Personal Headshot

Dennis Brookner


  • About Me
  • Resume

Education

Harvard University | Cambridge, MA
Ph.D. in Biochemistry (in progress) | 2019 - Present

Yale University | New Haven, CT
B.S. in Molecular Biophysics & Biochemistry | 2015-2019


Experience


Publications

Laue-DIALS: open-source software for polychromatic X-ray diffraction data, Structural Dynamics, 2024

MatchMaps: non-isomorphous difference maps for X-ray crystallography, J. Appl. Cryst., 2024

Perturbative diffraction methods resolve a conformational switch that facilitates a two-step enzymatic mechanism, PNAS, 2024

Uncovering the Molecular Interactions in the Catalytic Loop That Modulate the Conformational Dynamics in Protein Tyrosine Phosphatase 1B, JACS, 2019

Targeted protein unfolding uncovers a Golgi-specific transcriptional stress response, MBoC, 2018


Skills

X-Ray Crystallography
  • Protein crystallization and screen design using vapor diffusion, lipidic cubic phase methods
  • DIALS, CCP4, PHENIX, and Coot for data processing and structure determination
  • Modeling of multiple loop states and unknown ligands
  • Customized handling of unusual diffraction data via reciprocalspaceship
  • Phasing via selenomethionine labelling and single-wavelength anomalous dispersion
Biochemistry & Biophysics
  • Protein expression and purification (IMAC, IEX, SEC) using FPLC and manual methods
  • Enzyme kinetics assays in both steady-state and pre-steady-state regimes
  • Immunoprecipitation (pulldown) to determine protein binding partners
  • Protein stability quantification via limited proteolysis, melting-point analysis, colorometric assays
  • Diazarine labelling for analysis of solvent-accessible surface area
  • Two-dimensional 1H 13C HSQC NMR for investigation of enzyme dynamics
  • One-dimensional 31P NMR for study of phosphoenzyme species
Cell & Molecular Biology
  • DNA cloning for creation of novel protein constructs including fusion proteins and point mutants
  • Mammalian tissue culture including transfection of plasmids of interest
  • Western blot analysis of protein levels in cell lysate
  • Confocal microscopy to assess subcellular localization of fluorescent fusion proteins
Programming
  • Python, bash, R, Java

Site by Dennis Brookner | Hosted on GitHub Pages | Templated from Sean Kross

Personal Headshot

Dennis Brookner


  • About Me
  • Resume


Education

Harvard University | Cambridge, MA
Ph.D. in Biochemistry (in progress) | 2019 - Present

Yale University | New Haven, CT
B.S. in Molecular Biophysics & Biochemistry | 2015-2019


Experience


Publications

Laue-DIALS: open-source software for polychromatic X-ray diffraction data, Structural Dynamics, 2024

MatchMaps: non-isomorphous difference maps for X-ray crystallography, J. Appl. Cryst., 2024

Perturbative diffraction methods resolve a conformational switch that facilitates a two-step enzymatic mechanism, PNAS, 2024

Uncovering the Molecular Interactions in the Catalytic Loop That Modulate the Conformational Dynamics in Protein Tyrosine Phosphatase 1B, JACS, 2019

Targeted protein unfolding uncovers a Golgi-specific transcriptional stress response, MBoC, 2018


Skills

X-Ray Crystallography
  • Protein crystallization and screen design using vapor diffusion, lipidic cubic phase methods
  • DIALS, CCP4, PHENIX, and Coot for data processing and structure determination
  • Modeling of multiple loop states and unknown ligands
  • Customized handling of unusual diffraction data via reciprocalspaceship
  • Phasing via selenomethionine labelling and single-wavelength anomalous dispersion
Biochemistry & Biophysics
  • Protein expression and purification (IMAC, IEX, SEC) using FPLC and manual methods
  • Enzyme kinetics assays in both steady-state and pre-steady-state regimes
  • Immunoprecipitation (pulldown) to determine protein binding partners
  • Protein stability quantification via limited proteolysis, melting-point analysis, colorometric assays
  • Diazarine labelling for analysis of solvent-accessible surface area
  • Two-dimensional 1H 13C HSQC NMR for investigation of enzyme dynamics
  • One-dimensional 31P NMR for study of phosphoenzyme species
Cell & Molecular Biology
  • DNA cloning for creation of novel protein constructs including fusion proteins and point mutants
  • Mammalian tissue culture including transfection of plasmids of interest
  • Western blot analysis of protein levels in cell lysate
  • Confocal microscopy to assess subcellular localization of fluorescent fusion proteins
Programming
  • Python, bash, R, Java

Site by Dennis Brookner
Hosted on GitHub Pages
Templated from Sean Kross