{"id":2337,"date":"2020-03-03T16:19:01","date_gmt":"2020-03-03T07:19:01","guid":{"rendered":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/?p=2337"},"modified":"2020-03-04T09:40:23","modified_gmt":"2020-03-04T00:40:23","slug":"%e3%82%bf%e3%83%b3%e3%83%91%e3%82%af%e8%b3%aa-%e3%83%aa%e3%82%ac%e3%83%b3%e3%83%89%e8%a4%87%e5%90%88%e4%bd%93%e3%81%ae%e8%84%82%e8%b3%aa%e4%ba%8c%e9%87%8d%e8%86%9c%e3%81%b8%e3%81%ae%e6%8c%bf%e5%85%a5","status":"publish","type":"post","link":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/2020\/03\/03\/%e3%82%bf%e3%83%b3%e3%83%91%e3%82%af%e8%b3%aa-%e3%83%aa%e3%82%ac%e3%83%b3%e3%83%89%e8%a4%87%e5%90%88%e4%bd%93%e3%81%ae%e8%84%82%e8%b3%aa%e4%ba%8c%e9%87%8d%e8%86%9c%e3%81%b8%e3%81%ae%e6%8c%bf%e5%85%a5\/","title":{"rendered":"\u30bf\u30f3\u30d1\u30af\u8cea-\u30ea\u30ac\u30f3\u30c9\u8907\u5408\u4f53\u306e\u8102\u8cea\u4e8c\u91cd\u819c\u3078\u306e\u633f\u5165"},"content":{"rendered":"

\u7814\u7a76\u5ba4\u5185\u30e1\u30e2<\/p>\n

\u74b0\u5883: CentOS 7, GROMACS 2019.5.<\/p>\n

\u4e0b\u306e\u6587\u732e\u306e\u30b7\u30df\u30e5\u30ec\u30fc\u30b7\u30e7\u30f3\u306e\u6700\u521d\u306e\u90e8\u5206\u3060\u3051\u3084\u3063\u3066\u307f\u307e\u3057\u305f\u3002<\/p>\n

Ryckbosch, S. M.; Wender, P. A.; Pande, V. S. Molecular dynamics simulations reveal ligand-controlled positioning of a peripheral protein complex in membranes. Nat. Commun.<\/span> 2017<\/span>, 8<\/span>, 6. DOI: 10.1038\/s41467-016-0015-8<\/a>.<\/p>\n

\u8ad6\u6587\u4e2d\u306e\u5206\u5b50\u52d5\u529b\u5b66\uff08MD\uff09\u30b7\u30df\u30e5\u30ec\u30fc\u30b7\u30e7\u30f3\u306e\u624b\u9806\u306f<\/p>\n

