2.3 Viral proteins and their functions

Viral proteins are the workhorses of viruses, performing crucial roles in their life cycles. From building the virus structure to hijacking host cells, these proteins come in different types: structural, non-structural, and regulatory. Each type has specific jobs that help viruses survive and spread.

Viral proteins are incredibly diverse and multifunctional. They protect the viral genome, help viruses enter cells, replicate, and even dodge our immune system. Some viral proteins are so sneaky they can take over our cellular machinery, turning our own cells into virus factories.

Viral Protein Types and Roles

Structural, Non-Structural, and Regulatory Proteins

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• Viral proteins categorized into structural, non-structural, and regulatory proteins serve distinct functions in viral life cycle
• Structural proteins form physical structure of virus particle and protect viral genome
  • Include capsid proteins and envelope proteins
• Non-structural proteins involved in viral genome replication, transcription, and protein processing
  • Include viral enzymes and replication proteins
• Regulatory proteins control viral gene expression and modulate host cell processes to favor viral replication
• Accessory proteins enhance viral fitness and contribute to pathogenesis
  • Not essential for viral replication

Multifunctionality and Diversity

• Many viral proteins perform different roles at various stages of viral life cycle
• Composition and functions of viral proteins vary significantly between virus families
  • Reflect diverse replication strategies
• Protein functions can include genome protection, host cell entry, replication, and immune evasion
• Some viral proteins interact with host cellular components to hijack cellular machinery (ribosomes)

Capsid Proteins in Virus Structure

Structural Role and Assembly

• Capsid proteins form primary structural components of viral protein shell (capsid) encasing and protecting viral genome
• Self-assemble into specific geometric structures determined by virus type and size
  • Icosahedral formations (adenoviruses)
  • Helical formations (tobacco mosaic virus)
• Binding sites on capsid proteins facilitate packaging of genetic material during virus assembly
• In enveloped viruses, capsid proteins interact with envelope proteins maintaining structural integrity of virion
• Assembly of capsid proteins highly regulated process
  • Often involves interactions with cellular chaperones and other viral proteins

Functional Aspects of Capsid Proteins

• Some capsid proteins play role in receptor recognition and binding during initial stages of viral entry into host cells
• Undergo conformational changes in response to environmental triggers
  • Facilitate processes such as cell entry or genome release
• Can shield viral genome from host immune responses (nucleocapsid proteins of coronaviruses)
• May contain nuclear localization signals guiding viral genome to host cell nucleus (hepatitis B virus core protein)

Viral Enzymes in Replication

RNA Virus Replication Enzymes

• RNA-dependent RNA polymerases essential for replication of RNA virus genomes
  • Transcribe viral mRNAs in negative-sense RNA viruses (influenza virus)
• Reverse transcriptases in retroviruses convert viral RNA genomes into DNA for integration into host genome (HIV)
• Some RNA viruses encode methyltransferases and other enzymes for capping and modifying viral mRNAs
  • Mimic host cell mRNAs and evade immune detection (flaviviruses)

DNA Virus Replication Enzymes

• DNA-dependent DNA polymerases utilized by some DNA viruses for genome replication
  • Used when host cell polymerases are insufficient (poxviruses)
• Helicases unwind double-stranded DNA during replication (herpes simplex virus)
• Primases synthesize short RNA primers for DNA replication initiation (bacteriophage T7)

Proteases and Integrases

• Proteases cleave viral polyproteins into functional individual proteins
  • Critical step in maturation of many viruses (HIV protease)
• Integrases in retroviruses catalyze integration of viral DNA into host cell genome (HIV integrase)

Attachment and Fusion Proteins in Entry

Attachment Proteins and Viral Tropism

• Attachment proteins on viral surface recognize and bind to specific receptors on host cells
  • Initiate entry process
• Specificity of attachment proteins largely determines viral tropism
  • Influences which cell types and organisms virus can infect
• Examples of attachment proteins include:
  • Hemagglutinin in influenza viruses
  • Spike protein in coronaviruses

Fusion Proteins and Membrane Merging

• Fusion proteins mediate merging of viral and cellular membranes
  • Allow viral genome to enter host cell cytoplasm
• Undergo conformational changes triggered by receptor binding or environmental factors like pH
  • Expose fusion peptides
• Some viruses use single protein for both attachment and fusion
  • Others have separate proteins for these functions
• Examples of fusion proteins:
  • Gp41 in HIV
  • F protein in paramyxoviruses

Impact on Viral Infectivity

• Efficiency of attachment and fusion processes significantly impact viral infectivity
• Affect speed of viral spread within host
• Understanding structure and function of attachment and fusion proteins crucial for:
  • Developing antiviral therapies
  • Creating vaccines targeting viral entry