Robert W Arnold Week 7
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Electronic Lab Notebook 7
Journal Club 2 - Stanfield et. al 2003
HIV Structure Project
- New partners assigned.
- Isaiah and I will be working together to present the Stanfield 2003 paper in Journal Club next week.
- Began work for Week 8 Journal Club.
Week 8 Journal Club
Word Definitions
- lentivirus - a genus of retroviruses that cause persistent infection that typically results in chronic, progressive, usually fatal disease; it includes the human immunodeficiency viruses
- Free Online Medical Dictionary October 12 2011
- oligomeric - a polymer formed by the combination of relatively few monomers
- Free Online Medical Dictionary October 12 2011
- syncitia - A mass of cytoplasm having many nuclei but no internal cell boundaries
- Free Online Medical Dictionary October 12 2011
- rhinovirus - a genus of viruses of the family Picornaviridae that infect the upper respiratory tract and cause the common cold
- Free Online Medical Dictionary October 12 2011
- chimeric - Composed of parts of different origin
- Free Online Medical Dictionary October 12 2011
- hybridoma - a somatic cell hybrid formed by fusion of normal lymphocytes and tumor cells
- Free Online Medical Dictionary October 12 2011
- monoclonal - Of or relating to a protein from a single clone of cells, all molecules of which are the same
- Free Online Medical Dictionary October 12 2011
- hypervariable region - a chromosomal segment characterized by multiple alleles within a population for a single genetic locus
- Free Online Medical Dictionary October 12 2011
- conformation - chemical structure, also called the chemical conformation, the spatial arrangement of atoms and chemical bonds in a molecule
- Free Online Medical Dictionary October 12 2011
- twinning - in crystallography, crystal twinning refers to intergrown crystal forms that display a twin boundary
- Free Online Medical Dictionary October 12 2011
Journal Club Outline - Stanfield 2003
Introduction
- HIV-1 is a virus with spikes made of gp120 and gp41 embedded in its outer layer
- gp120 and gp41 are envelope proteins, both are encoded by gp160
- gp41 is responsible for staying attached to membrane, which in turn allows for gp120 to bind to cell receptors like CD4 along with coreceptors such as CCR5 and CXCR4
- gp120 has 5 variable regions, labeled V1-V5
- the V3 region of gp120 is especially important for HIV-1:
- V3 is a loop region with 40 residues at the base of the loop
- V3 is able to vary due to cellular environment
- it is able to neutralize antibodies
- Attempts at a vaccine based on the gp120 V3 specific region have been abandoned because they have only been successful in laboratory isolates and small strains
- Initial viral isolates use the CCR5 coreceptor to infect and are very hard to neutralize by any antibody, including those that target V3
- The V3 loop can be blocked by interactions within the gp120 complex
- As the infection progresses to AIDS, V3 regions in gp120 change
- V3 acquires more positively charged residues
- becomes easier to neutralize, likely because it is more accessible due to conformational change in gp120
- gp120 changes its conformational state many times
- After gp160 codes for gp120 and gp 41
- After coreceptor interaction
- The only crystal structures for gp120 are gp120 core regions from HXB2 and YU2, with some parts of V3 deleted
- Stanfield et al are trying to determine the different conformational changes of gp120 by studying V3 conformation states and why it is recognized differently by different antibodies
- they have discovered that certain antibodies recognize one type of V3 conformation while others recognize another type but that both V3 conformations have a B-strand followed by a double B-turn
- V3 is presumed to be able to adjust its conformation to different antibody binding sites
- NMR studies have shown V3 peptides are disordered in water solution
- peptide cyclization, peptide glycosylation, attaching to bacteriophage viral coats, attaching to carrier proteins are all methods that have been used to stabilize V3 loop peptide conformation
- Stabilized peptides are much more ordered increasing likelihood of GPGRAF region
- Antibody 83.1 is a group of 5 antibodies
