Anne Brown

Instructor, BCHM 1024: Introduction to Biochemistry Research Skills, January 2019 – present

Instructor, BCHM 5024: Computational Biochemistry for Bioinformatics, Spring 2014 – present

Undergraduate Research (BCHM 2994, BCHM 4994)

Program Focus

My research lab is focused on studying protein structure-function relationships across species and diseases by developing and using cutting-edge molecular dynamics (MD) simulation techniques and computational, data-rich method. We use MD simulations and computer aided drug design (CADD) to target proteins involved in a variety of disease, including Alzheimer’s, Type 2 Diabetes, and more, and are developing novel approaches towards drug repurposing in virtual screening pipelines. We also extensively collaborate on the utilization of computational thinking, data science, and discipline-specific computational tools into their research labs and classrooms. In brief, what we can explore at the atomistic level via simulations can lead us to greater insight and connections to cellular level phenomenon, and our group seeks to have long-term impact and add into the translational science approach of multiscale modeling of proteins in both functional and disease states. I am also involved in the training, pedagogical impact research, and mentorship of undergraduate research students in these areas.

Experience in Molecular Modeling and Informatics (EMMI) is a summer research opportunity for high school students interested in bioinformatics and computational biochemistry. In this program, we employ the Experiential Learning Theory, which has been extensively researched as a practice for actively teaching through the dynamic learning cycle driven by problem solving and reflection on the experience.

This program focuses on learning and employing various computational techniques to research in the biochemistry, biophysical, and pharmacological domains at Virginia Tech. Students learn how to successfully utilize computational practices in answering research questions, explore protein structure-function relationships, and contribute new knowledge and data to research projects.  

Brown Lab YouTube Channel [LINK]

1040 subscribers, 60K+ views, numerous positive comments (99% positive comments). Content on molecular visualization, molecular docking, and more computational techniques that need enhanced documentation and tutorials. Transcripts are available for all videos in English and Spanish. I oversee and maintain the site and aid in the production of all videos.

Google Scholar, PubMed

* indicates undergraduate research mentee(n=13) ^† indicates graduate student mentee  ^# indicates corresponding author (n=11)

