Lehninger Principles of Biochemistry (3rd edition). David L. Nelson, Michael M.
Cox. Biochemistry (5th edition). Jeremy M. Berg, John L. Tymoczko, Lubert Stryer.
Outline Protein structure
Fundamentals of Protein Structure
• • • •
Primary Secondary Tertiary Quaternary
Protein folding/binding Yu (Julie) Chen and Thomas Funkhouser Princeton University CS597A, Fall 2005
Levels of Protein Structure
• Forces and factors
Outline Protein structure Primary • Secondary • Tertiary • Quaternary
Protein folding/binding • Forces and factors
Lehninger Principles of Biochemistry (3rd edition) David L. Nelson, Michael M. Cox
Primary Structure DNA
Primary Structure Transcription and translation (DNA→Protein)
GGGGCTACGGGGGGTGGGGCTTCGCGCCCCGCCGGCCTAIAAGCGGGCCGCCGCGGCTCCGTGCCQTTGCCGACCTTGCCT GcCGCCGCTGCTGCTTCGCGCCCGTCGCCTCCGCCATGGCTCCCAGGAAGTTCTTCGTGGGTGGCAACTGGAAGATGAACG GCGACAAGAAGAGCTTGGGCGAGCTCATCCACACGCTGAATGGCGCCAAGCTCTCGGCCGACACCGAGGTGGTTTGCGGAG CCCCTTCAATCTACCTTGATTTTGCCCGCCAGAAGCTTGATGCAAAGATTGGAGTTGCAGCACAAAACTGTTACAACGTAC CGAAGGGTGCTTTCACAGGAGAGATCAGCCCAGCAATGATCAAAGATATTGGAGCTGCATGGGTGATCCTGGGCCACTCAG AGCGGAGGCATGTTTTTGGAGAGTCTGATGAGTTGATTGGGCAGAAGGTGGCTCATGCTCMTGCTGAAGGC .[Straus85] . .
Sequence of Nucleic Acids
http://www.accessexcellence.org
1
Primary Structure
Primary Structure
Transcription and translation (DNA→Protein) First Position |
Transcription and translation (DNA→Protein)
Second Position Third ------------------------------------ Position U(T) C A G |
U(T)
Phe Phe Leu Leu
Ser Ser Ser Ser
Tyr Tyr STOP STOP
Cys Cys STOP Trp
U(T) C A G
C
Leu Leu Leu Leu
Pro Pro Pro Pro
His His Gln Gln
Arg Arg Arg Arg
U(T) C A G
A
Ile Ile Ile Met
Thr Thr Thr Thr
Asn Asn Lys Lys
Ser Ser Arg Arg
U(T) C A G
G
Val Val Val Val
Ala Ala Ala Ala
Asp Asp Glu Glu
Gly Gly Gly Gly
U(T) C A G
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
Primary Structure
Transcription and translation (DNA→Protein)
Transcription and translation (DNA→Protein)
GGGGCTACGGGGGGTGGGGCTTCGCGCCCCGCCGGCCTAIAAGCGGGCCGCCGCGGCTCCGTGCCQTTGCCGACCTTGCCT GcCGCCGCTGCTGCTTCGCGCCCGTCGCCTCCGCCATGGCTCCCAGGAAGTTCTTCGTGGGTGGCAACTGGAAGATGAACG GCGACAAGAAGAGCTTGGGCGAGCTCATCCACACGCTGAATGGCGCCAAGCTCTCGGCCGACACCGAGGTGGTTTGCGGAG CCCCTTCAATCTACCTTGATTTTGCCCGCCAGAAGCTTGATGCAAAGATTGGAGTTGCAGCACAAAACTGTTACAACGTAC CGAAGGGTGCTTTCACAGGAGAGATCAGCCCAGCAATGATCAAAGATATTGGAGCTGCATGGGTGATCCTGGGCCACTCAG AGCGGAGGCATGTTTTTGGAGAGTCTGATGAGTTGATTGGGCAGAAGGTGGCTCATGCTCMTGCTGAAGGC . . .
