Fundamentals of Protein Structure · Introduction to protein structure (2nd edition) Carl Branden, John Tooze Supersecondary structure / motifs Secondary Structure Visualization Secondary

11

Fundamentals ofProtein Structure

Yu (Julie) Chen and Thomas Funkhouser

Princeton University

CS597A, Fall 2005

Outline

Protein structure• Primary• Secondary• Tertiary• Quaternary

Protein folding/binding• Forces and factors

Levels of Protein Structure

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

Outline

Protein structureØ Primary• Secondary• Tertiary• Quaternary


Primary Structure

DNA

Sequence of Nucleic Acids

GGGGCTACGGGGGGTGGGGCTTCGCGCCCCGCCGGCCTAIAAGCGGGCCGCCGCGGCTCCGTGCCQTTGCCGACCTTGCCTGcCGCCGCTGCTGCTTCGCGCCCGTCGCCTCCGCCATGGCTCCCAGGAAGTTCTTCGTGGGTGGCAACTGGAAGATGAACGGCGACAAGAAGAGCTTGGGCGAGCTCATCCACACGCTGAATGGCGCCAAGCTCTCGGCCGACACCGAGGTGGTTTGCGGAGCCCCTTCAATCTACCTTGATTTTGCCCGCCAGAAGCTTGATGCAAAGATTGGAGTTGCAGCACAAAACTGTTACAACGTACCGAAGGGTGCTTTCACAGGAGAGATCAGCCCAGCAATGATCAAAGATATTGGAGCTGCATGGGTGATCCTGGGCCACTCAGAGCGGAGGCATGTTTTTGGAGAGTCTGATGAGTTGATTGGGCAGAAGGTGGCTCATGCTCMTGCTGAAGGC . . .[Straus85]

Primary Structure

Transcription and translation (DNA→Protein)

http://www.accessexcellence.org

22

Primary Structure

Transcription and translation (DNA→Protein)First Second Position ThirdPosition ------------------------------------ Position

| U(T) C A G |

U(T) Phe Ser Tyr Cys U(T)Phe Ser Tyr Cys CLeu Ser STOP STOP ALeu Ser STOP Trp G

C Leu Pro His Arg U(T)Leu Pro His Arg CLeu Pro Gln Arg ALeu Pro Gln Arg G

A Ile Thr Asn Ser U(T)Ile Thr Asn Ser CIle Thr Lys Arg AMet Thr Lys Arg G

G Val Ala Asp Gly U(T)Val Ala Asp Gly CVal Ala Glu Gly AVal Ala Glu Gly G

Primary Structure


Alanine Ala ACysteine Cys CAspartic Acid Asp DGlutamic Acid Glu EPhenylalanine Phe FGlycine Gly GHistidine His HIsoleucine Ile ILysine Lys KLeucine Leu LMethionine Met MAsparagine Asn NProline Pro P Glutamine Gln QArginine Arg RSerine Ser SThreonine Thr TValine Val VTryptophan Trp WTyrosine Tyr Y

Short-hand Names for Amino Acids

Primary Structure


APRKFFVGGNWKMNGDKKSLGELIHTLNGAKLSADTEVVCGAPSIYLDFARQKLDAKIGVAAQNCYKVPKGAFTGEISPAMIKDIGAAWVILGHSERRHVFGESDELIGQKVAHALAEGLGVIACIGEKLDEREAGITEKVVFEQTKAIADNVKDWSKVVLAYEPVWAIGTGKTATPQQAQEVHEKLRGWLKSHVSDAVAQSTRIIYGGSVTGGNCKELASQHDVDGFLVGGASLKPEFVDIINAKH

Sequence of Amino Acids


GGGGCTACGGGGGGTGGGGCTTCGCGCCCCGCCGGCCTAIAAGCGGGCCGCCGCGGCTCCGTGCCQTTGCCGACCTTGCCTGcCGCCGCTGCTGCTTCGCGCCCGTCGCCTCCGCCATGGCTCCCAGGAAGTTCTTCGTGGGTGGCAACTGGAAGATGAACGGCGACAAGAAGAGCTTGGGCGAGCTCATCCACACGCTGAATGGCGCCAAGCTCTCGGCCGACACCGAGGTGGTTTGCGGAGCCCCTTCAATCTACCTTGATTTTGCCCGCCAGAAGCTTGATGCAAAGATTGGAGTTGCAGCACAAAACTGTTACAACGTACCGAAGGGTGCTTTCACAGGAGAGATCAGCCCAGCAATGATCAAAGATATTGGAGCTGCATGGGTGATCCTGGGCCACTCAGAGCGGAGGCATGTTTTTGGAGAGTCTGATGAGTTGATTGGGCAGAAGGTGGCTCATGCTCMTGCTGAAGGC . . .

