Mengiste, A.A.; McDonald, J.L.; Tran, M.T.N.; Plank, A.V.; Wilson, R.H.; Butty, V.L.; Shoulders, M.D. "MutaT7GDE: A Single Chimera for the Targeted, Balanced, and Efficient Installation of All Possible Transition Mutations In Vivo" in review (2024).

Yammine, K.M.; Abularach, S.M.; Kim, S.; Bikovtseva, A.A.; Lilianty, J.; Butty, V.L.; Schiavoni, R.P.; Bateman, J.F.; Lamandé, S.R.; Shoulders, M.D. "ER Procollagen Storage Defect Without Coupled Unfolded Protein Response Drives Precocious Arthritis” bioRxiv in review (2023). DOI: 10.1101/2023.10.19.562780.

Yoon, J.; Zhang, Y.M.; Her, C.; Grant, R.A.; Ponomarenko, A.I.; Ackermann, B.E.; Hui, T.; Lin, Y.-S.; Debelouchina, G.T.; Shoulders, M.D. "The Immune-Evasive Proline-283 Substitution in Influenza Nucleoprotein Increases Aggregation Propensity Without Altering the Native Structure" Science Advances 10, eadl6144 (2024). 

Chen, K.; Shoulders, M.D. "Protein Glycosylation Patterns Shaped By the IRE1-XBP1s Arm of the Unfolded Protein ResponseIsrael Journal of Chemistry e202300162 (2024). Invited article for issue recognizing Prof. Jeffery W. Kelly's Wolf Prize in Chemistry.

Ogbunugafor, C.B.; Guerrero, R.F.; Miller-Dickson, M.D.; Shakhnovich, E.I.; Shoulders, M.D. "Epistasis and Pleiotropy Shape Biophysical Protein Subspaces Associated with Drug Resistance" Physical Review E 108, e054408 (2023).

Yammine, K.M.; Abularach, S.M.; Sampurno, L.; Bateman, J.F.; Lamandé, S.R.; Shoulders, M.D. "Using CRISPR/Cas9 to Generate a Heterozygous COL2A1 p.R719C iPSC Line (MCRIi019-A-6)" Stem Cell Research 51, e103020 (2023).

Guerrero, R.F.; Dorgi, T.; Harris, R.M.; Shoulders, M.D.; Ogbunugafor, C.B. "Evolutionary Druggability: Leveraging Low-Dimensional Fitness Landscapes Towards New Metrics for Antimicrobial ApplicationseLife 12, e88480 (2023).

Yoon, J.; Patrick, J.E.; Ogbunugafor, C.B.; Shoulders, M.D. "Viral Evolution Shaped By Host Proteostasis NetworksAnnual Review of Virology 10, 77–98 (2023). 

Mengiste, A.A.; Wilson, R.H.; Weissman, R.F.; Papa, L.J., III; Hendel, S.J.; Moore, C.L.; Butty, V.L.; Shoulders, M.D. "Expanded MutaT7 Toolkit Efficiently and Simultaneously Accesses All Possible Transition Mutations in BacteriaNucleic Acids Research 51, e31 (2023).

Yoon, J.#; Nekongo, E.E.#; Patrick, J.E.; Hui, T.; Phillips, A.M.; Ponomarenko, A.I.; Hendel, S.J.; Sebastian, R.M.; Zhang, Y.M.; Butty, V.L.; Ogbunugafor, C.B.; Lin, Y.-S.; Shoulders, M.D. "The Endoplasmic Reticulum Proteostasis Network Profoundly Shapes the Protein Sequence Space Accessible to HIV EnvelopePLoS Biology 20, e3001569 (2022). #Co-First Authors.

Choudhury, A.; Lim, A.; Sebastian, R.M.; Moore, C.L.; Filliol, A.; Bledsoe, J.; Dai, C.; Schwabe, R.; Shoulders, M.D.; Mandrekar, P. "Loss of Heat Shock Factor I Promotes Hepatic Stellate Cell Activation and Drives Liver Fibrosis" Hepatology Communications 6, 2781–2797 (2022).

