Introduction

  • Fibrous protien, Globular protein
  • Simple proteinm Conjugated protein (with nonprotein)
    • Conjugated protein : apoprotein + prosthetic group = holoprotein
      • Glycoprotein
      • Lipoprotein
      • Metalloprotein
      • Phosphoprotein
      • Hemoprotein

Molecular Modeling

image [REF|16]

  • conventional ball-and-stick molecular model
  • sphere model
  • ribbon model




Amino Acids

image [REF|2] Amino acids comprise amino(–NH2, hydrophobic) and carboxyl(–COOH, hydrophobic) functional groups along with a side chain(R group) specific to each amino acid. (+ alpha carborn)

Proteinogenic Amino Acid : 20 AAc(20 Amino Acids)

image [REF|1,2]

  • L-Alanine(Ala / A)
  • L-Arginine(Arg / R)
  • L-Asparagine(Asn / N)
  • L-Aspartic acid(Asp / D)
  • L-Cysteine(Cys / C)
  • L-Glutamic acid(Glu / E)
  • L-Glutamine(Gln / Q)
  • Glycine(Gly / G)
  • L-Histidine(His / H)
  • L-Isoleucine(Ile / I)
  • L-Leucine(Leu / L)
  • L-Lysine(Lys / K)
  • L-Methionine(Met / M)
  • L-Phenylalanine(Phe / F)
  • L-Proline(Pro / P)
  • L-Serine(Ser / S)
  • L-Threonine(Thr / T)
  • L-Tryptophan(Trp / W)
  • L-Tyrosine(Tyr / Y)
  • L-Valine(Val / V)
  • L-Selenocysteine(Sec / U)
  • L-Pyrrolysine(Pyl / O)

Polypeptide

image [REF|3]

  • Residues, N-terminal(amino, begin), C-terminal(carboxyl, end)
  • Main Chain(backbone), Side Chain(R-group)

Peptide bond

image [REF|4]

Ramachandran Plot




Levels of protein structure

Primary structure

  • Homoogous : ex) cytochrome > invariant
  • Protein evolution : variable

Secondary structure

  • $\alpha$-helix, $\beta$-pleated sheet
  • Supersecondary structure

Tertiary structure

  • Denaturation/Renaturation : Primary > Tertiary
  • Globular Structure
  • Protein Folding
  • Interaction with ligands

Quaternary structure

  • Oligomer, Protomer




Structural Units

Domains

Motifs

Folds

　

　

　

Reference
  1. Proteinogenic amino acid
  2. Amino acid
  3. Peptide
  4. Peptide bond
  5. RCSB PDB
  6. PDB101
  7. List of types of proteins
  8. List of proteins
  9. List of topics related to protein
  10. List of protein structure prediction software
  11. List of protein secondary structure prediction programs
  12. List of protein-ligand docking software
  13. Protein-protein interaction
  14. Protein design
  15. PyMol
  16. Molecular Representation
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