Research Specialist (Contractor)
National Center for Biotechnology Information (NCBI)
National Library of Medicine (NLM)
National Institutes of Health (NIH)
Bldg. 38A, Room 6N611A
9000 Rockville Pike, MSC 3829
Bethesda, MD 20894, USA
Tel: (301) 402-3010
Fax: (301) 480-2288
e-mail: obolensk <at> ncbi.nlm.nih.gov
Current Research Projects
Mass Spectrometry (MS):
Fundamental physics for protein identification in biomedical research
In biomedical research it is often necessary to identify proteins present in a sample.
Tandem mass spectrometry (MS/MS) techniques are routinely used for this purpose.
The protein in question is digested into smaller pieces (peptides) and then these pieces
are further fragmented in mass spectrometers. Finally, thus obtained experimental mass
spectra are scored for similarity with theoretical mass spectra of candidate peptides.
Currently, in most of the peptide identification tools, all theoretically possible b-
and y-peaks of a candidate peptide are scored. The similarity scores can be made more
accurate if the scoring function does not take into account theoretical peaks which
cannot be observed in real-life product ion spectra due to various physical, chemical,
or thermodynamic reasons. We have suggested and demonstrated that the role of this
observability predictor can be played by dissociation energy.
Energy minimization formulation of electrostatics suitable to biomolecular systems
The cell is a crowded environment in which proteins and other large molecules constantly collide,
interact and drift away unless they meet a very specific, complementary partner.
In order to understand, describe and eventually predict the dynamics and kinetics of the
formation of molecular complexes, one needs to be able to calculate the forces between
large biomolecules in a fast but accurate way.
We have developed a novel formulation of electrostatics specifically suited for applications
to biomolecular systems.
The formulation allows one to correctly account for the effects arising due to the presence of water,
while remaining computationally efficient.
1. Obolensky OI, Wu WW, Shen RF, Yu YK (2013) Using dissociation energies to predict observability of b- and y-peaks in mass spectra of short peptides. II. Results for hexapeptides with non-polar side chains. Rapid Commun Mass Spectrom
2. Obolensky OI, Wu WW, Shen RF, Yu YK (2012) Using dissociation energies to predict observability of b- and y-peaks in mass spectra of short peptides. Rapid Commun Mass Spectrom
3. Obolensky OI, Doerr TP, Ray R, Yu YK (2009) Rigorous treatment of electrostatics for spatially varying dielectrics based on energy minimization. Phys Rev E Stat Nonlin Soft Matter Phys