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DNA Distortion and Damage
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Nucleotide substrate binding characterization in human pancreatic-type ribonucleases.

Khushboo Bafna1, Chitra Narayanan2, S Chakra Chennubhotla3

  • 1Genome Science and Technology, University of Tennessee, Knoxville, Tennessee, United States of America.

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|August 9, 2019
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Summary
This summary is machine-generated.

Human pancreatic-type ribonucleases (hRNases) exhibit diverse functions and binding preferences despite sequence similarity. Computer simulations reveal distinct substrate interactions and highlight the impact of temperature on enzyme-dynamics and binding.

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Genomics

Background:

  • The human genome encodes over a dozen homologous genes, producing human pancreatic-type ribonucleases (hRNases).
  • These hRNases share structural folds for binding and cleaving ribonucleic acid (RNA) but exhibit varied biological functions, localization, and catalytic efficiencies.
  • Limited data exists on the structural and dynamic factors driving this diversity.

Purpose of the Study:

  • To investigate the structural and dynamic properties influencing substrate interactions among hRNases.
  • To characterize substrate binding, electrostatics, and dynamics of hRNases 1-7 using computational simulations.
  • To explore the role of temperature variations on enzyme-substrate interactions.

Main Methods:

  • Utilized computer simulations to analyze substrate interactions, electrostatics, and dynamics.
  • Focused on hRNases 1-7 and their binding to two specific nucleotide substrates (ACAC and AUAU).
  • Compared enzyme-substrate interactions at 300 K and 310 K.

Main Results:

  • Significant differences in substrate interactions were observed among hRNases, despite conserved active-site catalytic triads.
  • Both binding site interactions (electrostatic, van der Waals) and dynamics of distal regions contribute to substrate binding.
  • A minor temperature shift from 300 K to 310 K markedly altered enzyme-substrate interactions.

Conclusions:

  • Enzyme-substrate interactions in hRNases are complex, influenced by factors beyond the active site, including remote protein dynamics.
  • Temperature plays a critical role in modulating hRNase activity and substrate binding, with implications for physiological conditions.
  • Computational simulations provide valuable insights into the molecular mechanisms underlying hRNase functional diversity.