Fundamentals of Protein Structure
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1 Outline Fundamentals of Protein Structure Yu (Julie) Chen and Thomas Funkhouser Princeton University CS597A, Fall 2005 Protein structure Primary Secondary Tertiary Quaternary Forces and factors Levels of Protein Structure Outline Protein structure Primary Secondary Tertiary Quaternary Forces and factors Lehninger Principles of Biochemistry (3 rd edition) DNA GGGGCTACGGGGGGTGGGGCTTCGCGCCCCGCCGGCCTAIAAGCGGGCCGCCGCGGCTCCGTGCCQTTGCCGACCTTGCCT GcCGCCGCTGCTGCTTCGCGCCCGTCGCCTCCGCCATGGCTCCCAGGAAGTTCTTCGTGGGTGGCAACTGGAAGATGAACG GCGACAAGAAGAGCTTGGGCGAGCTCATCCACACGCTGAATGGCGCCAAGCTCTCGGCCGACACCGAGGTGGTTTGCGGAG CCCCTTCAATCTACCTTGATTTTGCCCGCCAGAAGCTTGATGCAAAGATTGGAGTTGCAGCACAAAACTGTTACAACGTAC CGAAGGGTGCTTTCACAGGAGAGATCAGCCCAGCAATGATCAAAGATATTGGAGCTGCATGGGTGATCCTGGGCCACTCAG AGCGGAGGCATGTTTTTGGAGAGTCTGATGAGTTGATTGGGCAGAAGGTGGCTCATGCTCMTGCTGAAGGC.[Straus85].. Sequence of Nucleic Acids 1
2 First Second Position Third Position Position U(T) C A G U(T) Phe Ser Tyr Cys U(T) Phe Ser Tyr Cys C Leu Ser STOP STOP A Leu Ser STOP Trp G C Leu Pro His Arg U(T) Leu Pro His Arg C Leu Pro Gln Arg A Leu Pro Gln Arg G A Ile Thr Asn Ser U(T) Ile Thr Asn Ser C Ile Thr Lys Arg A Met Thr Lys Arg G G Val Ala Asp Gly U(T) Val Ala Asp Gly C Val Ala Glu Gly A Val Ala Glu Gly G Alanine Ala A Cysteine Cys C Aspartic Acid Asp D Glutamic Acid Glu E Phenylalanine Phe F Glycine Gly G Histidine His H Isoleucine Ile I Lysine Lys K Leucine Leu L Methionine Met M Asparagine Asn N Proline Pro P Glutamine Gln Q Arginine Arg R Serine Ser S Threonine Thr T Valine Val V Tryptophan Trp W Tyrosine Tyr Y Short-hand Names for Amino Acids GGGGCTACGGGGGGTGGGGCTTCGCGCCCCGCCGGCCTAIAAGCGGGCCGCCGCGGCTCCGTGCCQTTGCCGACCTTGCCT GcCGCCGCTGCTGCTTCGCGCCCGTCGCCTCCGCCATGGCTCCCAGGAAGTTCTTCGTGGGTGGCAACTGGAAGATGAACG GCGACAAGAAGAGCTTGGGCGAGCTCATCCACACGCTGAATGGCGCCAAGCTCTCGGCCGACACCGAGGTGGTTTGCGGAG CCCCTTCAATCTACCTTGATTTTGCCCGCCAGAAGCTTGATGCAAAGATTGGAGTTGCAGCACAAAACTGTTACAACGTAC CGAAGGGTGCTTTCACAGGAGAGATCAGCCCAGCAATGATCAAAGATATTGGAGCTGCATGGGTGATCCTGGGCCACTCAG AGCGGAGGCATGTTTTTGGAGAGTCTGATGAGTTGATTGGGCAGAAGGTGGCTCATGCTCMTGCTGAAGGC... Sequence of Nucleic Acids GGGGCTACGGGGGGTGGGGCTTCGCGCCCCGCCGGCCTAIAAGCGGGCCGCCGCGGCTCCGTGCCQTTGCCGACCTTGCCT GcCGCCGCTGCTGCTTCGCGCCCGTCGCCTCCGCCATGGCTCCCAGGAAGTTCTTCGTGGGTGGCAACTGGAAGATGAACG GCGACAAGAAGAGCTTGGGCGAGCTCATCCACACGCTGAATGGCGCCAAGCTCTCGGCCGACACCGAGGTGGTTTGCGGAG