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selected publications

*Western Washington University undergraduate or †Masters student or ^High school student or #Post-bac scholar



†Vogel BA‡, #Blount JM‡, *Kodama HM‡, *Goodwin-Rice NJ, *Andaluz DJ, †Jackson SN, Antos JM, Amacher JF. A unique binding mode of P1' Leu-containing target sequences for Streptococcus pyogenes Sortase A results in alternative cleavage. RSC Chem BiolAccepted. (‡ these authors contributed equally)

^Godse S, ^Sapar T, Amacher JF. An idea to explore: Engaging high school students in structure-function studies of bacterial sortase enzymes and inhibitors - A comprehensive computational experimental pipeline. Biochem Mol Biol Educ (2023). doi: 10.1002/bmb.21769.

*Tahti EF, *Blount JM, Jackson SN, *Gao M, Gill NP, Smith SN, *Pederson NJ, **Rumph SN, *Struyvenberg SA, *Mackley IGP, Madden DR, Amacher JF. Additive energetic contributions of multiple peptide positions determine the relative promiscuity of viral and human sequences for PDZ domain targets. Protein Science (2023). e4611. (**REU student from Bowdoin College)


Hobbs HT, Shah NH, Shoemaker SR, Amacher JF, Marqusee S, Kuriyan J. Saturation mutagenesis of a predicted ancestral Syk-family kinase. Protein Science (2022). 31(10):e4411.

*Johnson DA‡, *Piper IM‡, †Vogel BA‡, †Jackson SN‡, *Svendsen JE, *Kodama HM, *Lee DE, *Lindblom KM, McCarty J, Antos JM, Amacher JF. Structures of Streptococcus pyogenes Class A sortase in complex with substrate and product mimics provide key details of target recognition. J Biol Chem (2022). 298(10):102446. (‡ these authors contributed equally)

*Valgardson JD, †Struyvenberg SA, Sailer ZR, *Piper IM, *Svendsen JE, *Johnson DA, *Vogel BA, Antos JM, Harms MJ, Amacher JF. Comparative Analysis and Ancestral Sequence Reconstruction of Bacterial Sortase Family Proteins Generates Functional Ancestral Mutants with Different Sequence Specificities. Bacteria (2022). 1:121-135.

*Gao M‡, *Johnson DA‡, *Piper IM, *Kodama HM, *Svendsen JE, *Tahti E, *Longshore-Neate FA, *Vogel BA, Antos JM, Amacher JF. Structural and biochemical analyses of selectivity determinants in chimeric Streptococcus Class A sortase enzymes. Protein Science (2022). 31(3):701-715. (‡ these authors contributed equally)


Wofford HA‡, *Myers-Dean J‡, *Vogel BA, *Alamo KAE, *Longshore-Neate FA, Jagodzinski F, Amacher JF. Domain Analysis and Motif Matcher (DAMM): A Program to Predict Selectivity Determinants in Monosiga brevicollis PDZ Domains Using Human PDZ Data. Molecules (2021). 5;26(19):6034.

*Piper IM‡, †Struyvenberg SA‡, *Valgardson JD, *Johnson DA, *Gao M, *Johnston K, *Svendsen JE, *Kodama HM, Hvorecny KL, Antos JM, Amacher JF. (2021) Sequence variation in the β7-β8 loop of bacterial class A sortase enzymes alters substrate selectivity. J Biol Chem (2021). 297(2):100981.


*Gao M, *Mackley IGP, Mesbahi-Vasey S, †Bamonte HA, †Struyvenberg SA, *Landolt L, *Pederson NJ, *Williams LI, Bahl CD, Brooks L, Amacher JF. Structural Characterization and Computational Analysis of PDZ domains in Monosiga brevicollis. Protein Science (2020). In press.


Amacher JF, Brooks L, Hampton TH, Madden DR. Specificity in PDZ-peptide interaction networks: Computational analysis and review. J Struct Biol X. 4:100022. 


*Valgardson J‡, *Cosbey R‡, *Houser P‡, *Rupp M, *Van Bronkhorst R, *Lee M, Jagodzinski F, Amacher JFMotifAnalyzer-PDZ: A computational program to investigate the evolution of PDZ-binding target specificity. Protein Sci. 28(12): 2127-43.


Shah NH, Amacher JF, Nocka L, Kuriyan J. The Src module: an ancient scaffold in the evolution of cytoplasmic tyrosine kinases. Crit Rev Biochem Mol Biol. 2018. Sep 5: 1-29. Review.


Amacher JF, Hobbs HT, Cantor AC, Shah L, Rivero MJ, Mulchand SA, Kuriyan J. Phosphorylation control of the ubiquitin ligase Cbl is conserved in choanoflagellates. Protein Sci. 2018. 27(5): 923-32.



Courtney AH, Amacher JF, Kadlecek TA, Mollenauer MN, Au-Yeung BB, Kuriyan J, Weiss A. A Phosphosite within the SH2 Domain of Lck Regulates Its Activation by CD45. Mol Cell. 2017. 67(3):498-511



Amacher JF, Zhong F, Lisi GP, Zhu MQ, Alden SL, Hoke KR, Madden DR, Pletneva EV. A Compact Structure of Cytochrome c Trapped in a Lysine-Ligated State: Loop Refolding and Functional Implications of a Conformational Switch. J Am Chem Soc. 2015. 137(26):8435-49.


Qian Z, Xu X, Amacher JF, Madden DR, Cormet-Boyaka E, Pei D. Intracellular Delivery of Peptidyl Ligands by Reversible Cyclization: Discovery of a PDZ Domain Inhibitor that Rescues CFTR Activity. Angew Chem. 2015. 54(20):5874-8.



Amacher JF, Zhao R, Spaller MR, Madden DR. Chemically modified peptide scaffolds target the CFTR-associated ligand PDZ domain. PLoS One. 2014. 9(8):e103650.


Amacher JF, Cushing PR, Brooks L 3rd, Boisguerin P, Madden DR. Stereochemical preferences modulate affinity and selectivity among five PDZ domains that bind CFTR: comparative structural and sequence analyses. Structure. 2014. 22(1):82-93.



Amacher JF, Cushing PR, Bahl CD, Beck T, Madden DR. Stereochemical determinants of C-terminal specificity in PDZ peptide-binding domains: a novel contribution of the carboxylate-binding loop. J Biol Chem. 2013. 288(7):5114-26.

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