Bioinformatics

Biological Basics

1. Amino acids I 2. Peptide bond I 3. Proteins I 4. DNA I 5. Miscellaneous

3. Proteins

• macromolecules / polymers
• 'workhorses of the cell'
• made up of various L-amino acids connected by peptide bonds
• linear chains (unbranched)
  • protein molecule that consists of a single polypeptide chain is said to be monomeric
  • proteins made up of more than one polypeptide chain are called oligomeric
• interact with other proteins, nucleic acids, small molecules, ions, etc.

Protein Structure

Secondary structure

• 3D arrangement of only the polypeptide main chain
• determined by hydrogen bond interactions between adjacent amino acid residues in the polypeptide chain
• polypeptide chain can arrange itself into characteristic repeating patterns such as helices, or pleated sheets
• two basic secondary structures that are stabilized by hydrogen bonds
  • α-helix and ß-pleated sheet
• other important structures include ß-turns and ß-bulges

α-helix
regular secondary structure in which successive amino acids adopt the same Φ (Phi) and Ψ (Psi) dihedral angles (peptide bonds all trans) Φ  ≈  Ψ  ≈  - 60°	From Biochemistry2nd Ed. by Garrett and Grisham (Harcourt, Brace & Company)
coiled arrangement of amino acid residues with all carbonyl groups oriented in the same direction parallel with the axis of the helix
'backbone' of the peptide forms the inner part of the coil
side chains projected outward
'shorthand' - cartoon presentation ribbons or cylinders
H-bonds between C=O of residue n and NH of residue n+4	3.6 residues per turn (5.4 Å) 1.5 Å per residue rise 100° per residue turn
dipole moment (N-terminus with positive and C-terminus with negative charge)
Average Conformational Parameters of Helical Elements Conformation Phi Psi Omega Residues per turn Translation per residue alpha helix -57 -47 180 3.60 1.50 3-10 helix -49 -26 180 3.00 2.00 pi-helix 57 -70 180 4.40 1.15 Polyproline I -83 +158 0 3.33 1.90 Polyproline II -78 +149 180 3.00 3.12 Polyproline III -80 +150 180 3.00 3.10
helix can be either right-handed or left-handed in the sense of threads on a screw	all α-helices that are composed of D-amino acids, are left-handed helice
all α-helices that are composed of L-amino acids, are right-handed helices naturally occurring α-helixes found in proteins are all right-handed	mixtures of D- and L-amino acids will not allow α-helices to form
alanine, glutamine, methionine and leucine favor α-helices valine, tyrosin, serine, aspartic acid and asparagine tend to destabilze α-helices proline and glycine are helix breaker
To determine the handedness of an α-helix, close either your left hand or your right hand, and point your thumb upwards. If the helix spirals up in the same direction as the fingers of your right hand, it is a right handed helix. If it spirals up in the same direction as the fingers of your left hand, then it is a left-handed helix.
helical wheel
tool to visualize the position of amino acids around an α-helix 'wheel' = view along the long axis of the helix, with numbered positions and residues indicated colors of the residues indicate the nature of each residue (non-polar, polar uncharged, acidic or basic) allows quick visualization of whether a side of a helix posses specific chemical properties often 'dual-natured' half hydrophobic and half hydrophilic shown helix forms a Leucine-Zipper
Examples:   PDB code 1enh 1bcf 1ao6 Fold DNA/RNA-binding 3-helical bundle Ferritin-like Serum albumin-like Fold description core: 3-helices; bundle, closed or partly opened, right-handed twist; up-and down core: 4 helices; bundle, closed, left-handed twist; 1 crossover connection multihelical; one domain consists of two similar disulfide-linked subdomains Superfamily Homeodomain-like Ferritin-like Serum albumin-like Family Homeodomain Ferritin Serum albumin-like Protein Engrailed Homeodomain Bacterioferritin (cytochrome b1) Serum albumin Species Drosophila melanogaster Escherichia coli Human (Homo sapiens)

