Towards Physical Understanding of Molecular Recognition in the Cell: Recent Evolution of Molecular Dynamics Techniques and Free Energy Theories

Yamashita T. Towards Physical Understanding of Molecular Recognition in the Cell: Recent Evolution of Molecular Dynamics Techniques and Free Energy Theories Biomedical Sciences 2016, V. 2 (5), pp. 34-47 doi: 10.11648/j.bs.20160205.11

On the accurate molecular dynamics analysis of biological molecules

Yamashita T. On the accurate molecular dynamics analysis of biological molecules AIP Conf Proc. 2016, 1790, 020026; doi: http://dx.doi.org/10.1063/1.4968652

Molecular dynamics analysis to evaluate docking pose prediction.

Sakano T, Mahamood MI, Yamashita T, Fujitani H. Molecular dynamics analysis to evaluate docking pose prediction. Biophys Physicobiol. 2016 Jul 14;13:181-194. eCollection 2016.

Middle-Down and Chemical Proteomic Approaches to Reveal Histone H4 Modification Dynamics in Cell Cycle: Label-Free Semi-Quantification of Histone Tail Peptide Modifications Including Phosphorylation and Highly Sensitive Capture of Histone PTM Binding Proteins Using Photo-Reactive Crosslinkers.

Masuda K, Kitakami JI, Kozasa T, Kodama T, Ihara S, Hamakubo T. Middle-Down and Chemical Proteomic Approaches to Reveal Histone H4 Modification Dynamics in Cell Cycle: Label-Free Semi-Quantification of Histone Tail Peptide Modifications Including Phosphorylation and Highly Sensitive Capture of Histone PTM Binding Proteins Using Photo-Reactive Crosslinkers. FASEB J. 2017 Mar;31(3):910-919. doi: 10.1096/fj.201601102R. Epub 2016 Nov 23.

QRFP-Deficient Mice Are Hypophagic, Lean, Hypoactive and Exhibit Increased Anxiety-Like Behavior.

Okamoto K, Yamasaki M, Takao K, Soya S, Iwasaki M, Sasaki K, Magoori K, Sakakibara I, Miyakawa T, Mieda M, Watanabe M, Sakai J, Yanagisawa M, Sakurai T. QRFP-Deficient Mice Are Hypophagic, Lean, Hypoactive and Exhibit Increased Anxiety-Like Behavior. PLoS One. 2016 Nov 11;11(11):e0164716. doi: 10.1371/journal.pone.0164716. eCollection 2016.

CASTIN: a system for comprehensive analysis of cancer-stromal interactome.

Komura D, Isagawa T, Kishi K, Suzuki R, Sato R, Tanaka M, Katoh H, Yamamoto S, Tatsuno K, Fukayama M, Aburatani H, Ishikawa S. CASTIN: a system for comprehensive analysis of cancer-stromal interactome. BMC Genomics. 2016 Nov 9;17(1):899.

TET2 functions as a resistance factor against DNA methylation acquisition during Epstein-Barr virus infection.

Namba-Fukuyo H, Funata S, Matsusaka K, Fukuyo M, Rahmutulla B, Mano Y, Fukayama M, Aburatani H, Kaneda A. TET2 functions as a resistance factor against DNA methylation acquisition during Epstein-Barr virus infection. Oncotarget. 2016 Dec 6;7(49):81512-81526. doi: 10.18632/oncotarget.13130.

Base-Resolution Analysis of 5-Hydroxymethylcytosine by One-Pot Bisulfite-Free Chemical Conversion with Peroxotungstate.

Hayashi G, Koyama K, Shiota H, Kamio A, Umeda T, Nagae G, Aburatani H, Okamoto A. Base-Resolution Analysis of 5-Hydroxymethylcytosine by One-Pot Bisulfite-Free Chemical Conversion with Peroxotungstate. J Am Chem Soc. 2016 Nov 2;138(43):14178-14181. Epub 2016 Oct 24.

Effects of Chronic Low-Dose Radiation on Human Neural Progenitor Cells.

Ishimoto K, Kawamata N, Uchihara Y, Okubo M, Fujimoto R, Gotoh E, Kakinouchi K, Mizohata E, Hino N, Okada Y, Mochizuki Y, Tanaka T, Hamakubo T, Sakai J, Kodama T, Inoue T, Tachibana K, Doi T. Effects of Chronic Low-Dose Radiation on Human Neural Progenitor Cells. PLoS One. 2016 Oct 31;11(10):e0165766. doi: 10.1371/journal.pone.0165766. eCollection 2016.

