Scientific Interests

Projects in the Bauer lab are typically driven by undergraduate and graduate researchers in collaboration with other labs at HWI or the BioXFEL Science and Technology Center (STC). Please contact Dr. Bauer if you are interested in participating in one of our graduate or undergraduate internship programs.

Nanolipoprotein particles (NLPs), also referred to as “nanodiscs”, are discoidal particles that contain a lipid bilayer surrounded by apolipoproteins. NLPs are of great interest due to their ability to act as a membrane system that can incorporate and solubilize membrane proteins. The resulting complexes can then be studied by serial femtosecond crystallography (SFX) at X-ray free electron lasers (XFELs), or cryo-electron microscopy (cryo-EM) and electron diffraction (ED). We are currently investigating mechanisms of promoting regular interactions between the NLPs to enhance crystal growth. The utilization of a functionalized NLPs represents a powerful approach for studying the structure of membrane proteins, which are traditionally difficult to crystallize as large single crystals capable of producing high-quality diffraction.

Dr. Bauer has a long history of working with proteins that interact with nucleic acids (DNA and RNA). Another project involves the structural elucidation of proteins and protein complexes from the homeobox superfamily of transcription factors which contain a highly conserved DNA-binding domain known as the homeodomain (HD). These proteins are essential to the embryonic development of all vertebrates, they are involved in many adult physiological functions, and they are implicated in several types of cancer, namely leukemias. The current target is the conserved DNA binding region of the PBX-regulating Protein (Prep-1). The biochemistry of Prep-1 has been studied and characterized extensively, however, a structure that demonstrates its overall fold and mode of interaction with DNA regulatory elements and other HD proteins remains unresolved. We are working to get a better understanding of how this protein functions during our development and in disease models.

BioXFEL – Education and Diversity

As the Education and Diversity Director for BioXFEL, Dr. Bauer is responsible for the design, implementation, and management of an extensive education and diversity program. One of the main goals of our initiatives is to prepare a diverse group of scholars for scientific careers in a broad range of STEM disciplines and create the next generation of diverse scientists. We achieve this by offering customized programming that includes internships, fellowships, workshops, and professional development events. Our programs have been extremely effective in recruiting and retaining a diverse group of students, preparing them for research careers, and helping them transition to the next stage of their careers.

University of Puerto Rico Collaborations

Through BioXFEL we have established a scientific and education collaboration with faculty and students at several University of Puerto Rico (UPR) campuses. We regularly organize customized workshops for the UPR researchers and have hosted many undergraduate and graduate interns. Shortly after Hurricane Maria hit Puerto Rico, HWI was able to relocate 9 UPR graduate students and their families to help them to recover and complete their thesis projects. As an adjunct faculty member of the UPR Mayagüez Chemistry Department, Dr. Bauer is able to serve on thesis committees and provide additional scientific and mentoring support to graduate students. No fewer than twelve students from the University of Puerto Rico (5 undergraduate, 7 graduate) have rotated through Dr. Bauer’s lab at HWI and have contributed to BioXFEL projects.

Recent Publications

Journal Articles

    1. Bauer, W. J. & Woodruff, S. B. A science education model for large collaborative centers. Struct Dynam-us 8, 020402 (2021).
    2. Marchany‐Rivera, D. et al. SAXS structure of homodimeric oxyHemoglobin III from bivalve Lucina pectinata. Biopolymers e23427 (2021) doi:10.1002/bip.23427.
    3. Shelby, M. L. et al. Crystallization of ApoA1 and ApoE4 Nanolipoprotein Particles and Initial XFEL-Based Structural Studies. Crystals 10, 886 (2020).
    4. Kennedy, S. D., Bauer, W. J., Wang, W. & Kielkopf, C. L. Dynamic stacking of an expected branch point adenosine in duplexes containing pseudouridine-modified or unmodified U2 snRNA sites. Biochem Bioph Res Co 511, 416–421 (2019).
    5. Bauer, W. J. et al. Structural characterization and modeling of the Borrelia burgdorferi hybrid histidine kinase Hk1 periplasmic sensor: A system for sensing small molecules associated with tick feeding. J Struct Biol 192, 48–58 (2015).
    6. Wang, W. et al. Structure of Phosphorylated SF1 Bound to U2AF65 in an Essential Splicing Factor Complex. Structure 21, 197–208 (2013).
    7. Bauer, W. J., Heath, J., Jenkins, J. L. & Kielkopf, C. L. Three RNA Recognition Motifs Participate in RNA Recognition and Structural Organization by the Pro-Apoptotic Factor TIA-1. J Mol Biol 415, 727–740 (2012).

