Research
Currently interested in understanding the dynamics of proteins, nucleic acids and protein-nucleis acid complexes.
NMR of large protein assemblies
A majority of cellular functions are mediated through protein-protein interaction/association. However, large assemblies of megadalton size pose a great challenge to structural investigations either by X-ray Crystallography or by NMR. This is due to the fact that the line widths in the NMR spectra of such large assemblies are extremely large and often the signals are buried in the noise. These include efforts to narrow down lines by relaxation optimization, both by appropriate sample preparation and by the design of NMR pulse sequences. We have proposed a “bottom-up strategy”, where the assembly is dissociated into monomers with the help of external agents and then reconstituted in a controlled fashion. It is during reconstitution, we get the signals in NMR and get the information about the assembly.
More details are available at
PROTEIN SCIENCE (Accelerated Communication); 2008, 17(8), 1319-1325.
Specific Labels in HSQC type spectra of uniformly labeled proteins
We have developed a new pulse sequence, termed as (HC)NH, which results in identifying alanines and serines/threonines in two different experiments in 1H-15N HSQC spectrum of uniformly (15N, 13C) labeled proteins. This affords to characterize any local environment around those residues using NMR. This becomes specially useful for biologists/chemists who are not interested in the laborious job of complete backbone assignment.
More details are available at
JOURNAL OF MAGNETIC RESONANCE; 2008, 194(2), 289-294.
The pulse sequence and a sample data set can be downloaded here.
Tuning the HNN experiment for Rapid Backbone Resonance Assignment of (un)folded Proteins
We have demonstrated the unrecognized versatility and potential of the previously described HNN and HN(C)N experiments to obtain residue specific peak patterns in the spectra of the (15N, 13C) labeled proteins during backbone resonance assignment. This modification leads to the rapid resonance assignment of backbone amide protons and nitrogens. HNN-ST along with HNN and HNN-A [and similarly HN(C)N-ST along with HN(C)N and HN(C)N-A] provides a substantial boost to the assignment process by scanning the scattered glycines, alanines, serines, and threonines in the protein sequence under study. The peak patterns obtained in the neighborhood of these four amino acids in the protein chain would be very helpful for assignment of large proteins because of increased number of anchor points along the sequence. Moreover, in the light of more and more unfolded/denatured proteins being getting attention worldwide because of several important reports of intrinsically unfolded proteins, in vivo, the main strength of HNN suite of experiments, as against the standard triple resonance experiments, is to deal with these unfolded proteins.
More details are available at
JOURNAL OF BIOMOLECULAR NMR; 2008, 40(2), 145-52
Pulse Sequence can be downloaded here: HNN-ST pulse sequence