CCCCTTCAATCTACCTTGATTTTGCCCGCCAGAAGCTTGATGCAAAGATTGGAGTTGCAGCACAAAACTGTTACAACGTAC CGAAGGGTGCTTTCACAGGAGAGATCAGCCCAGCAATGATCAAAGATATTGGAGCTGCATGGGTGATCCTGGGCCACTCAG AGCGGAGGCATGTTTTTGGAGAGTCTGATGAGTTGATTGGGCAGAAGGTGGCTCATGCTCMTGCTGAAGGC... Sequence of Nucleic Acids [Straus85] [Straus85] GGGGCTACGGGGGGTGGGGCTTCGCGCCCCGCCGGCCTAIAAGCGGGCCGCCGCGGCTCCGTGCCQTTGCCGACCTTGCCT GcCGCCGCTGCTGCTTCGCGCCCGTCGCCTCCGCCATGGCTCCCAGGAAGTTCTTCGTGGGTGGCAACTGGAAGATGAACG GCGACAAGAAGAGCTTGGGCGAGCTCATCCACACGCTGAATGGCGCCAAGCTCTCGGCCGACACCGAGGTGGTTTGCGGAG CCCCTTCAATCTACCTTGATTTTGCCCGCCAGAAGCTTGATGCAAAGATTGGAGTTGCAGCACAAAACTGTTACAACGTAC CGAAGGGTGCTTTCACAGGAGAGATCAGCCCAGCAATGATCAAAGATATTGGAGCTGCATGGGTGATCCTGGGCCACTCAG AGCGGAGGCATGTTTTTGGAGAGTCTGATGAGTTGATTGGGCAGAAGGTGGCTCATGCTCMTGCTGAAGGC... Sequence of Nucleic Acids GGGGCTACGGGGGGTGGGGCTTCGCGCCCCGCCGGCCTAIAAGCGGGCCGCCGCGGCTCCGTGCCQTTGCCGACCTTGCCT GcCGCCGCTGCTGCTTCGCGCCCGTCGCCTCCGCCATGGCTCCCAGGAAGTTCTTCGTGGGTGGCAACTGGAAGATGAACG GCGACAAGAAGAGCTTGGGCGAGCTCATCCACACGCTGAATGGCGCCAAGCTCTCGGCCGACACCGAGGTGGTTTGCGGAG CCCCTTCAATCTACCTTGATTTTGCCCGCCAGAAGCTTGATGCAAAGATTGGAGTTGCAGCACAAAACTGTTACAACGTAC CGAAGGGTGCTTTCACAGGAGAGATCAGCCCAGCAATGATCAAAGATATTGGAGCTGCATGGGTGATCCTGGGCCACTCAG AGCGGAGGCATGTTTTTGGAGAGTCTGATGAGTTGATTGGGCAGAAGGTGGCTCATGCTCMTGCTGAAGGC... Sequence of Nucleic Acids [Straus85] [Straus85] 2
3 Amino acid: Twenty amino acids: (Amino group) (Carboxyl group) COO (Alpha carbon) OH H3N (Side chain) H R Lehninger Principles of Biochemistry (3rd edition) Amino acids are linked by peptide bonds Lehninger Principles of Biochemistry (3rd edition) C Biochemistry (5th edition) Jeremy M. Berg, John L. Tymoczko, Lubert Stryer Polypeptide chain: Polypeptide chain: Polypeptide chain: Backbone Side chain 3
4 Polypeptide chain: Polypeptide chain: Side chain Side chain Outline Protein structure Primary Secondary Tertiary Quaternary Forces and factors Peptide bond: Most bond angles are constrained Peptide bond: N-C and C -C bonds can rotate Most atoms in peptide bond are co-planar Lehninger Principles of Biochemistry (3 rd edition) 4
![Peptide bond: Ramachandran plot for 1tim: omega Peptides have at most two free torsion angles (omega is 180 (trans) or 0 cis) [PDBSUM] Beta sheet](/docs-images/76/74351631/images/5-1.jpg "Alpha helix Beta sheet Alpha helix Beta sheet Alpha helix Beta sheet Lehninger Principles of Biochemistry (3rd edition) [chemed.chem.purdue.")