King, D.T.; Serrano-Negron, J.E.; Zhu, Y.; Moore, C.L.; Shoulders, M.D.; Foster, L.J.; Vocadlo, D.J. "Thermal Proteome Profiling Reveals the O-GlcNAc-Dependent MeltomeJournal of the American Chemical Society 144, 3833–3842 (2022).

Bateman, J.F.; Shoulders, M.D.; Lamandé, S.R. "Collagen Misfolding Mutations: The Contributions of the Unfolded Protein Response to the Molecular PathologyConnective Tissue Research 63, e2036735 (2022).

Molina, R.; Rix, G.; Mengiste, A.A.; Alvarez, B.; Seo, D.; Chen, H.; Hurtado, J.; Zhang, Q.; Garcia-Garcia, J.D.; Heins, Z.; Almhjell, P.J.; Arnold, F.H.; Kahlil, A.S.; Hanson, A.; Dueber, J.; Schaffer, D.; Chen, F.; Kim, S.; Fernandez, L.; Shoulders, M.D.; Liu, C. "In Vivo Hypermutation and Continuous EvolutionNature Reviews Methods Primers 2, e36 (2022).

DiChiara, A.S.; Doan, N.-D.; Bikovtseva, A.A.; Rowley, L.; Butty, V.L.; Weis, M.E.; Eyre, D.R.; Lamandé, S.R.; Bateman, J.F.; Shoulders, M.D. "XBP1s-Mediated Endoplasmic Reticulum Proteostasis Network Enhancement Can Selectively Improve Folding and Secretion of an Osteogenesis Imperfecta-Causing Collagen-I Variant" BioRxiv (2021). DOI: 10.1101/2021.04.15.439909.

Li, R.C.; Wong, M.Y.; DiChiara, A.S.; Hosseini, A.S.; Shoulders, M.D. "Collagen's Enigmatic, Highly Conserved N-Glycan Has an Essential Proteostatic FunctionProceedings of the National Academy of Sciences, USA 118, e2026608118 (2021).

Hendel, S.J.; Shoulders, M.D. "Directed Evolution in Mammalian CellsNature Methods 18, 346–357 (2021).

Dickinson, B.C.; Shoulders, M.D. "Molecular Synthetic Biology: From Understanding Life to Creating Smart Therapeutics" Current Opinion in Chemical Biology 64, A1–A2 (2021).

Doan, N.-D.#; Hosseini, A.S.#; Bikovtseva, A.A.#; Huang, M.S.; DiChiara, A.S.; Papa, L.J., III; Koller, A.; Shoulders, M.D. "Elucidation of Proteostasis Defects Caused by Osteogenesis Imperfecta Mutations in the Collagen-α2(I) C-Propeptide Domain" Journal of Biological Chemistry 295, 9959–9973 (2020). #Co-First Authors.

Nekongo, E.E.#; Ponomarenko, A.I.#; Dewal, M.B.; Butty, V.L.; Browne, E.P.; Shoulders, M.D. "HSF1 Activation Can Restrict HIV ReplicationACS Infectious Diseases 6, 1659–1666 (2020). #Co-First Authors.

Sebastian, R.M.; Shoulders, M.D. "Chemical Biology Framework to Illuminate Proteostasis" Annual Review of Biochemistry 89, 529–555 (2020).

Kung, L.H.W.; Sampurno, L.; Yammine, K.M.; Graham, A.; McDonald, P.; Bateman, J.F.*; Shoulders, M.D.*; Lamandé, S.R. "CRISPR/Cas9 Editing to Generate a Heterozygous COL2A1 p.G1170S Human Chondrodysplasia iPSC Line, MCRIi019-A-2, in a Control iPSC Line, MCRIi019-AStem Cell Research 48, e101962 (2020). *Co-Corresponding Authors.

Liebelt, F.#; Sebastian, R.M.#; Moore, C.L.; Mulder, M.P.C.; Ovaa, H.; Shoulders, M.D.*; Vertegaal, A.C.O.* "SUMOylation and the HSF1-Regulated Chaperone Network Converge to Promote Proteostasis in Response to Heat ShockCell Reports 26, 236–249 (2019). #Co-First Authors; *Co-Corresponding Authors.

