
Hydrophobic (nonpolar) resiidues generally pack together away from polar solutions (water)
e.g., in core of proteins in water, in binding sites, on the surface of proteins in membranes, etc.
Cysteines can be oxidized to form covalent S-S bonds between amino acids distant in primary sequence
Outline
Protein structure
Secondary Structure
Loop
Alpha Helix Beta Sheet

1tim
[Jena]
Secondary Structure
Some repeating sequences of torsion angles are very stable
Alpha helix Beta sheet
Secondary Structure
Secondary Structure
Secondary Structure
[chemed.chem.purdue.edu]
Secondary Structure
Secondary Structure
Secondary Structure
Secondary Structure
Secondary Structure
Secondary Structure
[chemed.chem.purdue.edu]
Antiparallel
Parallel
Secondary Structure
Secondary Structure
Parallel
AntiParallel
Secondary Structure
Others form loops, turns etc.
Secondary Structure
[PDBSUM]
Secondary Structure
Supersecondary structure / motifs
Helix loop helix
Helix loop helix Calcium-binding motif
Introduction to protein structure (2nd edition) Carl Branden, John Tooze

Four classes:
Geek Key motif
All All / +

- - motif
Hairpin motif
Secondary Structure Visualization
Secondary Structure Visualization

Loop
Beta Sheet
Outline
Protein structure
Tertiary Structure
Arrangement of atoms:
Alpha Helix
1tim
[Jena]
[pymol]
1atp
10
Tertiary Structure
How protein folds:
Tertiary Structure
How protein folds:
[pymol]
1atp
[pymol]
1atp
Tertiary Structure

Tertiary Structure
Function Structural classifications
Fold similarities Evolutionary relationships Sequence similarities
Sequence
Structure
Examples:
CATH SCOP
The globin fold is resilient to amino acid changes. V. stercoraria (bacterial) hemoglobin (left) and P. marinus (eukaryotic) hemoglobin (right) share just 8% sequence identity, but their overall fold and function is identical.
Slide courtesy of Philip Bourne
Tertiary Structure
CATH hierarchy:
Class Architecture Topology Homology S35 (Family) S95 S100
Tertiary Structure
SCOP hierarchy:
Class Fold Superfamily Family Protein Domain Species PDB
SCOP: 1gsa
1. Root: scop 2. Class: Alpha and beta proteins (a/b) [51349] 3. Fold: PreATP-grasp domain [52439] 4. Superfamily: PreATP-grasp domain [52440] 5. Family: Prokaryotic glutathione synthetase, N-terminal domain [52457] 6. Protein: Prokaryotic glutathione synthetase, N-terminal domain [52458] 7. Species: Escherichia coli [52459] http://scop.mrc-lmb.cam.ac.uk/scop/ [Murzin95]
Structural Layout
http://cathwww.biochem.ucl.ac.uk/ [Orengo97]
11
Tertiary Structure
SCOP hierarchy:
7 945 1,539 2,845 70,859 SCOP: Structural Classification of Proteins (1.69 release)
Outline
Protein structure
Quatenary Structure
How multiple chains/proteins form a complex:
Quatenary Structure
Active binding site may be at interface between two chains
[Rasurf]
1tim
[Rasurf]
1tim
Quatenary Structure
Chain may take a new (active) conformation when bound to another
Quaternary structure
[Rasurf]
1tim
Ribbon diagram of a heptameric, 63 kDa cleavage fragment (PA63) of the protective antigen (PA) protein, produced by Bacillus anthracis as part of the anthrax toxin. The quaternary structure is that of a pre-pore, which later forms a channel that allows other toxins into the cytosol of the target cell, so the pathogen can cause damage to the host. [http://www3.niaid.nih.gov/]
12
Quaternary structure
Protein Structure Level Summary

Protein structure description

amino acid sequence local fold pattern of small subsequence fold of entire protein chain complex of multiple chains
Quorum Sensing Activity in Vibrio harveyi [Megan Pomianek, Chemistry, Princeton University]
Protein Structure Databases

Repositories:


