Membrane-bound pyrophosphatases couple the hydrolysis of inorganic pyrophosphate to the pumping of ions (sodium or protons) across a membrane in order to generate an electrochemical gradient. This class of membrane protein is widely conserved across plants, fungi, archaea, and bacteria, but absent in multicellular animals, making them a viable target for drug design against protozoan parasites such as Plasmodium falciparum. An excellent understanding of many of the catalytic states throughout the enzymatic cycle has already been afforded by crystallography. However, the dynamics and kinetics of the catalytic cycle between these static snapshots remain to be elucidated. Here, we employ single-molecule Förster resonance energy transfer (FRET) measurements to determine the dynamic range and frequency of conformations available to the enzyme in a lipid bilayer during the catalytic cycle. First, we explore issues related to the introduction of fluorescent dyes by cysteine mutagenesis; we discuss the importance of residue selection for dye attachment, and the balance between mutating areas of the protein that will provide useful dynamics while not altering highly conserved residues that could disrupt protein function. To complement and guide the experiments, we used all-atom molecular dynamics simulations and computational methods to estimate FRET efficiency distributions for dye pairs at different sites in different protein conformational states. We present preliminary single-molecule FRET data that points to insights about the binding modes of different membrane-bound pyrophosphatase substrates and inhibitors.
- MeSH
- bakteriální proteiny chemie genetika izolace a purifikace metabolismus MeSH
- buněčná membrána metabolismus MeSH
- enzymatické testy přístrojové vybavení metody MeSH
- fluorescenční barviva chemie MeSH
- fluorescenční mikroskopie přístrojové vybavení metody MeSH
- mutageneze MeSH
- protozoální proteiny chemie genetika izolace a purifikace metabolismus MeSH
- pyrofosfatasy chemie genetika izolace a purifikace metabolismus MeSH
- racionální návrh léčiv MeSH
- rekombinantní proteiny chemie genetika izolace a purifikace metabolismus MeSH
- rezonanční přenos fluorescenční energie přístrojové vybavení metody MeSH
- Saccharomyces cerevisiae MeSH
- sekvenční seřazení MeSH
- simulace molekulární dynamiky * MeSH
- software MeSH
- zobrazení jednotlivé molekuly přístrojové vybavení metody MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
We combined atomistic molecular-dynamics simulations with quantum-mechanical calculations to investigate the sequence dependence of the stretching behavior of duplex DNA. Our combined quantum-mechanical/molecular-mechanical approach demonstrates that molecular-mechanical force fields are able to describe both the backbone and base-base interactions within the highly distorted nucleic acid structures produced by stretching the DNA from the 5' ends, which include conformations containing disassociated basepairs, just as well as these force fields describe relaxed DNA conformations. The molecular-dynamics simulations indicate that the force-induced melting pathway is sequence-dependent and is influenced by the availability of noncanonical hydrogen-bond interactions that can assist the disassociation of the DNA basepairs. The biological implications of these results are discussed. Copyright 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.
