LSM2104/CZ2251 Essential Bioinformatics and Biocomputing Essential Bioinformatics and Biocomputing Protein Structure and Visualization Chen Yu Zong

Three Lectures Lecture 9: BioMacromolecular Visualization I Principles of protein chemistry and structure Lecture 10: BioMacromolecular Visualization II Protein structure databases; visualization; and classifications Lecture 11: Receptor Ligand Binding, Energy Minimization and docking concepts- Structural Modeling LSM2104/CZ2251 Essential Bioinformatics and Biocomputing Essential Bioinformatics and Biocomputing

Lecture 9 Principles of Protein Chemistry and Structure 1. Why protein structure? 2. Structure organization Building blocks (amino acids), primary structure Secondary structure Super-secondary structure Tertiary structure Quaternary structure Multi-domain proteins LSM2104/CZ2251 Essential Bioinformatics and Biocomputing Essential Bioinformatics and Biocomputing

The advent of the post-genomic era In the post-genomic era, focus has been extended from sequence to structure Why protein structure?

Mechanism of Protein function

Drug Receptors

Mad cows disease and the Prion protein Protein mis-folding can cause diseases Prion protein Memory?

Mad cows disease and the Prion protein Protein mis-folding can cause diseases Prion protein Memory?

Specific disease proteins are targets for drug discovery Knowledge of their structure useful for drug design HIV-1 protease Drug Design: Success Story of Anti-HIV

Protein sequence-structure-function relationship Protein structure determines its function Function of Proteins is determined by their four level structures Primary - Sequence of amino acids Secondary - Shape of specific region along chain mostly through H- bonding Tertiary - 3 Dimensional structure of globular protein through molecular folding Quaternary - Combination of separate polypeptide and prosthetic group. Aggregation and prosthetic.

1. Primary structure The general formula for α-amino acid. 20 different R groups in the commonly occurring amino acids. Proteins are polymers of a set of 20 amino acids. 20 amino acids = building units. Chiral Center asymmetric carbon

The CORN method for L isomers: put the hydrogen towards you and read off CO R N clockwise around the Ca This works for all amino acids. All naturally occurring amino acids that make up proteins are in the L conformation

Classification of 20 R groups Aliphatic residues

Aromatic residues

Acidic Basic Charged residues Negatively charged Positively charged

Neutral-Polar residues

Side chain = H Imino CC CC CC CC CC The unique couple H

Through hydrolysis reactions, amino acids are connected through peptide bond to form a peptide/protein. + H 2 O Structure of peptide bonds

Key features: –1. Planar –2. Rigid due to partial double bond character. –3. Almost always in trans configuration. –4. Polar. Can form at least two hydrogen bonds.

Peptide Unit The peptide unit is a planar, rigid structure The peptide bond has a partial double-bonded character due to delocalization of the electron pair of the C=O group. Its bond length 1.33 Å is shorter than the C-N bond length (1.45 Å), about 40% double bond character.

Each unit can rotate around two bonds (two degrees of freedom): C  -C bond angle of rotation psi (  ) N- C  bond angle of rotation phi (  ) The peptide unit is a planar, rigid structure

Computed Ramachandran Plot White = sterically disallowed conformations (atoms come closer than sum of van der Waals radii) Blue = sterically allowed conformations

Van der Waals Interactions van der Waals attraction occurs at short range, and rapidly dies off as the interacting atoms move apart. Repulsion occurs when the distance between interacting atoms becomes even slightly less than the sum of their contact distance. Van der Waals radii is the value of rij of the lowest van der Waals energy

2. Secondary structure Local organization mainly involving the protein backbone:  -helix,  -strand (further assemble into  -sheets)  turn and interconnecting loop

The (right-handed)  -helix First structure to be predicted (Pauling, Corey, Branson: 1951) and experimentally solved (Kendrew et al. 1958) – myoglobin Turn: 3.6 residues Pitch: 5.4 Å/turn Rise: 1.5 Å/residue Hydrogen bond i+4 i+8 i ++ --

Helix and Ramachandran Plot

The  -sheet Side chains project alternately up or down  strand

 -Sheet and Ramachandran Plot

Turn Structures

Loop structures

Ramachandran plot and Secondary Structure

3. Super secondary structure & motif Super secondary & motif: Secondary structures organized in specific geometric arrangements  -hairpins: the most simple super secondary structure 4.2.  -corners 4.3. Helix hairpins 4.4. The  corner 4.5. Helix-turn-helix 4.6.  motifs Details: Combination of basic secondary structures

3.1.  -hairpins

3.2.  -corners

3.3. Helix hairpins

3.4. The  corner

3.5. Helix-turn-helix

3.6.  motifs

4. Tertiary structure –secondary structure elements pack into a compact spatial unit –“Two methods now available to determine 3D structures of proteins: X-ray crystallography and Nuclear Magnetic Resonance (NMR)

Secondary Structural Components of Protein

The three-dimensional structure of a protein is determined by non-covalent interactions among amino acids 1. Hydrophobic region (nonpolar R- interactions) R-CH H 3 C-R 2. H-bonding between R-group G-OH --- N=R 3. Salt bridge R-COO NH 3 -R 4. van der Waals forces

Hydrophobic Interactions in Protein

Hydrogen Bond Interactions in Protein

The classic experiment by Anfinsen in 1950s on Ribonuclease Native state catalytically active addition of urea and mercaptoethanol Unfolded state ; inactive. Disulfide reduced removal of urea and mercaptoethanol Native, catalytically active state. Disulfide correctly re-formed.

Disulfide Bridges Disulfide bridges in extracellular proteins oxidation of 2 cysteine SH groups Covalent S-S bond formed.

Driving Forces in Folding Hydrophobic effect – bury hydrophobic side chains – expose polar/charged side chains to solvent – ion-pair or “salt-bridge” for buried charges Hydrogen bonding – between backbone N and O atoms – between N, O and S side chain atoms

Amino acid side- chains interact with each other and irresponsible for the globular shape of the protein. Side-chain Interaction

Highest level of protein organization Referring to the arrangement of homo- or heteromeric subunits (i.e., chains) and prosthetic groups i.e.,non-amino acid portion) fit as an organized whole. 5. Quaternary Structure

The quaternary structure of deoxyhemoglobin Hemoglobin - 4 chains: 2-  chain, 2-  chain (Heme- four iron groups)

Viral particles Nano-structures

6. Multi-Domain Protein Beads-on-a-string: sequential location: tyrosine-protein kinase receptor TIE-1 (immunoglobulin, EGF, fibronectin type-3 and protein kinase); Grb4 adaptor protein Domain insertions: “plugged-in” - pyruvate kinase (1pkn) All-  -1  -2  -1

SH2SH3SH2PHC2 Example of the Multi-domain Proteins Beads-on-a-string

Domain insertions: “plugged-in” pyruvate kinase

Summary Why protein structure? Protein structure organizations Primary, secondary, tertiary, quaternary structure, viral particles, multi-domain proteins