    \n
  1. PKC\u03b4 C1B\u30c9\u30e1\u30a4\u30f3\u3068\u30ea\u30ac\u30f3\u30c9\uff08Bryostatin-1, Wender’s bryolog, PDBu, prostratin\uff09\u306e\u8907\u5408\u4f53\u3042\u308b\u3044\u306f\u30c9\u30e1\u30a4\u30f3\u306e\u307f\u3092\u6eb6\u6db2\u4e2d\u304b\u3089\u8102\u8cea\u4e8c\u91cd\u819c\uff08POPS 128\u5206\u5b50\uff09\u3078Z\u8ef8\u306b\u6cbf\u3063\u3066200 ns\u304b\u3051\u3066\u5f15\u3063\u5f35\u308a\u4e0a\u3052\u308b\u3002\u5f15\u3063\u5f35\u308b\u306e\u306f\u30dd\u30b1\u30c3\u30c8\u5f62\u6210\u3059\u308b\u30a2\u30df\u30ce\u9178\u6b8b\u57fa\uff08\u5168\u4f53\u306e\u7d043\u5206\u306e1\uff09\u3068\uff08\u5b58\u5728\u3059\u308b\u306a\u3089\uff09\u30ea\u30ac\u30f3\u30c9\u3002<\/li>\n
  2. \u8ecc\u8de1\uff08\u30c8\u30e9\u30b8\u30a7\u30af\u30c8\u30ea\uff09\u304b\u3089\u53cd\u5fdc\u5ea7\u6a19\u306b\u6cbf\u3063\u3066100\u500b\u306e\u521d\u671f\u5ea7\u6a19\u3092\u53d6\u308b\u3002<\/li>\n
  3. \u305d\u308c\u305e\u308c\u306e\u521d\u671f\u5ea7\u6a19\u3092\u4f7f\u3063\u305f\u30b7\u30df\u30e5\u30ec\u30fc\u30b7\u30e7\u30f3\u309240\u30af\u30ed\u30fc\u30f3\uff0820 ns\uff09\u884c\u3046\u3002<\/li>\n
  4. \u3053\u308c\u3089\u306e\u30b7\u30df\u30e5\u30ec\u30fc\u30b7\u30e7\u30f3\u304b\u3089\u3001\u30bf\u30f3\u30d1\u30af\u8cea\u30ea\u30ac\u30f3\u30c9\u8907\u5408\u4f53\u306e\u819c\u306b\u5bfe\u3059\u308b\u8ddd\u96e2\u3068\u89d2\u5ea6\u3067\u4e8c\u6b21\u5143\u30d7\u30ed\u30d5\u30a1\u30a4\u30eb\u3092\u5f97\u308b\u3002\u3053\u306e\u914d\u7f6e\u3092\u5168\u3066\u7db2\u7f85\u3059\u308b\u3088\u3046\u306b\u65b0\u305f\u306b1000\u500b\u306e\u521d\u671f\u5ea7\u6a19\u3092\u53d6\u308b\u3002<\/li>\n
  5. \u3053\u306e1000\u500b\u306e\u521d\u671f\u5ea7\u6a19 \u00d7 4\u30af\u30ed\u30fc\u30f3 \u00d7 30 ns\u79d2\u306e\u30b7\u30df\u30e5\u30ec\u30fc\u30b7\u30e7\u30f3\u3092\u884c\u3046\u3002<\/li>\n
  6. \u30de\u30eb\u30b3\u30d5\u72b6\u614b\u30e2\u30c7\u30eb\uff08MSM\uff09\u306b\u3088\u308b\u81ea\u7531\u30a8\u30cd\u30eb\u30ae\u30fc\u89e3\u6790<\/li>\n<\/ol>\n

    \u5168\u3066\u5408\u308f\u305b\u305f\u30b7\u30df\u30e5\u30ec\u30fc\u30b7\u30e7\u30f3\u6642\u9593\u306fBryostatin-1\u3001PDBu\u3001\u30bf\u30f3\u30d1\u30af\u8cea\u306e\u307f\u304c400\u30de\u30a4\u30af\u30ed\u79d2\u3001prostratin\u304c580\u30de\u30a4\u30af\u30ed\u79d2\u3001Bryolog\u304c300\u30de\u30a4\u30af\u30ed\u79d2\u3002\u9014\u65b9\u3082\u306a\u304f\u9577\u3044\u3002<\/p>\n

    \u8a08\u7b97\u30d7\u30ed\u30b0\u30e9\u30e0\u3001\u529b\u5834: \u30d7\u30ed\u30b0\u30e9\u30e0, GROMACS 4.5.3; \u8a08\u7b97\u6a5f, Folding@home; \u529b\u5834 –
    \nAMBER99SB-ILDN\uff08\u30bf\u30f3\u30d1\u30af\u8cea\uff09, GAFF2\uff08\u30ea\u30ac\u30f3\u30c9\uff09, Slipids\uff08\u8102\u8cea\uff09, TIP3P\uff08\u6c34\uff09\u3002<\/p>\n