- They were taken from mice during HIV-1 studies
- all were raised against a 40-mer peptide containing the V3 sequence from the MN viral isolate
- These 5 were chosen of 85,000 due to their neutralizing strengths
- Some monoclonal antibodies are very specific while others are very broad
- 83.1 and 58.2 neutralize M-tropic isolates
Results and Discussion
- R-values were higher than expected even with good electron density maps
- Twinning tests were negative
- The R-values being higher show a noncrystallographic translation which would result in reflections
- Table 1 shows average reflection intensity
- The loops focus in on the V3 region of gp120 and its conformations
- All of the CDR (complementarity determining region) loops fall into expected classes with the exception of L1
- The L1 CDR loop tip bends away from the antigen binding site which is unusual
- When compared with 83.1 it is seen that it moves away from its corresponding site
- The loop collides with residues such as Pro^H41 and Gly^H42
- Table 2 summarizes all of the crystallographic data including wavelength, resolution, number of observations, reflections, and completeness
- CDR H3 has a bulged base that is atypical of its sequence
- Fab 83.1 is normally able to form a salt bridge between Asp^H101 with a charged residue of Arg or Lys at H94 allowing side chain Trp^H103 will hydrogen bond to the carbonyl oxygen, kinking the base
- Fab 26-10 and Fab B02C11 also have kinked H3 bases that are not predicted by their sequences
- 26-10 has its Asp^H101 is stabilized by a hydrogen bond and B02C11 Asp^H101 makes two hydrogen bonds to Asp^H96 and Ala^H99
- Table 3 shows the sequences of the anti-V3 Fabs 83.1 and 59.1 with CDR sequences in bold
- weak electron density is seen at both ends of 10-mer peptides
- the residues at the N-terminus have extended conformation with a type-1 turn around GPGR and then a type-2 turn around GRA
- different locations of the carbonyl oxygens in 83.1 and 59.1 peptides change torsion angles but the overall shape is the same
- the peptide contacts with Fab's heavy and light chains,these interactions include:
- 7 hydrogen bonds with no charge-charge interactions
- 6 hydrogen bonds to peptide main-chain atoms, one of which goes to the Arg^P315
- The order of the CDR loops which make the most contact from most to least are:
- H3
- H1
- L1
- L2
- L3
- H3
- Then light chain residues are next, followed by heavy chain residues
- the conformations of 3 of the peptides, 83.1, 50.1, and 59.1 are all very similar while the fourth, 58.2 has varying residues at the tip of V3
- The similarly conformed peptides all bind in different ways and locations when binding with the antibody
- these peptide conformations are thus believed to be the most common or preferential due to the antibody selection for high neutralizing ability
- the x-ray crystallography is being used to determine all the different conformations that can be used by V3
- Table 4 shows hydrogen bonding distances between the Fab and the peptide used
Materials and Methods
- 83.1 was taken from the mice used in early stages of HIV-1
- Fab fragments were collected, purified, then concentrated to 15.0 mg/ml for crystallization
- Then it was mixed with a linear peptide
- crystals grew as clusters of thin plates
- data was taken as quick as possible because the crystals suffered radiation induced decay
- a single crystal was used and the data can be seen in Table 2
- again, noncrystallographic translation was seen between two Fab molecules
- Fab 59.1 showed strong rotation function with elbow angles around 135 degrees
- Fab 58.2 was then used as a model to construct only this time with elbow angles like Fab 59.1
- The hybrid was then mutated to sequence for 83.1
- all Fab molecules were numbered, light and heavy connections measured, hydrogen bonds counted, and van der Waals interactions counted
Links
- Robert W Arnold Week 2
- Robert W Arnold Week 3
- Robert W Arnold Week 4
- Robert W Arnold Week 5
- Robert W Arnold Week 6
- Robert W Arnold Week 7
- Robert W Arnold Week 8
- Robert W Arnold Week 9
- Robert W Arnold Week 10
- Robert W Arnold Week 11
- Robert W Arnold Week 12
- Robert W Arnold Week 14
- Week 2 Assignment
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