Donnie Berkholz

Current

• Guest author at LWN.net
• Graduate research assistant at P. Andrew Karplus lab, Oregon State University
• Council member at Gentoo Linux

see less...

Past

• Undergraduate researcher at Ellis Bell lab, University of Richmond
• Undergraduate researcher at Brian O'Brien lab, Gustavus Adolphus College
• Undergraduate researcher at Jonathan Smith lab, Gustavus Adolphus College

• Undergraduate researcher at Len Banaszak lab, University of Minnesota

see less...

1 more...

Education

• Oregon State University
• University of Richmond
• Gustavus Adolphus College

see less...

Connections

187 connections

Industry

Biotechnology

Donnie Berkholz’s Summary

My Ph.D. thesis work focuses on understanding and leveraging protein structure at atomic resolution. I've used a combination of crystallography and computation to pursue this goal.

In one project, analysis of a vast database of nearly 20,000 residues uncovered significant conformation-dependent trends in the backbone's covalent geometry for all bond angles and lengths. Conformation-dependent averages for the N-Ca-C angle, which varied most dramatically, range from 107°–114° in well-populated regions. Tests suggest that accounting for these systematic variations will improve the accuracy of protein modeling and crystallographic refinement.

In another project, a series of catalytically relevant, atomic-resolution "snapshots" of the flavoenzyme glutathione reductase enabled us to reach numerous insights into how radiation can affect active sites and how exquisitely detailed structural changes can drive catalytic power.

I expect to finish my Ph.D. this summer, so I'm looking for a postdoctoral fellowship in structural biology that will challenge & teach me, where I can do great science with great people.

Donnie Berkholz’s Specialties:

* Biotech: Crystallography, molecular biology, computational techniques
* Linux/Open source: Gentoo Linux, shell scripting, Python
* Journalism: Copy editing and page design

Donnie Berkholz’s Experience

• Guest author

  LWN.net

  (Newspapers industry)

  December 2006 — Present (2 years 8 months)

  Wrote numerous articles about Gentoo Linux, other Linux distributions, and occasional conference coverage.
  
  * Earned 3 pay increases for the quality of my work. I now receive double my initial pay.
  * LWN.net is one of the top Linux and open-source news sites, best known for its high-quality developer community.

• Graduate research assistant

  P. Andrew Karplus lab, Oregon State University

  (Educational Institution; Higher Education industry)

  April 2005 — Present (4 years 4 months)

  Protein crystallography and computational modeling.
  
  * Analyzed the reaction pathway of the enzyme glutathione reductase using "snapshots" at 1.0 Å resolution.
  * Characterizing the distributions of bond lengths and angles as a function of the peptide backbone torsion angles. Leveraging these distributions in X-ray refinement and homology modeling programs.
  * 4 papers published or in-press; 4 more in preparation, expected to be submitted by summer 2009.

• Council member

  Gentoo Linux

  (Non-Profit; Computer Software industry)

  June 2003 — Present (6 years 2 months)

  Leading Gentoo to greatness.
  
  * Decide on global issues and policies as council member
  * Public relations: Revive Gentoo's PR with better communication as public relations team lead
  * Management: Deal with bureaucracy as desktop project lead so other developers can focus on their work. Manage 5-10 people who provide and maintain "ebuild" build scripts as X subproject lead
  * Project management: Led the graphical installer from its founding until it was near the 1.0 release.
  * Founded effort to provide clustering support, documentation and package maintenance
  * Maintain packages: Lead maintainer of the core X11 implementation, xorg-x11 (~320 packages). Maintain scientific packages.
  * Designed and implemented a reproduceable, consistent funding request process as a trustee of the charitable foundation that holds Gentoo's intellectual property and finances
  * Developer relations: Resolved interdeveloper disputes. Worked to determine consequences for violating Gentoo's rules. Recruited new developers
  * Mentoring: 4 new volunteer developers. Also mentored 1 full-time summer masters student through the Google Summer of Code.
  * Administer involvement in the Google Summer of Code program, which encourages college students to become involved in open-source development

• Undergraduate researcher

  Ellis Bell lab, University of Richmond

  (Biotechnology industry)

  September 2000 — May 2004 (3 years 9 months)

  Probing the active site of D-3-phosphoglycerate dehydrogenase: The role of acid-base catalysis and the local charge environment of the transition state in V-type regulation by serine.
  
