Wood Laboratory for Applied Protein Engineering
In Brief:
Since receiving his PhD from Rensselaer Polytechnic Institute (RPI) in 2001, Professor Wood has developed groundbreaking new technologies in downstream bioprocessing, with a focus on self-cleaving affinity tag methods. His work has led to several issued patents in this area, and he is now an active consultant in the area of biosimilars development and intellectual property, as well as a co-founder of Protein Capture Science, a startup company commercializing his self-cleaving affinity tag technology.
Background:
Professor Wood's interest in protein engineering started when he was an undergraduate at Caltech, where he received a dual degree in Chemical Engineering and Molecular Biology in 1990.
During this time, he did undergraduate research in the laboratories of Frances Arnold in Chemical Engineering, and William A. Goddard III, in Chemistry and Applied Physics. Both of these professors are well-known in protein engineering and protein structure prediction.
Wood then worked one year at Kelco in bioprocess development for commodity-scale mucopolysaccharide products, and two years at Amgen Inc. working with the Neupogen® manufacturing process.
After these industrial experiences, he returned to graduate school at RPI in 1993, where he was co-advised by Georges Belfort (at RPI) and Marlene Belfort (at the NY State Dept of Health, Division of Genetic Disorders).
During his graduate work, he combined rational protein engineering with evolutionary approaches to develop a novel self-cleaving intein for applications in protein purification. This intein provides a means to make any protein purification tag self-cleaving and has now been patented (US patent # 6,933,362) and incorporated into several new technologies.
Wood completed his PhD in 2001 and joined the faculty at Princeton University in the Department of Chemical Engineering. At Princeton, he continued working in protein engineering to develop new biotechnologies at the molecular level. This work now continues at The Ohio State University, where an important advance has been the development of several new self-cleaving tag modules that allow proteins and protein complexes to be purified in a variety of formats, and a new effort in split-intein methods.
As of April 2021, Wood's work in engineered proteins for biosensing and bioseparations has led to 60+ peer-reviewed journal papers, 11 book chapters, and one co-edited volume, in addition to over 40 invited conference presentations and seminars at prestigious institutions.
Strains developed in Wood's laboratory have also been requested by over 180 researchers worldwide, primarily for applications in bioseparations.
Self-Cleaving Affinity Tag Technology
Professor Wood's research focuses on biotechnology development through protein engineering. He is known for groundbreaking research in self-cleaving affinity tag technology for the purification of recombinant proteins. Current applications include new ways to purify recombinant proteins, bacterial biosensors that incorporate human drug targets, and new capabilities in drug discovery and drug delivery.
Since the mid-1980s, the use of affinity tag technology has been a ubiquitous method for laboratories to purify virtually any arbitrary recombinant protein through a single general and simple method. While dozens of different tags, kits and accessories are now commercially available, this method has not been adopted for large-scale bioprocessing, largely due to the expense of removing the affinity tag after the target protein is purified.
The Wood Lab is currently developing new protein elements that effectively make the affinity tags self-cleaving after purification, therefore enabling many new tag-based protein purification methods that address the biotech industry's needs for scale, simplicity and cost control.
EXPERTISE
Novel and/or non-chromatographic recombinant protein bioseparations; pharmaceutical bioprocess development; incorporation of functional human drug targets into bacterial reporter proteins; design of controllable, self-activating proteins for medical and research applications; detection and identification of environmental endocrine disrupting compounds.
KEY DISTINCTIONS
- Seven patents
- Developed self-cleaving affinity tag technology for the purification of recombinant proteins
- Founder, Protein Capture Science, LLC. Wood's patents and main sales product of his startup company comprises a new platform technology for purifying recombinant proteins, which have the potential to accelerate research and simplify the manufacture of therapeutic proteins. The result would be faster patient care and new and cheaper biopharmaceuticals entering the market.
- National Science Foundation CAREER Award, 2003
- Ohio State University Lumley Research Award, 2016
The development of affinity tag technology in the mid 1980's provided a means to purify virtually any arbitrary recombinant protein through a single general and simple method. This method is now ubiquitous in the laboratory, where dozens of different tags, kits and accessories are now commercially available. Surprisingly, this method has not been adopted for large-scale bioprocessing, largely due to the expense of removing the affinity tag after the target protein is purified. Thus the promise of this method has been severely limited due to basic limitations in the proteins involved.
We are currently developing new protein elements that effectively make the affinity tags self-cleaving after purification, and therefore enable many new tag-based protein purification methods. These methods retain the simplicity and generality of conventional affinity tag technology, and can potentially make tag technology a ubiquitous and critical platform in protein bioseparations. Although our early methods are very effective for proteins expressed in E. coli, we must adapt this technology for proteins expressed in Pichia and CHO, as well as transgenic and other expression hosts. Further, the tags we use must be attractive to the biotech industry, and address its needs for scale, simplicity and expense.
