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Items: 1 to 50 of 62

1.

Controlling the Circadian Clock with High Temporal Resolution through Photodosing.

Kolarski D, Sugiyama A, Breton G, Rakers C, Ono D, Schulte A, Tama F, Itami K, Szymanski W, Hirota T, Feringa BL.

J Am Chem Soc. 2019 Sep 11. doi: 10.1021/jacs.9b05445. [Epub ahead of print]

PMID:
31509406
2.

Reconstruction of low-resolution molecular structures from simulated atomic force microscopy images.

Dasgupta B, Miyashita O, Tama F.

Biochim Biophys Acta Gen Subj. 2019 Aug 28:129420. doi: 10.1016/j.bbagen.2019.129420. [Epub ahead of print]

PMID:
31472175
3.

Crystal contact-free conformation of an intrinsically flexible loop in protein crystal: Tim21 as the case study.

Bala S, Shinya S, Srivastava A, Ishikawa M, Shimada A, Kobayashi N, Kojima C, Tama F, Miyashita O, Kohda D.

Biochim Biophys Acta Gen Subj. 2019 Aug 23:129418. doi: 10.1016/j.bbagen.2019.129418. [Epub ahead of print]

PMID:
31449839
4.

Conformational ensemble of an intrinsically flexible loop in mitochondrial import protein Tim21 studied by modeling and molecular dynamics simulations.

Srivastava A, Bala S, Motomura H, Kohda D, Tama F, Miyashita O.

Biochim Biophys Acta Gen Subj. 2019 Aug 21:129417. doi: 10.1016/j.bbagen.2019.129417. [Epub ahead of print]

PMID:
31445064
5.

Bipartite anchoring of SCREAM enforces stomatal initiation by coupling MAP kinases to SPEECHLESS.

Putarjunan A, Ruble J, Srivastava A, Zhao C, Rychel AL, Hofstetter AK, Tang X, Zhu JK, Tama F, Zheng N, Torii KU.

Nat Plants. 2019 Jul;5(7):742-754. doi: 10.1038/s41477-019-0440-x. Epub 2019 Jun 24.

PMID:
31235876
6.

Cell-based screen identifies a new potent and highly selective CK2 inhibitor for modulation of circadian rhythms and cancer cell growth.

Oshima T, Niwa Y, Kuwata K, Srivastava A, Hyoda T, Tsuchiya Y, Kumagai M, Tsuyuguchi M, Tamaru T, Sugiyama A, Ono N, Zolboot N, Aikawa Y, Oishi S, Nonami A, Arai F, Hagihara S, Yamaguchi J, Tama F, Kunisaki Y, Yagita K, Ikeda M, Kinoshita T, Kay SA, Itami K, Hirota T.

Sci Adv. 2019 Jan 23;5(1):eaau9060. doi: 10.1126/sciadv.aau9060. eCollection 2019 Jan.

7.

Cryo-Cooling Effect on DHFR Crystal Studied by Replica-Exchange Molecular Dynamics Simulations.

Nagai T, Tama F, Miyashita O.

Biophys J. 2019 Feb 5;116(3):395-405. doi: 10.1016/j.bpj.2018.11.3139. Epub 2018 Dec 13.

PMID:
30638963
8.

Hybrid Methods for Macromolecular Modeling by Molecular Mechanics Simulations with Experimental Data.

Miyashita O, Tama F.

Adv Exp Med Biol. 2018;1105:199-217. doi: 10.1007/978-981-13-2200-6_13. Review.

PMID:
30617831
9.

Gaussian mixture model for coarse-grained modeling from XFEL.

Nagai T, Mochizuki Y, Joti Y, Tama F, Miyashita O.

Opt Express. 2018 Oct 1;26(20):26734-26749. doi: 10.1364/OE.26.026734.

PMID:
30469754
10.

Role of Computational Methods in Going beyond X-ray Crystallography to Explore Protein Structure and Dynamics.

Srivastava A, Nagai T, Srivastava A, Miyashita O, Tama F.

