The Martin Lab

UC Berkeley


Jonsson, E., Htet, Z.H., Bard, J.A.M., Dong, K. & Martin, A. Ubiquitin modulates 26S proteasome conformational dynamics and promotes substrate degradation. bioRxiv. August 2021. doi: https://doi.org/10.1101/2021.08.18.456915


Chen, X., Htet, Z.H., López-Alphonso, E., Martin, A. & Walters, K.J. Proteasome interaction with ubiquitinated substrates: from mechanisms to therapies. The FEBS Journal. November 2020. https://doi.org/10.1111/febs.15638

Castanzo, D.T., LaFrance, B., & Martin, A The AAA+ ATPase Msp1 is a processive protein translocase with robust unfoldase activity. Proceedings of the National Academies of Science (USA). June 2020. https://doi.org/10.1073/pnas.1920109117

Carroll, E.C., Greene, E.R., Martin, A., & Marqusee S.M. Site-specific ubiquitination affects protein energetics and proteasomal degradation. Nature Chemical Biology. June 2020. https://doi.org/10.1038/s41589-020-0556-3 [News and Views: Unraveling proteasome engagement]

Greene, E.R., Dong, K.C., & Martin, A. Understanding the 26S proteasome molecular machine from a structural and conformational dynamics perspective. Current Opinion in Structural Biology. April 2020. doi:10.1016/j.sbi.2019.10.004


Greene, E.R., Goodall, E.A., de la Peña, A.H., Matyskela, M.E., Lander, G.C., & Martin, A. Specific lid-base contacts in the 26s proteasome control the conformational switching required for substrate degradation. eLife, 2019 Nov 28. DOI: 10.7554/eLife.49806 .

Gates, S.N., & Martin, A. Stairway to translocation: AAA+ motor structures reveal the mechanisms of ATP‐dependent substrate translocation. Protein Science, 2019 Oct 09. doi: 10.1002/pro.3743.

Blythe E.E., Gates S.N., Deshaies R.J., Martin A. Multisystem Proteinopathy Mutations in VCP/p97 Increase NPLOC4·UFD1L Binding and Substrate Processing. Structure. 2019 Oct 08. PMID: 31623962.

Bard, J.A.M., Bashore, C., Dong, K.C. & Martin, A. The 26S Proteasome Utilizes a Kinetic Gateway to Prioritize Substrate Degradation. Cell 177, 1-13 (2019). doi:10.1016.cell.2019.02.031

Olszewski, M. M., Williams, C., Dong, K. C. & Martin, A. The Cdc48 unfoldase prepares well-folded protein substrates for degradation by the 26S proteasome. Communications Biology 2, 29 (2019). doi:10.103/s42003-019-0283-z


de la Peña, A.H.*, Goodall, E.A.*, Gates, S.N.*, Lander, G.C., Martin, A. Substrate-engaged 26S proteasome structures reveal mechanisms for ATP-hydrolysis–driven translocation. Science 362, 6418 (2018). doi:10.1126/science.aav0725

Proteasome in Action

Bard J.A.M., Martin A. (2018) Recombinant Expression, Unnatural Amino Acid Incorporation, and Site-Specific Labeling of 26S Proteasomal Subcomplexes. In: Mayor T., Kleiger G. (eds) The Ubiquitin Proteasome System. Methods in Molecular Biology, vol. 1844. Humana Press, New York, NY

Bard, J.A.M.*, Goodall, E.A.*, Greene, E.R., Jonsson, E., Dong, K.C., Martin, A. Structure and Function of the 26S Proteasome. Annu Rev Biochem (2018). doi:10.1146/annurev-biochem-062917-011931

Gardner, B.M., Castanzo, D.T., Chowdhury, S., Stjepanovic, G., Stefely, M.S., Hurley, J.H., Lander, G.C., Martin, A. The peroxisomal AAA-ATPase Pex1/Pex6 unfolds substrates by processive threading. Nat Commun 9, 135 (2018).


San Martín, Á., Rodriguez-Aliaga, P., Molina, J.A., Martin, A., Bustamante, C., & Baez, M. Knots can impair protein degradation by ATP-dependent proteases. Proc Natl Acad Sci USA 114, 9864–9869 (2017).

Worden, E.J., Dong, K.C., & Martin, A. An AAA Motor-Driven Mechanical Switch in Rpn11 Controls Deubiquitination at the 26S Proteasome. Mol Cell. 67, 1–22 (2017).


Rodriguez-Aliaga, P., Ramirez, L., Kim, F., Bustamante, C. & Martin, A. Substrate-translocating loops regulate mechanochemical coupling and power production in AAA+ protease ClpXP. Nat Struct Mol Biol 23, 974–981 (2016).

