3-picolyl azide adenine dinucleotide as a probe of femtosecond to picosecond enzyme dynamics

J Phys Chem B. 2012 Jan 12;116(1):542-8. doi: 10.1021/jp208677u. Epub 2011 Dec 15.

Abstract

Functionally relevant femtosecond to picosecond dynamics in enzyme active sites can be difficult to measure because of a lack of spectroscopic probes that can be located in the active site without altering the behavior of the enzyme. We have developed a new NAD(+) analog 3-Picolyl Azide Adenine Dinucleotide (PAAD(+)), which has the potential to be a general spectroscopic probe for NAD-dependent enzymes. This analog is stable and binds in the active site of a typical NAD-dependent enzyme formate dehydrogenase (FDH) with characteristics similar to those of natural NAD(+). It has an isolated infrared transition with high molar absorptivity that makes it suitable for observing enzyme dynamics using 2D IR spectroscopy. 2D IR experiments show that in aqueous solution, the analog undergoes complete spectral diffusion within hundreds of femtoseconds consistent with the water hydrogen bonding dynamics that would be expected. When bound to FDH in a binary complex, it shows picosecond fluctuations and a large static offset, consistent with previous studies of the binary complexes of this enzyme. These results show that PAAD(+) is an excellent probe of local dynamics and that it should be a general tool for probing the dynamics of a wide range of NAD-dependent enzymes.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Formate Dehydrogenases / chemistry*
  • Formate Dehydrogenases / metabolism
  • Hydrogen Bonding
  • NAD / analogs & derivatives*
  • NAD / chemistry*
  • Spectrophotometry, Infrared
  • Time Factors

Substances

  • 3-picolyl azide adenine dinucleotide
  • NAD
  • formate dehydrogenase (NADP+)
  • Formate Dehydrogenases