Book Chapters and Published Protocols

    1. Kielkopf, C. L., Bauer, W. & Urbatsch, I. L. Subcellular Localization of Signal Peptide Fusion Proteins Expressed in E. coli. Cold Spring Harb Protoc 2021, pdb.prot102145 (2021).
    2. Kielkopf, C. L., Bauer, W. & Urbatsch, I. L. Solubilization of Expressed Proteins from Inclusion Bodies. Cold Spring Harb Protoc 2021, pdb.prot102210 (2021).
    3. Kielkopf, C. L., Bauer, W. & Urbatsch, I. L. Preparation of Cell Extracts for Purification of Soluble Proteins Expressed in E. coli. Cold Spring Harb Protoc 2021, pdb.prot102178 (2021).
    4. Kielkopf, C. L., Bauer, W. & Urbatsch, I. L. Expression of Cloned Genes in Pichia pastoris Using the Methanol-Inducible Promoter AOX1. Cold Spring Harb Protoc 2021, pdb.prot102160 (2021).
    5. Kielkopf, C. L., Bauer, W. & Urbatsch, I. L. Expression of Cloned Genes in E. coli Using IPTG-Inducible Promoters. Cold Spring Harb Protoc 2021, pdb.prot102137 (2021).
    6. Kielkopf, C. L., Bauer, W. & Urbatsch, I. L. Expressing Cloned Genes for Protein Production, Purification, and Analysis. Cold Spring Harb Protoc 2021, pdb.top102129 (2021).
    7. Kielkopf, C. L., Bauer, W. & Urbatsch, I. L. Considerations for Membrane Protein Purification. Cold Spring Harb Protoc 2021, pdb.top102285 (2021).
    8. Kielkopf, C. L., Bauer, W. & Urbatsch, I. L. Purification of Polyhistidine-Tagged Proteins by Immobilized Metal Affinity Chromatography. Cold Spring Harb Protoc 2020, pdb.prot102194 (2020).
    9. Kielkopf, C. L., Bauer, W. & Urbatsch, I. L. Purification of Fusion Proteins by Affinity Chromatography on Glutathione Resin. Cold Spring Harb Protoc 2020, pdb.prot102202 (2020).
    10. Kielkopf, C. L., Bauer, W. & Urbatsch, I. L. Methods for Measuring the Concentrations of Proteins. Cold Spring Harb Protoc 2020, pdb.top102277 (2020).
    11. Kielkopf, C. L., Bauer, W. & Urbatsch, I. L. Expression of Cloned Genes Using the Baculovirus Expression System. Cold Spring Harb Protoc 2020, pdb.prot102152 (2020).
    12. Kielkopf, C. L., Bauer, W. & Urbatsch, I. L. Bradford Assay for Determining Protein Concentration. Cold Spring Harb Protoc 2020, pdb.prot102269 (2020).

Our Group

For more information on our NSF-funded Science and Technology Center (STC) visit


  • B.A. in Molecular Biology from Elmira College – 2002
    Graduated Cum Laude from a liberal arts program and a minor in Art


  • Ph.D. in Structural Biology from University at Buffalo – 2008
    Graduated with a 3.85 GPA and a thesis focusing on protein/DNA interactions of the HOX family of transcription factors in the laboratory of Dr. Timothy Umland.


William Bauer, PhD

T: 716 898 8620