Selected Publications

1. Breiner, L. M., *Briganti, A. J., McCord, J. P., Heifetz, M. E., Philbrook, S. Y., Slebodnick, C., Brown, A. M., Lowell, A. N. (2022).Synthesis, testing, and computational modeling of pleuromutilin 1,2,3-triazole derivatives in the ribosome. Tetrahedron Chem. 100034. [DOI]
2. ^†King, K.M., Bevan, D.R., and Brown, A.M.^# (2022). “Molecular Dynamics Simulations Indicate Aromaticity as a Key Factor in Inhibition of IAPP_(20-29) Aggregation.” ACS Chem. Neur. 13(11) pp. 615–1626. [DOI] 5.08
3. ^†Sharp, A.K., Newman, D., Libonate, G., Stern, M.B., Bevan, D.R., Anandakrishnan, R., and Brown, A.M.^# (2022). Biophysical insights into OR2T7: Investigation of a potential prognostic marker for glioblastoma. Biophys. J. 121(19) pp.3706-3718. [DOI]
4. *Kawecki, G., ^†King, K.M., *Cramer, N., Bevan, D.R. and Brown, A.M.^# (2022). Simulations of Cross-Amyloid Aggregation of Amyloid-β and Islet Amyloid Polypeptide Fragments. Biophys. J. 121 (11) pp. 2002-2013 [DOI]
5. ^†King, K.M., ^†Sharp, A.K., Davidson, D.S., Lemkul, J.A., and Brown, A.M.^# (2021). Impact of Electronic Polarization on Preformed, β-Strand Rich Homogenous and Heterogeneous Amyloid Oligomers. J. Comp. Biophys. Chem. 21(4) pp. 449-460. [DOI]
6. Kang, L., He, G., ^†Sharp, A.K., Wang, X., Brown, A.M., Michalak, P. and Weger-Lucarelli, J., 2021. A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation. Cell, 184(17) pp. 4392-4400. [DOI]
7. Piai, A., Fu, Qingshan, F., ^†Sharp, A.K., Bighi, B., Brown, A.M.^#, and Chou, J.J.NMR Model of the Entire Membrane-Interacting Region of the HIV-1 Fusion Protein and Its Perturbation of Membrane Morphology. J. Am. Chem. Soc. 43(17) pp. 6609-6615. [DOI] *co-corresponding author
8. Wu, L., Velander, P., Brown, A.M., Wang, Y., Liu, D., Bevan, D.R., Zhang, S. and Xu, B. (2021). Rosmarinic Acid Potently Detoxifies Amylin Amyloid and Ameliorates Diabetic Pathology in a Transgenic Rat Model of Type 2 Diabetes. ACS Pharmacol. Transl. Sci. 4(4) pp.1322-1337. [DOI]
9. Wind, L.L., Briganti, J.S., Brown, A.M., Neher, T.P., Davis, M.F., Durso, L.M., *Spicer, T., Lansing, S. (2021) Finding What Is Inaccessible: Antimicrobial Resistance Language Use among the One Health Domains. Antibiotics. 10, 385. [DOI]
10. Congdon, M., Fritzemeier, R. G., Kharel, Y., Brown, A. M., Serbulea, V., Bevan, D. R., Lynch, K. R., & Santos, W. L. (2021). Probing the substitution pattern of indole-based scaffold reveals potent and selective sphingosine kinase 2 inhibitors. Eur J Med Chem. 212, 113121. [DOI]
11. Dailing, A., Mitchell, K., Vuong, N., Lee, K. H., Joshi, R., Espina, V., Haymond Still, A., *Gottschalk, C. J., Brown, A. M., Paige, M., Liotta, L. A., and Luchini, A. (2021). Characterization and Validation of Arg286 Residue of IL-1RAcP as a Potential Drug Target for Osteoarthritis. Front Chem. 8, 601477. [DOI]
12. Kim, C., Brown, A.M., Grove, T., and Etzkorn F. (2021) Designed Leucine-Rich Repeat Proteins Bind Muramyl Dipeptide with High Affinity. Protein Sci. 30, 804-817. [DOI]
13. Briganti, J.S., and Brown, A.M.^# (2020) Implementing, Strengthening, and Iterating Digital-First Undergraduate Research Operational Procedures during Major Disruptions. SPUR. 4(2) pp. 62-63. [DOI]
14. Sharp, A. K., *Gottschalk, C.J., and Brown, A.M.^# (2020) Utilization of Computational Techniques and Tools to Introduce or Reinforce Knowledge of Biochemistry and Protein Structure-Function Relationships, Biochem Mol Biol Educ. 48, 662-664. [DOI]
15. Briganti, J.S., Ogier, A., and Brown, A.M.^# (2020) Piloting a Community of Student Data Consultants that Supports and Enhances Research Data Services. Int. J. Dig. Cur. 15(1). [DOI]
16. Song, W., *Gottschalk, C.J., Tang, T.-X., Biscardi, A., Ellena, J.F., Finkielstein, C.V., Brown, A.M., and Capelluto, D. G. S. (2020) Structural, in silico, and functional analysis of a Disabled-2-derived peptide for recognition of sulfatides, Sci Rep. 10, 13520.  [DOI]
17. Sibley, C. D., Morris, E. A., Kharel, Y., Brown, A.M., Huang, T., Bevan, D. R., Lynch, K. R., and Santos, W. L. (2020) Discovery of a Small Side Cavity in Sphingosine Kinase 2 that Enhances Inhibitor Potency and Selectivity, J. Med. Chem. 63 (3) pp. 1178-1198. [DOI] (Journal Cover Art for February 2020)
18. Liu, J., Zou, X., Gotoh, T., Brown, A.M., Jiang, L., Wisdom, E. L., Kim, J. K., and Finkielstein, C. V. (2018) “Distinct Control of PERIOD2 Degradation and Circadian Rhythms by the Oncoprotein and Ubiquitin Ligase MDM2.” Science Signaling. 11 (556), eaau0715. [DOI] [VT News Story]
19. Davidson, D.S., Brown, A.M., and Lemkul, J.A. (2018) "Insights into Stabilizing Forces in Amyloid Fibrils of Differing Sizes from Polarizable Molecular Dynamics Simulations." J. Mol. Biol. 430(20), 3819-3834. F1000 recommended paper. [DOI] [VT News Story]

Oral Presentations

Brown, A.M. and Lowell, A.L. "Overcoming AMR Through Antibiotic Redesign: Coupling Computational and Experimental Science". CeZAP (Center for Emerging, Zoonotic, and Arthropod-borne Pathogens) Distinguished Speaker Seminar Series in Infectious Diseases. February 2022.

Brown, A.M. “How Does HPC Help with Your Scientific Research”. Virginia Women in HPC program (VA-WHPC). January 2022. 

Poster Presentations

^†King. K., Bevan, D.R., Brown, A.M. (2022) Using molecular dynamics simulations to explore natural product inhibitors against IAPP_(20-29) aggregation. American Chemical Society (ACS) National Meeting & Expo.

^†Sharp, A.S., Bevan, D.R., Brown, A.M., and Anandakrishnan, R. (2020) Molecular insights into OR2T7: Coupled computational and experimental techniques reveal a novel prognostic marker for glioblastoma multiform. American Chemical Society (ACS) National Meeting & Expo. 

2023: Data Science Faculty Fellow

2022-2027: NSF Career Award, Resolving the influence of biologically relevant microenvironments on Amyloid Aggregation [LINK]

2021: Virginia Tech Department of Biochemistry Outstanding Service Award

2020: Virginia Tech Office of First-Year Experiences Outstanding First-Year Student Advocate

2020: Council of Undergraduate Research (CUR) Biology Division Mentor Award

2019: Virginia Tech Outstanding Undergraduate Research Faculty Mentor Award

2019: Virginia Tech Scholarship of Teaching and Learning Award

2017, 2018: Virginia Tech Favorite Faculty (2018 – Civility Award Winner)

2016: North American Colleges and Teachers of Agriculture (NACTA) Graduate Student Teaching Award of Merit

2015: Virginia Tech Graduate School Outstanding Graduate Student Service Excellence Award