Sequence of Nucleic Acids
GGGGCTACGGGGGGTGGGGCTTCGCGCCCCGCCGGCCTAIAAGCGGGCCGCCGCGGCTCCGTGCCQTTGCCGACCTTGCCT GcCGCCGCTGCTGCTTCGCGCCCGTCGCCTCCGCCATGGCTCCCAGGAAGTTCTTCGTGGGTGGCAACTGGAAGATGAACG GCGACAAGAAGAGCTTGGGCGAGCTCATCCACACGCTGAATGGCGCCAAGCTCTCGGCCGACACCGAGGTGGTTTGCGGAG CCCCTTCAATCTACCTTGATTTTGCCCGCCAGAAGCTTGATGCAAAGATTGGAGTTGCAGCACAAAACTGTTACAACGTAC CGAAGGGTGCTTTCACAGGAGAGATCAGCCCAGCAATGATCAAAGATATTGGAGCTGCATGGGTGATCCTGGGCCACTCAG AGCGGAGGCATGTTTTTGGAGAGTCTGATGAGTTGATTGGGCAGAAGGTGGCTCATGCTCMTGCTGAAGGC . . .
Sequence of Nucleic Acids
APRKFFVGGNWKMNGDKKSLGELIHTLNGAKLSADTEVVCGAPSIYLDFAR QKLDAKIGVAAQNCYKVPKGAFTGEISPAMIKDIGAAWVILGHSERRHVFGES DELIGQKVAHALAEGLGVIACIGEKLDEREAGITEKVVFEQTKAIADNVKDW SKVVLAYEPVWAIGTGKTATPQQAQEVHEKLRGWLKSHVSDAVAQSTRI IYGGSVTGGNCKELASQHDVDGFLVGGASLKPEFVDIINAKH
Sequence of Amino Acids
APRKFFVGGNWKMNGDKKSLGELIHTLNGAKLSADTEVVCGAPSIYLDFAR QKLDAKIGVAAQNCYKVPKGAFTGEISPAMIKDIGAAWVILGHSERRHVFGES DELIGQKVAHALAEGLGVIACIGEKLDEREAGITEKVVFEQTKAIADNVKDW SKVVLAYEPVWAIGTGKTATPQQAQEVHEKLRGWLKSHVSDAVAQSTRI IYGGSVTGGNCKELASQHDVDGFLVGGASLKPEFVDIINAKH
Sequence of Amino Acids [Straus85]
Primary Structure
[Straus85]
Primary Structure
Transcription and translation (DNA→Protein)
Transcription and translation (DNA→Protein)
GGGGCTACGGGGGGTGGGGCTTCGCGCCCCGCCGGCCTAIAAGCGGGCCGCCGCGGCTCCGTGCCQTTGCCGACCTTGCCT GcCGCCGCTGCTGCTTCGCGCCCGTCGCCTCCGCCATGGCTCCCAGGAAGTTCTTCGTGGGTGGCAACTGGAAGATGAACG GCGACAAGAAGAGCTTGGGCGAGCTCATCCACACGCTGAATGGCGCCAAGCTCTCGGCCGACACCGAGGTGGTTTGCGGAG CCCCTTCAATCTACCTTGATTTTGCCCGCCAGAAGCTTGATGCAAAGATTGGAGTTGCAGCACAAAACTGTTACAACGTAC CGAAGGGTGCTTTCACAGGAGAGATCAGCCCAGCAATGATCAAAGATATTGGAGCTGCATGGGTGATCCTGGGCCACTCAG AGCGGAGGCATGTTTTTGGAGAGTCTGATGAGTTGATTGGGCAGAAGGTGGCTCATGCTCMTGCTGAAGGC . . .
Sequence of Nucleic Acids
GGGGCTACGGGGGGTGGGGCTTCGCGCCCCGCCGGCCTAIAAGCGGGCCGCCGCGGCTCCGTGCCQTTGCCGACCTTGCCT GcCGCCGCTGCTGCTTCGCGCCCGTCGCCTCCGCCATGGCTCCCAGGAAGTTCTTCGTGGGTGGCAACTGGAAGATGAACG GCGACAAGAAGAGCTTGGGCGAGCTCATCCACACGCTGAATGGCGCCAAGCTCTCGGCCGACACCGAGGTGGTTTGCGGAG CCCCTTCAATCTACCTTGATTTTGCCCGCCAGAAGCTTGATGCAAAGATTGGAGTTGCAGCACAAAACTGTTACAACGTAC CGAAGGGTGCTTTCACAGGAGAGATCAGCCCAGCAATGATCAAAGATATTGGAGCTGCATGGGTGATCCTGGGCCACTCAG AGCGGAGGCATGTTTTTGGAGAGTCTGATGAGTTGATTGGGCAGAAGGTGGCTCATGCTCMTGCTGAAGGC . . .
