Selected Publications

Ramsey KM, Barrick D. Unraveling paralog-specific Notch signaling through thermodynamics of ternary complex formation and transcriptional activation of chimeric receptors. Protein Sci. 2024 Apr;33(4):e4947. doi: 10.1002/pro.4947. PMID: 38511488; PMCID: PMC10962485.

Petersen M, Fang R, Majumdar A, Barrick D. Stability Islands and the Folding Cooperativity of a Seven-Repeat Array from Topoisomerase V. J Am Chem Soc. 2023 Jun 14;145(23):12641-12650. doi: 10.1021/jacs.3c02193. Epub 2023 Jun 1. PMID: 37262333; PMCID: PMC10416711.

Carter AA, Ramsey KM, Hatem CL, Sherry KP, Majumdar A, Barrick D. Structural features of the Notch ankyrin domain-Deltex WWE₂ domain heterodimer determined by NMR spectroscopy and functional implications. Structure. 2023 May 4;31(5):584-594.e5. doi: 10.1016/j.str.2023.03.003. Epub 2023 Mar 27. PMID: 36977409; PMCID: PMC10338078.

Baxter-Koenigs AR, El Nesr G, Barrick D. Singular value decomposition of protein sequences as a method to visualize sequence and residue space. Protein Sci. 2022 Oct;31(10):e4422. doi: 10.1002/pro.4422. PMID: 36173173; PMCID: PMC9514065.

Sternke M, Tripp KW, Barrick D. Surface residues and nonadditive interactions stabilize a consensus homeodomain protein. Biophys J. 2021 Dec 7;120(23):5267-5278. doi: 10.1016/j.bpj.2021.10.035. Epub 2021 Oct 30. PMID: 34757081; PMCID: PMC8715166.

Petersen M, Barrick D. Analysis of Tandem Repeat Protein Folding Using Nearest-Neighbor Models. Annu Rev Biophys. 2021 May 6;50:245-265. doi: 10.1146/annurev-biophys-102220-083020. Epub 2021 Feb 19. PMID: 33606943; PMCID: PMC8105288.

Marold JD, Sforza K, Geiger-Schuller K, Aksel T, Klein S, Petersen M, Poliakova-Georgantas E, Barrick D. A collection of programs for one-dimensional Ising analysis of linear repeat proteins with point substitutions. Protein Sci. 2021 Jan;30(1):168-186. doi: 10.1002/pro.3977. Epub 2020 Nov 2. PMID: 33058322; PMCID: PMC7737774.

Sternke M, Tripp KW, Barrick D. The use of consensus sequence information to engineer stability and activity in proteins. Methods Enzymol. 2020;643:149-179. doi: 10.1016/bs.mie.2020.06.001. Epub 2020 Jul 17. PMID: 32896279; PMCID: PMC8098710.

Klein SA, Majumdar A, Barrick D. A Second Backbone: The Contribution of a Buried Asparagine Ladder to the Global and Local Stability of a Leucine-Rich Repeat Protein. Biochemistry. 2019 Aug 20;58(33):3480-3493. doi: 10.1021/acs.biochem.9b00355. Epub 2019 Aug 6. PMID: 31347358; PMCID: PMC7184636.

Sternke M, Tripp KW, Barrick D. Consensus sequence design as a general strategy to create hyperstable, biologically active proteins. Proc Natl Acad Sci U S A. 2019 Jun 4;116(23):11275-11284. doi: 10.1073/pnas.1816707116. Epub 2019 May 20. PMID: 31110018; PMCID: PMC6561275.

Geiger-Schuller, K.P., Mitra, J., Ha, T., & Barrick, D (2019) Functional instability allows access to DNA in longer Transcription Activator-Like Effector (TALE) arrays.  eLife 8. pii: e38298.

Geiger-Schuller, K., Sforza, K., Yuhas, M., Parmeggiani, F., Baker, D., & Barrick, D. (2018) Extreme stability in de novo-designed repeat arrays is determined by unusually stable short-range interactions. Proc. of the Natl. Acad. of Sci. USA 115, 7539-7544.

Sherry, K.P., Das, R., Pappu, R.V., & Barrick D (2017) Control of transcriptional activity by design of charge patterning in the intrinsically disordered RAM region of the Notch Receptor.  Proc. Nat. Acad. Sci. USA 114, E9243-E9252.

Tripp, K. W., Sternke, M., & Barrick, D. (2017) Creating a homeodomain with high stability and DNA binding by sequence averaging.  J. Am. Chem. Soc., 139, 5051-5060.

Geiger-Schuller, K., & Barrick (2016) Broken TALES: Transcriptional activation-like effectors populate partly folded states.  Biophysical Journal 111, 2395-2403.

Fossat, M.J., Dao, T.P., Kenkins, K., Dellarole, M., Yang, Y., McCallum, S.A., Garcia, A.E., Barrick, D., Roumestand, C., & Royer, C.A, (2016)  High-resolution mapping of a repeat protein folding free energy landscape, Biophysical Journal 111, 2368-2376 .

Cunha, E., Hatem, C.L, & Barrick, D. (2016) Synergistic enhancement of cellulose pairs linked by consensus ankyrin repeats: determination of the roles of spacing, orientation, and enzyme identity.  Proteins: Struct. Funct.&  Bioinf. 84, 1043-1054.