Repositories:
Primary Secondary Tertiary Quaternary UniProt DSSP PDB PQS
Chain 1GSA:_ Compound Glutathione Synthetase Type Protein Molecular Weight 35547 Number of Residues 316 Number of Alpha 9 Content of Alpha 27.22 Number of Beta 19 Content of Beta 28.16
1 MIKLGIVMDP IANINIKKDS SFAMLLEAQR RGYELHYMEM GDLYLINGEA EEEEE S GGGTTTTTTH HHHHHHHHHH HT EEEEE G GGEEEETTEE

Repositories:

UniProt DSSP PDB PQS
Chain 1GSA:_ Compound Glutathione Synthetase Type Protein Molecular Weight 35547 Number of Residues 316
1 MIKLGIVMDP IANINIKKDS SFAMLLEAQR RGYELHYMEM GDLYLINGEA
51 RAHTRTLNVK QNYEEWFSFV GEQDLPLADL DVILMRKDPP FDTEFIYATY
51 RAHTRTLNVK QNYEEWFSFV GEQDLPLADL DVILMRKDPP FDTEFIYATY EEEEEEEEE S SS EEE EEEEEGGGS SEEEE HHHHHHHH
101 ILERAEEKGT LIVNKPQSLR DCNEKLFTAW FSDLTPETLV TRNKAQLKAF
101 ILERAEEKGT LIVNKPQSLR DCNEKLFTAW FSDLTPETLV TRNKAQLKAF HHHHHHHTT EEES HHHHH HTTTTGGGGG GTTTB EEE ES HHHHHHH
151 WEKHSDIILK PLDGMGGASI FRVKEGDPNL GVIAETLTEH GTRYCMAQNY
201 LPAIKDGDKR VLVVDGEPVP YCLARIPQGG ETRGNLAAGG RGEPRPLTES
251 DWKIARQIGP TLKEKGLIFV GLDIIGDRLT EINVTSPTCI REIEAEFPVS
H = helix B = residue in isolated beta bridge E = extended beta strand G = 310 helix T = hydrogen bonded turn S = bend
151 WEKHSDIILK PLDGMGGASI FRVKEGDPNL GVIAETLTEH GTRYCMAQNY HHHHSSEEEE SS TTTT EEE TTTTTH HHHHHHHTTT TTS EEEEE
201 LPAIKDGDKR VLVVDGEPVP YCLARIPQGG ETRGNLAAGG RGEPRPLTES GGGGG EEE EEEETTEE S EEEEEE SS S GGGT EEEEEE HH
251 DWKIARQIGP TLKEKGLIFV GLDIIGDRLT EINVTSPTCI REIEAEFPVS HHHHHHHHHT HHHHTT EE EEEEETTEE EEE SS H HHHHHHSS
301 ITGMLMDAIE ARLQQQ
301 ITGMLMDAIE ARLQQQ HHHHHHHHHH HHT
http://www.uniprot.org/ [Apweiler04]
[Kabsch83]

Repositories:
Primary Secondary Tertiary Quaternary UniProt DSSP PDB PQS
[Kabsch83]
http://www.rcsb.org/pdb/ [Berman00]
13

Repositories:

Summary
Protein structure description

References
Information and figures were taken from:
Introduction to protein structure (2nd edition)
Carl Branden, John Tooze
Lehninger Principles of Biochemistry (3rd edition)

David L. Nelson, Michael M. Cox
Biochemistry (5th edition)

Jeremy M. Berg, John L. Tymoczko, Lubert Stryer
http://www.cs.cryst.bbk.ac.uk http://www.accessexcellence.org http://chemmed.chem.purdue.edu
Example: Hemoglobin
Chain A Tertiary Structure
Deoxyhemoglobin (alpha chain). Chain: a. Engineered: yes. Mutation: yes. Deoxyhemoglobin (beta chain). Chain: b, d. Engineered: yes. Mutation: yes 1C7D E.A.Brucker
amino acid sequence local fold pattern of small subsequence fold of entire protein chain complex of multiple chains
Protein folding/binding

http://pqs.ebi.ac.uk/ [Hendrick98]
Disulfide linkages Hydrogen bonding Electrostatic interactions Hydrophobic interactions Van der Waals forces
[Jena]
1tim
Example: Hemoglobin
Chain A Primary structure: 284 residues
Chain A Secondary structure and motifs: 19 Helices 50 Helices-helices interacs 14 Beta turns 2 gamma turns
Example: Hemoglobin
Deoxyhemoglobin Quaternary Structure
14

