Structural study on HIV viral tropism Olga V. Kalinina Max Planck - - PowerPoint PPT Presentation

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Structural study on HIV viral tropism Olga V. Kalinina Max Planck - - PowerPoint PPT Presentation

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Structural study on HIV viral tropism Olga V. Kalinina Max Planck Institute for Informatics 1 Two step entry into host cell 2 Two step entry into host cell 2 Two step entry into host cell CD4, bound by gp120 (V1 & V2 loops)

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Structural study

  • n HIV viral tropism

Olga V. Kalinina Max Planck Institute for Informatics

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Two step entry into host cell

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Two step entry into host cell

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Two step entry into host cell

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  • CD4, bound by gp120

(V1 & V2 loops)

  • CCR5 & CXCR4, bound

by gp120’s V3 loop

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  • Tropism is largely defined

by V3 loop of gp120

  • Known predictors of co-

receptor tropism:

  • 11/25 rule (positive charge

at positions 11 & 25 of V3): 62% sensitivity at 5% FPR

  • Sequence-based SVM: 71%
  • Incorporating structure into

SVM: up to 80%

  • Physico-chemical basis:

unknown

Can we predict tropism?

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Sander et al., PLoS Comp Biol 2007

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CCR5 & CXCR4

  • G-protein coupled receptors (7 TM bundles, transfer

extracellular signals into the cell)

  • Structure of CXCR4 solved in 2012
  • Structure of CCR5 modelled on that template

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Interaction between HIV’s gp120 and host receptors

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Wu et al., 2010 Science

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Interaction between HIV’s gp120 and host receptors

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Wu et al., 2010 Science

This is pure imagination!

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Data

  • Experimentally verified sequences (Bozek et al.,

Retrovirology 2012): 7 R5 & 13 X4

  • Prototypical sequences from geno2pheno-C[NGS-Sanger]

(Pfeifer et al., Bioinformatics 2012): 47 R5 & 49 X4

  • Prototypical sequences from geno2pheno-C[NGS-Sanger]

and geno2pheno[coreceptor]: 31 R5 & 27 X4

  • V3 loop structure from PDB entry 2b4c
  • CXCR4 structure from PDB entry 2oe0
  • CCR5 structure model (33% identity, 55% positives to

CXCR4)

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Sequence comparison does not work

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Pfeifer & Lengauer, Bioinformatics, 2012

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Sequence comparison does not work

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Predicted Experimental R5 X4

Pfeifer & Lengauer, Bioinformatics, 2012

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What else can we measure?

  • Charge (recall 11/25 rule)
  • Statistical preferences in peptide binding (PepSite,

Trabuco et al., Nucl Acids Res 2012)

  • Docking energy of receptor-loop complex

(FlexPepDock, London et al., Nucl Acids Res 2011)

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Charge

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p=0.07 p=0.003 p=7e-5

R5_exp X4_exp R5_pred2 X4_pred2 R5_pred X4_pred

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PepSite: how it works

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PepSite: amino acid preferences

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Proline Positively charged Phe

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PepSite: score for V3 loops

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CCR5_R5 CCR5_X4 CXCR4_R5 CXCR4_X4 195 200 205 210 215 220 CCR5_R5 CCR5_X4 CXCR4_R5 CXCR4_X4 190 195 200 205 210 215

Experimentally tested Predicted Predicted w/2 methods

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FlexPepDock

  • Protein-peptide docking protocol
  • Side chains and backbone of peptide flexible
  • Side chains of protein flexible, backbone fixed

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FlexPepDock: results

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All-complex energy Interface energy Experimentally tested Prediction, 2 methods Prediction, NGS-Sanger

Extremely weak difference

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FlexPepDock: loop split in halves

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Left-hand half Right-hand half

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Back to receptors

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CCR5 CXCR4 side top

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Electrostatic potential

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CCR5 CXCR4 side top

  • 5 kT/e

+5 kT/e

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Endogenous ligands

  • CCR5: CCL5, CCL3, CCL4 (all chemokines)
  • CXCR4: SDF-1 (chemokine), extracellular ubiquitin

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Ligand electrostatic potential

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  • 5 kT/e

+5 kT/e

CCR5 ligands CXCR4 ligands

CCL5 CCL3 CCL4 SDF-1 Ubiquitin

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Ligand electrostatic potential

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  • 5 kT/e

+5 kT/e

CCR5 ligands CXCR4 ligands

CCL5 CCL3 CCL4 SDF-1 Ubiquitin

Glycosylated!

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Interaction model

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CCR5 with its ligands CXCR4 with its ligands

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What does this imply for tropism?

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  • Appears to be defined by charge

What does this imply for tropism?

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  • Appears to be defined by charge
  • Glycans often confer negative charge

What does this imply for tropism?

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  • Appears to be defined by charge
  • Glycans often confer negative charge
  • There is a glycosylation site in pos 301 in 47/47 R5 and 46/49 X4

sequences, but it is not necessarily occupied

What does this imply for tropism?

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  • Removal of a glycosylation site switches tropism from R5 to X4

(Pollakis et al, 2001)

  • Appears to be defined by charge
  • Glycans often confer negative charge
  • There is a glycosylation site in pos 301 in 47/47 R5 and 46/49 X4

sequences, but it is not necessarily occupied

What does this imply for tropism?

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Acknowledgements

  • Nico Pfeifer
  • Thomas Lengauer
  • Department for Applied Algorithmics and Computational

Biology, MPII

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