  * Characterized native and four active-site mutants using UV/Vis spectroscopy, size-exclusion chromatography, and fluorescence.
  * Techniques: Protein growth & purification, enzyme kinetics, fluorescence resonance energy transfer (FRET).
  * Presented work at multiple conferences and won prizes.
  * 3 papers are expected from this work; 1 is actively in preparation.

• Undergraduate researcher

  Brian O'Brien lab, Gustavus Adolphus College

  (Chemicals industry)

  February 2001 — December 2002 (1 year 11 months)

  Synthesis of organometallic compounds. As a structural biologist, this gives me insight into the synthetic work that future collaborators may perform.
  
  * Presented my work at the Sigma Xi conference at Gustavus

• Undergraduate researcher

  Jonathan Smith lab, Gustavus Adolphus College

  (Chemicals industry)

  September 2001 — August 2002 (1 year)

  Studied conformations of serotonin in physiological conditions using quantum-mechanical calculations, molecular dynamics, and resonance Raman spectroscopy. Architected Linux cluster. As a structural biologist, this gives me experience with high-level quantum-mechanical simulations and advanced computing techniques, both of which are becoming increasingly common for macromolecular systems.
  
  * Created a prototype Linux cluster as proof-of-concept for a Smith group joint NSF grant for $380,000 in July 2005.
  * Awarded a Presidential Student-Faculty Collaboration Grant for research in summer 2002.
  * Presented my work at the MERCURY Conference in Computational Chemistry (Hamilton College, NY).

• Undergraduate researcher

  Len Banaszak lab, University of Minnesota

  (Educational Institution; Higher Education industry)

  June 2001 — August 2001 (3 months)

  Visualizing mitochondrial surfaces and characterizing D-3-phosphoglycerate dehydrogenase (PGDH) mutants. This was my first experience doing research full-time and convinced me that I truly enjoyed research, not just one mentor. It was also my first experience in a graduate-level lab, which encouraged me to continue on for my Ph.D.
  
  * Accepted into prestigious NSF-REU program
  * Created a PGDH mutant using site-directed mutagenesis and characterized it.
  * Developed and refined an improved mitochondrial isolation procedure, for use in visualizing mitochondrial proteins via AFM.

Donnie Berkholz’s Education

• Oregon State University

  Ph.D. , Biochemistry and Biophysics , 2004 — 2009

  Thesis work in protein X-ray crystallography and structural modeling.

• University of Richmond

  B.S., B.A. , Biochemistry and Molecular Biology, Chemistry , 2002 — 2004

  * Journalism minor
  * GPA: 3.32
  * National Merit Scholar
  * Extensive undergraduate research

  Activities and Societies:

  Student newspaper

• Gustavus Adolphus College

  Biochemistry, Chemistry, Biology 2000 — 2004

  * GPA: 3.55
  * National Merit Scholar
  * Recipient, Partners in Scholarship ($12,500/year)
  * Recipient, Presidential Scholarship $(10,000/year)
  * Extensive undergraduate research
  * Worked 20 hours/week while in school

  Activities and Societies:

  Student newspaper, Writing Center tutor (science-writing specialist), chemistry tutor

Additional Information

Donnie Berkholz’s Groups:

•    The Personal MBA Community
•    Gentoo
•    Lifesciences Opportunities in US
•    Open Source Developers
•    Krav Maga on LI (MMA, Kapap, Lotar...)
•    Linux Expert
•    Eagle Scouts, Boy Scouts of America
•    Biotech & Pharma Professionals Network
•    National Merit Scholars
•    Tweeters
•    Life Science Professionals
•    Open Source Bridge

Donnie Berkholz’s Honors:

* Best Student Talk award, West Coast Protein Crystallography Workshop, 2009
* Finn Wold award, Protein Society, 2008
* Presidential Student/Faculty Collaboration Grant, Gustavus, summer 2002
* 1st place undergraduate poster, ASBMB national meeting, 2002
* John C. Johnson award (poster), Tri-Beta (biology honor society) national meeting, 2002
* National Merit Scholar
* Eagle Scout

Donnie Berkholz’s Contact Settings

Interested In:

• career opportunities
• consulting offers
• new ventures
• job inquiries
• expertise requests
• business deals
• reference requests
• getting back in touch