Fundamentals of Protein Structure

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Outline

Fundamentals of Protein Structure

Levels of Protein Structure

Lehninger Principles of Biochemistry (3rd edition) David L. Nelson, Michael M. Cox

Sequence of Nucleic Acids

Short-hand Names for Amino Acids

Sequence of Nucleic Acids

APRKFFVGGNWKMNGDKKSLGELIHTLNGAKLSADTEVVCGAPSIYLDFAR QKLDAKIGVAAQNCYKVPKGAFTGEISPAMIKDIGAAWVILGHSERRHVFGES DELIGQKVAHALAEGLGVIACIGEKLDEREAGITEKVVFEQTKAIADNVKDW SKVVLAYEPVWAIGTGKTATPQQAQEVHEKLRGWLKSHVSDAVAQSTRI IYGGSVTGGNCKELASQHDVDGFLVGGASLKPEFVDIINAKH

APRKFFVGGNWKMNGDKKSLGELIHTLNGAKLSADTEVVCGAPSIYLDFAR QKLDAKIGVAAQNCYKVPKGAFTGEISPAMIKDIGAAWVILGHSERRHVFGES DELIGQKVAHALAEGLGVIACIGEKLDEREAGITEKVVFEQTKAIADNVKDW SKVVLAYEPVWAIGTGKTATPQQAQEVHEKLRGWLKSHVSDAVAQSTRI IYGGSVTGGNCKELASQHDVDGFLVGGASLKPEFVDIINAKH

Sequence of Amino Acids

Sequence of Amino Acids

APRKFFVGGNWKMNGDKKSLGELIHTLNGAKLSADTEVVCGAPSIYLDFAR QKLDAKIGVAAQNCYKVPKGAFTGEISPAMIKDIGAAWVILGHSERRHVFGES DELIGQKVAHALAEGLGVIACIGEKLDEREAGITEKVVFEQTKAIADNVKDW SKVVLAYEPVWAIGTGKTATPQQAQEVHEKLRGWLKSHVSDAVAQSTRI IYGGSVTGGNCKELASQHDVDGFLVGGASLKPEFVDIINAKH

APRKFFVGGNWKMNGDKKSLGELIHTLNGAKLSADTEVVCGAPSIYLDFAR QKLDAKIGVAAQNCYKVPKGAFTGEISPAMIKDIGAAWVILGHSERRHVFGES DELIGQKVAHALAEGLGVIACIGEKLDEREAGITEKVVFEQTKAIADNVKDW SKVVLAYEPVWAIGTGKTATPQQAQEVHEKLRGWLKSHVSDAVAQSTRI IYGGSVTGGNCKELASQHDVDGFLVGGASLKPEFVDIINAKH

Sequence of Amino Acids

Sequence of Amino Acids

Lehninger Principles of Biochemistry (3rd edition) David L. Nelson, Michael M. Cox

Biochemistry (5th edition) Jeremy M. Berg, John L. Tymoczko, Lubert Stryer

APRKFFVGGNWKMNGDKKSLGELIHTLNGAKLSADTEVVCGAPSIYLDFAR QKLDAKIGVAAQNCYKVPKGAFTGEISPAMIKDIGAAWVILGHSERRHVFGES DELIGQKVAHALAEGLGVIACIGEKLDEREAGITEKVVFEQTKAIADNVKDW SKVVLAYEPVWAIGTGKTATPQQAQEVHEKLRGWLKSHVSDAVAQSTRI IYGGSVTGGNCKELASQHDVDGFLVGGASLKPEFVDIINAKH

Sequence of Amino Acids

APRKFFVGGNWKMNGDKKSLGELIHTLNGAKLSADTEVVCGAPSIYLDFAR QKLDAKIGVAAQNCYKVPKGAFTGEISPAMIKDIGAAWVILGHSERRHVFGES DELIGQKVAHALAEGLGVIACIGEKLDEREAGITEKVVFEQTKAIADNVKDW SKVVLAYEPVWAIGTGKTATPQQAQEVHEKLRGWLKSHVSDAVAQSTRI IYGGSVTGGNCKELASQHDVDGFLVGGASLKPEFVDIINAKH