ß-sheet
formed of stretches of 5 - 10 residues in extended conformation characterized by hydrogen bonds crossing between chains H-bonds formed between the amide carbonyl on one chain of the sheet and the amide nitrogen in a neighboring chain 2 amino acid residues / repeat
multiple chains lie next to each other to form the sheet pleated = each Cα a bit above or below the previous (Φ  ≈  - 135 ° ; Ψ  ≈  + 135°) ß-sheets are often twisted	'shorthand' - cartoon presentation flat arrows
amino acid side chains stick out from both the top and bottom surfaces of the sheet
ß-sheet strands are not fully extended due to sidechain steric inteferences
two H-bonding chains may run parallel or anti-parallel parallel ß-sheets backbones in same direction each residue H-bonds with the residues before and after the adjacent residue must be significant amount of primary structure between them to get back to same side for next parallel run anti-parallel ß-sheets opposite direction of backbones each residue H-bonds with the residue across from it sligthly energetically favored often directly connected by a small loop ß-bulges region of irregularity in anti-parallel ß-structures ('break') normal pattern of hydrogen bonding is disrupted e.g. by the insertion of an extra residue extra residue is 'bulged out' thus changing H-bond pairing
valine, isoleucine and phenylalanine enhance ß-sheets proline doesn't fit well into ß-sheets

Non-repetitive structures (turns, loops & random coils)

connect secondary structure elements allow protein to quickly change direction and keep it's compact shape often hydrophilic (tend to be located on the protein surface) many loops or turns contain functional residues (e.q. binding sites for metal ions [calmodulin]) structures are of varying size, from perhaps 3 to 15-16 residues turns usually short and tight region in the range of 3-5 monomers (short loop) typically self-hydrogen bonded involves a sharp reversal in the direction of a polypeptide chain over just four amino acid residues glycine (flexible !) and proline (adopt cis configuration !) are usually involved sterically demanding glycine residue is often located in the middle of a ß-turn exception: junction of 2 anti-parallel strands 'shorthand' - cartoon presentation ß-turns specific subclass often connect anti-parallel ß-strands polypeptide region of 4 amino acids (i, i+1, i+2 and i+3) hydrogen bond from the carbonyl O of the 1st residue (i) to the N of the 4th residue (i+3) further classification based on the Φ and Ψ angles of residue i+1 and i+2 most common types: type I type II loops longer regions larger stretches with no secondary structure often define an enzyme active site generally near the protein surface often disordered loop regions that connect two adjacent anti-parallel strands are called 'hairpin loops' random coils all other local arrangements of amino acids are described as random coils (everything that isn't a helix, sheet or turn), although they are random only in the sense of not being periodic

Super-secondary structure (ExPASy) Protein Structure: Understanding Protein Conformation (by H. Jakubowski, St. John's University) Koehl, P.; Levitt, M.; Proc. Natl. Acad. Sci. USA 1999, 96(22), 12524-12529. Structure-based conformational preferences of amino acids. [PDF I PubMed]

