Research

Main interests:

(1) To study the basic molecular and mechanistic underpinnings of cellular metabolism using large-scale systems and computational biology.

(2) To understand cellular processes that span across different time and length scales, by leveraging structure-based methods with systems biology approaches.

(3) To gain insight into enzyme catalysis and reaction mechanisms using atomistic simulations.


Current Projects


Characterizing strain / population variation                               Link to research

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  • phenotype differences in E. coli biofuel strains
  • SNPs and dysfunction in metabolic diseases
  • apply novel statistical, bioinformatics, and data mining algorithms to identify biological patterns
  • analysis of genomic, metabolomic, proteomic and phenotypic information

Integration of systems and structural biology                                 Link to research

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  • Bridging systems and biomolecular sciences
  • Expand genome-scale models of metabolism to include protein structure and other data
  • comparative systems biology of the structural proteome

Projects during graduate studies


Synthetic pathway design/ Metabolic Engineering                   Link to research

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  • Retrofitting re-engineered proteins to synthetic pathways
  • Biosynthesis of desired chemicals and products
  • Engineering routes using pathway design algorithms
  • Coupling the design of biocatalysts with atomistic simulations
  • In collaboration with Prof. Vassily Hatzimanikatis and the LCSB (EPFL)

Protein Engineering/ Biomimetics                                                   Link to researchGA_alg

  • Coiled-coil peptidic scaffolds as designed biomimetics
    • genetic algorithm to guide site-directed mutation
  • Directed evolution of SNAP-tag, a stable protein label
    • In collaboration with Prof. Kai Johnsson and the LIP
    • Molecular dynamics simulations coupled to proteolysis

Modeling enzyme catalysis                                                                   Link to researchhomolysis

  • Modeling radical species with all-atom simulations
  • B12-dependent reaction mechanisms
  • hybrid QM/MM MD simulations to follow the full catalytic cycle enzymatic reactions
  • Mutation of nearby glutamate residue prevents/inhibits homolysis & abstraction

Modeling Protein-DNA interactions/ DNA Repair                   Link to research

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  • Hydrolysis and excising of mispaired bases – MutY
  • O6-alkylguanine-DNA alkyltransferase – DNA repair
  • Atomistic simulations show specific organization pattern of water molecules in active site
  • Mechanisms initiate degradation post-repair

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