{"id":45,"date":"2012-12-07T23:18:24","date_gmt":"2012-12-07T23:18:24","guid":{"rendered":"http:\/\/localhost:8888\/wordpress\/?page_id=45"},"modified":"2023-08-04T11:37:54","modified_gmt":"2023-08-04T15:37:54","slug":"publications","status":"publish","type":"page","link":"https:\/\/research.cbc.osu.edu\/sotomayor.8\/publications\/","title":{"rendered":"Publications"},"content":{"rendered":"

PUBLICATIONS<\/em><\/p>\n

(see also google scholar<\/a>\u00a0and\u00a0researcherID<\/a>) <\/em><\/p>\n

(54) A. P. J. Giese*, W-H. Weng<\/em>*, K. S. Kindt, V. H. H. Chang, J. S. Montgomery, E. M. Ratzan, A. J. Beirl, R. Aponte Rivera, J. M. Lotthammer\u00a7<\/sup>, S. Walujkar, <\/em>M. P. Foster, O. A. Zobeiri, J. R. Holt, S. Riazuddin, K. E. Cullen, M. Sotomayor<\/em>, Z. M. Ahmed\u2020<\/sup>. “Complexes of vertebrate TMC1\/2 and CIB2\/3 proteins form hair-cell mechanotransduction cation channels”. Submitted. <\/em>bioRxiv version<\/a>.<\/p>\n

(53) S. Walujkar*<\/em>, J. M. Lotthammer\u00a7*<\/sup>, C. R. Nisler, J. C. Sudar\u00a7<\/sup>, <\/em>C. Klaus<\/em>, A. Ballesteros, M. Sotomayor<\/em>\u2020<\/sup>. “In-Silico <\/em>Electrophysiology of Inner-Ear Mechanotransduction Channel TMC1 Models”. Submitted. <\/em>bioRxiv version<\/a>.<\/p>\n

.<\/span><\/p>\n

(52) W. Zheng, S. Rawson, Z. Shen, E. Tamilselvan<\/em>, H. E. Smith<\/em>, J. Halford, C. Shen, S. E. Murthy, M. H. Ulbrich, M. Sotomayor<\/em>, T-M. Fu\u2020<\/sup>, J. R. Holt\u2020<\/sup>. \u201cTMEM63 Proteins Function as Monomeric High-threshold Mechanosensitive Ion Channels\u201d. In press, Neuron.<\/em><\/p>\n

(51) M. V. Ivanchenko, D. M. Hathaway, A. J. Klein, B. Pan, O. Strelkova, P. De-la-Torre, X. Wu, C. W. Peters, E. M. Mulhall, K. T. Booth, C. Goldstein, J. Brower, M. Sotomayor, <\/em>A. A. Indzhykulian, D. P. Corey\u2020<\/sup>. “Mini-PCDH15 gene therapy rescues hearing in a mouse model of Usher syndrome type 1F”.\u00a0Nature communications,\u00a0<\/em>14:2400, 2023.<\/p>\n

(50) C. R. Nisler, <\/em>Y. Narui*,<\/em> E. Scheib\u00a7<\/sup>*<\/em>, D. Choudhary, <\/em>J. D. Bowman, H. Mandayam Bharathi<\/em>, V. J. Lynch, M. Sotomayor<\/em>\u2020<\/sup>. “Interpreting the Evolutionary Echoes of a Protein Complex Essential for Inner-Ear Mechanosensation”. Molecular Biology and Evolution,<\/em> 40:msad057, 2023. bioRxiv version<\/a>.<\/p>\n

.<\/span><\/p>\n

(49) B. L. Neel, C. R. Nisler, S. Walujkar, R. Araya-Secchi, M. Sotomayor<\/em>\u2020<\/sup>. “<\/em>Collective Mechanical Responses of Cadherin-Based Adhesive Junctions as Predicted by Simulations”. Biophysical Journal,<\/em> 121:991-1012, 2022. bioRxiv version<\/a>.<\/p>\n

