Alex J. George Week 7: Difference between revisions
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# Aib142- α- aminoisobutyric acid [NHC(CH3)2C(O)] | # Aib142- α- aminoisobutyric acid [NHC(CH3)2C(O)] | ||
# His loop and Ser loop- Histidine and Serine loops | # His loop and Ser loop- Histidine and Serine loops | ||
# residue- amino acid | |||
== Paper Outline== | == Paper Outline== | ||
===Introduction | ===Introduction=== | ||
* The third hypervariable (V3) loop of gp120 is required for viral entry into the cell membrane | * The third hypervariable (V3) loop of gp120 is required for viral entry into the cell membrane | ||
* Sequence changes in V3 can affect receptor usage- controlling which types of cells are infected | * Sequence changes in V3 can affect receptor usage- controlling which types of cells are infected | ||
* CXCR4 is the coreceptor for T-Cell tropic and CCR5 is the coreceptor for macrophage tropic | * CXCR4 is the coreceptor for T-Cell tropic and CCR5 is the coreceptor for macrophage tropic | ||
* | *V3 loop is about 40 amino acids | ||
* Exposure of V3 loop depends on viral type which affects tropism-- CD4 increases exposure | |||
* T-Tropic sequences around V3 loop are basic | |||
* Highly conserved sequences have key structural role to protein | |||
* Knowing conformations of loop could help explain progression of disease | |||
* Fab 50.1 and 59.1 have turns similar to Aib amino acid | |||
* Replacing Alanine with Aib residue didn't change rigidity of Fab 59.1 | |||
===Results/Discussion=== | |||
* '''Figure 1''' | |||
**Indicates Amino acid sequences of RP70, Histidine loop, Serine loop and Aib142 | |||
** RP70 loop has disulfide bond, the two loops have hydrazone bonds between J and Z (this is shown in detail) | |||
** J is called Arn(P1); Z is called Gly(P11) | |||
*'''Table 1''' | |||
** Data collection and refinement statistics | |||
**Rmsd- Deviation from ideal bond length/ angle | |||
* '''Figure 2''' | |||
** Views of Fab 58.2- A) with Aib142, B) with His loop C) with Ser loop | |||
**Cyan is the light chain, Blue is heavy chain, Red is highly conserved sequence | |||
*'''Figure 3''' | |||
** Comparing the H1 loop of different Fabs (58.2, AN02 and N10) | |||
** The structures are very similar until regions 32-37 | |||
* '''Figure 4''' | |||
** Electron density for the Aib142 peptide loop (a,b), His loop peptide (c) and Ser loop peptide (d) |
Revision as of 13:57, 4 March 2010
Dual conformations for the HIV-1 gp120 V3 loop in complexes with different neutralizing Fabs
Vocabulary
- X-Ray crystallography- a method of determining the arrangement of atoms within a molecule by looking at diffraction patterns of X-rays
- syncytium- a cell-like structure filled with cytoplasm containing many nuclei
- Fab fragment- "fragment antigen binding" region on antibody that binds to the antigen
- paucity- smallness or insufficient number; scarcity
- GPGR tip- a relatively conserved region within the V3 Loop
- Ramachandran space- way to visualize dihedral angles ψ against φ of amino acid residues in protein structure
- isomorphously- similarity in form
- hydrazone bond- a double bond between a Carbon atom and Nitrogen atom
- Aib142- α- aminoisobutyric acid [NHC(CH3)2C(O)]
- His loop and Ser loop- Histidine and Serine loops
- residue- amino acid
Paper Outline
===Introduction===
- The third hypervariable (V3) loop of gp120 is required for viral entry into the cell membrane
- Sequence changes in V3 can affect receptor usage- controlling which types of cells are infected
- CXCR4 is the coreceptor for T-Cell tropic and CCR5 is the coreceptor for macrophage tropic
- V3 loop is about 40 amino acids
- Exposure of V3 loop depends on viral type which affects tropism-- CD4 increases exposure
- T-Tropic sequences around V3 loop are basic
- Highly conserved sequences have key structural role to protein
- Knowing conformations of loop could help explain progression of disease
- Fab 50.1 and 59.1 have turns similar to Aib amino acid
- Replacing Alanine with Aib residue didn't change rigidity of Fab 59.1
Results/Discussion
- Figure 1
- Indicates Amino acid sequences of RP70, Histidine loop, Serine loop and Aib142
- RP70 loop has disulfide bond, the two loops have hydrazone bonds between J and Z (this is shown in detail)
- J is called Arn(P1); Z is called Gly(P11)
- Table 1
- Data collection and refinement statistics
- Rmsd- Deviation from ideal bond length/ angle
- Figure 2
- Views of Fab 58.2- A) with Aib142, B) with His loop C) with Ser loop
- Cyan is the light chain, Blue is heavy chain, Red is highly conserved sequence
- Figure 3
- Comparing the H1 loop of different Fabs (58.2, AN02 and N10)
- The structures are very similar until regions 32-37
- Figure 4
- Electron density for the Aib142 peptide loop (a,b), His loop peptide (c) and Ser loop peptide (d)