Salomon Garcia: Week 7: Difference between revisions

Revision as of 14:32, 8 March 2010

Ten New words from the 2003 Stanfield Article:

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
CDR- complementarity determining region (CDR) is a relatively short amino acid sequence found in the variable (V) domains of antigen receptors
Fab proteins- fragment of immunoglobulin prepared by papain treatment.
Deglycosylated-The removal of the sugar entity from a glycogen
Peptide cyclization- Changing an open-chain hydrocarbon to a closed ring in a peptide bond
TOM/FRODO- a computer program that builds graphic images of a particular model.
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.
Matthews coefficient- is used in machine learning as a measure of the quality of binary (two-class) classifications.
ASW mice- a hybrid mice often used in experimentation
BALB/c mice-is an albino, laboratory-bred strain of the House Mouse from which a number of common substrains are derived.

http:wikipedia.org

http:biology-online.org/dictionary

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

- 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

@@ Line 23: / Line 23: @@
 ====Introduction====
+*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
 ====Results====
 ====Discussion====