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Viral Mutations00:36

Viral Mutations

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A mutation is a change in the sequence of bases of DNA or RNA in a genome. Some mutations occur during replication of the genome due to errors made by the polymerase enzymes that replicate DNA or RNA. Unlike DNA polymerase, RNA polymerase is prone to errors because it is not capable of “proofreading” its work. Viruses with RNA-based genomes, like HIV, therefore accrue mutations faster than viruses with DNA-based genomes. Because mutation and recombination provide the raw material...
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Retroviruses have a single-stranded RNA genome that undergoes a special form of replication. Once the retrovirus has entered the host cell, an enzyme called reverse transcriptase synthesizes double-stranded DNA from the retroviral RNA genome. This DNA copy of the genome is then integrated into the host’s genome inside the nucleus via an enzyme called integrase. Consequently, the retroviral genome is transcribed into RNA whenever the host’s genome is transcribed, allowing the...
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The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
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Mutations are heritable changes in an organism’s genome involving alterations in the base sequence of DNA or RNA. These changes can influence cellular processes and phenotypic traits, potentially transforming the unaltered wild type into a mutant form. Such changes, termed forward mutations, are pivotal in shaping the genetic diversity of organisms.RNA viruses exhibit the highest mutation rates due to the absence of robust proofreading mechanisms during genome replication. In contrast,...
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During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA.  Marilyn Kozak discovered that the sequence RCCAUGG (where R...
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Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors
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Small Conformational Changes Underlie Evolution of Resistance to NNRTI in HIV Reverse Transcriptase.

Ashutosh Srivastava1, Varun Birari2, Somdatta Sinha2

  • 1Institute of Transformative Bio-Molecules (WPI), Nagoya University, Nagoya, Aichi, Japan.

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Summary

Understanding HIV drug resistance is key to effective treatment. This study reveals how single mutations in reverse transcriptase (RT) disrupt drug function without major structural changes, offering insights for new antiretroviral therapy (ART) development.

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Drug Discovery

Background:

  • Antiretroviral therapy (ART) for HIV/AIDS faces challenges from drug resistance.
  • Non-nucleoside reverse transcriptase inhibitors (NNRTIs) are crucial ART components, but single resistance mutations can render them ineffective.
  • Resistance mutations in HIV reverse transcriptase (RT) can abolish drug efficacy despite minimal structural changes.

Purpose of the Study:

  • To investigate the structural mechanism by which single resistance mutations in nevirapine-bound RT lead to significant loss of drug function.
  • To analyze how small local conformational variations translate into large functional effects in RT.

Main Methods:

  • Protein contact network analysis of static structures of wild-type and mutant RT.
  • Molecular dynamics simulations of inhibitor-bound RT variants.
  • Analysis of network structure and dynamics using various measures.

Main Results:

  • Single resistance mutations alter the protein contact network and communication pathways within RT.
  • These mutations cause RT to exhibit dynamics similar to unbound states, even with the inhibitor present.
  • The study demonstrates that significant functional changes can occur with negligible overall conformational variations.

Conclusions:

  • Protein contact network analysis combined with molecular dynamics is a powerful approach to study structure-function relationships in proteins.
  • This method can elucidate mechanisms of drug resistance where small structural changes have large functional impacts.
  • Findings provide insights for developing novel antiretroviral drugs that overcome resistance mutations.