Enzyme Selectivity of HIV Reverse Transcriptase: Conformations, Ligands, and Free Energy Partition

Serdal Kirmizialtin, Kenneth A. Johnson, Ron Elber

Research output: Contribution to journalArticle

Abstract

Atomically detailed simulations of HIV RT are performed to investigate the contributions of the conformational transition to the overall rate and specificity of enzyme catalysis. A number of different scenarios are considered within Milestoning theory to provide a more complete picture of the process of opening and closing the enzyme. We consider the open to closed transition in the absence of and with the correct and incorrect substrates. We also consider the free energy profile and the kinetics of the conformational change after the chemistry step in which a new base was added to the DNA, but the DNA was not yet displaced. We partition the free energy along the reaction coordinate and analyze the importance of different protein domains. Strikingly, significant influence on the free energy profile is detected for amino acids far from the active site. The overall long-range impact is about 50 percent of the total. We also illustrate that the overall rate is not necessarily determined by the highest free energy barrier along the reaction path (with respect to the free enzyme and substrate) and that the specificity is not necessarily determined by the same reaction step that determines the rate. (Graph Presented).

Original languageEnglish (US)
Pages (from-to)11513-11526
Number of pages14
JournalJournal of Physical Chemistry B
Volume119
Issue number35
DOIs
StatePublished - Sep 3 2015

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HIV Reverse Transcriptase
human immunodeficiency virus
Catalyst selectivity
Free energy
Conformations
enzymes
partitions
Enzymes
selectivity
free energy
Ligands
ligands
DNA
deoxyribonucleic acid
energy
Energy barriers
Substrates
closing
profiles
Catalysis

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Surfaces, Coatings and Films
  • Materials Chemistry

Cite this

Enzyme Selectivity of HIV Reverse Transcriptase : Conformations, Ligands, and Free Energy Partition. / Kirmizialtin, Serdal; Johnson, Kenneth A.; Elber, Ron.

In: Journal of Physical Chemistry B, Vol. 119, No. 35, 03.09.2015, p. 11513-11526.

Research output: Contribution to journalArticle

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