Sequence of Nucleic Acids
APRKFFVGGNWKMNGDKKSLGELIHTLNGAKLSADTEVVCGAPSIYLDFAR QKLDAKIGVAAQNCYKVPKGAFTGEISPAMIKDIGAAWVILGHSERRHVFGES DELIGQKVAHALAEGLGVIACIGEKLDEREAGITEKVVFEQTKAIADNVKDW SKVVLAYEPVWAIGTGKTATPQQAQEVHEKLRGWLKSHVSDAVAQSTRI IYGGSVTGGNCKELASQHDVDGFLVGGASLKPEFVDIINAKH
Sequence of Amino Acids
APRKFFVGGNWKMNGDKKSLGELIHTLNGAKLSADTEVVCGAPSIYLDFAR QKLDAKIGVAAQNCYKVPKGAFTGEISPAMIKDIGAAWVILGHSERRHVFGES DELIGQKVAHALAEGLGVIACIGEKLDEREAGITEKVVFEQTKAIADNVKDW SKVVLAYEPVWAIGTGKTATPQQAQEVHEKLRGWLKSHVSDAVAQSTRI IYGGSVTGGNCKELASQHDVDGFLVGGASLKPEFVDIINAKH
Sequence of Amino Acids [Straus85]
[Straus85]
2
Primary Structure
Primary Structure
Amino acid:
Twenty amino acids:
(Amino group) (Carboxyl group)
COO (Alpha carbon)
OH H3N
(Side chain)
H
R
Lehninger Principles of Biochemistry (3rd edition) David L. Nelson, Michael M. Cox
[http://www.cryst.bbk.ac.uk]
Primary Structure
Primary Structure
Amino acids are linked by peptide bonds
Lehninger Principles of Biochemistry (3rd edition) David L. Nelson, Michael M. Cox
C
Biochemistry (5th edition) Jeremy M. Berg, John L. Tymoczko, Lubert Stryer
Polypeptide chain:
APRKFFVGGNWKMNGDKKSLGELIHTLNGAKLSADTEVVCGAPSIYLDFAR QKLDAKIGVAAQNCYKVPKGAFTGEISPAMIKDIGAAWVILGHSERRHVFGES DELIGQKVAHALAEGLGVIACIGEKLDEREAGITEKVVFEQTKAIADNVKDW SKVVLAYEPVWAIGTGKTATPQQAQEVHEKLRGWLKSHVSDAVAQSTRI IYGGSVTGGNCKELASQHDVDGFLVGGASLKPEFVDIINAKH
Sequence of Amino Acids
[http://www.cryst.bbk.ac.uk]
Primary Structure
Primary Structure
Polypeptide chain:
Polypeptide chain: Backbone
Side chain
APRKFFVGGNWKMNGDKKSLGELIHTLNGAKLSADTEVVCGAPSIYLDFAR QKLDAKIGVAAQNCYKVPKGAFTGEISPAMIKDIGAAWVILGHSERRHVFGES DELIGQKVAHALAEGLGVIACIGEKLDEREAGITEKVVFEQTKAIADNVKDW SKVVLAYEPVWAIGTGKTATPQQAQEVHEKLRGWLKSHVSDAVAQSTRI IYGGSVTGGNCKELASQHDVDGFLVGGASLKPEFVDIINAKH
Sequence of Amino Acids
[http://www.cryst.bbk.ac.uk]
APRKFFVGGNWKMNGDKKSLGELIHTLNGAKLSADTEVVCGAPSIYLDFAR QKLDAKIGVAAQNCYKVPKGAFTGEISPAMIKDIGAAWVILGHSERRHVFGES DELIGQKVAHALAEGLGVIACIGEKLDEREAGITEKVVFEQTKAIADNVKDW SKVVLAYEPVWAIGTGKTATPQQAQEVHEKLRGWLKSHVSDAVAQSTRI IYGGSVTGGNCKELASQHDVDGFLVGGASLKPEFVDIINAKH
Sequence of Amino Acids
[http://www.cryst.bbk.ac.uk]
3
Primary Structure
Primary Structure
Polypeptide chain:
Polypeptide chain: Side chain
Side chain
APRKFFVGGNWKMNGDKKSLGELIHTLNGAKLSADTEVVCGAPSIYLDFAR QKLDAKIGVAAQNCYKVPKGAFTGEISPAMIKDIGAAWVILGHSERRHVFGES DELIGQKVAHALAEGLGVIACIGEKLDEREAGITEKVVFEQTKAIADNVKDW SKVVLAYEPVWAIGTGKTATPQQAQEVHEKLRGWLKSHVSDAVAQSTRI IYGGSVTGGNCKELASQHDVDGFLVGGASLKPEFVDIINAKH
APRKFFVGGNWKMNGDKKSLGELIHTLNGAKLSADTEVVCGAPSIYLDFAR QKLDAKIGVAAQNCYKVPKGAFTGEISPAMIKDIGAAWVILGHSERRHVFGES DELIGQKVAHALAEGLGVIACIGEKLDEREAGITEKVVFEQTKAIADNVKDW SKVVLAYEPVWAIGTGKTATPQQAQEVHEKLRGWLKSHVSDAVAQSTRI IYGGSVTGGNCKELASQHDVDGFLVGGASLKPEFVDIINAKH
Sequence of Amino Acids
Sequence of Amino Acids
