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

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Protein structure visualization molecular story l.jpg
Protein structureVisualizationMolecular Story


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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


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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)


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Structure based analysis  Molecular profile and story

Protein structure: Primary

Secondary

Tertiary -Folding

quaternary

Protein structure determination:

X-ray crystallography

NMR spectroscopy

Protein structure prediction:

Secondary structure prediction

Homology modeling

Protein 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


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Protein Molecular Structure

a) Protein is a polymer of amino acids.

20 Amino Acids ( Functional Groups)

Peptide Bond Formation


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c) The Secondary Structure and Tertiary Structure of Protein

Elements of Secondary Structure:

Helix

Loop

Turn

β-Strand

Helix

β-Strand

in β-Sheet

Turn

Loop

Turn




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Many alpha helices are

Amphipathic

100 degree per residue


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Molscript Representations of

Typical Protein Architectures.

β 7 Propellor (2bbkH)

α 4-Layer Sandwich (2dnjA)

β Barrel (2por)

Sandwich (2hlaB)


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Molscript Representations of

Typical Protein Architectures.

α β Barrel (4timA)

α Helix Bundle (2ccy)

α Horseshoe (1bnh)

2 Solenoid (1tsp)


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Schematic Illustrations of Isologous and Heterologous Association between Protein Subunits

b

a

c d

d

c

b

a

c

a b

d

--b

a----b

a-----b

d

a

c

b

a

d--c

b--a

--d

b a

c---d

c---d

c-

Heterologous Tetramer

d c

Heterologous Association

Isologous Association


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Examples of Protein Quarternary Structure. Association between Protein Subunits

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

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


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DNA Quadruplex & Association between Protein Subunits

G Quartets

+

K


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NMR Spectroscopy Association between Protein Subunits

Sample-Spectrum-Structure


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X-Ray Crystallography Association between Protein Subunits

Crystal Diffraction Electron Density Structure


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Protein Function and Structure (Architecture) Association between Protein Subunits

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


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  • The Second Project Association between Protein Subunits

  • Go to www.pdb.org,

  • 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.


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