Publications

PUBLICATIONS

(see also google scholar and researcherID)

(40) D. Choudhary*, Y. Narui*, B. L. Neel*, L. N. Wimalasena, C. F. Klanseck, P. De-la-Torre, C. Chen, R. Araya-Secchi, E. Tamilselvan, M. Sotomayor. “Structural Determinants of Protocadherin-15 Elasticity and Function in Inner- Ear Mechanotransduction”. Submitted, bioRxiv version.

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(39) D. Modak and M. Sotomayor. “Identification of an Adhesive Interface for the Non-Clustered δ1 Protocadherin-1 Involved in Respiratory Diseases”. Communications Biology, 2:354, 2019. Journal version, bioRxiv version.

(38) J. W. Slater, S. C. Marguet, M. E. Gray, H. A. Monaco, M. Sotomayor, H. S. Shafaat. “Power of the Secondary Sphere: Modulating Hydrogenase Activity in Nickel-Substituted Rubredoxin”. ACS Catalysis, 9:8928-8942, 2019.

(37) J. M. Nicoludis*, A. Green*, S. Walujkar, E. May, M. Sotomayor, D. Marks, and R. Gaudet. “Interaction specificity of clustered protocadherins inferred from sequence covariation and structural analysis”. PNAS, 116:17825-17830, 2019. Journal version, bioRxiv version.

(36) M. S. Park*, R. Araya-Secchi*, J. A. Brackbill*, H-D. Phan*, A. C. Kehling, E. W. Abd-El-Wahab, D. M. Dayeh, M. Sotomayor, K. Nakanishi. “Multidomain convergence of Argonaute during RISC assembly correlates with the formation of internal water clusters”. Molecular Cell, 75:725-740, 2019.

(35) T. H. Chen, M. Sotomayor, and V. Gopalan. “Biochemical Studies Provide Insights into the Necessity for Multiple Arabidopsis thaliana Protein-Only RNase P Isoenzymes” Journal of Molecular Biology, 431:615-624, 2019.

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(34) P. De-la-Torre, D. Choudhary, R. Araya-Secchi, Y. Narui, and M. Sotomayor. “A Mechanically Weak Extracellular Membrane-Adjacent Domain Induces Dimerization of Protocadherin-15” Biophysical Journal, 115:2368-2385, 2018. Journal version, bioRxiv version.

(33) B. Pan*, N. Akyuz*, X-P. Liu*, Y. Asai, C. Nist-Lund, K. Kurima, B. H. Derfler, B. György, W. Limapichat, S. Walujkar, L. N. Wimalasena, M. Sotomayor, D. P. Corey, and J. R. Holt. “TMC1 Forms the Pore of Mechanosensory Transduction Channels in Vertebrate Inner Ear Hair Cells” Neuron, 99:736-753, 2018.

(32) A. Jaiganesh, P. De-la-Torre, A. A. Patel, D. J. Termine, F. Velez-Cortes, C. Chen, and M. Sotomayor. “Zooming in on cadherin-23: Structural diversity and potential mechanisms of inherited deafness” Structure, 25:1210-1225, 2018.

(31) T. Fecker*, P. Galaz-Davison*, F. Engelberger, Y. Narui, M. Sotomayor, L. P. Parra, and C. A. Ramirez-Sarmiento. “Active Site Flexibility as a Hallmark for Efficient PET Degradation by I. sakaiensis PETase” Biophysical Journal, 114:1302-1312, 2018.

(30) Y. Narui and M. Sotomayor. “Tunning Inner-Ear Tip-Link Affinity Through Alternatively Spliced Variants of Protocadherin-15” Biochemistry, 57:1702-1710, 2018.

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(29) D. Choudhary, A. Kumar, T. J. Magliery, and M. Sotomayor. “Using thermal scanning assays to test protein-protein interactions of inner-ear cadherins” PLoS ONE, 12(12):e0189546, 2017.

(28) A. Jaiganesh, Y. Narui, R. Araya-Secchi, and M. Sotomayor. “Beyond Cell-Cell Adhesion: Sensational Cadherins for Hearing and Balance” Cold Spring Harbor Perspectives in Biology – Cell-Cell Junctions, 2017.

(27) R. E. Powers, R. Gaudet, and M. Sotomayor. “A partial calcium-free linker confers flexibility to inner-ear protocadherin-15” Structure, 25:482-495, 2017.

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(26) R. Araya-Secchi, B. L. Neel, and M. Sotomayor. “An elastic element in the protocadherin-15 tip link of the inner ear” Nature Communications, 7:13458, 2016.

(25) S. R. Cooper, J. D. Jontes, and M. Sotomayor. “Structural determinants of adhesion by Protocadherin-19 and implications for its role in epilepsy” eLife, 5:e18529, 2016.

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(24) M. Sotomayor R. Gaudet, and D. P. Corey. “Sorting out a promiscuous superfamily: towards cadherin connectomics” Trends in Cell Biology, 24:524-536, 2014.

(23) M. A. Koussa, M. Sotomayor, and W. Wong. “Protocol for sortase-mediated construction of DNA-protein hybrids and functional nanostructures” Methods, 67:134-141, 2014.

