The Martin Lab

UC Berkeley


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, (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 (2015). doi:10.1038/nsmb.3015

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).

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).