Thus our focus is on the development of new tags that meet these needs. For example, these tags must bind at high capacity, and have chemistries that lend themselves to disposable technologies, and the self-cleaving reaction must be more controllable and reliable in every expression host. Our approaches range from simple chemistry to complex protein re-design, and require a variety of backgrounds.
- Wood, D., Derbyshire, V., Wu, W., Chartrain, M., Belfort, M. and Belfort, G., “Optimized Single-Step Affinity Purification with a Self-Cleaving Intein Applied to Human Acidic Fibroblast Growth Factor,” Biotechnology Progress, Vol. 16, pp. 1055-1063, (2000).
- Wu, W., Wood, D., Belfort, G., Derbyshire, V. & Belfort, M., “Intein-Mediated Purification of Cytotoxic Endonuclease I-TevI by Insertional Inactivation and pH-Controllable Splicing,” Nucleic Acids Research, Vol. 30, pp. 4864-71, (2002).
- US Patent # 6,933,362: Belfort, G., Belfort, M., Derbyshire, V., Wood, D., and Wu, W., “Genetic System and Self-Cleaving Inteins therefrom, Bioseparations Employing Same, Protein Purification by Inactivation with Inteins in Linker Region and pH Controllable Intein Splicing, and Methods for Determining Critical, Generalizable Residues for Varying Intein Activity.”
- Coolbaugh, M. J., Shakalli Tang, M. J., Wood, D. W., “High-throughput purification of recombinant proteins using self-cleaving intein tags,” Analytical Biochemistry, Vol. 516, pp. 65-74, (2017).
back to Research
The Applied Protein Engineering Lab has also worked in the area of general intein design and mechanistic understanding, including basic understanding of the intein splicing and cleaving mechanisms, as well as overall intein structure.
These contributions have aided the development of several new intein technologies over the years, and are summarized in several review papers and an edited volume. Most importantly, Wood's work in this area has also led to collaborations in more general areas of basic structure and activity relationships for engineered metalloproteins, which will be particularly relevant to the group's intended design of PloyHb molecules.
- Skretas, G. & Wood, D.W., “Regulation of Protein Activity with Small-Molecule-Controlled Inteins,” Protein Science, Vol. 14, pp. 523-532, (2005).
- Shi, C., Qing Meng, Q. & Wood, D. W., “Analysis of the roles of mutations in thyroid hormone receptor- β by a bacterial biosensor system,” Journal of Molecular Endocrinology, Vol. 52 (1), pp. 55–66, (2014).
- Cronin, M., Coolbaugh, M. J., Nellis, D., Zhu, J., Wood, D. W., Nussinov, R. & Ma, B., “Dynamics differentiate between active and inactive inteins,” European Journal of Medicinal Chemistry, Vol. 91, pp. 51-62, (2015).
- US Patent # 9,796,967 B2: Nellis, D., Wood, D. W., Zhu, J. & Ma, B., “Reversible Regulation Of Intein Activity Through Engineered New Zinc Binding Domain”.
As part of the full body of published research for this group, a description of Hormone Receptors follows, although this is not a current focus.
The nuclear hormone receptors (NHRs) are involved in vital functions of the cell, such as development, differentiation, homeostasis, reproduction and metabolism. Accordingly, NHRs comprise one of the most important classes of drug targets, and about 4% of all currently marketed therapeutics interfere with the activity of one or more of these proteins. Importantly, they are also targets for naturally occurring and synthetic endocrine disrupting compounds, and interference with their function has been connected to breast cancer, decreased fertility, and other disorders in humans and in animals.
We have developed a very simple reporter system in E. coli that can sense human hormone-like compounds, and report their presence and activity through changes in growth phenotype. Our sensor is based on a chimeric fusion protein where genetically inserting various hormone ligand-binding domains yields sensors with altered specificity. We have now constructed sensors using the alpha and beta subtypes of the human estrogen receptor, as well as the human thyroid receptor and insect ecdysone receptor. These designs are not only able to detect hormone-like compounds for these targets, but they are also able to discriminate between estrogen agonistic and antagonistic activities, distinguish subtype-selective estrogen receptor modulators, and report rough estimates of binding affinity. Our current goal is to understand the structure, energy and kinetics of our designed proteins, and generate new rules for engineering allosteric protein chimeras. In the short term we hope to modify this system for screening large natural-product libraries, and libraries derived from combinatorial synthesis techniques. The ability of this system to work effectively with three examples of human nuclear hormone receptors suggests that it will be generally useful for identifying natural product ligands that modulate this family or targets.
David Wood has developed a groundbreaking new method for purifying recombinant proteins from complex mixtures. This method can be applied to any protein made in any cell, and has the potential to accelerate research on new lifesaving biopharmaceuticals while making them less expensive to produce.
Wood has received several patents for this innovation, along with significant industry interest and external funding. Most recently, he has helped to start Protein Capture Science, LLC to commercialize the technology and make it available to academic and industry researchers throughout the world.
