Publications

PUBLICATIONS

(see also google scholar and researcherID)

(51) C. R. Nisler, Y. Narui, D. Choudhary, J. D. Bowman, V. J. Lynch, M. Sotomayor. “Interpreting the Evolutionary Echoes of a Protein Complex Essential for Inner-Ear Mechanosensation.”. Submitted. bioRxiv version.

(50) S. Walujkar*, J. M. Lotthammer§*, C. R. Nisler, , J. C. Sudar§, Angela Ballesteros, M. Sotomayor. “In-Silico Electrophysiology of Inner-Ear Mechanotransduction Channel TMC1 Models”. Submitted. bioRxiv version.

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(49) B. L. Neel, C. R. Nisler, S. Walujkar, R. Araya-Secchi, M. Sotomayor. “Collective Mechanical Responses of Cadherin-Based Adhesive Junctions as Predicted by Simulations”. In press, Biophysical Journal, 2022. bioRxiv version.

(48) B. L. Neel*, C. R. Nisler*, S. Walujkar*, R. Araya-Secchi, M. Sotomayor. “Elastic versus Brittle Mechanical Responses Predicted for Dimeric Cadherin Complexes”. In press, Biophysical Journal, 2022. bioRxiv version.

(47) Y. Chen, M. Sotomayor, S. Capponi, B. Hariharan, I. D. Sahu, M. Haase, G. A. Lorigan, A. Kuhn, S. H. White, R. E. Dalbey. “A Hydrophilic Microenvironment in the Substrate-Translocating Groove of the YidC Membrane Insertase is Essential for Enzyme Function”. In press, Journal of Biological Chemistry, 2022.

(46) T. Ahmed,  C. R. Nisler, E. C. Fluck III, S. Walujkar, M. Sotomayor, V. Y. Moiseenkova-Bell. “Structure of the ancient TRPY1 channel from Saccharomyces cerevisiae reveals mechanisms of modulation by lipids and calcium”. Structure, 30:139-155, 2022. Journal version, bioRxiv version, commentary, cover!

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(45) M. E. Gray*, Z. R. Johnson§*, D. Modak*, E. Tamilselvan, M. J. Tyska, M. Sotomayor. “Heterophilic and Homophilic Cadherin Interactions in Intestinal Intermicrovillar Links are Species-Dependent”. PLoS Biology 19(12):e3001463, 2021. Journal version, bioRxiv version.

(44) J. D. Hudson, E. Tamilselvan, M. Sotomayor, S. R. Cooper. “A complete Protocadherin-19 ectodomain model for evaluating epilepsy-causing mutations and its protein interaction network”. Structure, 29:1128-1143, 2021. Journal version, cover!

(43) B. J. Caldwell, A. Norris, E. Zakharova, C. E. Smith, C. T. Wheat, D. Choudhary, M. Sotomayor, V. H. Wysocki, C. E. Bell. “Oligomeric complexes formed by Redβ single strand annealing protein in its different DNA bound states”. Nucleic Acids Res. 49:3441-3460, 2021.

(42) M. E. Gray and M. Sotomayor. “Crystal structure of the nonclassical cadherin-17 N-terminus and implications for its adhesive binding mechanism”. Acta Crystallogr. F Struct. Biol. Commun. 77:85-94, 2021.

(41) H. Smith, N. Pinkerton, D. B. Heisler, E. Kudryashova, A. R. Hall, K. R. Karch, A. Norris, V. Wysocki, M. Sotomayor, E. Reisler, D. Vavylonis, D. S. Kudryashov. “Rounding Out the Understanding of ACD Toxicity with the Discovery of Cyclic Forms of Actin Oligomers”.  Int. J. Mol. Sci. 22:718, 2021.

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(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 Mechanics and Function in Hearing and Balance Perception”. PNAS, 117:24837-24848, 2020. Journal version, 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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