Molecular Pathology and Novel Clinical Therapy for Uterine Leiomyosarcoma.

Hayashi T, Kawano M, Ichimura T, Ida K, Ando H, Zharhary D, Kanai Y, Aburatani H, Tonegawa S, Shiozawa T, Yaegashi N, Konishi I. Molecular Pathology and Novel Clinical Therapy for Uterine Leiomyosarcoma. Anticancer Res. 2016 Oct;36(10):4997-5007. Review.

Ubiquitination of Lysine 867 of the Human SETDB1 Protein Upregulates Its Histone H3 Lysine 9 (H3K9) Methyltransferase Activity.

Ishimoto K, Kawamata N, Uchihara Y, Okubo M, Fujimoto R, Gotoh E, Kakinouchi K, Mizohata E, Hino N, Okada Y, Mochizuki Y, Tanaka T, Hamakubo T, Sakai J, Kodama T, Inoue T, Tachibana K, Doi T. Ubiquitination of Lysine 867 of the Human SETDB1 Protein Upregulates Its Histone H3 Lysine 9 (H3K9) Methyltransferase Activity. PLoS One. 2016 Oct 31;11(10):e0165766. doi: 10.1371/journal.pone.0165766. eCollection 2016.

Loss of YAP1 defines neuroendocrine differentiation of lung tumors.

Ito T, Matsubara D, Tanaka I, Makiya K, Tanei ZI, Kumagai Y, Shiu SJ, Nakaoka HJ, Ishikawa S, Isagawa T, Morikawa T, Shinozaki-Ushiku A, Goto Y, Nakano T, Tsuchiya T, Tsubochi H, Komura D, Aburatani H, Dobashi Y, Nakajima J, Endo S, Fukayama M, et al. Loss of YAP1 defines neuroendocrine differentiation of lung tumors. Cancer Sci. 2016 Oct;107(10):1527-1538. doi: 10.1111/cas.13013. Epub 2016 Sep 9.

MDM2 is a potential therapeutic target and prognostic factor for ovarian clear cell carcinomas with wild type TP53.

Makii C, Oda K, Ikeda Y, Sone K, Hasegawa K, Uehara Y, Nishijima A, Asada K, Koso T, Fukuda T, Inaba K, Oki S, Machino H, Kojima M, Kashiyama T, Mori-Uchino M, Arimoto T, Wada-Hiraike O, Kawana K, Yano T, Fujiwara K, Aburatani H, et al. MDM2 is a potential therapeutic target and prognostic factor for ovarian clear cell carcinomas with wild type TP53. Oncotarget. 2016 Nov 15;7(46):75328-75338. doi: 10.18632/oncotarget.12175.

Smad4 is required to inhibit osteoclastogenesis and maintain bone mass.

Morita M, Yoshida S, Iwasaki R, Yasui T, Sato Y, Kobayashi T, Watanabe R, Oike T, Miyamoto K, Takami M, Ozato K, Deng CX, Aburatani H, Tanaka S, Yoshimura A, Toyama Y, Matsumoto M, Nakamura M, Kawana H, Nakagawa T, Miyamoto T. Smad4 is required to inhibit osteoclastogenesis and maintain bone mass. Sci Rep. 2016 Oct 12;6:35221. doi: 10.1038/srep35221.

Histone H2A T120 Phosphorylation Promotes Oncogenic Transformation via Upregulation of Cyclin D1.

Aihara H, Nakagawa T, Mizusaki H, Yoneda M, Kato M, Doiguchi M, Imamura Y, Higashi M, Ikura T, Hayashi T, Kodama Y, Oki M, Nakayama T, Cheung E, Aburatani H, Takayama KI, Koseki H, Inoue S, Takeshima Y, Ito T. Histone H2A T120 Phosphorylation Promotes Oncogenic Transformation via Upregulation of Cyclin D1. Mol Cell. 2016 Oct 6;64(1):176-188. doi: 10.1016/j.molcel.2016.09.012.

Targeted nucleotide editing using hybrid prokaryotic and vertebrate adaptive immune systems

Nishida K, Arazoe T, Yachie N, Banno S, Kakimoto M, Tabata M, Mochizuki M, Miyabe A, Araki M, Hara KY, Shimatani Z & Kondo A Targeted nucleotide editing using hybrid prokaryotic and vertebrate adaptive immune systems Science 353, aaf8729

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