Kevin E. Hauser

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100 Laufer Center for Physical & Quantitative Biology

Stony Brook University

Stony Brook, NY 11794-5252

+1 (561) 635-1848

This email address is being protected from spambots. You need JavaScript enabled to view it.

hauserresearch.org

 


 

Education

 

PhD, Chemical Biology, expected August 2016

Stony Brook University, Department of Chemistry, Stony Brook, NY

Dissertation: A protein-DNA binding & recognition mechanism

Committee: Orlando Schärer (chair), Carlos Simmerling, Miguel Garcia-Diaz, Robert Rizzo

 

BSc, Chemistry, 2008

University of Florida, Department of Chemistry, Gainesville, FL

Research advisor: Adrian Roitberg

 


 

Research Experience

 

PhD student with Dr. Carlos L. Simmerling & Dr. Miguel Garcia-Diaz, 2009-present

Stony Brook University, Department of Chemistry, Stony Brook, NY

  • Discovered helical motions of a human transcription factor (MTERF1) underlie its interactions with DNA, its sliding along the DNA helical groove in search of the target sequence and its unwinding of the target DNA.
  • Designed an approach to estimate energy landscapes.
  • Developed high-temperature torsion grid search method for force field training.
  • Simplified a theory of helical geometry and implemented it in a program that evaluates helical parameters of irregular helices (e.g. protein, DNA, protein tertiary structure).

PhD rotation student with Dr. Daniel P. Raleigh, Fall 2010

Stony Brook University, Department of Chemistry, Stony Brook, NY

  • Designed, synthesized, purified, verified, characterized 10-residue chignolin-like polyamide (β-hairpin) with a p-cyanophenylalanine (21st pair methodology) fluorescent probe.

Post-Baccalaureate Researcher with Dr. Rodney J. Bartlett, Summer 2009

Quantum Theory Project, Gainesville, FL

  • Derived infinite basis set extrapolation functions for ab initio Coupled Cluster theory.
  • Investigated basis set extrapolation for vibrational and geometric atomic properties.

Undergraduate Researcher with Dr. Adrian E. Roitberg, 2007-2008

Quantum Theory Project, Gainesville, FL

  • Examined mixing efficiency of temperature-replica exchange molecular dynamics (REMD) simulations.

 


 

Publications

 

A method to calculate helical properties of biomolecules, Hauser, K., Simmerling, C., Coutsias, E., in preparation 

 

The two codes of DNA (review), Hauser, K., Perez, A., Garcia-Diaz, M., Simmerling, C., in preparation

 

A mechanism of protein diffusion along DNA, Hauser, K., Migues, A. N., Schiffer, B., Coutsias, E.,Garcia-Diaz, M., Simmerling, C., in preparation

 

A human transcription factor in search mode, Hauser, K., Essuman, B., Coutsias, E., Garcia-Diaz, M., Simmerling, C., Nucleic Acids Research, Vol. 44, No. 1, Pages 63-74, 2016, DOI:10.1093/nar/gkv1091 

 

Base flipping by MTERF1 can accommodate multiple conformations and occurs in a stepwise fashion, Byrnes, J.L.*, Hauser, K.*, Mejia, E., Norona, L., Simmerling, C., Garcia-Diaz, M., Journal of Molecular Biology, In Press, (*co-first authors) DOI:10.1016/j.jmb.2015.10.021

 

ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB, Maier, J.A., Martinez, C., Kasavajala, K., Wickstrom, L., Hauser, K.E., Simmerling, C., Journal of Chemical Theory and Computation, Vol. 11, Issue 8, Pages 3696-3713, 2015, DOI:10.1021/acs.jctc.5b00255

 


 

Professional Presentations

 

A Human Transcription Factor in Search Mode, Hauser, K., Essuman, B., He, Y., Coutsias, E., Garcia-Diaz, M., Simmerling, C., American Chemical Society National Meeting, San Diego, CA, 2016, oral presentation

A Human Transcription Factor in Search Mode, Hauser, K., Essuman, B., Coutsias, E., Garcia-Diaz, M., Simmerling, C., The New York Structural Biology Discussion Group 10th Winter Meeting, New York, NY, 2015, poster

A Human Transcription Factor in Search Mode, Hauser, K., Essuman, B., Coutsias, E., Garcia-Diaz, M., Simmerling, C., Biophysical Society Annual Meeting, Baltimore, MD, 2015, poster

A Human Transcription Factor in Search Mode, Hauser, K., Essuman, B., Coutsias, E., Garcia-Diaz, M., Simmerling, C., Biophysical Society Annual Meeting, Baltimore, MD, 2015, oral presentation

A Human Transcription Factor in Search Mode, Hauser, K., Essuman, B., Coutsias, E., Garcia-Diaz, M., Simmerling, C., Institute of Chemical Biology and Drug Discovery Annual Symposium, Stony Brook, NY, 2014, poster