Marold, J.D., Kavran, J.M., Bowman, G.D., & Barrick, D. (2015).  A naturally occurring repeat protein with high internal sequence identity defines a new class of TPR-like proteins.  Structure 23,2206-2265.

Sherry, K.P., Johnson, S.E., Hatem, C.L., Majumdar, A., Johnson, S., Hatem, D. & Barrick, D. (2015).  Effects of linker length and transient secondary structure elements in the intrinsically disordered RAM region on Notch signaling.  J. Mol. Biol. 427, 3587-3597.

Dao, T., Majumdar, A., & Barrick D. (2015) The highly polarized C-terminal transition state of the leucine-rich repeat domain of PP32 is governed by local stability. PNAS, 112 (18), E2298-306.

Preimesberger, M.R., Majumdar, A., Aksel, T., Sforza, K., Leckta, T., Barrick, D, & Lecomte, J.T.J. (2015) Direct NMR Detection of Bifurcated Hydrogen Bonding in the a-Helix N-Caps of Ankyrin Repeat Proteins. J. Am. Chem. Soc., in press.

Aksel, T., & Barrick, D (2014) Direct observation of parallel folding pathways revealed using a symmetric repeat protein system. Biophysical Journal 107, 220-232.

Dao, T., Majumdar, A., & Barrick, D (2014). The role of the capping motifs in stabilizing the structure of the PP32 leucine-rich repeat domain. Protein Science 23 (6), 801-811.

Cunha, E., Hatem, C., & Barrick, D (2013) Insertion of Endocellulase Catalytic Domains into Thermostable Consensus Ankyrin Scaffolds: Effects on Stability and Cellulolytic Activity. Applied Environmental Microbiology 79, 6684-6696.

Johnson, S.E. & Barrick, D. (2012) Dissecting and cirumventing the requirement for RAM in Notch signaling. PLos One 7(8) 39093.

Allgood, A.G, & Barrick, D. (2011) Mapping the Deltex binding surface on the Notch Ankyrin domain using analytical ultracentrifugation. J. Mol. Biol. 414, 243-259.

Cunha, E., Hatem, C.L., & Barrick, D. (2011). Natural and designed enzymes for cellulose degradation, in Advanced Biofuels and Bioproducts, Springer Publishing, 339-370.

Vieux, E.F., & Barrick, D. (2011). Deletion of internal structured repeats increases the stability of a leucine-rich repeat protein, YopM. Biophysical Chemistry 159, 152-161.

Rouget, J. B., Aksel, T., Roche, J., Saldana, J. L., Garcia, A. E., Barrick, D., & Royer, C. A. (2011). Size and Sequence and the volume change of protein folding. J. Am. Chem. Soc., 133, 6020-6027.

Sosnick, T.R., & Barrick, D. (2011). The folding of single domain proteins – have we reached a consensus? Curr. Op. Struct. Biol. 21, 12-24.

Aksel, T., Majumdar, A., & Barrick, D. (2011) The contribution of entropy, enthalpy, and hydrophobic desolvation ito cooperativity in repeat-protein folding. Structure, 19, 349-360.

Johnson, S.E. Ilagan, M.X.G., Kopan, R., & Barrick, D (2010) Thermodynamic analysis of the CSL:Notch interaction: Distribution of binding energy of the Notch RAM region to the CSL beta-trefoil domain and the mode of competition with the viral transactivator EBNA2. J. Biol. Chem, 285, 6681-6692.

Kloss, E. & Barick, D. (2009) C-terminal deletion of leucine-rich repeats from YopM reveals a heterogeneous distribution of stability in a cooperatively folded protein. Protein Science, 18, 1948-1960.

Aksel, T., & Barrick, D. (2009) Analysis of repeat-protein folding using nearest-neighbor statistical mechanical models. Meth. Enzymol. 455, 95-125.

Street, T.O., Bradley, C.M., & Barrick, D. (2009) Predicting repeat-protein folding kinetics from an experimentally determined folding energy landscape. Prot. Sci. 18, 58-68.

Kloss, E., & Barrick, D. (2008) Thermodynamics, kinetics, and salt dependence of folding of YopM, a large leucine-rich repeat protein. J. Mol. Biol. 383, 1195-1209.

Courtemanche, N., & Barrick, D. (2008) The leucine-rich repeat domain of Internalin B folds along a polarized N-terminal pathway. Structure 16, 705-712.

Tripp, K.W., & Barrick, D. (2008) Rerouting the folding pathway of the Notch ankyrin domain by reshaping the energy landscape. J. Am. Chem. Soc. 130, 5681-5688.

Bertagna, A., Toptygin, D., Brand, L., & Barrick, D. (2008) The effects of conformational heterogeneity on the binding of the Notch intracellular domain to effector proteins: a case of biologically tuned disorder. Biochem. Soc. Trans. 36, 157-166.

Courtemanche, N., & Barrick, D. (2008) Folding thermodynamics and kinetics of the Leucine-rich repeat domain of the virulence factor Internalin B. Protein Science 17, 43-53.

Kloss, E., Courtemanche, N., & Barrick, D. (2007) Repeat-protein folding: new insights into origins of cooperativity, stability, and topology. Archives of Biochemistry and Biophyics 469, 83-99.

Street, T.O., Courtemanche, N., & Barrick, D. (2007B) Protein folding and stability using denaturants. Methods in Cell Biology: Biophysical Tools for Biologists. Correia, J.J. & Detrich, H.W. III, eds. Academic Press, Vol 84, 295-325.