Dambacher, C.M.*, Worden, E.J.*, Herzik, M.A., Martin, A. & Lander, G.C. Atomic structure of the 26S proteasome lid reveals the mechanism of deubiquitinase inhibition. eLife 5, 1-17 (2016).


Bashore, C., Dambacher, C.M., Goodall, E.A., Matyskiela, M.E., Lander, G.C., Martin, A. Ubp6 deubiquitinase controls conformational dynamics and substrate degradation of the 26S proteasome. Nat Struct Mol Biol 22, 712–719 (2015).

Yang, B., Stjepanovic, G., Shen, Q., Martin, A. & Hurley, J. H. Vps4 disassembles an ESCRT-III filament by global unfolding and processive translocation. Nat Struct Mol Biol 22, 492–498 (2015)

Gardner, B.M., Chowdhury, S., Lander, G.C., Martin, A. The Pex1/Pex6 Complex Is a Heterohexameric AAA+ Motor with Alternating and Highly Coordinated Subunits. J Mol Biol 427, 1375–1388 (2015).


Worden, E.J., Padovani, C. & Martin, A. Structure of the Rpn11-Rpn8 dimer reveals mechanisms of substrate deubiquitination during proteasomal degradation. Nat Struct Mol Biol 21, 220–227 (2014).

Nyquist, K. & Martin, A. Marching to the beat of the ring: polypeptide translocation by AAA+ proteases. Trends Biochem Sci 39, 53-60 (2014).


Sen, M.*, Maillard, R.A.*, Nyquist, K.*, Rodriguez-Aliaga, P., Pressé, S., Martin, A. & Bustamante, C. The ClpXP protease unfolds substrates using a constant rate of pulling but different gears. Cell 155, 636-46 (2013).

Beckwith, R., Estrin, E., Worden, E.J. & Martin, A. Reconstitution of the 26S proteasome reveals functional asymmetries in its AAA+ unfoldase. Nat Struct Mol Biol 10, 1164-72 (2013).

AAA+ Asymmetries

Estrin, E., Lopez-Blanco, J.R., Chacon, P. & Martin, A. Formation of an intricate helical bundle dictates the assembly of the 26S proteasome lid. Structure 21, 1-12 (2013).

Matyskiela, M.E., Lander, G. C. & Martin, A. Conformational switching of the 26S proteasome enables substrate degradation. Nat Struct Mol Biol 20, 781-8 (2013).

Lander, G.C., Martin, A. & Nogales, E. The proteasome under the microscope: the regulatory particle in focus. Curr Opin Struct Biol 23, 243-51 (2013).

Matyskiela, M.E., & Martin, A. Design principles of a universal protein degradation machine. J Mol Bio 425, 199-213 (2013).


Lander, G.C.*, Estrin, E.*, Matyskiela, M.E.*, Bashore, C., Nogales, E. & Martin, A. Complete subunit architecture of the proteasome regulatory particle. Nature 482, 186-91 (2012).


Maillard, R.A., Chistol, G., Sen, M., Righini, M., Tan, J., Kaiser, C. M., Hodges, C., Martin, A. & Bustamante, C. ClpX(P) generates mechanical force to unfold and translocate its protein substrates. Cell 145, 459-69 (2011).


Glynn, S.E., Martin, A., Nagar, A. R., Baker, T. A. & Sauer, R. T. Structures of asymmetric ClpX hexamers reveal nucleotide-dependent motions in a AAA+ protein-unfolding machine. Cell 139, 744-56 (2009).


Martin, A., Baker, T.A. & Sauer, R.T. Pore loops of the AAA+ ClpX machine grip substrates to drive translocation and unfolding. Nat Struct Mol Biol 15, 1147-51 (2008).

Martin, A., Baker, T.A. & Sauer, R.T. Protein unfolding by a AAA+ protease is dependent on ATP-hydrolysis rates and substrate energy landscapes. Nat Struct Mol Biol 15, 139-45 (2008).

Martin, A., Baker, T.A. & Sauer, R.T. Diverse pore loops of the AAA+ ClpX machine mediate unassisted and adaptor-dependent recognition of ssrA-tagged substrates. Mol Cell 29, 441-50 (2008).


Martin, A., Baker, T.A. & Sauer, R.T. Distinct static and dynamic interactions control ATPase-peptidase communication in a AAA+ protease. Mol Cell 27, 41-52 (2007).


Martin, A., Baker, T.A. & Sauer, R.T. Rebuilt AAA + motors reveal operating principles for ATP-fuelled machines. Nature 437, 1115-20 (2005).