(48) B. L. Neel*, C. R. Nisler*, S. Walujkar*, R. Araya-Secchi, M. Sotomayor<\/em>\u2020<\/sup>. “<\/em>Elastic versus Brittle Mechanical Responses Predicted for Dimeric Cadherin Complexes”. Biophysical Journal,<\/em> 121:1013-1028, 2022. bioRxiv version<\/a>.<\/p>\n

(47) Y. Chen, M. Sotomayor<\/em>, S. Capponi, B. Hariharan, I. D. Sahu, M. Haase, G. A. Lorigan, A. Kuhn, S. H. White, R. E. Dalbey\u2020<\/sup>. \u201cA Hydrophilic Microenvironment in the Substrate-Translocating Groove of the YidC Membrane Insertase is Essential for Enzyme Function\u201d. Journal of Biological Chemistry<\/em>, 298:101690, 2022.<\/em>
\n<\/span><\/span><\/p>\n

(46) T. Ahmed,\u00a0 C. R. Nisler<\/em>, E. C. Fluck III, S. Walujkar<\/em>, M. Sotomayor<\/em>, V. Y. Moiseenkova-Bell\u2020<\/sup>. \u201cStructure of the ancient TRPY1 channel from Saccharomyces cerevisiae <\/em> reveals mechanisms of modulation by lipids and calcium\u201d.\u00a0Structure, <\/em>30:139-155, 2022. Journal version<\/a>, bioRxiv version,<\/a> commentary<\/a>, cover<\/a>!<\/p>\n

.<\/span><\/p>\n

(45) M. E. Gray<\/em>*, Z. R. Johnson<\/em>\u00a7<\/sup>*, D. Modak<\/em>*, E. Tamilselvan<\/em>, M. J. Tyska, M. Sotomayor<\/em>\u2020<\/sup>. \u201cHeterophilic and Homophilic Cadherin Interactions in Intestinal Intermicrovillar Links are Species-Dependent\u201d. PLoS Biology <\/em>19(12):e3001463, 2021. Journal version<\/a>, bioRxiv version<\/a>.<\/p>\n

(44) J. D. Hudson, E. Tamilselvan<\/em>, M. Sotomayor, <\/em>S. R. Cooper\u2020<\/sup>. \u201cA complete Protocadherin-19 ectodomain model for evaluating epilepsy-causing mutations and its protein interaction network\u201d. Structure,<\/em> 29:1128-1143, 2021. Journal version,<\/a> cover<\/a>!<\/p>\n

(43) B. J. Caldwell, A. Norris, E. Zakharova, C. E. Smith, C. T. Wheat, D. Choudhary<\/em>, M. Sotomayor<\/em>, V. H. Wysocki, C. E. Bell\u2020<\/sup>. “Oligomeric complexes formed by Red\u03b2 single strand annealing protein in its different DNA bound states”. Nucleic Acids Res. <\/em>49:3441-3460, 2021.<\/p>\n

(42) M. E. Gray <\/em>and M. Sotomayor<\/em>\u2020<\/sup>. “Crystal structure of the nonclassical cadherin-17 N-terminus and implications for its adhesive binding mechanism”. Acta Crystallogr. F Struct. Biol. Commun.<\/em> 77:85-94, 2021.<\/p>\n

(41) H. Smith, N. Pinkerton, D. B. Heisler, E. Kudryashova, A. R. Hall, K. R. Karch, A. Norris, V. Wysocki, M.<\/em> Sotomayor<\/em>, E. Reisler, D. Vavylonis, D. S. Kudryashov\u2020<\/sup>. “Rounding Out<\/em> the Understanding of ACD Toxicity with the Discovery of Cyclic Forms of Actin Oligomers”.\u00a0 Int. J. Mol. Sci.\u00a0<\/em>22:718, 2021.<\/p>\n

.<\/span><\/p>\n

(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<\/em>\u2020<\/sup>. \u201cStructural Determinants of Protocadherin-15 Mechanics and Function in Hearing and Balance Perception\u201d. PNAS, <\/em>117:24837-24848, 2020. Journal version<\/a>, bioRxiv version<\/a>.<\/p>\n

.<\/span><\/p>\n

(39) D. Modak<\/em> and M. Sotomayor\u2020<\/sup>. <\/em>“Identification of an Adhesive Interface for the Non-Clustered \u03b41 Protocadherin-1 Involved in Respiratory Diseases”. Communications Biology<\/em>, 2:354, 2019. Journal version<\/a>, bioRxiv version<\/a>.<\/p>\n

(38) J. W. Slater, S. C. Marguet, M. E. Gray<\/em>, H. A. Monaco, M. Sotomayor<\/em>, H. S. Shafaat\u2020<\/sup>. “Power of the Secondary Sphere: Modulating Hydrogenase Activity in Nickel-Substituted Rubredoxin”. ACS Catalysis, <\/em>9:8928-8942, 2019.<\/p>\n

(37) J. M. Nicoludis*, A. Green*, S. Walujkar<\/em>, E. May, M. Sotomayor<\/em>, D. Marks\u2020<\/sup>, and R. Gaudet\u2020<\/sup>. “Interaction specificity of clustered protocadherins inferred from sequence covariation and structural analysis”.\u00a0PNAS<\/em>, 116:17825-17830, 2019. Journal version<\/a>, bioRxiv version<\/a>.<\/p>\n

(36) M. S. Park*, R. Araya-Secchi<\/em>*, J. A. Brackbill*, H-D. Phan*, A. C. Kehling, E. W. Abd-El-Wahab, D. M. Dayeh, M. Sotomayor<\/em>, K. Nakanishi\u2020<\/sup>.<\/em> \u201cMultidomain convergence of Argonaute during RISC assembly correlates with the formation of internal water clusters\u201d. Molecular Cell,<\/em> 75:725-740, 2019.<\/em><\/p>\n

(35) T. H. Chen, M. Sotomayor<\/em>, and V. Gopalan\u2020<\/sup>. “Biochemical Studies Provide Insights into the Necessity for Multiple Arabidopsis thaliana<\/em> Protein-Only RNase P Isoenzymes” Journal of Molecular Biology<\/em>, 431:615-624, 2019.<\/p>\n

.<\/span><\/p>\n

(34) P. De-la-Torre<\/em>, D. Choudhary<\/em>, R. Araya-Secchi<\/em>, Y. Narui<\/em>, and M. Sotomayor\u2020<\/sup><\/em>. “A Mechanically Weak Extracellular Membrane-Adjacent Domain Induces Dimerization of Protocadherin-15” Biophysical Journal<\/em>, 115:2368-2385, 2018. Journal version<\/a>, bioRxiv version<\/a>.<\/p>\n

(33) B. Pan*, N. Akyuz*, X-P. Liu*, Y. Asai, C. Nist-Lund, K. Kurima, B. H. Derfler, B. Gy\u00f6rgy, W. Limapichat, S. Walujkar<\/em>, L. N. Wimalasena<\/em>, M. Sotomayor, <\/em>D. P. Corey\u2020<\/sup>, and J. R. Holt\u2020<\/sup>. “TMC1 Forms the Pore of Mechanosensory Transduction Channels in Vertebrate Inner Ear Hair Cells” Neuron, <\/em>99:736-753, 2018.<\/p>\n

(32) A. Jaiganesh<\/em>, P. De-la-Torre<\/em>, A. A. Patel<\/em>,<\/em> D. J. Termine<\/em>, F. Velez-Cortes<\/em>, C. Chen<\/em>, and M. Sotomayor\u2020<\/sup><\/em>. “Zooming in on cadherin-23: Structural diversity and potential mechanisms of inherited deafness” Structure, <\/em>25:1210-1225, 2018.<\/p>\n

(31) T. Fecker*, P. Galaz-Davison*, F. Engelberger,\u00a0Y. Narui<\/em>, M. Sotomayor\u2020<\/sup>,<\/em> L. P. Parra\u2020<\/sup>, and C. A. Ramirez-Sarmiento\u2020<\/sup>. “Active Site Flexibility as a Hallmark for Efficient PET Degradation by\u00a0I. sakaiensis <\/em>PETase” Biophysical Journal, <\/em>114:1302-1312, 2018.<\/p>\n

(30) Y. Narui <\/em>and M. Sotomayor\u2020<\/sup>. <\/em>“Tunning Inner-Ear Tip-Link Affinity Through Alternatively Spliced Variants of Protocadherin-15” Biochemistry, <\/em>57:1702-1710, <\/em>2018.<\/p>\n

.<\/span><\/p>\n

(29) D. Choudhary<\/em>, A. Kumar, T. J. Magliery, <\/em>and M. Sotomayor\u2020<\/sup><\/em>. “Using thermal scanning assays to test protein-protein interactions of inner-ear cadherins” PLoS ONE<\/em>, 12(12):e0189546, 2017.<\/p>\n

(28) A. Jaiganesh<\/em>, Y. Narui<\/em>, R. Araya-Secchi, <\/em>and M. Sotomayor\u2020<\/sup><\/em>. “Beyond Cell-Cell Adhesion: Sensational Cadherins for Hearing and Balance”\u00a0Cold Spring Harbor Perspectives in Biology<\/em> – Cell-Cell Junctions, 2017.<\/p>\n

(27) R. E. Powers, R. Gaudet\u2020<\/sup>, and M. Sotomayor\u2020<\/sup><\/em>. \u201cA partial calcium-free linker confers flexibility to inner-ear protocadherin-15\u201d Structure,<\/em>\u00a025:482-495, 2017.<\/p>\n

.<\/span><\/p>\n

(26) R. Araya-Secchi, B. L. Neel, <\/em>and M. Sotomayor\u2020<\/sup><\/em>. \u201cAn elastic element in the protocadherin-15 tip link of the inner ear\u201d Nature Communications,<\/em> 7:13458, 2016.<\/p>\n

(25) S. R. Cooper<\/em>, J. D. Jontes\u2020<\/sup>, and M. Sotomayor\u2020<\/sup>. \u201c<\/em>Structural determinants of adhesion by Protocadherin-19 and implications for its role in epilepsy\u201d eLife, <\/em>5:e18529, 2016.<\/p>\n

.<\/span><\/p>\n

(24) M. Sotomayor<\/em>\u2020<\/sup><\/em> R. Gaudet\u2020<\/sup>, and D. P. Corey.\u2020<\/sup> “Sorting out a promiscuous superfamily: towards cadherin connectomics” Trends in Cell Biology<\/em>, 24:524-536, 2014.<\/p>\n

(23) M. A. Koussa, M. Sotomayor<\/em>, and W. Wong\u2020<\/sup>. “Protocol for sortase-mediated construction of DNA-protein hybrids and functional nanostructures” Methods<\/em>, 67:134-141, 2014.<\/p>\n

.<\/span><\/p>\n

(22) R. Geng, M. Sotomayor<\/em>, 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\u2020<\/sup>. “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<\/em>, 33:4395-4404, 2013. Recommended by F1000Prime<\/em>.<\/p>\n

.<\/span><\/p>\n

(21) M. Sotomayor<\/em>, W. A. Weihofen, R. Gaudet\u2020<\/sup>, and D. P. Corey\u2020<\/sup>. “Structure of a Force-Conveying Cadherin Bond Essential for Inner-Ear Mechanotransduction” Nature<\/em>, 492:128-132, 2012.<\/p>\n

(20) H. Inada, E. Procko, M. Sotomayor<\/em>, and R. Gaudet\u2020<\/sup>. “Structural and biochemical consequences of disease-causing mutations in the ankyrin repeat domain of the human TRPV4 channel” Biochemistry<\/em>, 51:6195-6206, 2012. Recommended by F1000Prime<\/em>.<\/p>\n

(19) J. Gumbart, F. Khalili-Araghi, M. Sotomayor<\/em>, and B. Roux\u2020<\/sup>. “Constant Electric Field Simulations of the Membrane Potential Illustrated with Simple Systems” BBA – Biomembranes<\/em>, 1818:294-302, 2012.<\/p>\n

.<\/span><\/p>\n

(18) R. Gamini, M. Sotomayor<\/em>, C. Chipot, and K. Schulten\u2020<\/sup>. “Cytoplasmic domain filter function in the mechanosensitive channel of small conductance” Biophysical Journal<\/em>, 101:80-89, 2011. (pdf<\/a>)<\/p>\n

(17) D. Asenjo, F. Lund\u2020<\/sup>, S. Poblete, R. Soto, and M. Sotomayor<\/em>. “Characterization of the melting transition in two dimensions at vanishing external pressure using molecular dynamics simulations” Physical Review B<\/em>, 83:174110, 2011.<\/p>\n

.<\/span><\/p>\n

(16) M. Sotomayor*<\/em>, W. A. Weihofen*, R. Gaudet\u2020<\/sup>, and D. P. Corey\u2020<\/sup>. “Structural Determinants of Cadherin-23 Function in Hearing and Deafness” Neuron<\/em>, 66:85-100, 2010. Recommended by F1000Prime<\/em>.
\n\"\"<\/p>\n

.<\/span><\/p>\n

(15) E. H. Lee, J. Hsin, G. Comellas, M. Sotomayor<\/em>, and K. Schulten\u2020<\/sup>. “Discovery through the computational microscope” Structure<\/em>, 17:1295-1306, 2009. (pdf<\/a>)<\/p>\n

(14) F. Khalili-Araghi, J. Gumbart, P. Wen, M. Sotomayor<\/em>, E. Tajkhorshid, and K. Schulten\u2020<\/sup>. “Molecular Dynamics Simulations of Membrane Channels and Transporters” Current Opinion in Structural Biology<\/em>, 19:128-137, 2009. (pdf<\/a>)<\/p>\n

.<\/span><\/p>\n

(13) V. Vasquez, M. Sotomayor<\/em>, J. Cordero-Morales, K. Schulten, and E. Perozo\u2020<\/sup>. “A Structural Mechanism for MscS gating in lipid bilayers” Science<\/em>, 321:1210-1214, 2008. (pdf<\/a>)<\/p>\n

(12) M. Sotomayor<\/em> and K. Schulten\u2020<\/sup>. “The Allosteric Role of the Ca++ Switch in Adhesion and Elasticity of C-Cadherin” Biophysical Journal<\/em>, 94:4621-4633, 2008. (pdf<\/a>)<\/p>\n

(11) B. Lim, E. H. Lee, M. Sotomayor<\/em>, and Klaus Schulten\u2020<\/sup>. “Molecular basis of fibrin clot elasticity” Structure<\/em>, 16:449-459, 2008. (pdf<\/a>)<\/p>\n

(10) V. Vasquez, M. Sotomayor<\/em>, D. Marien Cortes, Benoit Roux, Klaus Schulten, and Eduardo Perozo\u2020<\/sup>. “Three dimensional architecture of membrane-embedded MscS in the closed conformation” Journal of Molecular Biology<\/em>, 378:55-70, 2008. (pdf<\/a>)<\/p>\n

.<\/span><\/p>\n

(9) M. Sotomayor<\/em> and K. Schulten\u2020<\/sup>. “Single-Molecule Experiments in Vitro<\/em> and in Silico<\/em>” Science<\/em>, 316:1144-1148, 2007. (pdf<\/a>)
\n\"\"<\/p>\n

