Structure and function of biomolecules are closely linked. Knowledge of structure can help predict and understand function, and information on function can be tremendously useful to repair or modulate the system for a desired output.
One approach to understand structure-function relationship is to build from basics—study molecules in isolation and when in midst of a defined biological environment. Gas phase spectroscopic techniques are ideal in achieving this task, and together with theoretical calculations, can reveal structure and possible interactions at the molecular level.
Hydrogen bonding and dispersion forces are important stabilizing elements in the structure of biomolecules. For instance, DNA structure is stabilized by a combination of base pairing (involving hydrogen bonding) and base stacking (involving dispersive forces). Recent work from Aloke Das’s group at IISER-Pune provides insights into the nature of such forces using gas phase spectroscopy.
“It is technically challenging to study both these forces simultaneously in the same system. We have been able to achieve this using gas phase methods on complexes of indole and pyridine, which are typical chemical moieties found in proteins,” says Das.
Indole and pyridine complexes were studied in a home-built REMPI-TOF (Resonance Enhanced Multiphoton Ionization–Time of Flight) mass spectrometer. An initial time-of-flight (TOF) mass spectrum suggested the presence of indole-pyridine dimers and trimers. The structure of these dimers and trimers was then investigated using resonant two-photon ionization (R2PI) and IR-UV double resonance spectroscopic techniques combined with theoretical quantum chemical calculations aimed at identifying lowest energy conformations.
Unique signatures suggesting a V-shape geometry in the case of dimer and a cyclic geometry in the case of trimer were identified in this study.
“Such geometry provides them maximum stability and allows effective use of both hydrogen bond and dispersion force interactions,” points Das. He adds, “Suspending molecules in a bulk solvent can obscure information and so we prefer to study isolated molecules. Water molecules, however, have a key role to play in the structure and function of biomolecules and we would like to add measured number of water molecules in the system and test how that changes molecular interactions.”
The study “Competition between hydrogen bonding and dispersion interactions in indole…pyridine dimer and (indole)2…pyridine trimer studied in a supersonic jet” is co-authored by Sumit Kumar, Partha Biswas, and Indu Kaul and has appeared online ahead of print as an ASAP article in the Journal of Physical Chemistry A.
The article is available online here
Research work in Aloke Das’s laboratory is supported by funds from IISER-Pune, the DST nanoscience unit of IISER and research fellowships from CSIR and IISER-Pune.
-Reported by Shanti Kalipatnapu