Doan, N.-D.; DiChiara, A.S.; Del Rosario, A.M.; Schiavoni, R.P.; Shoulders, M.D. "Mass Spectrometry-Based Proteomics to Define Intracellular Collagen InteractomesMethods in Molecular Biology 1944, 95–114 (2019).

Papa, L.J., III; Shoulders, M.D. "Genetic Engineering by DNA RecombineeringCurrent Protocols in Chemical Biology 11, e70 (2019).

Wong, M.Y.; Shoulders, M.D. "Targeting Defective Proteostasis in the CollagenopathiesCurrent Opinion in Chemical Biology 50, 80–88 (2019).

Wong, M.Y.#; Chen, K.#; Antonopoulos, A.#; Kasper, B.T.#; Dewal, M.B.; Taylor, R.J.; Whittaker, C.A.; Hein, P.P.; Dell, A.; Genereux, J.C.; Haslam, S.M.; Mahal, L.K.; Shoulders, M.D. "XBP1s Activation Can Globally Remodel N-Glycan Structure Distribution PatternsProceedings of the National Academy of Sciences, USA 115, E10089–E10098 (2018). #Co-First Authors.

DiChiara, A.S.; Li, R.C.; Suen, P.H.; Hosseini, A.S.; Taylor, R.J.; Weickhardt, A.F.; Malhotra, D.; McCaslin, D.R.; Shoulders, M.D. "A Cysteine-Based Molecular Code Informs Collagen C-Propeptide AssemblyNature Communications 9, e4206 (2018).

Phillips, A.M.#; Ponomarenko, A.I.#; Chen, K.; Ashenberg, O.; Miao, J.; McHugh, S.M.; Butty, V.L.; Whittaker, C.A.; Moore, C.L.; Bloom, J.D.; Lin, Y.-S.; Shoulders, M.D. "Destabilized Adaptive Influenza Variants Critical for Innate Immune System Escape are Potentiated by Host ChaperonesPLoS Biology 16, e3000008 (2018). #Co-First Authors.

Phillips, A.M.; Doud, M.B.; Gonzalez, L.O.; Butty, V.L.; Lin, Y.-S.; Bloom, J.D.; Shoulders, M.D. "Enhanced ER Proteostasis and Temperature Differentially Impact the Mutational Tolerance of Influenza HemagglutinineLife 7, e38795 (2018).

Berman, C.M.#; Papa, L.J., III#; Hendel, S.J.#; Moore, C.L.; Suen, P.H.; Weickhardt, A.F.; Doan, N.-D.; Kumar, C.S.; Uil, T.G.; Butty, V.L.; Hoeben, R.C.; Shoulders, M.D. "An Adaptable Platform for Directed Evolution in Human CellsJournal of the American Chemical Society 140, 18093–18103 (2018). #Co-First Authors.

Moore, C.L.#; Papa, L.J., III#; Shoulders, M.D. "A Processive Protein Chimera Introduces Mutations across Defined DNA Regions In VivoJournal of the American Chemical Society 140, 11560–11564 (2018). #Co-First Authors.

Richardson, C.E.R.; Cunden, L.S.; Butty, V.L.; Nolan, E.M.; Lippard, S.J.; Shoulders, M.D. "A Method for Selective Depletion of Zn(II) Ions from Complex Biological Media and Evaluation of Cellular Consequences of Zn(II) DeficiencyJournal of the American Chemical Society 140, 2413–2416 (2018).

Richardson, C.E.R.; Nolan, E.M.; Shoulders, M.D.*; Lippard, S.J.* "A Sensitive, Non-Radioactive Assay for Zn(II) Uptake into Metazoan CellsBiochemistry 57, 6807–6815 (2018). *Co-Corresponding Authors.

