1 / 21

Protein Structure Analysis: Sample Problem Solution

This sample problem guides the analysis of a 20 amino acid polypeptide sequence through trypsin and cyanogen bromide cleavages to determine N- and C-termini and assemble the peptide. Explore primary, secondary, tertiary, and quaternary protein structure concepts.

jbaca
Download Presentation

Protein Structure Analysis: Sample Problem Solution

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Amino Acids, Peptides and Proteins

  2. Sample Problem Give the sequence for a 20 amino acid polypeptide with amino acid analysis: gly2ala4leu4phe3trp1lys2met2ser1arg1 • Step 1: Terminal residue analysis: • N-terminus = ala • C-terminus = phe

  3. Sample Problem Step 2: Trypsin hydrolysis (cleaves at lys and arg) gave four fragments: • trpphearg • alaleuglymetlys • leuglyleuleuphe • alaalasermetalaphelys

  4. Sample Problem Step 2: Trypsin hydrolysis (cleaves at lys and arg) gave four fragments: • trpphearg • alaleuglymetlys • leuglyleuleuphe • alaalasermetalaphelys Fragment III represents the last five amino acids (trypsin does not cleave at phenylalanine).

  5. Sample Problem Step 2: Trypsin hydrolysis (cleaves at lys and arg) gave four fragments: • trpphearg • alaleuglymetlys • leuglyleuleuphe • alaalasermetalaphelys Either fragment II or IV must be N-terminus (cannot know which).

  6. Sample Problem Step 3: Cyanogen bromide cleavage gave three fragments: • alaleuglymet • alaphelysleuglyleuleuphe • lystrppheargalaalasermet

  7. Sample Problem Step 3: Cyanogen bromide cleavage gave three fragments: • alaleuglymet • alaphelysleuglyleuleuphe • lystrppheargalaalasermet Fragment 2 must be the C-terminus.

  8. Sample Problem Step 3: Cyanogen bromide cleavage gave three fragments: • alaleuglymet • alaphelysleuglyleuleuphe • lystrppheargalaalasermet Fragment 1 must be the N-terminus.

  9. Sample Problem Step 4: We can now assemble the peptide:

  10. Sample Problem Step 4: We can now assemble the peptide:

  11. Proteins • Protein function depends on structure. • Depends on various amino acids. • Primary Structure: The amino acid sequence.

  12. Proteins • Secondary Structure: The “local” hydrogen-bonding scheme. • a-Helix Hydrogen bonds

  13. Proteins • Secondary Structure: The “local” hydrogen-bonding scheme. • a-Helix

  14. Proteins • Secondary Structure: The “local” hydrogen-bonding scheme. • b-Sheet Interchainhydrogen bonds

  15. Proteins • Tertiary Structure: How the protein, with all of its regions of secondary structure (a-helix, b-sheet) has folded over upon itself • Interaction between R-groups is important • All intermolecular forces we have studied are at play

  16. Proteins • Tertiary Structure: Chemical bonds between cysteines Disulfide bonds

  17. Proteins • Tertiary Structure: Interaction between R-groups Hydrophobic interactions Hydrogen bonding Ionic bonding (“salt bridge”) Hydrophilic interactions

  18. Proteins • Tertiary Structure: How the protein, with all of its regions of secondary structure (a-helix, b-sheet) has folded over upon itself.

  19. Proteins • Tertiary Structure: How the protein, with all of its regions of secondary structure (a-helix, b-sheet) has folded over upon itself. a-Helix regions

  20. Proteins • Tertiary Structure: How the protein, with all of its regions of secondary structure (a-helix, b-sheet) has folded over upon itself. b-Sheet regions

  21. Proteins • Quaternary Structure: How protein subunits aggregate into a larger functional unit. Hemoglobin has two  and two  subunits that fit together to form the whole hemoglobin molecule with four hemes and their associated iron atoms to transport O2 and CO2

More Related