[http://www.cryst.bbk.ac.uk]
Outline
[http://www.cryst.bbk.ac.uk]
Primary Structure
Protein structure
Peptide bond:
• Primary Secondary • Tertiary • Quaternary
Protein folding/binding • Forces and factors
Most bond angles are constrained
[http://www.cryst.bbk.ac.uk]
Primary Structure
Primary Structure
Peptide bond:
N-C and C -C bonds can rotate
Lehninger Principles of Biochemistry (3rd edition) David L. Nelson, Michael M. Cox
Most atoms in peptide bond are co-planar [http://www.cryst.bbk.ac.uk]
4
Secondary Structure
Secondary Structure
Peptide bond:
Ramachandran plot for 1tim:
omega
Peptides have at most two free torsion angles (omega is 180° (trans) or 0° cis) [http://www.cryst.bbk.ac.uk]
Secondary Structure
[PDBSUM]
Secondary Structure
Some repeating sequences of torsion angles are very stable • Alpha helix • Beta sheet
Some repeating sequences of torsion angles are very stable Alpha helix • Beta sheet
[http://www.cryst.bbk.ac.uk]
Secondary Structure Some repeating sequences of torsion angles are very stable Alpha helix • Beta sheet
[http://www.cryst.bbk.ac.uk]
Secondary Structure Some repeating sequences of torsion angles are very stable Alpha helix • Beta sheet
[http://www.cryst.bbk.ac.uk]
Lehninger Principles of Biochemistry (3rd edition) David L. Nelson, Michael M. Cox
[chemed.chem.purdue.edu]
5
Secondary Structure
Secondary Structure
Some repeating sequences of torsion angles are very stable Alpha helix • Beta sheet
Some repeating sequences of torsion angles are very stable Alpha helix • Beta sheet
[http://www.cryst.bbk.ac.uk]
Secondary Structure
[http://www.cryst.bbk.ac.uk]
Secondary Structure
Some repeating sequences of torsion angles are very stable • Alpha helix Beta sheet
Some repeating sequences of torsion angles are very stable • Alpha helix Beta sheet
[http://www.cryst.bbk.ac.uk]
Secondary Structure
[http://www.cryst.bbk.ac.uk]
Secondary Structure
Some repeating sequences of torsion angles are very stable • Alpha helix Beta sheet
Some repeating sequences of torsion angles are very stable • Alpha helix Beta sheet
[chemed.chem.purdue.edu]
Antiparallel
Parallel [http://www.cryst.bbk.ac.uk]
6
Secondary Structure
Secondary Structure
Some repeating sequences of torsion angles are very stable
Some repeating sequences of torsion angles are very stable
• Alpha helix Beta sheet
• Alpha helix Beta sheet
AntiParallel
Parallel Lehninger Principles of Biochemistry (3rd edition) David L. Nelson, Michael M. Cox
[http://www.cryst.bbk.ac.uk]
Secondary Structure
Secondary Structure
Others form loops, turns etc.
Others form loops, turns etc.
Lehninger Principles of Biochemistry (3rd edition) David L. Nelson, Michael M. Cox
[PDBSUM]
Secondary Structure
Supersecondary structure / motifs
Others form loops, turns etc.