Int J Mol Sci. 2018 Oct 30;19(11). pii: E3401. doi: 10.3390/ijms19113401. Review.

11.

Computational investigation of the conformational dynamics in Tom20-mitochondrial presequence tethered complexes.

Srivastava A, Tama F, Kohda D, Miyashita O.

Proteins. 2019 Jan;87(1):81-90. doi: 10.1002/prot.25625. Epub 2018 Nov 16.

PMID:
30367523
12.

Acceleration of cryo-EM Flexible Fitting for Large Biomolecular Systems by Efficient Space Partitioning.

Mori T, Kulik M, Miyashita O, Jung J, Tama F, Sugita Y.

Structure. 2019 Jan 2;27(1):161-174.e3. doi: 10.1016/j.str.2018.09.004. Epub 2018 Oct 18.

PMID:
30344106
13.

Searching for 3D structural models from a library of biological shapes using a few 2D experimental images.

Tiwari SP, Tama F, Miyashita O.

BMC Bioinformatics. 2018 Sep 12;19(1):320. doi: 10.1186/s12859-018-2358-0.

14.

Single-particle XFEL 3D reconstruction of ribosome-size particles based on Fourier slice matching: requirements to reach subnanometer resolution.

Nakano M, Miyashita O, Jonic S, Tokuhisa A, Tama F.

J Synchrotron Radiat. 2018 Jul 1;25(Pt 4):1010-1021. doi: 10.1107/S1600577518005568. Epub 2018 May 30.

PMID:
29979162
15.

Conformational dynamics of human protein kinase CK2α and its effect on function and inhibition.

Srivastava A, Hirota T, Irle S, Tama F.

Proteins. 2018 Mar;86(3):344-353. doi: 10.1002/prot.25444. Epub 2017 Dec 25.

PMID:
29243286
16.

Three-dimensional reconstruction for coherent diffraction patterns obtained by XFEL.

Nakano M, Miyashita O, Jonic S, Song C, Nam D, Joti Y, Tama F.

J Synchrotron Radiat. 2017 Jul 1;24(Pt 4):727-737. doi: 10.1107/S1600577517007767. Epub 2017 Jun 14.

17.

Editorial overview: Macromolecular assemblies.

Shimizu T, Tama F.

Curr Opin Struct Biol. 2017 Apr;43:vii-ix. doi: 10.1016/j.sbi.2017.04.009. No abstract available.

PMID:
28477856
18.

Flexible fitting to cryo-EM density map using ensemble molecular dynamics simulations.

Miyashita O, Kobayashi C, Mori T, Sugita Y, Tama F.

J Comput Chem. 2017 Jun 15;38(16):1447-1461. doi: 10.1002/jcc.24785. Epub 2017 Apr 1.

PMID:
28370077
19.

Hybrid approach for structural modeling of biological systems from X-ray free electron laser diffraction patterns.

Tokuhisa A, Jonic S, Tama F, Miyashita O.

J Struct Biol. 2016 Jun;194(3):325-36. doi: 10.1016/j.jsb.2016.03.009. Epub 2016 Mar 10.

PMID:
26972893
20.

Thermodynamic properties of water molecules in the presence of cosolute depend on DNA structure: a study using grid inhomogeneous solvation theory.

Nakano M, Tateishi-Karimata H, Tanaka S, Tama F, Miyashita O, Nakano S, Sugimoto N.

Nucleic Acids Res. 2015 Dec 2;43(21):10114-25. doi: 10.1093/nar/gkv1133. Epub 2015 Nov 3.

21.

Hybrid Electron Microscopy Normal Mode Analysis graphical interface and protocol.

Sorzano CO, de la Rosa-Trevín JM, Tama F, Jonić S.

J Struct Biol. 2014 Nov;188(2):134-41. doi: 10.1016/j.jsb.2014.09.005. Epub 2014 Sep 27.

PMID:
25268657
22.

Replica exchange molecular dynamics simulations provide insight into substrate recognition by small heat shock proteins.

Patel S, Vierling E, Tama F.