Wong, M.Y.; Doan, N.-D.; DiChiara, A.S.; Papa, L.J., III; Cheah, J.H.; Soule, C.K.; Watson, N.; Hulleman, J.D.; Shoulders, M.D. "High-Throughput Assay for Collagen Secretion Suggests an Unanticipated Role for Hsp90 in Collagen ProductionBiochemistry 57, 2814–2827 (2018)

Cole, K.S.; Grandjean, J.M.D.; Chen, K.; Witt, C.H.; O'Day, J.; Shoulders, M.D.; Wiseman, R.L.; Weerapana, E. "Characterization of an A-Site Selective Protein Disulfide Isomerase A1 Inhibitor" Biochemistry 57, 2035–2043 (2018).

Wong, M.Y.; DiChiara, A.S.; Suen, P.H.; Chen, K.; Doan, N.-D.; Shoulders, M.D. "Adapting Secretory Proteostasis and Function Through the Unfolded Protein ResponseCurrent Topics in Microbiology and Immunology 414125 (2018).

Phillips, A.M.; Gonzalez, L.O.; Nekongo, E.E.; Ponomarenko, A.I.; McHugh, S.M.; Butty, V.; Levine, S.S.; Lin, Y.-S.; Mirny, L.A.; Shoulders, M.D. "Host Proteostasis Modulates Influenza EvolutioneLife 6, e28652 (2017).

Maji, B.#; Moore, C.L.#; Zetsche, B.; Volz, S.E.; Zhang, F.; Shoulders, M.D.*; Choudhary, A.* "Multidimensional Chemical Control of CRISPR-Cas9" Nature Chemical Biology 13, 911 (2017). #Co-First Authors; *Co-Corresponding Authors.

DiChiara, A.S.; Taylor, R.J.; Wong, M.Y.; Doan, N.-D.; Del Rosario, A.M.; Shoulders, M.D. "Mapping and Exploring the Collagen-I Proteostasis Network" ACS Chemical Biology 11, 1408–1421 (2016).

Moore, C.L.; Dewal, M.B.; Nekongo, E.E.; Santiago, S.; Lu, N.B.; Levine, S.S.; Shoulders, M.D. "Transportable, Chemical Genetic Methodology for the Small Molecule-Mediated Inhibition of Heat Shock Factor 1ACS Chemical Biology 11200–210 (2016).

Phillips, A.M.; Shoulders, M.D. "The Path of Least Resistance: Mechanisms to Reduce Influenza's Sensitivity to OseltamivirJournal of Molecular Biology 428533–537 (2016).

Dewal, M.B.; DiChiara, A.S.; Antonopoulos, A.; Taylor, R.J.; Harmon, C.J.; Haslam, S.M.; Dell, A.; Shoulders, M.D. "XBP1s Links the Unfolded Protein Response to the Molecular Architecture of Mature N-GlycansChemistry and Biology 22, 1301–1312 (2015).

Genereux, J.C.; Qu, S.; Zhou, M.; Ryno, L.M.; Wang, S.; Shoulders, M.D.; Kaufman, R.J.; Lasmézasm C.I.; Kelly, J.W.; Wiseman, R.L. "Unfolded Protein Response-Induced ERdj3 Secretion Links Endoplasmic Reticulum Stress to Extracellular ProteostasisEMBO Journal 34, 419 (2015).

Choudhary, A.#; Kamer, K.J.#; Shoulders, M.D.#; Raines, R.T. "4-Ketoproline: An Electrophilic Proline Analog for BioconjugationBiopolymers: Peptide Science 104, 110115 (2015). #Co-First Authors.

Chen, J.J.#; Genereux, J.C.#; Hulleman, J.D.; Shoulders, M.D.; Wiseman, R.L. “ATF6 Activation Reduces the Secretion and Extracellular Aggregation of Destabilized Variants of an Amyloidogenic ProteinChemistry and Biology 2115641574 (2014)#Co-First Authors.

Ryno, L.M.; Genereux, J.C.; Naito, T.; Morimoto, R.I.; Powers, E.T.; Shoulders, M.D.; Wiseman, R.L. "Characterizing the Altered Cellular Proteome Induced by the Stress-Independent Activation of Heat Shock Factor I" ACS Chemical Biology 9, 12731283 (2014).

