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HIV Structure and Function
Background: Basic Virology and Pathogenesis
Structure: Virion structure, genomic structure,
and accessory molecules
Lifecycle: Infection and Expression
Viruses
Microscopic infectious agents that can infect the cells of a
biological organism.
Viruses can only replicate themselves by infecting a host cell
and are incapable to reproduce on their own.
A complete viral particle, known as a virion consists of nucleic
acid surrounded by a protective coat of protein called a capsid.
Types of Viruses
(Baltimore Classification)
I: Double-stranded DNA (Adenoviruses; Herpesviruses; Poxviruses, etc)
Herpesviridae (Herpes, CMV, EBV), Poxviridae (Smallpox, Chickenpox,
Vaccinia), Papilloma virus, Adenovirus
II: Single-stranded (+) sense DNA (Parvoviruses)
Erythema infectiosum, Phages
III: Double-stranded RNA (Reoviruses; Birnaviruses)
Rotavirus, Reovirus
IV: Single-stranded (+) sense RNA (Picornaviruses; Togaviruses, etc)
Polio, SARS, Hep A, Hep C, Rubella, Yellow fever
V: Single-stranded (-) sense RNA (Orthomyxoviruses, Rhabdoviruses, etc)
Rubella, Influenza, Rabies, Measles, Mumps, Ebola
VI: Single-stranded (+) sense RNA with DNA intermediate (Retroviruses)
HTLV, HIV
VII: Double-stranded DNA with RNA intermediate (Hepadnaviruses)
Hep B
HIV Classification
Group:
Group VI (ssRNA-RT)
Family:
Retroviridae
Genus:
Lentivirus (Enveloped)
Species:
Human immunodeficiency virus 1
Species:
Human immunodeficiency virus 2
Species Virulence
Infectivity
Prevalence
Inferred origin
HIV-1
HIV-2
High
Low
Global
West Africa
Chimpanzee
Sooty Mangabey
High
Lower
CRF14_BG
HIV-1 Tropism
www.hivmedicine.com/textbook/pathogen.htm
Human immunodeficiency virus (HIV) is a retrovirus that
causes acquired immunodeficiency syndrome (AIDS).
AIDS has killed nearly 30 million people since it was first
recognized in 1981.
At the end of 2010, an estimated 34 million people were
living with HIV worldwide.
In 2010 alone, AIDS claimed an estimated 1.8 million
lives, of which 250,000 were children.
HIV primarily infects vital cells in the human immune
system such as helper T cells (CD4+ T cells),
macrophages and dendritic cells. HIV infection leads to
low levels of CD4+ T cells.
http://www.unaids.org/en/
Transmission
Sexual route.
Blood or blood product route.
Mother-to-child transmission (MTCT).
Viral RNA
gp120
p24
RT & other
virion
proteins
Fusion & Entry
Binding
Reverse
transcription
CD4
CXCR4
Nuclear
localization
& entry
Integration
Viral RNA
gp120
p24
Cellular Activation
Assembly
RT & other
virion prteins
Post-translational
processing
Budding
Translation
Viral Gene
Transcription
HIV Structure
Virion
Genomic
Proteomic
HIV Structure
SIV
HIV
HIV Structure
Virion
Genomic
Proteomic
Viral RNA
gp120
p24
RT & other
virion
proteins
Fusion & Entry
Binding
Reverse
transcription
CD4
CXCR4
Nuclear
localization
& entry
Integration
HIV-1 RNA
Nature Reviews Microbiology 2, 461-472 (June 2004)
Nature 460, 711-716 (6 August 2009)
HIV-1 Integrated DNA
Source: The AmFAR AIDS Handbook, D Ward, pp. 348
RNA Splicing
Translational
Frameshift
Source: The Molecular Biology of HIV/AIDS, D Ward, pp. 19
Dr. Isabelle BOUALLAGA Institut Pasteur. http://www.123bio.net/
Source: Atlas of Infectious Diseases, Mandell & Mildvan (ed.), pp. 3.13
Source: Atlas of
Infectious Diseases,
Mandell & Mildvan
(ed.), pp. 3.13
HIV Structure
Virion
Genomic
Proteomic
HIV Proteins
Structural Proteins
Gag: Matrix, Capsid, NC, p6
Pol: Protease, Reverse Transcriptase, Integrase
Env: gp120, gp41
Regulatory Proteins
Tat
Rev
Nef
Accessory proteins
Vif
Vpr
Vpu
Source: The Molecular Biology of HIV/AIDS, D Ward, pp. 19
Source: BioAfrica Bioinformatics for HIV Research. http://bioafrica.mrc.ac.za/
Gene/Protein
gag
(Pr) 55gag
Mass, KDa
Function
p55
Gag precursor protein
MA - Matrix
p17
Aids nuclear import and viral assembly
CA - Capsid
p24
HIV central core – contains HIV genome and enzymes
NC - Nucleocapsid
p15 (p6,p9) p6 – Precise location in virion unknown, not generally present in
other retroviruses, may direct proteins to secretory path of cell.
p9 – Assoc. with HIV RNA, involved in packaging of HIV
RNA into virions
myristate
Association with
membrane
Matrix p17
Envelope
Incorporation
Viral Entry
RNA binding
RNA packing
Formation of Gag
multimers
Capsid p24
p2
NC p9
p1
p6
Viral Budding
Source: BioAfrica Bioinformatics for HIV Research. http://bioafrica.mrc.ac.za/
Gene/Protein
Mass, KDa
Function
pol
(Pr) 160gag-pol
p160
Gag-Pol precursor protein
PR - protease
p10
Cleaves Gag and Gag-Pol
IN - integrase
p32
Integrates viral genome into host DNA
RT – reverse
transcriptase
p66/p51
p66 – copies RNA genome. RNAse H
p51 – regulatory?
