Salomon Garcia: Week 7

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Preparation for Journal Club 2

Ten New words from the 2003 Stanfield Article:

  1. Twinning- The assemblage of two or more crystals, or parts of crystals, in reversed position with reference to each other in accordance with some definite law
  2. CDR- complementarity determining region (CDR) is a relatively short amino acid sequence found in the variable (V) domains of antigen receptors
  3. Fab proteins- fragment of immunoglobulin prepared by papain treatment.
  4. Deglycosylated-The removal of the sugar entity from a glycogen
  5. Peptide cyclization- Changing an open-chain hydrocarbon to a closed ring in a peptide bond
  6. TOM/FRODO- a computer program that builds graphic images of a particular model.
  7. Ramachandran plot- is a way to visualize dihedral angles ψ against φ of amino acid residues in protein structure.[1] It shows the possible conformations of ψ and φ angles for a polypeptide.
  8. Matthews coefficient- is used in machine learning as a measure of the quality of binary (two-class) classifications.
  9. ASW mice- a hybrid mice often used in experimentation
  10. BALB/c mice-is an albino, laboratory-bred strain of the House Mouse from which a number of common substrains are derived.



  • HIV has an outer surface of glyco proteins
    • gp120 responsible for binding to CD4 receptors and coreceptors, CCR5 or CXCR4
    • gp41 anchors gp120 to the viral membrane providing noncovalent association

Materials and Methods

    • Mab 83.1 was made by immunization of an ASW mice with cyclic peptide RP70
    • Antibody was produced in ascites fluid of a mice and purified with an immobilized protein A column
    • Fab was made from immunoglobin by cleavage
    • Fab was concentrated to 15.0 mg/ml for crystallization studies
  • Fab Purification
    • Fab was mixed with 16-mer peptide MP1 in a 6:1 mole ration
    • Crystals were grown using sitting-drop vapor diffusion method with a reservoir solution of 1.6 M Na/K phosphate, 5% isopropanol, pH 6.0.
    • Crystals grow as clusters of thin plates
    • Crystals used for this experiments grew over a 2-week period
  • Fab Crystallization procedure
    • Were cryocooled to liquid nitrogen temperatures in order to collect the data in a rapid manner.
    • The crystals were protected by putting them in a solution containing the following 25% glycerol, 1.6 M Na/K phosphate, 5% isopropanol, pH 6.0
    • HKL2000 was used to format all of the data that was obtained
  • Structure determination
    • Matthew coefficient was obtained by two Fab molecules
    • Model was constructed from the constant region of Fab 58.2
    • EPMR program was used to position the model in the cell
    • EPMR also used to locate the first Fab molecule in the asymetric unit
  • Model building and refinement
    • TOM/FRODO was used to rebuild the mutated hybrid model and to correct the sequence and were subsequently refined with CNS version 1.1.
    • Refinement was carried with tight NCS restraints in the beginning and progressively released towards the end of refinement
  • Structural Analysis
    • Kabat convention was used to number the molecules
      • Light and heavy chains are labeled using “L” and “H”
      • Peptide labeled “P” and was numbered according to HXB2 isolate sequence
    • HBPLUS was used to evaluate the Hydrogen bonds
    • Contacsym program was used to assign van der waals contacts.

Results and Discussion

  • Electron Density maps were good quality
  • R-values were higher due to constant refinement and adjustment

BIOL 398-01: Bioinformatics Lab

  • Lab Journal
Salomon Garcia: Week 2 Salomon Garcia: Week 6 Salomon Garcia: Week 11
Salomon Garcia: Week 3 Salomon Garcia: Week 7 Salomon Garcia: Week 12
Salomon Garcia: Week 4 Salomon Garcia: Week 8 Salomon Garcia: Week 13
Salomon Garcia: Week 5 Salomon Garcia: Week 9 Salomon Garcia: Week 14

  • Shared Journal
  1. BIOL398-01/S10:Class Journal Week 2
  2. BIOL398-01/S10:Class Journal Week 3
  3. BIOL398-01/S10:Class Journal Week 4
  4. BIOL398-01/S10:Class Journal Week 5
  5. BIOL398-01/S10:Class Journal Week 6
  6. BIOL398-01/S10:Class Journal Week 7
  7. BIOL398-01/S10:Class Journal Week 8
  8. BIOL398-01/S10:Class Journal Week 9
  9. BIOL398-01/S10:Class Journal Week 11
  10. BIOL398-01/S10:Class Journal Week 12
  11. BIOL398-01/S10:Class Journal Week 13
  12. BIOL398-01/S10:Class Journal Week 14

  • Assignments
  1. BIOL398-01/S10:Week 2
  2. BIOL398-01/S10:Week 3
  3. BIOL398-01/S10:Week 4
  4. BIOL398-01/S10:Week 5
  5. BIOL398-01/S10:Week 6
  6. BIOL398-01/S10:Week 7
  7. BIOL398-01/S10:Week 8
  8. BIOL398-01/S10:Week 9
  9. BIOL398-01/S10:Week 11
  10. BIOL398-01/S10:Week 12
  11. BIOL398-01/S10:Week 13
  12. BIOL398-01/S10:Week 14