APRKFFVGGNWKMNGDKKSLGELIHTLNGAKLSADTEVVCGAPSIYLDFAR QKLDAKIGVAAQNCYKVPKGAFTGEISPAMIKDIGAAWVILGHSERRHVFGES DELIGQKVAHALAEGLGVIACIGEKLDEREAGITEKVVFEQTKAIADNVKDW SKVVLAYEPVWAIGTGKTATPQQAQEVHEKLRGWLKSHVSDAVAQSTRI IYGGSVTGGNCKELASQHDVDGFLVGGASLKPEFVDIINAKH

Sequence of Amino Acids

Sequence of Amino Acids

APRKFFVGGNWKMNGDKKSLGELIHTLNGAKLSADTEVVCGAPSIYLDFAR QKLDAKIGVAAQNCYKVPKGAFTGEISPAMIKDIGAAWVILGHSERRHVFGES DELIGQKVAHALAEGLGVIACIGEKLDEREAGITEKVVFEQTKAIADNVKDW SKVVLAYEPVWAIGTGKTATPQQAQEVHEKLRGWLKSHVSDAVAQSTRI IYGGSVTGGNCKELASQHDVDGFLVGGASLKPEFVDIINAKH

APRKFFVGGNWKMNGDKKSLGELIHTLNGAKLSADTEVVCGAPSIYLDFAR QKLDAKIGVAAQNCYKVPKGAFTGEISPAMIKDIGAAWVILGHSERRHVFGES DELIGQKVAHALAEGLGVIACIGEKLDEREAGITEKVVFEQTKAIADNVKDW SKVVLAYEPVWAIGTGKTATPQQAQEVHEKLRGWLKSHVSDAVAQSTRI IYGGSVTGGNCKELASQHDVDGFLVGGASLKPEFVDIINAKH

Sequence of Amino Acids

Sequence of Amino Acids

Most bond angles are constrained

Lehninger Principles of Biochemistry (3rd edition) David L. Nelson, Michael M. Cox

Alpha Helix Beta Sheet

Lehninger Principles of Biochemistry (3rd edition) David L. Nelson, Michael M. Cox

Lehninger Principles of Biochemistry (3rd edition) David L. Nelson, Michael M. Cox

Supersecondary structure / motifs

Helix loop helix

Helix loop helix Calcium-binding motif

Introduction to protein structure (2nd edition) Carl Branden, John Tooze

Supersecondary structure / motifs

Supersecondary structure / motifs

Geek Key motif

Introduction to protein structure (2nd edition) Carl Branden, John Tooze

Introduction to protein structure (2nd edition) Carl Branden, John Tooze

Secondary Structure Visualization

Secondary Structure Visualization

Active binding site may be at interface between two chains

Protein Structure Level Summary

Primary Secondary Tertiary Quaternary

Lehninger Principles of Biochemistry (3rd edition) David L. Nelson, Michael M. Cox

Protein Structure Databases

Protein Structure Databases

Protein Structure Databases

Primary Secondary Tertiary Quaternary

Primary Secondary Tertiary Quaternary

UniProt DSSP PDB PQS

1 MIKLGIVMDP IANINIKKDS SFAMLLEAQR RGYELHYMEM GDLYLINGEA

51 RAHTRTLNVK QNYEEWFSFV GEQDLPLADL DVILMRKDPP FDTEFIYATY

101 ILERAEEKGT LIVNKPQSLR DCNEKLFTAW FSDLTPETLV TRNKAQLKAF

151 WEKHSDIILK PLDGMGGASI FRVKEGDPNL GVIAETLTEH GTRYCMAQNY

201 LPAIKDGDKR VLVVDGEPVP YCLARIPQGG ETRGNLAAGG RGEPRPLTES

251 DWKIARQIGP TLKEKGLIFV GLDIIGDRLT EINVTSPTCI REIEAEFPVS

301 ITGMLMDAIE ARLQQQ

301 ITGMLMDAIE ARLQQQ HHHHHHHHHH HHT

Protein Structure Databases

UniProt DSSP PDB PQS

Protein Structure Databases