Gag
p6
PR p10
RT
p51
p66
IN p32
Anti-HIV drugs
Nucleoside/Nucleotide Reverse Transcriptase Inhibitors
lamivudine (3TC), zalcitabine (ddC), zidovudine (AZT), didanosine (ddI), stavudine (d4T)
Non-Nucleoside Reverse Transcriptase Inhibitors
Delavirdine, efavirenz, nevirapine
Protease Inhibitors
Amprenavir , indinavir, saquinavir, saquinavir, lopinavir/ritonavir, ritonavir, nelfinavir
Integrase Inhibitors
Isentress (Raltegravir or MK-0518) , JTK303/GS-9137
Fusion or Entry Inhibitors
Enfurvitide (Fuzeon or T20), Maraviroc (Selzentry -CCR5 antagonist-)
HAART (Highly Active Antiretroviral Therapy): three or more anti-HIV drugs (antiretrovirals)
from different classes in combination allows them to work together to keep HIV levels down
Gene/Protein
env
(Pr) 160 env
Mass, KDa
Function
gp160
Env precursor protein
SU – Envelope
gp120
Surface glycoprotein that binds CD4
TM - Transmembrane
gp41
Transmembrane protein that anchors gp120 to virus,
responsible for fusion between virus and host cell membrane.
Gene/Protein
gag
(Pr) 55gag
Mass, KDa
Function
p55
Gag precursor protein
MA - Matrix
p17
Aids nuclear import and viral assembly
CA - Capsid
p24
HIV central core – contains HIV genome and enzymes
NC - Nucleocapsid
p15 (p6,p9) p6 – Precise location in virion unknown, not generally present in
other retroviruses, may direct proteins to secretory path of cell.
p9 – Assoc. with HIV RNA, involved in packaging of HIV
RNA into virions
pol
(Pr) 160gag-pol
p160
Gag-Pol precursor protein
PR - protease
p10
Cleaves Gag and Gag-Pol precursor proteins
IN - integrase
p31
Integrates viral genome into host DNA
RT – reverse
transcriptase
p66/p51
p66 – copies RNA genome. RNAse H
env
(Pr) 160 env
p51 – regulatory?
gp160
Env precursor protein
SU – Envelope
gp120
Surface glycoprotein that binds CD4
TM - Transmembrane
gp41
Transmembrane protein that anchors gp120 to virus,
responsible for fusion between virus and host cell membrane.
Source: The Molecular Biology of HIV/AIDS, D Ward, pp. 19
Regulatory Proteins:
TAT: Trans-Activator of Transcription
REV: Regulator of Virion protein expression
NEF: Negative Regulatory Factor
Accessory Proteins:
VIF: Virion Infectivity Factor
VPU: Viral Protein U
VPR: Viral Protein R
TAT: Trans-Activator of Transcription
TAR
Recruitment of
CDK9
Poor transcription
Tat
Tat
Tat
Tat
Tat
CDK9
Release to extracellular medium:
Apoptosis bystander T-cells
CXCR4 negative interaction
Enhanced transcription
REV: Regulator of Virion protein expression
RRE = rev-response element
NEF: Negative Regulatory Factor
* Downmodulation the expression of several surface molecules
important in host immune function:
MHC I, MHC II, CD4
* Activation from latency? Extracellular Nef might activate NF kB.
T-cell activation (activates the production of MIP-1alpha and
MIP-1beta in macrophages)
VIF: Virion Infectivity Factor
www.hivmedicine.com/textbook/pathogen.htm
VPU: Viral Protein U
* Involved in viral budding, enhancing virion release from the cell
* Downregulation of CD4
VPR: Viral Protein R
* Regulation of nuclear import of the HIV-1 pre-integration
complex
* Required for virus replication in non-dividing cells such as
macrophages.
* Induces cell cycle arrest and apoptosis in proliferating cells
Gene/Protein
tat
Tat
rev
Rev
Mass, KDa
Function
p14
Transactivates HIV transcription (kinase adaptor to RNAP2).
p19
Nuclear export of unspliced & single-spliced RNA (via RRE).
p27
Internalizes cell-surface CD4 & MHC Class I molecules.
nef
Nef
May enhance cellular activation.
vif
Vif
p23
Overcomes a post-entry block to infection.
May influence virion assembly.
vpu
Vpu
p16
Facilitates virion release via ion channel formation.
Targets CD4 for destruction in ER (freeing bound env).
vpr
Vpr
p15
Targets the HIV pre-integration complex to the nucleus.
Arrests activated cells in G 2 phase of cell cycle.
Take-home points:
• Structure:
–
–
–
–
–
–
–
env is only exposed viral protein (neutralization resistant)
infectivity mediated by gp120 & gp41 (CD4 & CCR5 or CXCR4)
RNA genome -- requires HIV reverse transcription to DNA
integration requires HIV integrase
LTR/promoter requires cellular transcription factors
productive viral gene expression requires HIV protease activity
accessory genes modulate:
1) cellular function (e.g., nef, vpr)
2) viral gene expression (e.g., tat, rev)
– gag (p24) represents the primary structural component of virion
– small molecule inhibitors of these structure’s functional activity
represent the primary current antiviral therapeutic strategy