Biophys J. 2014 Jun 17;106(12):2644-55. doi: 10.1016/j.bpj.2014.04.048.

23.

Macromolecular structures probed by combining single-shot free-electron laser diffraction with synchrotron coherent X-ray imaging.

Gallagher-Jones M, Bessho Y, Kim S, Park J, Kim S, Nam D, Kim C, Kim Y, Noh do Y, Miyashita O, Tama F, Joti Y, Kameshima T, Hatsui T, Tono K, Kohmura Y, Yabashi M, Hasnain SS, Ishikawa T, Song C.

Nat Commun. 2014 May 2;5:3798. doi: 10.1038/ncomms4798.

PMID:
24786694
24.

Iterative elastic 3D-to-2D alignment method using normal modes for studying structural dynamics of large macromolecular complexes.

Jin Q, Sorzano CO, de la Rosa-Trevín JM, Bilbao-Castro JR, Núñez-Ramírez R, Llorca O, Tama F, Jonić S.

Structure. 2014 Mar 4;22(3):496-506. doi: 10.1016/j.str.2014.01.004. Epub 2014 Feb 6.

25.

Network visualization of conformational sampling during molecular dynamics simulation.

Ahlstrom LS, Baker JL, Ehrlich K, Campbell ZT, Patel S, Vorontsov II, Tama F, Miyashita O.

J Mol Graph Model. 2013 Nov;46:140-9. doi: 10.1016/j.jmgm.2013.10.003. Epub 2013 Oct 16.

26.

Allosteric regulation of DNA cleavage and sequence-specificity through run-on oligomerization.

Lyumkis D, Talley H, Stewart A, Shah S, Park CK, Tama F, Potter CS, Carragher B, Horton NC.

Structure. 2013 Oct 8;21(10):1848-58. doi: 10.1016/j.str.2013.08.012. Epub 2013 Sep 19.

27.

3DEM Loupe: Analysis of macromolecular dynamics using structures from electron microscopy.

Nogales-Cadenas R, Jonic S, Tama F, Arteni AA, Tabas-Madrid D, Vázquez M, Pascual-Montano A, Sorzano CO.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W363-7. doi: 10.1093/nar/gkt385. Epub 2013 May 13.

28.

Steered molecular dynamics simulations of a type IV pilus probe initial stages of a force-induced conformational transition.

Baker JL, Biais N, Tama F.

PLoS Comput Biol. 2013 Apr;9(4):e1003032. doi: 10.1371/journal.pcbi.1003032. Epub 2013 Apr 11.

29.

Consensus among multiple approaches as a reliability measure for flexible fitting into cryo-EM data.

Ahmed A, Tama F.

J Struct Biol. 2013 May;182(2):67-77. doi: 10.1016/j.jsb.2013.02.002. Epub 2013 Feb 13.

PMID:
23416197
30.

Molecular model of a soluble guanylyl cyclase fragment determined by small-angle X-ray scattering and chemical cross-linking.

Fritz BG, Roberts SA, Ahmed A, Breci L, Li W, Weichsel A, Brailey JL, Wysocki VH, Tama F, Montfort WR.

Biochemistry. 2013 Mar 5;52(9):1568-82. doi: 10.1021/bi301570m. Epub 2013 Feb 15.

31.

Twelve transmembrane helices form the functional core of mammalian MATE1 (multidrug and toxin extruder 1) protein.

Zhang X, He X, Baker J, Tama F, Chang G, Wright SH.

J Biol Chem. 2012 Aug 10;287(33):27971-82. doi: 10.1074/jbc.M112.386979. Epub 2012 Jun 21.

32.

Simulations of substrate transport in the multidrug transporter EmrD.

Baker J, Wright SH, Tama F.

Proteins. 2012 Jun;80(6):1620-32. doi: 10.1002/prot.24056. Epub 2012 Mar 20.

33.

Excited states of ribosome translocation revealed through integrative molecular modeling.

Whitford PC, Ahmed A, Yu Y, Hennelly SP, Tama F, Spahn CM, Onuchic JN, Sanbonmatsu KY.