Shoulders, M.D.#; Ryno, L.M.#; Kelly, J.W.; Wiseman, R.L. “Broadly Applicable Methodology for the Dosable, Rapid, and Small Molecule-Mediated Regulation of Transcription Factors in Human Cells” Journal of the American Chemical Society 135, 8129–8132 (2013). #Co-First Authors.

Shoulders, M.D.; Ryno, L.M.; Genereux, J.C.; Moresco, J.J.; Tu, P.G.; Wu, C.; Yates, J.R. III; Su, A.I.; Kelly, J.W.; Wiseman, R.L. “Stress-Independent Activation of XBP1s and/or ATF6 Reveals Three Functionally Diverse ER Proteostasis Environments” Cell Reports 3, 1279–1292 (2013).

Krow, G.R.; Shoulders, M.D.; Edupuganti, R.; Gandla, D.; Yu, F.; Sonnet, P.E.; Sender, M.; Choudhary, A.; DeBrosse, C.; Ross, C.W.,III; Carroll, P.; Raines, R.T. “Synthesis of 5-Fluoro- and 5-Hydroxymethanoprolines via Lithiation of N-BOC-Methanopyrrolidines. Constrained Cɣ-Exo and Cɣ-Endo Flp and Hyp Conformer Mimics” Journal of Organic Chemistry 77, 5331–5344 (2012). 

Shoulders, M.D.; Raines, R.T. “Interstrand Dipole-Dipole Interactions Can Stabilize the Collagen Triple Helix” Journal of Biological Chemistry 286, 22905–22912 (2011).

Krow, G.R.; Edupuganti, R.; Gandla, D.; Yu, F.; Sender, M.; Sonnet, P.E.; Zdilla, M.J.; DeBrosse, C.; Cannon, K.C.; Ross, C.W., III; Choudhary, A.; Shoulders, M.D.; Raines, R.T. “Synthesis of Conformationally Constrained 5-Fluoro- and 5-Hydroxymethanopyrrolidines. Ring Puckered Mimics of Gauche and Anti-3-Fluoro- and 3-Hydroxypyrrolidines” Journal of Organic Chemistry 76, 3626–3634 (2011).

Shoulders, M.D.; Kotch F.W.; Choudhary, A.; Guzei, I.A.; Raines, R.T. “The Aberrance of the 4S Diastereomer of 4-Hydroxyproline” Journal of the American Chemical Society, 132, 10857–10865 (2010).

Shoulders, M.D.; Satyshur, K.A.; Forest, K.T.; Raines, R.T. “Stereoelectronic and Steric Effects in Side Chains Preorganize a Protein Main Chain” Proceedings of the National Academy of Sciences, USA 107, 559–564 (2010).

Krow, G.R.; Liu, N.; Sender, M.; Lin, G.; Centafont, R.; Sonnet, P.E.; DeBrosse, C.; Ross, C.W., III; Carroll, P.J.; Shoulders, M.D.; Raines, R.T. “Oligomers of a 5-Carboxymethanopyrrolidine β-Amino Acid—A Search for Order” Organic Letters 12, 5438–5441 (2010).

Shoulders, M.D.; Kamer, K.J.; Raines, R.T. “Origin of the Stability Conferred upon Collagen by Fluorination” Bioorganic and Medicinal Chemistry Letters 19, 3859–3862 (2009).

Shoulders, M.D.; Raines, R.T. “Collagen Structure and Stability” Annual Review of Biochemistry 78, 929–958 (2009).

Shoulders, M.D.; Raines, R.T. “Modulating Collagen Triple-Helix Stability with 4-Chloro, 4-Fluoro, and 4-Methylprolines” Advances in Experimental Medicine and Biology 611, 251–252 (2009).

Shoulders, M.D.; Guzei, I.A.; Raines, R.T. “4-Chloroprolines: Synthesis, Conformational Analysis, and Effect on the Collagen Triple Helix” Biopolymers 89, 443–454 (2008).

Shoulders, M.D.; Hodges, J.A.; Raines, R.T. “Reciprocity of Steric and Stereoelectronic Effects in the Collagen Triple Helix” Journal of the American Chemical Society 128, 8112–8113 (2006).