Protein structure Visualization Molecular Story. Review “Central Dogma”: Sequence Structure function Sequence based analysis Structure based analysis.

Protein structureVisualization

Molecular Story

Review “Central Dogma”:

Sequence Structure function

Sequence based analysis

Structure based analysis

Gene Sequence Protein Structure Protein Function

(Genomics) (Structural Genomics) (Functional Genomics)

Primary Structure Protein - Protein

Secondary Structure Protein-DNA/RNA

Tertiary Structure Protein-Lipids

Quaternary Structure Protein-Small Molecules Determine Structure Drug Development

Sequence similarity

Conserved domain

Predict structure

Predict function

Bio-information data collection methods and major databases

Genome sequencing Genbank (www.ncbi.nih.gov)

Genechip gene expression database

X-ray crystallography, NMR protein structure database ( www.pdb.org)

2D gel, mass spectrometry proteomics database

Literature db PubMed (www.pubmed.org)

Inherent genetic disease db OMIM (www.ncbi.nih.gov)

Structure based analysis Molecular profile and story

Protein structure: Primary Secondary Tertiary -Folding quaternaryProtein structure determination: X-ray crystallography NMR spectroscopyProtein structure prediction: Secondary structure prediction Homology modelingProtein structure analysis: The structure character of the individual protein The structural basis of the protein function Protein family (based on conserved domain, motifs to predict their functions)Write the molecular profile and story

I. Protein Molecular Structure

a) Protein is a polymer of amino acids.

20 Amino Acids ( Functional Groups)

Peptide Bond Formation

c) The Secondary Structure and Tertiary Structure of Protein

Elements of Secondary Structure:

Helix

LoopTurn

β-Strandin β-Sheet

β-Strand Helix

Turn

Loop

Turn

Secondary Structure & Ramachandran Plot

Ramachandran Plot of CDC42-RhoGDI Complex [PDB Code 1DOA]

Many alpha helices are Amphipathic

100 degree per residue

Molscript Representations of Typical Protein Architectures.

β Barrel (2por)

β 7 Propellor (2bbkH) α 4-Layer Sandwich (2dnjA)

Sandwich (2hlaB)

Molscript Representations of Typical Protein Architectures.

α β Barrel (4timA) α Helix Bundle (2ccy)

2 Solenoid (1tsp) α Horseshoe (1bnh)

b a

c da b

d c

--b

a----b

a-----b

a

--d c---d c---d c

-

b

a

dc

a b

c dc

d

a

b

Isologous Association

Heterologous Tetramer

Heterologous Association

Schematic Illustrations of Isologous and Heterologous Association between Protein

Subunits

b--a

d--c

The Isologous tetrameric structure of rabbit skeletal muscle aldolase, with three twofold symmetry axes (1ado).

The prealbumin dimer, in which arrows depict the β-strands. The two monomers (left and right) associate to extend the two β-sheets (1bm7).

Examples of Protein Quarternary Structure.

DNA Quadruplex & G Quartets

K+

NMR SpectroscopySample-Spectrum-Structure

X-Ray CrystallographyCrystal Diffraction Electron Density Structure

Protein Function and Structure (Architecture)

a) Binding: Protein-DNA: transcription factors, eg TATA binding protein (PDB 1tgh) Protein-RNA: microRNA-target protein RNAi function Protein-small molecule: eg: Myoglobin-Heme/O2,Fe (PDB 1a6k) drug-target protein binding Protein-Protein: eg, chaperonin GroEL

b) Catalysis: Enzymes Catalyzes biochemical reactions eg: DNA Polymerase catalyzes DNA replication (PDB 1pbx) HIV protease cleaves protein catalyzing the HIV replication (PDB 1a8k)

c) Switching: eg: small GTPase Ras is a ‘Molecular switch’ for cell growth, GTP-bound, ‘ON’ (PDB 121p); GDP-bound, “off” (PDB 1pll)

d) Structural Proteins: Silk: a stack of anti-parallel beta-sheets (PDB 1slk) within a sheet: covalent bonding and hydrogen bond, between sheets: Van der Waals force F-actin: helical assemblies of actin and actin-associated proteins muscle contraction, cytoskeleton

The Second Project

Go to www.pdb.org,

a) Type a protein (or a disease) name, search for the structures

b) Download the structure text file, save it as a text file with .pdb extension.

c) Input the xxx.pdb file to Pymol (download from www.pymol.org) to see the molecular structure, notice its structural characters.d) Read the major reference paper (from www.pubmed.org) for this

protein structure and the corresponding gene, summarize the connection of the structure and the protein function. Write the molecular story for this gene.