super-secondary structures

α-helices and ß-structures are combined through loops to make recognizable higher order structures that commonly occur in proteins   helix-loop-helix © 2003 Thomas-Wadsworth   Chavali, G.B.; Vijayalakshmi, C.; Salunke, D.M.; Proteins 2001, 42(4), 471-480. Analysis of sequence signature defining functional specificity and structural stability in helix-loop-helix proteins. [PubMed] Massari, M.E.; Murre, C.; Mol. Cell. Biol. 2000, 20(2), 429-440. Helix-loop-helix proteins: regulators of transcription in eucaryotic organisms. [PDF I PubMed] Murre, C.; Bain, G.; van Dijk, M.A.; Engel, I.; Furnari, B.A.; Massari, M.E.; Matthews, J.R.; Quong, M.W.; Rivera, R.R.; Stuiver, M.H.; Biochim. Biophys. Acta 1994, 1218(2), 129-135. Structure and function of helix-loop-helix proteins. [PubMed] ß-α-ß unit   © 2003 Thomas-Wadsworth hairpin     greek-key Phosphatidylethanolamine binding protein, PEBP from Mouse (Mus musculus), PEBP-2 (PDB: 1kn3) © 2003 Thomas-Wadsworth four adjacent antiparallel ß-strands arranged in a pattern similar to the repeating unit of one of the ornamental patterns used in ancient Greece three up-and-down ß-strands connected by hairpins are followed by a longer connection to the fourth strand, which lies adjacent to the first folds including the greek-key topology have 5-13 strands   jelly-roll fold formed by the addition of an extra 'swirl' to a greek-key   Tumor necrosis factor (TNF) from Mouse (Mus musculus) (PDB: 2tnf) Stirk, H.J.; Woolfson, D.N.; Hutchinson, E.G.; Thornton, J.M.; FEBS Lett. 1992, 308(1), 1-3. Depicting topology and handedness in jellyroll structures. Feige, M.J.; Walter, S.; Buchner, J.; J. Mol. Biol. 2004, 344(1), 107-118. Folding mechanism of the CH2 antibody domain. [PubMed] Rizzuti, B.; Daggett, V.; Guzzi, R.; Sportelli, L.; Biochemistry 2004, 43(49), 15604-15609. The early steps in the unfolding of azurin. [PubMed] Wu, B.; Yee, A.; Pineda-Lucena, A.; Semesi, A.; Ramelot, T.A.; Cort, J.R.; Jung, J.W.; Edwards, A.; Lee, W.; Kennedy, M.; Arrowsmith, C.H.; Protein Sci. 2003, 12(12), 2831-2837. Solution structure of ribosomal protein S28E from Methanobacterium thermoautotrophicum.

Super-secondary structure (ExPASy) Protein Structure: Understanding Protein Conformation (by H. Jakubowski, St. John's University)

secondary structure preferences of amino acids
amino acid	helix	strand	turn
alanine	1.42	0.83	0.66
arginine	0.98	0.93	0.95
aspartic acid	1.01	0.54	1.46
asparagine	0.67	0.89	1.56
cysteine	0.70	1.19	1.19
glutamic acid	1.51	0.37	0.74
glutamine	1.11	1.10	0.98
glycine	0.57	0.75	1.56
histidine	1.00	0.87	0.95
isoleucine	1.08	1.60	0.47
leucine	1.21	1.30	0.59
lysine	1.14	0.74	1.01
methionine	1.45	1.05	0.60
phenylalanine	1.13	1.38	0.60
proline	0.57	0.55	1.52
serine	0.77	0.75	1.43
threonine	0.83	1.19	0.96
tryptophan	1.08	1.37	0.96
tyrosine	0.69	1.47	1.14
valine	1.06	1.70	0.50

• LIFE - The Science of Biology (7th edition) (by W.K. Purves, D. Sadava, G.H. Orians, H. Craig Heller)
• Protein Structure by Molecular Graphics (University of Cambridge)
• Protein Structure Classification (by O. Lund, Technical University of Denmark)
• Protein Structure: Understanding Protein Conformation (by H. Jakubowski, St. John's University)
• Cozzone, A.J.; Encyclopedia of Life Sciences 2002, 1-10. Proteins: fundamental chemical properties. [PDF]
• Hadley, C.; Jones, D.T.; Structure Fold. Des. 1999, 7(9), 1099-1112. A systematic comparison of protein structure classifications: SCOP, CATH and FSSP. [PubMed]
• Ouzounis, C.A.; Coulson, R.M.; Enright, A.J.; Kunin, V.; Pereira-Leal, J.B.; Nat. Rev. Genet. 2003, 4(7), 508-519. Classification schemes for protein structure and function. [PDF I PubMed]
• Saito, N.; Adv. Biophys. 1989, 25, 95-132. Principles of protein architecture. [PubMed]
• Shakhnovich, B.E.; Max Harvey, J.; J. Mol. Biol. 2004, 337(4), 933-949. Quantifying structure-function uncertainty: a graph theoretical exploration into the origins and limitations of protein annotation. [PubMed]

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