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(22) R. Geng, M. Sotomayor, K. J. Kinder, S. R. Gopal, J. Gerka-Stuyt, D. H.-C. Chen, R. E. Hardisty-Hughes, G. Ball, A. Parker, R. Gaudet, D. Furness, S. D. Brown, D. P. Corey, and K. N. Alagramam. “Noddy, a mouse harboring a missense mutation in protocadherin-15, reveals the impact of disrupting a critical interaction site between tip-link cadherins in inner ear hair cells” The Journal of Neuroscience, 33:4395-4404, 2013. Recommended by F1000Prime.

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(21) M. Sotomayor, W. A. Weihofen, R. Gaudet, and D. P. Corey. “Structure of a Force-Conveying Cadherin Bond Essential for Inner-Ear Mechanotransduction” Nature, 492:128-132, 2012.

(20) H. Inada, E. Procko, M. Sotomayor, and R. Gaudet. “Structural and biochemical consequences of disease-causing mutations in the ankyrin repeat domain of the human TRPV4 channel” Biochemistry, 51:6195-6206, 2012. Recommended by F1000Prime.

(19) J. Gumbart, F. Khalili-Araghi, M. Sotomayor, and B. Roux. “Constant Electric Field Simulations of the Membrane Potential Illustrated with Simple Systems” BBA – Biomembranes, 1818:294-302, 2012.

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(18) R. Gamini, M. Sotomayor, C. Chipot, and K. Schulten. “Cytoplasmic domain filter function in the mechanosensitive channel of small conductance” Biophysical Journal, 101:80-89, 2011. (pdf)

(17) D. Asenjo, F. Lund, S. Poblete, R. Soto, and M. Sotomayor. “Characterization of the melting transition in two dimensions at vanishing external pressure using molecular dynamics simulations” Physical Review B, 83:174110, 2011.

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(16) M. Sotomayor*, W. A. Weihofen*, R. Gaudet, and D. P. Corey. “Structural Determinants of Cadherin-23 Function in Hearing and Deafness” Neuron, 66:85-100, 2010. Recommended by F1000Prime.

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(15) E. H. Lee, J. Hsin, G. Comellas, M. Sotomayor, and K. Schulten. “Discovery through the computational microscope” Structure, 17:1295-1306, 2009. (pdf)

(14) F. Khalili-Araghi, J. Gumbart, P. Wen, M. Sotomayor, E. Tajkhorshid, and K. Schulten. “Molecular Dynamics Simulations of Membrane Channels and Transporters” Current Opinion in Structural Biology, 19:128-137, 2009. (pdf)

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(13) V. Vasquez, M. Sotomayor, J. Cordero-Morales, K. Schulten, and E. Perozo. “A Structural Mechanism for MscS gating in lipid bilayers” Science, 321:1210-1214, 2008. (pdf)

(12) M. Sotomayor and K. Schulten. “The Allosteric Role of the Ca++ Switch in Adhesion and Elasticity of C-Cadherin” Biophysical Journal, 94:4621-4633, 2008. (pdf)

(11) B. Lim, E. H. Lee, M. Sotomayor, and Klaus Schulten. “Molecular basis of fibrin clot elasticity” Structure, 16:449-459, 2008. (pdf)

(10) V. Vasquez, M. Sotomayor, D. Marien Cortes, Benoit Roux, Klaus Schulten, and Eduardo Perozo. “Three dimensional architecture of membrane-embedded MscS in the closed conformation” Journal of Molecular Biology, 378:55-70, 2008. (pdf)

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(9) M. Sotomayor and K. Schulten. “Single-Molecule Experiments in Vitro and in SilicoScience, 316:1144-1148, 2007. (pdf)

(8) M. Sotomayor*, V. Vasquez*, E. Perozo, and K. Schulten. “Ion Conduction through MscS as Determined by Electrophysiology and Simulation” Biophysical Journal, 92:886-902, 2007. (pdf)

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(7) M. Gao, M. Sotomayor, E. Villa, E. Lee, and K. Schulten. “Molecular Mechanisms of Cellular Mechanics” Physical Chemistry – Chemical Physics, 8:3692-3706, 2006. (pdf)

(6) M. Sotomayor*, T. A. van der Straaten*, U. Ravaioli, and K. Schulten. “Electrostatic Properties of the Mechanosensitive Channel of Small Conductance MscS” Biophysical Journal, 90:3496-3510, 2006. (pdf)

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(5) M. Sotomayor, D. P. Corey, and K. Schulten. “In Search of the Hair-Cell Gating Spring: Elastic Properties of Ankyrin and Cadherin Repeats” Structure, 13:669-682, 2005. (pdf)

(4) E. Tajkhorshid, J. Cohen, A. Aksimentiev, M. Sotomayor, and K. Schulten. “Towards understanding membrane channels” in Bacterial ion channels and their eukaryotic homologues, Boris Martinac and Andrzej Kubalski, editors, pp 153-190. ASM Press, Washington, DC, 2005. (pdf)

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(3) M. Sotomayor and K. Schulten. “Molecular Dynamics Study of Gating in the Mechanosensitive Channel of Small Conductance MscS” Biophysical Journal, 87:3050-3065, 2004. (pdf)

(2) D.P. Corey and M. Sotomayor. “Tightrope act” Nature, 428:901-902, 2004.

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(1) C.J. Clarke, A. Gendrin, and M. Sotomayor. “The dispersal of circumstellar discs: the role of the ultraviolet switch” Monthly Notices of the Royal Astronomical Society, 328:485-491, 2001. (pdf)

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