Helix – loop – helix
Helix – loop – helix Calcium-binding motif
[http://www.cryst.bbk.ac.uk]
Introduction to protein structure (2nd edition) Carl Branden, John Tooze
7
Supersecondary structure / motifs
Supersecondary structure / motifs Four classes:
Geek Key motif
All
All
- - motif
/
+
Hairpin 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 Loop
Alpha Helix Beta Sheet
1tim
[Jena]
Outline Protein structure
Tertiary Structure Arrangement of atoms:
• Primary • Secondary Tertiary • Quaternary
Protein folding/binding • Forces and factors
1atp
[pymol]
8
Tertiary Structure
Tertiary Structure
How protein folds:
Arrangement of secondary structures – plus amino acid side chains (not shown)
1atp
1atp
[pymol]
Outline
[pymol]
Quatenary Structure
Protein structure
How multiple chains/proteins form a complex:
• Primary • Secondary • Tertiary Quaternary
Protein folding/binding • Forces and factors
1tim
[Rasurf]
Quatenary Structure
Quatenary Structure
How multiple chains/proteins form a complex:
How multiple chains/proteins form a complex:
Active binding site may be at interface between two chains
1tim
[Rasurf]
Chain may take a new (active) conformation when bound to another
1tim
[Rasurf]
9
Quaternary structure
Protein Structure Level Summary Protein structure description • • • •
Primary Secondary Tertiary Quaternary
Igg2A Intact Antibody-Mab231; Chain: A, B, C, D 1IGT L.J.Harris, S.B.Larson, K.W.Hasel, A.Mcpherson
Example: Hemoglobin
amino acid sequence local fold pattern of small subsequence fold of entire protein chain complex of multiple chains
Lehninger Principles of Biochemistry (3rd edition) David L. Nelson, Michael M. Cox
Example: Hemoglobin Chain A Primary structure: 284 residues
Chain A Tertiary Structure
Chain A Secondary structure and motifs:
Deoxyhemoglobin
19 Helices 50 Helices-helices interacs 14 Beta turns 2 gamma turns
Quaternary Structure
Deoxyhemoglobin (alpha chain). Chain: a. Engineered: yes. Mutation: yes. Deoxyhemoglobin (beta chain). Chain: b, d. Engineered: yes. Mutation: yes 1C7D E.A.Brucker
Deoxyhemoglobin (alpha chain). Chain: a. Engineered: yes. Mutation: yes. Deoxyhemoglobin (beta chain). Chain: b, d. Engineered: yes. Mutation: yes 1C7D E.A.Brucker
Example: Hemoglobin
Outline Protein structure • • • •
Primary Secondary Tertiary Quaternary
Protein folding/binding Forces and factors
Deoxyhemoglobin (alpha chain). Chain: a. Engineered: yes. Mutation: yes. Deoxyhemoglobin (beta chain). Chain: b, d. Engineered: yes. Mutation: yes 1C7D E.A.Brucker
10
Folding/Binding
Folding/Binding
Factors determining tertiary/quaternary structure: 1. 2. 3. 4. 5.
Disulfide linkages Hydrogen bonding Electrostatic interactions Hydrophobic interactions Van der Waals forces
Important properties of amino acids: • • • • • •
Size Charge Polarity Aromaticity Hydrophobicity Conformational constraints
[http://www.cryst.bbk.ac.uk]
Folding/Binding
Folding/Binding
Important properties of amino acids: • • • • •
Important properties of amino acids:
Size Charge Polarity Aromaticity Hydrophobicity Conformational constraints
• Size Charge • Polarity • Aromaticity • Hydrophobicity • Conformational constraints
[http://www.cryst.bbk.ac.uk]
Folding/Binding
[http://www.cryst.bbk.ac.uk]
Folding/Binding
Important properties of amino acids:
Important properties of amino acids:
• Size • Charge Polarity • Aromaticity • Hydrophobicity • Conformational constraints
• Size • Charge • Polarity Aromaticity • Hydrophobicity • Conformational constraints
[http://www.cryst.bbk.ac.uk]
[http://www.cryst.bbk.ac.uk]
11
Folding/Binding
Folding/Binding
Important properties of amino acids:
Important properties of amino acids:
• • • •
Size Charge Polarity Aromaticity Hydrophobicity • Conformational constraints
• • • • •
Size Charge Polarity Aromaticity Hydrophobicity Conformational constraints
[http://www.cryst.bbk.ac.uk]
Summary
References
Protein structure description • • • •
Primary Secondary Tertiary Quaternary
Information and figures were taken from:
amino acid sequence local fold pattern of small subsequence fold of entire protein chain complex of multiple chains
• 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
Protein folding/binding • • • • •
[http://www.cryst.bbk.ac.uk]
http://www.cs.cryst.bbk.ac.uk • http://www.accessexcellence.org • http://chemmed.chem.purdue.edu
Disulfide linkages Hydrogen bonding Electrostatic interactions Hydrophobic interactions Van der Waals forces 1tim
[Jena]
Primary Structure Twenty amino acids:
[http://www.cryst.bbk.ac.uk]
12
