Alex J. George Week 7

Vocabulary

 * 1) X-Ray crystallography- a method of determining the arrangement of atoms within a molecule by looking at diffraction patterns of X-rays
 * 2) syncytium- a cell-like structure filled with cytoplasm containing many nuclei
 * 3) Fab fragment- "fragment antigen binding" region on antibody that binds to the antigen
 * 4) paucity- smallness or insufficient number; scarcity
 * 5) GPGR tip- a relatively conserved region within the V3 Loop
 * 6) Ramachandran space-  way to visualize dihedral angles ψ against φ of amino acid residues in protein structure
 * 7) isomorphously- similarity in form
 * 8) hydrazone bond- a double bond between a Carbon atom and Nitrogen atom
 * 9) Aib142- α- aminoisobutyric acid [NHC(CH3)2C(O)]
 * 10) His loop and Ser loop- Histidine and Serine loops
 * 11) residue- amino acid

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)
 * Figure 5
 * A surface picture of Fab 58.2 indicating acidic regions (red), basic regions (blue) and neutral regions (white)
 * a) Shows the acidic binding pocket for Arg(P322) of Aib142
 * b) Shows the charge-charge interaction between Arg of peptide and Glu/Asp of Fab
 * Table 2
 * Shows the number of Van der Waals contacts between Fab and the 3 peptides, Aib142, His loop and Ser loop
 * Table 3
 * Shows the number of Hydrogen bonds between Fab and the 3 peptides, Aib142, His loop and Ser loop


 * Various amino acids were substituted for other amino acids to determine their importance to the structure; Gly(P319) proved to be important, as did Arg (P322) and Pro(P320)
 * The conformation of the V3 loop is different than others when it is bound to Fab 58.2
 * Figure 6
 * The conformations of the V3 loop of 3 peptides bound to Fabs 50.1, 59.1 and 58.2
 * Fabs 50.1 and 59.1 overlap each other, but Fab 58.2 shows a different conformation (different turns)
 * Blue is the Aib142 peptide bound to V3, Green is the His loop
 * Table 4
 * Indicates that the residue binding angles are similar despite the different turns


 * NMR has supported the idea that glycosylation can affect V3 conformation

Discussion

 * The high degree of conservation of GPGR region at the tip of the V3 loop suggests this is significant to biological function
 * Altering the V3 loop changes tropism, but is it because the loop structure is different or just that the turn is different
 * The results here help to understand the conformational flexibility of the V3 loop
 * More knowledge of the V3 regions will always help to combating HIV-1

Group Journal Club
[[Media:Protein Structure Journal Club Presentation.ppt| Protein Structure Presentation]]