[Straus85]

Primary Structure






[Straus85]

Primary Structure






[Straus85]

Primary Structure






[Straus85]

33

Primary Structure

Amino acid:

OH

(Side chain)

(Alpha carbon)

(Amino group)

(Carboxyl group)

[http://www.cryst.bbk.ac.uk]

Primary Structure

Twenty amino acids:


CH3N

COO

H

RR

Primary Structure


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

Amino acids are linked by peptide bonds

Primary Structure

Polypeptide chain:


Sequence of Amino Acids[http://www.cryst.bbk.ac.uk]

Primary Structure

Polypeptide chain:



Backbone

Primary Structure

Polypeptide chain:



Side chain

44

Primary Structure

Polypeptide chain:



Side chain

Primary Structure

Polypeptide chain:



Side chain

Outline

Protein structure• PrimaryØ Secondary• Tertiary• Quaternary


Primary Structure

Peptide bond:

Most bond angles are constrained


Primary Structure

Peptide bond:

Most atoms in peptide bond are co-planar



Primary Structure

N-C� and C� -C bonds can rotate

55

Secondary Structure

Peptide bond:

Peptides have at most two free torsion angles(omega is 180° (trans) or 0° cis)

omega


Secondary Structure

Ramachandran plot for 1tim:

[PDBSUM]

Secondary Structure

Some repeating sequences of torsion angles are very stable

• Alpha helix• Beta sheet


Secondary Structure

Some repeating sequences of torsion angles are very stableØ Alpha helix• Beta sheet


Secondary Structure



Secondary Structure


[chemed.chem.purdue.edu]


66

Secondary Structure



Secondary Structure



Secondary Structure


• Alpha helixØ Beta sheet


Secondary Structure




Secondary Structure



[chemed.chem.purdue.edu]

Secondary Structure



Antiparallel Parallel


77

Secondary Structure



ParallelAnti-

Parallel


Secondary Structure




Secondary Structure

Others form loops, turns etc.

[PDBSUM]

Secondary Structure



Secondary Structure



Supersecondary structure / motifs

Helix – loop – helixHelix – loop – helix

Calcium-binding motif Introduction to protein structure (2nd edition)

Carl Branden, John Tooze

88

Hairpin motif

Geek Key motif

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


Four classes:

All �

All �

� /�

� +�

�- � -

�motif

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


Secondary Structure Visualization Secondary Structure Visualization

1tim[Jena]

Alpha Helix

Beta Sheet

Loop

Outline

Protein structure• Primary• SecondaryØ Tertiary• Quaternary


Tertiary Structure

Arrangement of atoms:

1atp[pymol]

99

Tertiary Structure

How protein folds:

1atp[pymol]

Tertiary Structure

Arrangement of secondary structures –plus amino acid side chains (not shown)

1atp[pymol]

Outline

Protein structure• Primary• Secondary• TertiaryØ Quaternary


Quatenary Structure

How multiple chains/proteins form a complex:

1tim[Rasurf]

Quatenary Structure


1tim[Rasurf]

Active binding sitemay be at interfacebetween two chains

Quatenary Structure


1tim[Rasurf]

Chain may takea new (active) conformation when bound to another

1010

Quaternary structure

Igg2A Intact Antibody-Mab231; Chain: A, B, C, D1IGTL.J.Harris, S.B.Larson, K.W.Hasel, A.Mcpherson

Protein Structure Level Summary

Protein structure description• Primary � amino acid sequence• Secondary � local fold pattern of small subsequence• Tertiary � fold of entire protein chain• Quaternary � complex of multiple chains


Example: Hemoglobin

Chain APrimary structure: 284 residues

Chain ASecondary structure and motifs:

19 Helices50 Helices-helices interacs

14 Beta turns2 gamma turns

Deoxyhemoglobin (alpha chain). Chain: a. Engineered: yes. Mutation: yes. Deoxyhemoglobin (beta chain). Chain: b, d. Engineered: yes. Mutation: yes1C7DE.A.Brucker

Chain A

Tertiary Structure


Deoxyhemoglobin

Quaternary Structure

Example: Hemoglobin


Example: Hemoglobin Outline

Protein structure• Primary• Secondary• Tertiary• Quaternary

Protein folding/bindingØ Forces and factors

1111

Folding/Binding

Factors determining tertiary/quaternary structure:1. Disulfide linkages2. Hydrogen bonding3. Electrostatic interactions4. Hydrophobic interactions5. Van der Waals forces


Folding/Binding

Important properties of amino acids:• Size• Charge• Polarity• Aromaticity• Hydrophobicity• Conformational

constraints

Folding/Binding

Important properties of amino acids:Ø Size• Charge• Polarity• Aromaticity• Hydrophobicity• Conformational

constraints


Folding/Binding

Important properties of amino acids:• SizeØ Charge• Polarity• Aromaticity• Hydrophobicity• Conformational

constraints


Folding/Binding

Important properties of amino acids:• Size• ChargeØ Polarity• Aromaticity• Hydrophobicity• Conformational

constraints


Folding/Binding

Important properties of amino acids:• Size• Charge• PolarityØ Aromaticity• Hydrophobicity• Conformational

constraints


1212

Folding/Binding

Important properties of amino acids:• Size• Charge• Polarity• AromaticityØ Hydrophobicity• Conformational

constraints


Folding/Binding

Important properties of amino acids:• Size• Charge• Polarity• Aromaticity• HydrophobicityØ Conformational

constraints


Summary

Protein structure description• Primary � amino acid sequence• Secondary � local fold pattern of small subsequence• Tertiary � fold of entire protein chain• Quaternary � complex of multiple chains

Protein folding/binding• Disulfide linkages• Hydrogen bonding• Electrostatic interactions• Hydrophobic interactions• Van der Waals forces

1tim[Jena]

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

Ø http://www.cs.cryst.bbk.ac.uk• http://www.accessexcellence.org• http://chemmed.chem.purdue.edu

Primary Structure

Twenty amino acids:


Documents

Fundamentals of Protein Structure · Introduction to protein structure (2nd edition) Carl Branden, John Tooze Supersecondary structure / motifs Secondary Structure Visualization Secondary