Loyola Marymount University Higher Structural Differences in Amino Acid Sequence of gp120 V3 Region in Patients With Rapid CD4+ T Cell Decline Versus Patients with High CD4+ T Cell Variability Kevin Paiz-Ramirez Janelle N. Ruiz Biology 398.01 Department of Biology Loyola Marymount University March 20, 2010

Outline Background on structure of HIV-1, core gp120, and gp120 complex with CD4 and CD4 co-receptors Are there structural differences in V3 region of HIV-1 gp120 between participants with rapid CD4+ T cell decline versus patients with high CD4+ T Cell variability? Results: comparing our groups Diversity and Divergence of gp120 V3 region structures Secondary structural predictions of amino sequences Location and nature of major a.a. changes Predicted post-translational modifications Interpretations in Light of Recent Studies Discussion and Further Studies

Entry of HIV Involves a Sequential Interaction in the Structure The entry of HIV involves specific interactions The envelope glycoprotein (gp120) CD4 glycoprotein CD4+ co-receptors

Structure of gp120 Core Kwong, et, al 1998

Importance of core gp120 structure and ternary complex to HIV-1 entry into host cell Kwong, et al. explored the structure of gp120 in complex with CD4 receptor. Gp120 is crucial for fusion of HIV-1 to cell surface Positioning Timing CD4 binding induced conformational change in gp120

Previous investigation revealed differences in diversity and divergence in DNA sequence of gp120 V3 variants Patients with high CD4 decline had greater diversity and divergence in DNA sequence of gp120 V3 variants than patients with high variability in CD4 count Are there structural differences in HIV-1 amino acid sequences between participants with a rapid CD4+ T cell decline versus patients with high CD4+ T Cell variability? Does this translate to differences in protein sequence and structure? Linear Progressors High Variability

Methodology for Determining Structural Differences in Sequence between Linear and High Variability Groups 1. Multiple amino acid sequence alignments from first four visits of each patient 2. Determined consensus sequence and sequence(s) with most differences from consensus sequence 3. Predicted secondary structures of sequences using PSIPRED 4. Performed Multiple Sequence alignments for sequences 5. Investigated sites of possible post-translational modifications using PROSITE

High Variability group has fewer sequences and less divergence in sequences: Subject 12 Multiple Sequence Alignments See less amino acid sequences in total and less major amino acid changes between sequences (purple) in High Variability group that Linear progressors Tables: Represent Major Amino Acid Differences between Consensus Sequence and Sequence with most differences b/w Consensus Sequence 8

High Variability group has fewer sequences and less divergence in sequences: Subject 8

High Variability group has fewer sequences and less divergence in sequences: Subject 6

Linear Progressors have greater number of sequences and greater divergence in sequences: Subject 4 Many more sequences and many more purple major amino acid changes, shown in chart 11

High Variability group have greater number of sequences and greater divergence in sequences: Subject 10

Structure-Based Sequence Alignment of Core Gp120 Gp120 sequence from Kwong et al.

Predicted Secondary Structures of the gp120 V3 Region shows six beta sheets and one alpha helix

High Variability shows six beta sheets and one alpha helix Subject 6 Subject 8 Subject 12

Linear Progressors show six beta sheets and one or two alpha helices Subject 4 Subject 10

High Variability Participants Have Greater Major Amino Acid Changes on Protein Surface Binding Site *Black 1: Coil region, nonpolar, hydrophobic  Polar Basic *Black 2: Coil Region, Polar BasicPolar, unchargednonpolar, hydrophobic *Black 3: Helix 2, Nonpolar, hydorphobicPolar Basic *Black 4: Coil Region, Polar, unchargednonpolar, hydorophobic Key: Blue: Single, fully conserved residues Green: Conservation of strong groups Purple: Conservation of weak groups Black: No consensus

Linear Progressor Participants Have Greater Major Amino Acid Changes on Protein Binding Sites Surface *Black 1: Beta Sheet 11, polar uncharged nonpolar, hydrophobic *Black 2: Coil Region, Polar basic nonpolar, hydrophobic *Black 3: Helix 2, polar uncharged nonpolar, hydrophobic *Black 4: Coil Region, Polar BasicPolar, uncharged 1st black coil  N-binding site 2nd black coil on Betasheet 3rd black coil On the surface not on a binding site 4th black coil binding site 5th black coil on the surface not on a binding sit Key: Blue: Single, fully conserved residues Green: Conservation of strong groups Purple: Conservation of weak groups Black: No consensus

Linear Progressor Participants Have Greater Major Amino Acid Changes on Protein Binding Sites *Black 1: Coil Region, nonpolar, hydrophobic & Polar Basic  Polar Acidic *Black 2: Beta Sheet 11, Nonpolar Basic  Polar Uncharged *Black 3: Coil Region, Polar basic nonpolar, hydrophobic *Black 4: Coil Region, Polar, uncharged  Polar Basic *Black 5: Coil Region, random *Black 6: Helix 2, Polar, uncharged & Polar Basic  nonpolar, hydrophobic *Black 7: Helix 2, nonpolar, hydrophobic & Polar Basic  Polar, uncharged & Polar Acidic *Black 9: Coil Region, Polar Basic  Polar Uncharged *Black 10: Coil Region, random Key: Blue: Single, fully conserved residues Green: Conservation of strong groups Purple: Conservation of weak groups Black: No consensus

Sites of Post Translational Modification: Linear Progressors Have Slightly Greater Post Translational Modifications than High Variability

Discussion Linear progressors had greater number of amino acid sequences (diversity) and greater amount of major amino acid changes (divergence) This could indicate greater structural differences in linear progressors Linear Progressors had greater number of major amino acid changes in CD4-binding regions Linear Progressors showed greater post-translational modifications Further studies could examine protein structural differences variants within gp41 region

Further Investigations Exploring Interactive Regions in gp120 Pancera, et al, examined the gp41 interactive region. Gp120 elements proximal to gp41 completed a 7 stranded Beta sandwich Invarient in conformation

Further Investigations Exploring Interactive Regions in gp120 Crystal structure was consistent presenting shape changing spacer Facilitated movement between outer domain and gp41 Provided conformational diversity Immune evasion

References Kwong PD, Wyatt R, Robinson J, Sweet RW, Sodroski J, and Hendrickson WA. Structure of glycoprotein in complex with the CD4 receptor and a neutralizing human antibody. Nature 1998 Jun 18; 398(6686) 648-59. Pancera M, Majeed S, Ban YE, Chen L, Huang CC, Kong L, Kown YD, Stuckey J, Zhou T, Robinson JE, Schief WR, Sodroski J, Wyatt R, and Kwong PD. Structure of HIV-1 gp120 with gp41-interactive region reveals layered envelope architecture and basis of conformational mobility. Proc Natl Acad Sci USA 2010 doi:10.1073