Computing for Bioinformatics Lecture 8: protein folding

Problem description ● Definition: Given the amino acid sequence of a protein, what is the protein's structure in three dimension? ● Importance: The structure of a protein provides a key to understanding its biological function. ● Assumption: The amino acid sequence contains all information about the native 3-D structure. ● Thermodynamic principle: (Christian Anfinsen's denaturation-renaturation experiments on ribonuclease.) If one changes the solvent condition, the protein will undergo a transition from the native state to an unfolded state and become inactive. When solvent condition is changed back, the protein refolds and becomes active again.

Methods of 3D structure determination ● Experimental approaches: expensive, slow ➢ Nuclear magnetic resonance (NMR) ➢ X-ray crystallography ● Today we have much more sequenced proteins than protein’s structures. The gap is rapidly increasing. ● Protein structure prediction is becoming increasingly important.

Protein Structure Primary structure – sequence of amino acids constituting polypeptide chain Secondary structure – local organization of polypeptide chain into secondary structures such as  -helices and  -sheets Tertiary structure –three dimensional arrangements of amino acids as they react to one another due to polarity and interactions between side chains Quaternary structure – Interaction of several protein subunits

Amino acids Hydrophobic: Glycine(G), Alanine(A), Valine(V), phenylalanine (F), Proline (P), Methionine (M), isoleucine (I), Leucine(L), Tryptophan (W) Charged: Aspartic acid (D), Glutamic Acid (E), Lysine (K), Arginine (R), Histidine (H) Polar: Serine (S), Theronine (T), Tyrosine (Y); Histidine (H), Cysteine (C), Asparagine (N), Glutamine (Q), Tryptophan (W)

Types of Secondary Structures ●  Sheets ●  -Helices ● Loops – Image source:

 Helix – Most abundant secondary structure – 3.6 amino acids per turn – Hydrogen bond formed between every fourth reside – Average length: 10 amino acids, or 3 turns – Varies from 5 to 40 amino acids

 Helix Every third amino acid tends to be hydrophobic Rich in alanine (A), gutamic acid (E), leucine (L), and methionine (M) Poor in proline (P), glycine (G), tyrosine (Y), and serine (S)

 Sheet Image source:

 Sheet Hydrogen bonds between 5-10 consecutive amino acids in one portion of the chain with another 5-10 farther down the chain Interacting regions may be adjacent with a short loop, or far apart with other structures in between – Directions: Same: Parallel Sheet Opposite: Anti-parallel Sheet Mixed: Mixed Sheet – Pattern of hydrogen bond formation in parallel and anti-parallel sheets is different

Interactions in Helices and Sheets

Loops Regions between  helices and  sheets Various lengths and three-dimensional configurations Located on surface of the structure More variable sequence structure Tend to have charged and polar amino acids Frequently a component of active sites

Classes of Protein Structure The classes are made based on the percentages of secondary structure components. 1) Class  :: bundles of  -helices connected by loops on surface of proteins 2) Class  antiparallel  sheets, usually two sheets in close contact forming sandwich 3) Class  /  : mainly parallel  sheets with intervening  helices; may also have mixed  sheets (metabolic enzymes) 4) Class  +  mainly segregated  -helices and antiparallel  sheets

 Class Protein (hemoglobin)

 Class Protein (T-Cell CD8)

 /  Class Protein (tryptohan synthase)

 +  Class Protein (1RNB)

Protein structure database Databases of three dimensional structures of proteins, where structure has been solved using X-ray or NMR techniques Protein Databases: – PDB – SCOP – Swiss-Prot – PIR Most extensive for 3-D structure is the Protein Data Bank (PDB). Current release of PDB (April 8, 2003) has 20,622 structures

Partial PDB File ATOM 1 N VAL A HHB 162 ATOM 2 CA VAL A HHB 163 ATOM 3 C VAL A HHB 164 ATOM 4 O VAL A HHB 165 ATOM 5 CB VAL A HHB 166 ATOM 6 CG1 VAL A HHB 167 ATOM 7 CG2 VAL A HHB 168 ATOM 8 N LEU A HHB 169 ATOM 9 CA LEU A HHB 170 ATOM 10 C LEU A HHB 171 ATOM 11 O LEU A HHB 172 ATOM 12 CB LEU A HHB 173 ATOM 13 CG LEU A HHB 174 ATOM 14 CD1 LEU A HHB 175 ATOM 15 CD2 LEU A HHB 176

Description of PDB File second column: amino acid position in the polypeptide chain fourth column: current amino acid Columns 7, 8, and 9: x, y, and z coordinates (in angstroms) The 11 th column: temperature factor -- can be used as a measurement of uncertainty

Visualization of Proteins Most popular program for viewing 3-dimensional structures is Rasmol Rasmol: Chime: Cn3D: Mage: Swiss 3D viewer: