You are here

Science

Staff Publications (2013 - 2022)

  1. Adaptable SEC-SAXS data collection for higher quality structure analysis in solution.
    Matsui, T.; Rajkovic, I.; Mooers, B.H.M.; Liu, P.; Weiss, T.M. Protein Science 33, (2024).
  2. Viscoelastic analysis of mussel threads reveals energy dissipative mechanisms.
    Areyano, M.; Valois, E.; Carvajal, I.Sanchez; Rajkovic, I.; Wonderly, W.R.; Kossa, A.; McMeeking, R.M.; Waite, H. J R Soc Interface 19, 20210828 (2022).
  3. Stabilization of glucose-6-phosphate dehydrogenase oligomers enhances catalytic activity and stability of clinical variants.
    Garcia, A.Ann; Mathews, I.I.; Horikoshi, N.; Matsui, T.; Kaur, M.; Wakatsuki, S.; Mochly-Rosen, D. J Biol Chem 298, 101610 (2022).
  4. The Influence of Calcium Ions (Ca2+) on the Enzymatic Hydrolysis of Lipopolysaccharide Aggregates to Liberate Free Fatty Acids (FFA) in Aqueous Solution
    Pazol, J.; Weiss, T.M.; Martínez, C.D.; Quesada, O.; Nicolau, E. Jcis Open 7, (2022).
  5. From Protein Design to the Energy Landscape of a Cold Unfolding Protein.
    Pulavarti, S.V.S.R.K.; Maguire, J.B.; Yuen, S.; Harrison, J.S.; Griffin, J.; Premkumar, L.; Esposito, E.A.; Makhatadze, G.I.; Garcia, A.E.; Weiss, T.M.; Snell, E.H.; Kuhlman, B.; Szyperski, T. J Phys Chem B 126, 1212-1231 (2022).
  6. A round-robin approach provides a detailed assessment of biomolecular small-angle scattering data reproducibility and yields consensus curves for benchmarking.
    Trewhella, J.; Vachette, P.; Bierma, J.; Blanchet, C.; Brookes, E.; Chakravarthy, S.; Chatzimagas, L.; Cleveland, T.E.; Cowieson, N.; Crossett, B.; Duff, A.P.; Franke, D.; Gabel, F.; Gillilan, R.E.; Graewert, M.; Grishaev, A.; Guss, M.; Hammel, M.; Hopkins, J.; Huang, Q.; Hub, J.S.; Hura, G.L.; Irving, T.C.; Jeffries, C.Michael; Jeong, C.; Kirby, N.; Krueger, S.; Martel, A.; Matsui, T.; Li, N.; Pérez, J.; Porcar, L.; Prangé, T.; Rajkovic, I.; Rocco, M.; Rosenberg, D.J.; Ryan, T.M.; Seifert, S.; Sekiguchi, H.; Svergun, D.; Teixeira, S.; Thureau, A.; Weiss, T.M.; Whitten, A.E.; Wood, K.; Zuo, X. Acta Crystallogr D Struct Biol 78, 1315-1336 (2022).
  7. Nanostructure-specific X-ray tomography reveals myelin levels, integrity and axon orientations in mouse and human nervous tissue.
    Georgiadis, M.; Schroeter, A.; Gao, Z.; Guizar-Sicairos, M.; Liebi, M.; Leuze, C.; McNab, J.A.; Balolia, A.; Veraart, J.; Ades-Aron, B.; Kim, S.; Shepherd, T.; Lee, C.H.; Walczak, P.; Chodankar, S.; DiGiacomo, P.; David, G.; Augath, M.; Zerbi, V.; Sommer, S.; Rajkovic, I.; Weiss, T.; Bunk, O.; Yang, L.; Zhang, J.; Novikov, D.S.; Zeineh, M.; Fieremans, E.; Rudin, M. Nat Commun 12, 2941 (2021).
  8. Early-Stage Aggregation and Crystalline Interactions of Peptoid Nanomembranes.
    Hammons, J.A.; Baer, M.D.; Jian, T.; Lee, J.R.I.; Weiss, T.M.; De Yoreo, J.J.; Noy, A.; Chen, C.L.; Van Buuren, A. J Phys Chem Lett 12, 6126-6133 (2021).
  9. Long-range structural defects by pathogenic mutations in most severe glucose-6-phosphate dehydrogenase deficiency.
    Horikoshi, N.; Hwang, S.; Gati, C.; Matsui, T.; Castillo-Orellana, C.; Raub, A.G.; Garcia, A.A.; Jabbarpour, F.; Batyuk, A.; Broweleit, J.; Xiang, X.; Chiang, A.; Broweleit, R.; Vöhringer-Martinez, E.; Mochly-Rosen, D.; Wakatsuki, S. Proc Natl Acad Sci U S A 118, (2021).
  10. Dynamics and stability in the maturation of a eukaryotic virus: a paradigm for chemically programmed large-scale macromolecular reorganization.
    Johnson, J.E.; Domitrovic, T.; Matsui, T.; Castells-Graells, R.; Lomonossoff, G. Arch Virol 166, 1547-1563 (2021).
  11. Antibody Probes of Module 1 of the 6-Deoxyerythronolide B Synthase Reveal an Extended Conformation During Ketoreduction.
    Cogan, D.P.; Li, X.; Sevillano, N.; Mathews, I.I.; Matsui, T.; Craik, C.S.; Khosla, C. J Am Chem Soc 142, 14933-14939 (2020).
  12. A bacterial surface layer protein exploits multistep crystallization for rapid self-assembly.
    Herrmann, J.; Li, P.N.; Jabbarpour, F.; Chan, A.C.K.; Rajkovic, I.; Matsui, T.; Shapiro, L.; Smit, J.; Weiss, T.M.; Murphy, M.E.P.; Wakatsuki, S. Proc Natl Acad Sci U S A 117, 388-394 (2020).
  13. Halogenation-Dependent Effects of the Chlorosulfolipids of on Lipid Bilayers.
    Iii, F.R.Moss; Cabrera, G.E.; McKenna, G.M.; Salerno, G.J.; Shuken, S.R.; Landry, M.L.; Weiss, T.M.; Burns, N.Z.; Boxer, S.G. ACS Chem Biol 15, 2986-2995 (2020).
  14. An ensemble of flexible conformations underlies mechanotransduction by the cadherin-catenin adhesion complex.
    Bush, M.; Alhanshali, B.M.; Qian, S.; Stanley, C.B.; Heller, W.T.; Matsui, T.; Weiss, T.M.; Nicholl, I.D.; Walz, T.; Callaway, D.J.E.; Bu, Z. Proc Natl Acad Sci U S A 116, 21545-21555 (2019).
  15. Structure of the full-length Clostridium difficile toxin B.
    Chen, P.; Lam, K.H.; Liu, Z.; Mindlin, F.A.; Chen, B.; Gutierrez, C.B.; Huang, L.; Zhang, Y.; Hamza, T.; Feng, H.; Matsui, T.; Bowen, M.E.; Perry, K.; Jin, R. Nat Struct Mol Biol 26, 712-719 (2019).
  16. STING Polymer Structure Reveals Mechanisms for Activation, Hyperactivation, and Inhibition.
    Ergun, S.L.; Fernandez, D.; Weiss, T.M.; Li, L. Cell 178, 290-301.e10 (2019).
  17. Interaction of dequalinium chloride with phosphatidylcholine bilayers: A biophysical study with consequences on the development of lipid-based mitochondrial nanomedicines.
    Sauvage, F.; Legrand, F.X.; Roux, M.; Rajkovic, I.; Weiss, T.M.; Varga, Z.; Augis, L.; Nugue, G.; Debouzy, J.C.; Vergnaud-Gauduchon, J.; Barratt, G. J Colloid Interface Sci 537, 704-715 (2019).
  18. Influence of micelle charge density on adsorption and exciton delocalization of conjugated polyelectrolytes
    Segura, C.J.; Johnston, A.R.; Hollingsworth, W.R.; Rajkovic, I.; Ayzner, A.L. Proc. SPIE 11084, Physical Chemistry of Semiconductor Materials and Interfaces XVIII , 110840A (2019).
  19. Quaternary structure of α-amino-β-carboxymuconate-ϵ-semialdehyde decarboxylase (ACMSD) controls its activity.
    Yang, Y.; Davis, I.; Matsui, T.; Rubalcava, I.; Liu, A. J Biol Chem 294, 11609-11621 (2019).
  20. The L Phase of Pulmonary Surfactant.
    Kumar, K.; Chavarha, M.; Loney, R.W.; Weiss, T.M.; Rananavare, S.B.; Hall, S.B. Langmuir 34, 6601-6611 (2018).
  21. A viral-fusion-peptide-like molecular switch drives membrane insertion of botulinum neurotoxin A1.
    Lam, K.H.; Guo, Z.; Krez, N.; Matsui, T.; Perry, K.; Weisemann, J.; Rummel, A.; Bowen, M.E.; Jin, R. Nat Commun 9, 5367 (2018).
  22. Structure-Function Analysis of the Extended Conformation of a Polyketide Synthase Module.
    Li, X.; Sevillano, N.; La Greca, F.; Deis, L.; Liu, Y.C.; Deller, M.C.; Mathews, I.I.; Matsui, T.; Cane, D.E.; Craik, C.S.; Khosla, C. J Am Chem Soc 140, 6518-6521 (2018).
  23. Discovery and Characterization of a Thioesterase-Specific Monoclonal Antibody That Recognizes the 6-Deoxyerythronolide B Synthase.
    Li, X.; Sevillano, N.; La Greca, F.; Hsu, J.; Mathews, I.I.; Matsui, T.; Craik, C.S.; Khosla, C. Biochemistry 57, 6201-6208 (2018).
  24. Ladderane phospholipids form a densely packed membrane with normal hydrazine and anomalously low proton/hydroxide permeability.
    Moss, F.R.; Shuken, S.R.; Mercer, J.A.M.; Cohen, C.M.; Weiss, T.M.; Boxer, S.G.; Burns, N.Z. Proc Natl Acad Sci U S A 115, 9098-9103 (2018).
  25. α-Catenin Structure and Nanoscale Dynamics in Solution and in Complex with F-Actin.
    Nicholl, I.D.; Matsui, T.; Weiss, T.M.; Stanley, C.B.; Heller, W.T.; Martel, A.; Farago, B.; Callaway, D.J.E.; Bu, Z. Biophys J 115, 642-654 (2018).
  26. Absence of Mixed Phase in Organic Photovoltaic Active Layers Facilitates Use of Green Solvent Processing
    Oosterhout, S.D.; Savikhin, V.; Burgers, M.A.; Zhang, J.; Zhang, Y.; Marder, S.R.; Bazan, G.C.; Toney, M.F. J. Phys. Chem. C 122, 11136-11144 (2018).
  27. Intrinsic disorder in the regulatory N-terminal domain of diacylglycerol acyltransferase 1 from Brassica napus.
    Panigrahi, R.; Matsui, T.; Song, A.H.; Caldo, K.Mark P.; Young, H.S.; Weselake, R.J.; Lemieux, J. Sci Rep 8, 16665 (2018).
  28. De Novo Design and Implementation of a Tandem Acyl Carrier Protein Domain in a Type I Modular Polyketide Synthase.
    Wang, Z.; Bagde, S.R.; Zavala, G.; Matsui, T.; Chen, X.; Kim, C.Y. ACS Chem Biol 13, 3072-3077 (2018).
  29. Controllable Activation of Nanoscale Dynamics in a Disordered Protein Alters Binding Kinetics.
    Callaway, D.J.E.; Matsui, T.; Weiss, T.; Stingaciu, L.R.; Stanley, C.B.; Heller, W.T.; Bu, Z. J Mol Biol 429, 987-998 (2017).
  30. Phospho-Priming Confers Functionally Relevant Specificities for Rad53 Kinase Autophosphorylation.
    Chen, E.ShengWen; Weng, J.H.; Chen, Y.H.; Wang, S.C.; Liu, X.X.; Huang, W.C.; Matsui, T.; Kawano, Y.; Liao, J.H.; Lim, L.H.; Bessho, Y.; Huang, K.F.; Wu, W.J.; Tsai, M.D. Biochemistry 56, 5112-5124 (2017).
  31. Environmental Calcium Controls Alternate Physical States of the Caulobacter Surface Layer.
    Herrmann, J.; Jabbarpour, F.; Bargar, P.G.; Nomellini, J.F.; Li, P.N.; Lane, T.J.; Weiss, T.M.; Smit, J.; Shapiro, L.; Wakatsuki, S. Biophys J 112, 1841-1851 (2017).
  32. Structural features of NS3 of Dengue virus serotypes 2 and 4 in solution and insight into RNA binding and the inhibitory role of quercetin.
    Pan, A.; Saw, W.Geok; Manimekalai, M.Sony Subra; Grüber, A.; Joon, S.; Matsui, T.; Weiss, T.M.; Grüber, G. Acta Crystallogr D Struct Biol 73, 402-419 (2017).
  33. Dynamic intramolecular regulation of the histone chaperone nucleoplasmin controls histone binding and release.
    Warren, C.; Matsui, T.; Karp, J.M.; Onikubo, T.; Cahill, S.; Brenowitz, M.; Cowburn, D.; Girvin, M.; Shechter, D. Nat Commun 8, 2215 (2017).
  34. Selective Binding of AIRAPL Tandem UIMs to Lys48-Linked Tri-Ubiquitin Chains.
    Rahighi, S.; Braunstein, I.; Ternette, N.; Kessler, B.; Kawasaki, M.; Kato, R.; Matsui, T.; Weiss, T.M.; Stanhill, A.; Wakatsuki, S. Structure 24, 412-22 (2016).
  35. Solution structure of an "open" E. coli Pol III clamp loader sliding clamp complex.
    Tondnevis, F.; Weiss, T.M.; Matsui, T.; Bloom, L.B.; McKenna, R. J Struct Biol 194, 272-81 (2016).
  36. Structure of Carbon Nanotube Porins in Lipid Bilayers: An in Situ Small-Angle X-ray Scattering (SAXS) Study.
    Tran, I.C.; Tunuguntla, R.H.; Kim, K.; Lee, J.R.I.; Willey, T.M.; Weiss, T.M.; Noy, A.; van Buuren, T. Nano Lett 16, 4019-24 (2016).
  37. Structure of a Bacterial Virus DNA-Injection Protein Complex Reveals a Decameric Assembly with a Constricted Molecular Channel.
    Zhao, H.; Speir, J.A.; Matsui, T.; Lin, Z.; Liang, L.; Lynn, A.Y.; Varnado, B.; Weiss, T.M.; Tang, L. PLoS One 11, e0149337 (2016).
  38. Prion Protein-Antibody Complexes Characterized by Chromatography-Coupled Small-Angle X-Ray Scattering.
    Carter, L.; Kim, S.Joong; Schneidman-Duhovny, D.; Stöhr, J.; Poncet-Montange, G.; Weiss, T.M.; Tsuruta, H.; Prusiner, S.B.; Sali, A. Biophys J 109, 793-805 (2015).
  39. Long-range ion-water and ion-ion interactions in aqueous solutions.
    Chen, C.; Huang, C.; Waluyo, I.; Weiss, T.; Pettersson, L.G.M.; Nilsson, A. Phys Chem Chem Phys 17, 8427-30 (2015).
  40. The accurate assessment of small-angle X-ray scattering data.
    Grant, T.D.; Luft, J.R.; Carter, L.G.; Matsui, T.; Weiss, T.M.; Martel, A.; Snell, E.H. Acta Crystallogr D Biol Crystallogr 71, 45-56 (2015).
  41. Structural Studies of Geosmin Synthase, a Bifunctional Sesquiterpene Synthase with αα Domain Architecture That Catalyzes a Unique Cyclization-Fragmentation Reaction Sequence.
    Harris, G.G.; Lombardi, P.M.; Pemberton, T.A.; Matsui, T.; Weiss, T.M.; Cole, K.E.; Köksal, M.; Murphy, F.V.; Vedula, S.; Chou, W.K.W.; Cane, D.E.; Christianson, D.W. Biochemistry 54, 7142-55 (2015).
  42. Protein Arginine Methyltransferase 8: Tetrameric Structure and Protein Substrate Specificity.
    Lee, W.C.; Lin, W.L.; Matsui, T.; Chen, E.S.W.; Wei, T.Y.Wade; Lin, W.H.; Hu, H.; Zheng, Y.George; Tsai, M.D.; Ho, M.C. Biochemistry 54, 7514-23 (2015).
  43. An encapsidated viral protein and its role in RNA packaging by a non-enveloped animal RNA virus.
    Mendes, A.; Vlok, M.; Short, J.R.; Matsui, T.; Dorrington, R.A. Virology 476, 323-333 (2015).
  44. Structural insight and flexible features of NS5 proteins from all four serotypes of Dengue virus in solution.
    Saw, W.Geok; Tria, G.; Grüber, A.; Manimekalai, M.Sony Subra; Zhao, Y.; Chandramohan, A.; Anand, G.Srinivasan; Matsui, T.; Weiss, T.M.; Vasudevan, S.G.; Grüber, G. Acta Crystallogr D Biol Crystallogr 71, 2309-27 (2015).
  45. Nematic director reorientation at solid and liquid interfaces under flow: SAXS studies in a microfluidic device.
    Silva, B.F.B.; Zepeda-Rosales, M.; Venkateswaran, N.; Fletcher, B.J.; Carter, L.G.; Matsui, T.; Weiss, T.M.; Han, J.; Li, Y.; Olsson, U.; Safinya, C.R. Langmuir 31, 4361-71 (2015).
  46. Architectures of whole-module and bimodular proteins from the 6-deoxyerythronolide B synthase.
    Edwards, A.L.; Matsui, T.; Weiss, T.M.; Khosla, C. J Mol Biol 426, 2229-45 (2014).
  47. CD4-induced activation in a soluble HIV-1 Env trimer.
    Guttman, M.; Garcia, N.K.; Cupo, A.; Matsui, T.; Julien, J.P.; Sanders, R.W.; Wilson, I.A.; Moore, J.P.; Lee, K.K. Structure 22, 974-84 (2014).
  48. Integrative structure-function mapping of the nucleoporin Nup133 suggests a conserved mechanism for membrane anchoring of the nuclear pore complex.
    Kim, S.Joong; Fernandez-Martinez, J.; Sampathkumar, P.; Martel, A.; Matsui, T.; Tsuruta, H.; Weiss, T.M.; Shi, Y.; Markina-Inarrairaegui, A.; Bonanno, J.B.; Sauder, M.; Burley, S.K.; Chait, B.T.; Almo, S.C.; Rout, M.P.; Sali, A. Mol Cell Proteomics 13, 2911-26 (2014).
  49. Structural basis of the pH-dependent assembly of a botulinum neurotoxin complex.
    Matsui, T.; Gu, S.; Lam, K.H.; Carter, L.G.; Rummel, A.; Mathews, I.I.; Jin, R. J Mol Biol 426, 3773-3782 (2014).
  50. A mechanistic understanding of processing additive-induced efficiency enhancement in bulk heterojunction organic solar cells.
    Schmidt, K.; Tassone, C.J.; Niskala, J.R.; Yiu, A.T.; Lee, O.P.; Weiss, T.M.; Wang, C.; Fréchet, J.M.J.; Beaujuge, P.M.; Toney, M.F. Adv Mater 26, 300-5 (2014).
  51. Ultrafast X-ray probing of water structure below the homogeneous ice nucleation temperature.
    Sellberg, J.A.; Huang, C.; McQueen, T.A.; Loh, N.D.; Laksmono, H.; Schlesinger, D.; Sierra, R.G.; Nordlund, D.; Hampton, C.Y.; Starodub, D.; DePonte, D.P.; Beye, M.; Chen, C.; Martin, A.V.; Barty, A.; Wikfeldt, K.T.; Weiss, T.M.; Caronna, C.; Feldkamp, J.; Skinner, L.B.; Seibert, M.M.; Messerschmidt, M.; Williams, G.J.; Boutet, S.; Pettersson, L.G.M.; Bogan, M.J.; Nilsson, A. Nature 510, 381-4 (2014).
  52. Structure of the bifunctional aminoglycoside-resistance enzyme AAC(6')-Ie-APH(2'')-Ia revealed by crystallographic and small-angle X-ray scattering analysis.
    Smith, C.A.; Toth, M.; Weiss, T.M.; Frase, H.; Vakulenko, S.B. Acta Crystallogr D Biol Crystallogr 70, 2754-64 (2014).
  53. Crystal structure of Streptococcus pyogenes EndoS, an immunomodulatory endoglycosidase specific for human IgG antibodies.
    Trastoy, B.; Lomino, J.V.; Pierce, B.G.; Carter, L.G.; Günther, S.; Giddens, J.P.; Snyder, G.A.; Weiss, T.M.; Weng, Z.; Wang, L.X.; Sundberg, E.J. Proc Natl Acad Sci U S A 111, 6714-9 (2014).
  54. Solvation structures of protons and hydroxide ions in water.
    Chen, C.; Huang, C.; Waluyo, I.; Nordlund, D.; Weng, T.C.; Sokaras, D.; Weiss, T.; Bergmann, U.; Pettersson, L.G.M.; Nilsson, A. J Chem Phys 138, 154506 (2013).
  55. Syntaxin1a variants lacking an N-peptide or bearing the LE mutation bind to Munc18a in a closed conformation.
    Colbert, K.N.; Hattendorf, D.A.; Weiss, T.M.; Burkhardt, P.; Fasshauer, D.; Weis, W.I. Proc Natl Acad Sci U S A 110, 12637-42 (2013).
  56. Virus assembly and maturation: auto-regulation through allosteric molecular switches.
    Domitrovic, T.; Movahed, N.; Bothner, B.; Matsui, T.; Wang, Q.; Doerschuk, P.C.; Johnson, J.E. J Mol Biol 425, 1488-96 (2013).
  57. The structure of yeast glutaminyl-tRNA synthetase and modeling of its interaction with tRNA.
    Grant, T.D.; Luft, J.R.; Wolfley, J.R.; Snell, M.E.; Tsuruta, H.; Corretore, S.; Quartley, E.; Phizicky, E.M.; Grayhack, E.J.; Snell, E.H. J Mol Biol 425, 2480-93 (2013).
  58. Structure of the arginine methyltransferase PRMT5-MEP50 reveals a mechanism for substrate specificity.
    Ho, M.C.; Wilczek, C.; Bonanno, J.B.; Xing, L.; Seznec, J.; Matsui, T.; Carter, L.G.; Onikubo, T.; Kumar, R.; Chan, M.K.; Brenowitz, M.; Cheng, H.; Reimer, U.; Almo, S.C.; Shechter, D. PLoS One 8, e57008 (2013).
  59. Structural study of hNck2 SH3 domain protein in solution by circular dichroism and X-ray solution scattering.
    Matsumura, Y.; Shinjo, M.; Matsui, T.; Ichimura, K.; Song, J.; Kihara, H. Biophys Chem 175-176, 39-46 (2013).
  60. Structure, dynamics, evolution, and function of a major scaffold component in the nuclear pore complex.
    Sampathkumar, P.; Kim, S.Joong; Upla, P.; Rice, W.J.; Phillips, J.; Timney, B.L.; Pieper, U.; Bonanno, J.B.; Fernandez-Martinez, J.; Hakhverdyan, Z.; Ketaren, N.E.; Matsui, T.; Weiss, T.M.; Stokes, D.L.; Sauder, M.; Burley, S.K.; Sali, A.; Rout, M.P.; Almo, S.C. Structure 21, 560-71 (2013).
  61. Scalable and selective dispersion of semiconducting arc-discharged carbon nanotubes by dithiafulvalene/thiophene copolymers for thin film transistors.
    Wang, H.; Mei, J.; Liu, P.; Schmidt, K.; Jiménez-Osés, G.; Osuna, S.; Fang, L.; Tassone, C.J.; Zoombelt, A.Pieter; Sokolov, A.N.; Houk, K.N.; Toney, M.F.; Bao, Z. ACS Nano 7, 2659-68 (2013).
  62. Dynamics in cryo EM reconstructions visualized with maximum-likelihood derived variance maps.
    Wang, Q.; Matsui, T.; Domitrovic, T.; Zheng, Y.; Doerschuk, P.C.; Johnson, J.E. J Struct Biol 181, 195-206 (2013).