Protein: Linear chain of amino acids called residues (4 in this toy protein) Ser Trp Leu O N N N N O O C C C C O O CαCα CαCα CαCα CαCα Lys H H H H H The.

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Presentation transcript:

Protein: Linear chain of amino acids called residues (4 in this toy protein) Ser Trp Leu O N N N N O O C C C C O O CαCα CαCα CαCα CαCα Lys H H H H H The backbone (red) is the same for all residues. The side-chains (green) vary.

The 20 amino acids found in nature 1-letter3-letterAmino acid AAlaAlanine CCysCysteine DAspAspartic Acid EGluGlutamic Acid FPhePhenylalanine GGlyGlycine HHisHistidine IIleIsoleucine KLysLysine LLeuLeucine 1-letter3-letterAmino Acid MMetMethionin NAsnAsparagine PProProline QGlnGlutamine RArgArginine SSerSerine TThrThreonin VValValine WTrpTryptophan YTyrTyrosine

Patrice Koehl

The Peptide Bond CC C N RnRn O H CC C N R O H n+1 H H Peptide bond The peptide bond is planar Patrice Koehl

Degrees of Freedom in Proteins Bond length Bond angle 12 Dihedral angle Patrice Koehl

Torsion angles avoid eclipsing

Torsion angles characterize residue conformation Backbone: 3 angles per residue :  ψ and  Sidechain: 1 to 7 angles,  ; each  has 3 favored values: 60 o, -60 o, 180 o. Patrice Koehl φ ψ

Proteins fall to lowest free energy conformation Protein Folding in the Landscape Perspective: Chevron Plots and Non-Arrhenius Kinetics Hue Sun Chan and Ken A. Dill, Proteins: Structure, Function, and Genetics, 30:1 Free energy (vertical axis) as a function of conformation. The two horizontal axes represent torsional degrees of freedom.

RAMACHANDRAN PLOTS All residues, but glycineGlycine   Acta Cryst. (2002). D58,

Small Amino acids: Glycine CAC H Highly flexible Patrice Koehl

Hydrophobic Amino acids (1) CA CB C CH3 Ala C CH CH3 CA CB CG1CG2 Val Patrice Koehl

C CH CH3 CH2 CA CB CG CD1 CD2 Hydrophobic Amino acids (2) C CH CH2CH3 CA CB CG1 CG2 CD Leu Ile Patrice Koehl

NC CH2 CA CB CG CD N Hydrophobic Amino acids (3) C CH2 C CH C H CA CB CG CD1 CE1 CZ CE2 CD2 Pro Phe Patrice Koehl

C CH2 CH3 CH2 S CA CB CG SD CE Hydrophobic Amino acids (4) C CH2 C CH N C C HC C C H H H CA CB CG CD2 CD1 NE1 CE2 CE3 CZ2 CZ3 CH Met Trp Patrice Koehl

Polar Amino acids (1) C OH CH2 CA CB OG C OH CH CA CB OG1 CG2 CH3 Ser Thr Patrice Koehl

C CH2 C CH C CA CB CG CD1 CE1 CZCE2 CD2 OH Polar Amino acids (2) Patrice Koehl

C CH2 C CA CBCG ND2 NH2O OD1 Polar Amino acids (3) C CH2 C CA CB CG CD NE2 NH2O OE1 Asn Gln Patrice Koehl

Polar Amino acids: Cysteine C S CH2 CA CB SG CB1 SG1 SG2 CB2 CA1 CA2 Can form disulphide bridges in proteins pKa sidechain: 8.3 Patrice Koehl

Polar Amino acids: Histidine C CH2 C CHN NC H H pKa sidechain: 6.04 CA CB CG ND1 CD2 NE2 CE1 Patrice Koehl

C CH2 C CHN NC H H C CH2 C CHN NCH C CH2 C CHN NC H H C CH2 C CHN NC H H H H + + H Different ionic states of the Histidine sidechain Patrice Koehl

C CH2 C CA CB CG OD2 Charged Amino acids (1) OO OD1 - pKa sidechain: 3.9 C CH2 C CA CB CG CD OE2 OO OE1 - pKa sidechain: 4.25 Asp Glu Patrice Koehl

C CH2 pKa sidechain: 9.2 CH2 NH3 + CA CB CG CD CE NZ Charged Amino acids (2) C CH2 NE CZ CA CB CG CD NE CZ NH1 NH2 NH2 + pKa sidechain: 12.5 Lys Arg Patrice Koehl

Molecular Visualization Software Pymol: the standard for publications youtube tutorial at: A more complete tutorial can be found at: Jmol DS Visualizer displays rotamers off of a common mainchain

Summary Proteins in nature are a string of residues, each of which is one of the 20 amino acids. Amino acids all have a backbone made of atoms N-C α -CO in a conformation characterized by the torsion angles,, and The remaining atoms form side-chains whose conformations are characterized by their torsion angles. Side-chains can be hydrophobic, polar or charged. Hydrophobic amino acids: GLY,ALA,VAL,ILE,LEU,PHE,PRO,MET,TRP Polar amino acids: CYS, SER, THR, HIS, ASN, GLN, TYR Charged amino acids: ASP, GLU, ARG, LYS  