Ligand binding and protein dynamics in lactate dehydrogenase

J. R Exequiel T Pineda, Robert Callender, Steven D Schwartz

Research output: Contribution to journalArticle

45 Citations (Scopus)

Abstract

Recent experimental studies suggest that lactate dehydrogenase (LDH) binds its substrate via the formation of a LDH/NADH·substrate encounter complex through a select-fit mechanism, whereby only a minority population of LDH/NADH is binding-competent. In this study, we perform molecular dynamics calculations to explore the variations in structure accessible to the binary complex with a focus on identifying structures that seem likely to be binding-competent and which are in accord with the known experimental characterization of forming binding-competent species. We find that LDH/NADH samples quite a range of protein conformations within our 2.148 ns calculations, some of which yield quite facile access of solvent to the active site. The results suggest that the mobile loop of LDH is perhaps just partially open in these conformations and that multiple open conformations, yielding multiple binding pathways, are likely. These open conformations do not require large-scale unfolding/melting of the binary complex. Rather, open versus closed conformations are due to subtle protein and water rearrangements. Nevertheless, the large heat capacity change observed between binding-competent and binding-incompetent can be explained by changes in solvation and an internal rearrangement of hydrogen bonds. We speculate that such a strategy for binding may be necessary to get a ligand efficiently to a binding pocket that is located fairly deep within the protein's interior.

Original languageEnglish (US)
Pages (from-to)1474-1483
Number of pages10
JournalBiophysical Journal
Volume93
Issue number5
DOIs
StatePublished - Sep 2007
Externally publishedYes

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L-Lactate Dehydrogenase
Carrier Proteins
Ligands
NAD
Protein Conformation
Molecular Dynamics Simulation
Freezing
Hydrogen
Catalytic Domain
Proteins
Hot Temperature
Water
Population

ASJC Scopus subject areas

  • Biophysics

Cite this

Ligand binding and protein dynamics in lactate dehydrogenase. / Pineda, J. R Exequiel T; Callender, Robert; Schwartz, Steven D.

In: Biophysical Journal, Vol. 93, No. 5, 09.2007, p. 1474-1483.

Research output: Contribution to journalArticle

Pineda, J. R Exequiel T ; Callender, Robert ; Schwartz, Steven D. / Ligand binding and protein dynamics in lactate dehydrogenase. In: Biophysical Journal. 2007 ; Vol. 93, No. 5. pp. 1474-1483.
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