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Ognjen Perišić      
Contact      
  Email op18 {at} nyu.edu
  Phone ----- ---------------
  Address

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Education


University of Illinois at Chicago, Department of Bioengineering
Ph.D. in Bioinformatics
Thesis: "The improvement of nonequilibrium free energy reconstruction using stochastic pulling protocol"

Belgrade University, School of Electrical Engineering, Department of Microelectronics and engineering physics
B.Sc. in Electrical Engineering (Dipl. Ing)
Thesis: "DC/DC converters controlled by fuzzy logic"

       
       
Research
I
Potential of Mean Force and free energy reconstruction
  
PMF reconstruction is one of the most expensive tasks in computational chemistry and molecular biology. The problem stems from the dissipation generated during the perturbation. In 1997 Chris Jarzynski presented a new theoretical framework able to directly connect free energy difference and external work, even when perturbation is far from equilibrium. The drawback of his relation is in the number of work samples (perturbation trajectories) required to generate a satisfying PMF (free energy) estimate. I focused my research toward new perturbation schemes which should be able to decrease the number of work trajectories needed for the accurate PMF reconstruction. Besides the exact nonequilibrium work relation I explore application of its cumulant expansion i.e. fluctuation-dissipation theorem.
     
II
Mechanical properties of proteins
  
I am interested in the behavior of proteins with known mechanical role (spectrin), or proteins with exceptional thermodynamical stability (Top7). That research is fueled by my interest in nanotechnology i.e. the design of nanoscale objects with predetermined mechanical roles.
Distribution of hydrogen bonds belonging to β sheet. Superficially, Top7 is structurally symmetric. Stretching reveals the true resistance mechanism which lies hidden below hydrogen bonds.
     
     
     
  1. Conformation of the protein after it had been pulled for 50 Angstroms.
  2. Force-extension diagram
  3. Number (moving average) of hydrogen bonds belonging to β sheet during pulling. Force peak is connected to the behavior of the second group (green set) of hydrogen bonds.

Distribution of hydrophobic residues corresponds to Top7's unfolding pattern (no matter if it is being stretched from N terminus or from C terminus). Nonbonded interactions guide protein through the unfolding landscape; protein backbone and hydrogen bonds are just a skeleton.

     
     
     
Stretching of the erythroid spectrin interface(s) using constant pulling velocity. Interfaces were modeled following the assumption that they resemble regular spectrin triple-helical repeats. Monomers first unfold and then start to unbind. Some of the mutants exhibit higher unfolding forces which may imply that they possess higher binding energy barriers than wild type interface(s). Unpublished results.
     
III
Analytical approach to drug design
  
With the guidance of Dr. Celerino Abad-Zapatero I analyzed large protein-ligand data sets in attempt to connect binding affinity of ligands to their polar surface area (number of polar atoms) and atomic mass. That approach, originaly proposed by Dr. Abad-Zapatero, should introduce new paradigm into the drug-design process.
     
IV
Protein-protein interactions
  
Prediction of the interfacial residues is a difficult task due the uniformity of the physical and chemical properties of protein surfaces. While protein-lipid and protein-DNA interactions are lead by the different charge of entites which interact, proteins which form complexes behave similarly and thus do not offer inital clues on the interfacial residues. The research is not yet completed, but I have some initial conclusions.
Schematic representation of the motor protein Kinesin (chain A) and its Kirchhoff (connectivity) map.
     
     
   
Publications
2008
    
1) On the improvement of free energy calculation from molecular dynamics experiments using adaptive stochastic perturbation protocols
  Ognjen Perišić and Hui Lu
  to be submitted
     
2) Ligand Efficiency Indices as Numerical Guides in Drug discovery. Applications to Database Analysis and the Characterization of Ligand:Inhibitor complexes
  Ognjen Perišić, Hui Lu, John Waas, John Overrington, Bissan Al-Lazikani, Michael Johnson and Cele Abad-Zapatero
  to be submitted
     
 
2007
    
3) Efficient free energy profile reconstruction using adaptive stochastic perturbation protocols
  Ognjen Perišić and Hui Lu
  submitted - (arXiv:0801.0178)
     
4) Single Molecule Force Spectroscopy Reveals a Novel Mechanically Stable Protein Fold and the Rational Tuning of its Mechanical Stability
  Deepak Sharma, Ognjen Perisic, Canaan Lam, Hui Lu and Hongbin Li
  Proceedings of the National Academy of Sciences (2007), v104, no.22, p9278-9283
  highlighted in SCIENCE VOL 316, (1395), 8 JUNE 2007.
     
2005
    
5) Improved protein fold assignment using support vector machines
  Robert E. Langlois, Alice Diec, Ognjen Perisic, Yang Dai, Hui Lu
  International Journal of Bioinformatics Research and Applications, 1(3):319, 2005
     
 
Book chapters
    
1) Physical and Chemical Basis for Structural Bioinformatics
  Hui Lu, Ognjen Perišić and Dong Xu
  Book: Computational Methods for Protein Structure Prediction and Modeling
  edited by Ying Xu, Dong Xu, and Jie Liang. Springer-Verlag. Vol. 2. Pages 267-297, 2007
  ISBN-10: 0387333215, ISBN-13: 978-0387333212
     
     
     
Work history
 
Official
  
1) January 1999 - August 2001, programmer, head of the software development team
Institute of Economic Sciences, Belgrade, Serbia.
Developed a software for share trading and stock exchange on the basis of the mathematical model created by Dr. Božo Drašković, then the head of the Institute. The software includes all of the characteristics of East-European economies in transition. Besides algorithm implementation, I developed functions for basic and complex data base management (data base engine), network communication and laser printer control which means that software is independent of the third party components. It was presented on Jisa Info (Yugoslav informatics alliance) congress in 2001, the largest meeting of the Serbian IT community.
Software was sold to companies across Serbia/Montenegro such as:
  • The Coca Cola Company - AD IBP Beograd, Belgrade, Serbia;
  • Vet pharm, Belgrade, Serbia;
  • Kikinda mill, Kikinda, Serbia;
  • . . . .
4)> 5)> ...........> >
   
2) May - August 2002, engineering internship: Biotechplex Chicago, Il.
Worked on a software for gamma camera control and image acquisition using Microsoft Visual C++ and Matlab.
     
3) Research and teaching assistant at UIC.

Teaching assistant, Bioinformatics Training Certificate Program.
     
Unofficial work history
    
1) Wrote first commerical application in high school.
     
2) In my senior year in high school worked as a data base operator; entered a bunch of data. That job helped me buy scuba equipment and join diving excursion.
     
3) As an undergrad student, with a friend, wrote software for a funeral company.