(8) M. Sotomayor*<\/em>, V. Vasquez*, E. Perozo, and K. Schulten\u2020<\/sup>. “Ion Conduction through MscS as Determined by Electrophysiology and Simulation” Biophysical Journal<\/em>, 92:886-902, 2007. (pdf<\/a>)<\/p>\n

.<\/span><\/p>\n

(7) M. Gao, M. Sotomayor<\/em>, E. Villa, E. Lee, and K. Schulten\u2020<\/sup>. “Molecular Mechanisms of Cellular Mechanics” Physical Chemistry – Chemical Physics<\/em>, 8:3692-3706, 2006. (pdf<\/a>)
\n\"\"<\/p>\n

(6) M. Sotomayor*<\/em>, T. A. van der Straaten*, U. Ravaioli, and K. Schulten\u2020<\/sup>. “Electrostatic Properties of the Mechanosensitive Channel of Small Conductance MscS” Biophysical Journal<\/em>, 90:3496-3510, 2006. (pdf<\/a>)<\/p>\n

.<\/span><\/p>\n

(5) M. Sotomayor<\/em>, D. P. Corey, and K. Schulten\u2020<\/sup>. “In Search of the Hair-Cell Gating Spring: Elastic Properties of Ankyrin and Cadherin Repeats” Structure<\/em>, 13:669-682, 2005. (pdf<\/a>)<\/p>\n

(4) E. Tajkhorshid, J. Cohen, A. Aksimentiev, M. Sotomayor<\/em>, and K. Schulten\u2020<\/sup>. “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<\/a>)<\/p>\n

.<\/span><\/p>\n

(3) M. Sotomayor<\/em> and K. Schulten\u2020<\/sup>. “Molecular Dynamics Study of Gating in the Mechanosensitive Channel of Small Conductance MscS” Biophysical Journal<\/em>, 87:3050-3065, 2004. (pdf<\/a>)<\/p>\n

(2) D.P. Corey\u2020<\/sup> and M. Sotomayor.<\/em> “Tightrope act” Nature<\/em>, 428:901-902, 2004.<\/p>\n

.<\/span><\/p>\n

(1) C.J. Clarke\u2020<\/sup>, A. Gendrin, and M. Sotomayor<\/em>. “The dispersal of circumstellar discs: the role of the ultraviolet switch” Monthly Notices of the Royal Astronomical Society<\/em>, 328:485-491, 2001. (pdf<\/a>)<\/p>\n","protected":false},"excerpt":{"rendered":"

PUBLICATIONS (see also google scholar\u00a0and\u00a0researcherID) (54) A. P. J. Giese*, W-H. Weng*, K. S. Kindt, V. H. H. Chang, J. S. Montgomery, E. M. Ratzan, A. J. Beirl, R. Aponte Rivera, J. M. Lotthammer\u00a7, S. Walujkar, M. P. Foster, O. … Continue reading →<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"open","ping_status":"open","template":"showcase.php","meta":{"footnotes":""},"class_list":["post-45","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/research.cbc.osu.edu\/sotomayor.8\/wp-json\/wp\/v2\/pages\/45","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/research.cbc.osu.edu\/sotomayor.8\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/research.cbc.osu.edu\/sotomayor.8\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/research.cbc.osu.edu\/sotomayor.8\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/research.cbc.osu.edu\/sotomayor.8\/wp-json\/wp\/v2\/comments?post=45"}],"version-history":[{"count":64,"href":"https:\/\/research.cbc.osu.edu\/sotomayor.8\/wp-json\/wp\/v2\/pages\/45\/revisions"}],"predecessor-version":[{"id":2386,"href":"https:\/\/research.cbc.osu.edu\/sotomayor.8\/wp-json\/wp\/v2\/pages\/45\/revisions\/2386"}],"wp:attachment":[{"href":"https:\/\/research.cbc.osu.edu\/sotomayor.8\/wp-json\/wp\/v2\/media?parent=45"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}