Structural biologist at Mayo Clinic, Open-source developer at Gentoo Linux
Rochester, Minnesota Area
- Current
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- Postdoctoral research fellow at Mayo Clinic
- Board of Directors at X.Org Foundation
- Guest author at LWN.net
- Developer at Gentoo Linux
- Past
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- Graduate research assistant at P. Andrew Karplus lab, Oregon State University
- 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
- Education
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- Oregon State University
- University of Richmond
- Gustavus Adolphus College
- Connections
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205
connections
- Industry
- Biotechnology
Donnie Berkholz’s Summary
My broad interest is using protein structure-function relationships to impact scientific research and improve people's lives.
Toward that end, I am now learning structure-based drug design at the Mayo Clinic, improving my skills in crystallography and in better understanding the medical relevance of my research.
My Ph.D. thesis work focused 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.
Donnie Berkholz’s Specialties:
* Biotech: Crystallography, structural enzymology, structural bioinformatics, homology modeling, molecular biology
* Linux/Open source: Gentoo Linux, shell scripting, Python
* Journalism: Copy editing and page design
Donnie Berkholz’s Experience
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Postdoctoral research fellow
Mayo Clinic
(Non-Profit; Hospital & Health Care industry)
September 2009 — Present (3 months)
Focus on solving the structures of mitochondrial proteins involved in fighting oxidative stress to better understand related diseases and to ameliorate them using structure-based drug design.
- Crystallography
- Fragment-based drug design
- Virtual screening -
Board of Directors
X.Org Foundation
(Computer Software industry)
March 2009 — Present (9 months)
Develop and execute strategies to provide worldwide stewardship of the X Window System technology and standards. Directors are elected by foundation members for two-year terms.
The X Window System is the base-level graphics subsystem used by Linux and Unix, and it's also available on Mac and Windows.
* Co-administer involvement in the Google Summer of Code program, which encourages college students to become involved in open-source development
* Maintainer of the Planet Freedesktop blog aggregator
* Maintainer of the x-packagers mailing list, created to improve collaboration among Linux distributions and other X packagers
* Lead of X team for Gentoo Linux
* Patch contributor to X.Org, primarily to packaging scripts -
Guest author
LWN.net
(Newspapers industry)
December 2006 — Present (3 years )
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. -
Developer
Gentoo Linux
(Non-Profit; Computer Software industry)
June 2003 — Present (6 years 6 months)
Leading Gentoo to greatness.
* Decide on global issues and policies as council member. Provide a critical voice on all key issues under discussion as exemplary behavior for the broader development community.
* 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 -
Graduate research assistant
P. Andrew Karplus lab, Oregon State University
(Educational Institution; Higher Education industry)
April 2005 — September 2009 (4 years 6 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; 1 accepted; 1 submitted; 4 more in preparation, expected to be submitted by fall 2009. -
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
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Oregon State University
Ph.D. , Biochemistry and Biophysics , 2004 — 2009
Thesis work in protein X-ray crystallography and structural modeling.
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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
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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:
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The Personal MBA Community -
Gentoo -
Open Source Developers -
Krav Maga on LI (MMA, Kapap, Lotar...) -
Linux Expert -
Eagle Scouts, Boy Scouts of America -
Computational Biology -
Molecular Modeling in Life Sciences -
National Merit Scholars -
Tweeters -
Protein engineering -
Fuel Rochester
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
