Suenaga A - Search Results

1

Structure and dynamics of RNA polymerase II elongation complex.

Suenaga A, Okimoto N, Futatsugi N, Hirano Y, Narumi T, Ohno Y, Yanai R, Hirokawa T, Ebisuzaki T, Konagaya A, Taiji M. Suenaga A, et al. Biochem Biophys Res Commun. 2006 Apr 28;343(1):90-8. doi: 10.1016/j.bbrc.2006.02.124. Epub 2006 Mar 2. Biochem Biophys Res Commun. 2006. PMID: 16529717

2

Tyr-317 phosphorylation increases Shc structural rigidity and reduces coupling of domain motions remote from the phosphorylation site as revealed by molecular dynamics simulations.

Suenaga A, Kiyatkin AB, Hatakeyama M, Futatsugi N, Okimoto N, Hirano Y, Narumi T, Kawai A, Susukita R, Koishi T, Furusawa H, Yasuoka K, Takada N, Ohno Y, Taiji M, Ebisuzaki T, Hoek JB, Konagaya A, Kholodenko BN. Suenaga A, et al. J Biol Chem. 2004 Feb 6;279(6):4657-62. doi: 10.1074/jbc.M310598200. Epub 2003 Nov 12. J Biol Chem. 2004. PMID: 14613932 Free article.

3

Cooperative motions of protein and hydration water molecules: molecular dynamics study of scytalone dehydratase.

Okimoto N, Nakamura T, Suenaga A, Futatsugi N, Hirano Y, Yamaguchi I, Ebisuzaki T. Okimoto N, et al. Among authors: suenaga a. J Am Chem Soc. 2004 Oct 13;126(40):13132-9. doi: 10.1021/ja048053u. J Am Chem Soc. 2004. PMID: 15469312

4

Bead-like passage of chloride ions through ClC chloride channels.

Suenaga A, Yeh JZ, Taiji M, Toyama A, Takeuchi H, Son M, Takayama K, Iwamoto M, Sato I, Narahashi T, Konagaya A, Goto K. Suenaga A, et al. Biophys Chem. 2006 Mar 1;120(1):36-43. doi: 10.1016/j.bpc.2005.10.004. Epub 2005 Nov 9. Biophys Chem. 2006. PMID: 16288955

5

Folding dynamics of 10-residue beta-hairpin peptide chignolin.

Suenaga A, Narumi T, Futatsugi N, Yanai R, Ohno Y, Okimoto N, Taiji M. Suenaga A, et al. Chem Asian J. 2007 May 4;2(5):591-8. doi: 10.1002/asia.200600385. Chem Asian J. 2007. PMID: 17465405

6

Molecular dynamics simulations reveal that Tyr-317 phosphorylation reduces Shc binding affinity for phosphotyrosyl residues of epidermal growth factor receptor.

Suenaga A, Hatakeyama M, Kiyatkin AB, Radhakrishnan R, Taiji M, Kholodenko BN. Suenaga A, et al. Biophys J. 2009 Mar 18;96(6):2278-88. doi: 10.1016/j.bpj.2008.11.018. Biophys J. 2009. PMID: 19289054 Free PMC article.

7

High-performance drug discovery: computational screening by combining docking and molecular dynamics simulations.

Okimoto N, Futatsugi N, Fuji H, Suenaga A, Morimoto G, Yanai R, Ohno Y, Narumi T, Taiji M. Okimoto N, et al. Among authors: suenaga a. PLoS Comput Biol. 2009 Oct;5(10):e1000528. doi: 10.1371/journal.pcbi.1000528. Epub 2009 Oct 9. PLoS Comput Biol. 2009. PMID: 19816553 Free PMC article.

8

An efficient computational method for calculating ligand binding affinities.

Suenaga A, Okimoto N, Hirano Y, Fukui K. Suenaga A, et al. PLoS One. 2012;7(8):e42846. doi: 10.1371/journal.pone.0042846. Epub 2012 Aug 20. PLoS One. 2012. PMID: 22916168 Free PMC article.

9

Molecular dynamics, free energy, and SPR analyses of the interactions between the SH2 domain of Grb2 and ErbB phosphotyrosyl peptides.

Suenaga A, Hatakeyama M, Ichikawa M, Yu X, Futatsugi N, Narumi T, Fukui K, Terada T, Taiji M, Shirouzu M, Yokoyama S, Konagaya A. Suenaga A, et al. Biochemistry. 2003 May 13;42(18):5195-200. doi: 10.1021/bi034113h. Biochemistry. 2003. PMID: 12731860

10

Computational studies on prion proteins: effect of Ala(117)-->Val mutation.

Okimoto N, Yamanaka K, Suenaga A, Hata M, Hoshino T. Okimoto N, et al. Among authors: suenaga a. Biophys J. 2002 May;82(5):2746-57. doi: 10.1016/S0006-3495(02)75615-4. Biophys J. 2002. PMID: 11964260 Free PMC article.

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