Modeling the MTERF1-DNA Binding and Recognition Mechanism, Hauser, K., Essuman, B., Coutsias, E., Garcia-Diaz, M., Simmerling, C., Biophysical Society Annual Meeting, San Francisco, CA, 2014, poster

Modeling the MTERF1-DNA Binding and Recognition Mechanism, Hauser, K., Garcia-Diaz, M., Simmerling, C., American Chemical Society National Meeting, Dallas, TX, 2014, poster

How proteins control our DNA: Computer Models Predict It's All About Being Flexible, Hauser, K., Simmerling, C., Boosting The Power Of SUNY, State Legislature, Albany, NY, 2013, poster

How Do Proteins Find The Right Sequence?, Hauser, K., Garcia-Diaz, M., Simmerling, C., Chemistry Research Day, Stony Brook, NY, 2013, poster

How Do Proteins Find The Right Sequence?, Hauser, K., Garcia-Diaz, M., Simmerling, C., Institute of Chemical Biology & Drug Discovery, Stony Brook, NY, 2013, poster

Modeling the Mechanism of MTERF1-DNA Binding & Recognition, Hauser, K., Garcia-Diaz, M., Simmerling, C., Institute of Chemical Biology & Drug Discovery, Stony Brook, NY, 2012, poster

Modeling the Mechanism of MTERF1-DNA Binding & Recognition, Hauser, K., Garcia-Diaz, M., Simmerling, C., Chemistry Research Day, Stony Brook, NY, 2012, poster

Studying How a DNA-Binding Protein Uses a Clamping Motion to Recognize DNA, Hauser, K., Simmerling, C., Celebrating Diversity & Academic Excellence, Stony Brook, NY, 2011, poster

Modeling the Mechanism of MTERF1-DNA Binding & Recognition, Hauser, K., Garcia-Diaz, M., Simmerling, C., Institute of Chemical Biology & Drug Discovery, Stony Brook, NY, 2011, poster

Modeling the Mechanism of MTERF1-DNA Binding & Recognition, Hauser, K., Garcia-Diaz, M., Simmerling, C., Chemistry Research Day, Stony Brook, NY, 2011, poster

Atomic Scale Mechanics of a Human DNA-Binding Protein: MTERF1, Hauser, K., Simmerling, C., Preparing for the Professoriate, SUNY Albany, NY, 2011, poster

Modeling a Molecular Mechanism of Mitochondrial DNA Targeting by a Human Mitochondrial Transcription Factor, Hauser, K., Byrnes, J., Garcia-Diaz, M., Simmerling, C., New York Theoretical and Computational Chemistry Conference, New York, NY, 2011, poster

 


 

Computational Skills 

 

Coding

  • Fortran
  • Bash
  • C/C++
  • CUDA/C
  • Python

Molecular Modeling

  • Partial Nudged Elastic Band

  • Targeted MD

  • Hamiltonian REMD

  • Umbrella Sampling

  • MMPBSA/GBSA

  • Jarzynski sampling (steered MD)

  • Loop modeling

  • Elastic Network Models & Anisotropic Network Models

 


 

Honors & Awards

 

Fellowship, NIH NRSA 2012-present

Fellowship, NSF AGEP-T 2014-present

Research Grant, NSF AGEP-T 2015

Travel Award, Biophysical Society 2015

Travel Award, NSF AGEP-T 2014

Poster Award Top-5, NVIDIA, ACS 2014

Researcher of Distinction Award, CIE 2014

The Lindau Meeting of Nobel Laureates 2013

Fellowship, NIH Chemical Biology Training Program 2011-2012

Fellowship Honoree, NSF GRFP 2011

Fellowship, NSF LSAMP-BD 2009-2011

 


 

Professional Development

 

Scientists Teaching Science  2015

The Compact for Faculty Diversity 2011, 2012, 2013, 2014

Improvisation for Scientists 2014

Alan Alda Center for Communicating Science, Distilling Your Message 2011

 


 

References

 

Carlos Simmerling, Ph.D.
Professor of Chemistry
Stony Brook University
This email address is being protected from spambots. You need JavaScript enabled to view it.
+1 (631) 632-5424

Miguel Garcia-Diaz, Ph.D.
Associate Professor of Pharmacological Sciences
Stony Brook University
This email address is being protected from spambots. You need JavaScript enabled to view it.
+1 (631) 444-3054

Evangelos Coutsias, Ph.D.
Professor of Applied Math & Statistics
Stony Brook University
This email address is being protected from spambots. You need JavaScript enabled to view it.
+1 (631) 632-1822

Orlando Schärer, Ph.D.
Professor of Chemistry
Stony Brook University
This email address is being protected from spambots. You need JavaScript enabled to view it.
+1 (631) 632-7545