5 Peptide bond: Ramachandran plot for 1tim: omega Peptides have at most two free torsion angles (omega is 180 (trans) or 0 cis) [PDBSUM] Beta sheet Alpha helix Beta sheet Alpha helix Beta sheet Alpha helix Beta sheet Lehninger Principles of Biochemistry (3rd edition) [chemed.chem.purdue.edu] 5
![edu]](/docs-images/76/74351631/images/6-2.jpg)
6 Alpha helix Beta sheet Alpha helix Beta sheet Beta sheet Beta sheet Beta sheet Beta sheet [chemed.chem.purdue.edu] Antiparallel Parallel 6
7 Beta sheet Beta sheet Parallel Anti- Parallel Lehninger Principles of Biochemistry (3 rd edition) Others form loops, turns etc. Others form loops, turns etc. Lehninger Principles of Biochemistry (3 rd edition) [PDBSUM] Others form loops, turns etc. Supersecondary structure / motifs Helix loop helix Introduction to protein structure (2 nd edition) Carl Branden, John Tooze Helix loop helix Calcium-binding motif 7
![Loop Alpha Helix Beta Sheet 1tim [Jena] Outline Protein structure Primary](/docs-images/76/74351631/images/8-2.jpg "Secondary Tertiary Quaternary Forces and factors Tertiary Structure Arrangement")
8 Supersecondary structure / motifs Supersecondary structure / motifs Geek Key motif Four classes: All All / motif Hairpin motif Introduction to protein structure (2 nd edition) Carl Branden, John Tooze Introduction to protein structure (2 nd edition) Carl Branden, John Tooze Visualization Visualization Loop Alpha Helix Beta Sheet 1tim [Jena] Outline Protein structure Primary Secondary Tertiary Quaternary Forces and factors Tertiary Structure Arrangement of atoms: 1atp [pymol] 8
![Tertiary Structure How protein folds: Tertiary Structure Arrangement of secondary structures plus amino acid side chains (not shown) 1atp [pymol] 1atp [pymol] Outline Protein structure Primary](/docs-images/76/74351631/images/9-0.jpg "Secondary Tertiary Quaternary Forces and factors Quatenary Structure How multiple chains/proteins form a complex: 1tim [Rasurf] Quatenary Structure How multiple chains/proteins form a complex:")
9 Tertiary Structure How protein folds: Tertiary Structure Arrangement of secondary structures plus amino acid side chains (not shown) 1atp [pymol] 1atp [pymol] Outline Protein structure Primary Secondary Tertiary Quaternary Forces and factors Quatenary Structure How multiple chains/proteins form a complex: 1tim [Rasurf] Quatenary Structure How multiple chains/proteins form a complex: Quatenary Structure How multiple chains/proteins form a complex: Active binding site may be at interface between two chains Chain may take a new (active) conformation when bound to another 1tim [Rasurf] 1tim [Rasurf] 9
10 Quaternary structure 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 Igg2A Intact Antibody-Mab231; Chain: A, B, C, D 1IGT L.J.Harris, S.B.Larson, K.W.Hasel, A.Mcpherson Lehninger Principles of Biochemistry (3 rd edition) Example: Hemoglobin Chain A Primary structure: 284 residues Example: Hemoglobin Chain A Tertiary Structure Chain A Secondary structure and motifs: 19 Helices 50 Helices-helices interacs 14 Beta turns 2 gamma turns Deoxyhemoglobin 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 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
11 Folding/Binding Factors determining tertiary/quaternary structure: 1. Disulfide linkages 2. Hydrogen bonding 3. Electrostatic interactions 4. Hydrophobic interactions 5. Van der Waals forces Folding/Binding Size Charge Polarity Aromaticity Hydrophobicity Conformational Folding/Binding Size Charge Polarity Aromaticity Hydrophobicity Conformational Folding/Binding Size Charge Polarity Aromaticity Hydrophobicity Conformational Folding/Binding Size Charge Polarity Aromaticity Hydrophobicity Conformational Folding/Binding Size Charge Polarity Aromaticity Hydrophobicity Conformational 11
12 Folding/Binding Size Charge Polarity Aromaticity Hydrophobicity Conformational Folding/Binding Size Charge Polarity Aromaticity Hydrophobicity Conformational 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 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) Biochemistry (5th edition) Jeremy M. Berg, John L. Tymoczko, Lubert Stryer Twenty amino acids: 12
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