Proc Natl Acad Sci U S A. 2011 Nov 22;108(47):18943-8. doi: 10.1073/pnas.1108363108. Epub 2011 Nov 11.

34.

Phosphorylated smooth muscle heavy meromyosin shows an open conformation linked to activation.

Baumann BA, Taylor DW, Huang Z, Tama F, Fagnant PM, Trybus KM, Taylor KA.

J Mol Biol. 2012 Jan 13;415(2):274-87. doi: 10.1016/j.jmb.2011.10.047. Epub 2011 Nov 4.

35.

Consensus among flexible fitting approaches improves the interpretation of cryo-EM data.

Ahmed A, Whitford PC, Sanbonmatsu KY, Tama F.

J Struct Biol. 2012 Feb;177(2):561-70. doi: 10.1016/j.jsb.2011.10.002. Epub 2011 Oct 13.

36.

Structure modeling from small angle X-ray scattering data with elastic network normal mode analysis.

Miyashita O, Gorba C, Tama F.

J Struct Biol. 2011 Mar;173(3):451-60. doi: 10.1016/j.jsb.2010.09.008. Epub 2010 Sep 17. Review.

PMID:
20850542
37.
38.

Three-dimensional structure of the anthrax toxin pore inserted into lipid nanodiscs and lipid vesicles.

Katayama H, Wang J, Tama F, Chollet L, Gogol EP, Collier RJ, Fisher MT.

Proc Natl Acad Sci U S A. 2010 Feb 23;107(8):3453-7. doi: 10.1073/pnas.1000100107. Epub 2010 Feb 8.

39.

Biased coarse-grained molecular dynamics simulation approach for flexible fitting of X-ray structure into cryo electron microscopy maps.

Grubisic I, Shokhirev MN, Orzechowski M, Miyashita O, Tama F.

J Struct Biol. 2010 Jan;169(1):95-105. doi: 10.1016/j.jsb.2009.09.010. Epub 2009 Oct 2.

PMID:
19800974
40.

Flexible fitting of high-resolution x-ray structures into cryoelectron microscopy maps using biased molecular dynamics simulations.

Orzechowski M, Tama F.

Biophys J. 2008 Dec 15;95(12):5692-705. doi: 10.1529/biophysj.108.139451. Epub 2008 Oct 10.

41.
42.
43.

Removal of divalent cations induces structural transitions in red clover necrotic mosaic virus, revealing a potential mechanism for RNA release.

Sherman MB, Guenther RH, Tama F, Sit TL, Brooks CL, Mikhailov AM, Orlova EV, Baker TS, Lommel SA.

J Virol. 2006 Nov;80(21):10395-406. Epub 2006 Aug 18.

44.

Symmetry, form, and shape: guiding principles for robustness in macromolecular machines.

Tama F, Brooks CL.

Annu Rev Biophys Biomol Struct. 2006;35:115-33. Review.

PMID:
16689630
45.

Structure of the E. coli protein-conducting channel bound to a translating ribosome.

Mitra K, Schaffitzel C, Shaikh T, Tama F, Jenni S, Brooks CL 3rd, Ban N, Frank J.

Nature. 2005 Nov 17;438(7066):318-24.

46.

Electrostatic properties of cowpea chlorotic mottle virus and cucumber mosaic virus capsids.

Konecny R, Trylska J, Tama F, Zhang D, Baker NA, Brooks CL 3rd, McCammon JA.

Biopolymers. 2006 Jun 5;82(2):106-20.

47.

The 13 angstroms structure of a chaperonin GroEL-protein substrate complex by cryo-electron microscopy.

Falke S, Tama F, Brooks CL 3rd, Gogol EP, Fisher MT.

J Mol Biol. 2005 Apr 22;348(1):219-30.

PMID:
15808865
48.
49.
50.

Normal mode based flexible fitting of high-resolution structure into low-resolution experimental data from cryo-EM.

Tama F, Miyashita O, Brooks CL 3rd.

J Struct Biol. 2004 Sep;147(3):315-26.

PMID:
15450300

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