    \u666e\u901a\u3001C1\u30c9\u30e1\u30a4\u30f3-\u30ea\u30ac\u30f3\u30c9\u8907\u5408\u4f53\u3092\u8102\u8cea\u4e8c\u91cd\u819c\u306b\u57cb\u3081\u8fbc\u3093\u3060\u521d\u671f\u69cb\u9020\u3092PPM server\u3068CHARMM-GUI\u3067\u4f5c\u308b\u3068\u30bf\u30f3\u30d1\u30af\u8cea\u304c\u57cb\u307e\u3063\u305f\u5074\uff08inner leaflet\uff09\u306e\u30ea\u30f3\u8102\u8cea\u5206\u5b50\u6570\u304c6\u500b\u7a0b\u5c11\u304f\u306a\u308a\u307e\u3059\u3002\u4e0a\u4e0b\u306e\u5206\u5b50\u6570\u306e\u5dee\u3092\u5f15\u3063\u5f35\u308a\u4e0a\u3052\u308b\u6642\u306b\u3069\u3046\u3057\u3066\u3044\u308b\u306e\u304b\u3068\u601d\u3063\u305f\u3089\u3001outer leaflet\u3068inner leaflet\u306e\u30ea\u30f3\u8102\u8cea\u5206\u5b50\u6570\u306f\u540c\u3058\uff0864\u5206\u5b50\u305a\u3064\uff09\u3067\u7121\u7406\u77e2\u7406\u30bf\u30f3\u30d1\u30af\u8cea\u30ea\u30ac\u30f3\u30c9\u8907\u5408\u4f53\u3092\u5f15\u3063\u5f35\u308a\u4e0a\u3052\u3066\u3044\u307e\u3057\u305f\u3002\u305d\u3053\u306e\u7d30\u304b\u3044\u3068\u3053\u308d\u306f\u6c17\u306b\u3057\u3066\u3044\u306a\u3044\u3088\u3046\u3067\u3059\u3002<\/p>\n

    \u5f15\u3063\u5f35\u308a\u4e0a\u3052\u308b\u3068\u3053\u308d\u3060\u3051\u306a\u3089\u307e\u305a\u51fa\u6765\u305d\u3046\u3060\u3068\u601d\u3063\u3066PKC\u03b4 C1B\u30c9\u30e1\u30a4\u30f3\u3068TPA\u306e\u8907\u5408\u4f53\u3067\u3084\u3063\u3066\u307f\u308b\u3053\u3068\u306b\u3057\u307e\u3057\u305f\u3002TPA\u306e\u3088\u3046\u306a\u758e\u6c34\u6027\u304c\u9ad8\u3044\u5206\u5b50\u306f\u306f\u3058\u3081\u304b\u3089\u819c\u4e2d\u306b\u5206\u914d\u3057\u3066\u3044\u308b\u3068\u601d\u3044\u307e\u3059\u304c\u3001\u7d30\u304b\u3044\u3053\u3068\u306f\u6c17\u306b\u305b\u305a\u3084\u3063\u3066\u307f\u307e\u3059\u3002<\/p>\n

    COM-pulling<\/h2>\n

    \u30d5\u30a1\u30a4\u30eb<\/h3>\n

    COM\u306f “center of mass” \u300c\u8cea\u91cf\u4e2d\u5fc3\u300d\u306e\u7565\u79f0\u3067\u3059\u3002CHARMM-GUI\u30b5\u30fc\u30d0\u3092\u4f7f\u3063\u30661PTR.pdb\u304b\u3089\u4f5c\u6210\u3057\u305fPKC\u03b4-C1B\u30c9\u30e1\u30a4\u30f3\u3068TPA\u306e\u8907\u5408\u4f53\u69cb\u9020\u3092POPS\u4e8c\u91cd\u819c\u306e\u5c11\u3057\u4e0b\u5074\u306b\u914d\u7f6e\u3057\u307e\u3057\u305f\u3002CHARMM-GUI\u304c\u51fa\u529b\u3059\u308b\u901a\u5e38\u306e\u5e73\u8861\u5316\uff08step6.6\u307e\u3067\uff09\u3092\u884c\u3063\u305f\u5f8c\u3001step6.6\u306e\u6761\u4ef6\uff08\u30bf\u30f3\u30d1\u30af\u8cea\u3068\u30ea\u30ac\u30f3\u30c9\u306e\u91cd\u539f\u5b50\u306b\u4f4d\u7f6e\u62d8\u675f\u304c\u304b\u304b\u3063\u3066\u3044\u308b\uff09\u3067\u3055\u3089\u306b100 ns\u5e73\u8861\u5316\u3092\u884c\u3044\u307e\u3057\u305f\u3002\u6b21\u306b\u3001mdp\u30d5\u30a1\u30a4\u30eb\u306b\u4ee5\u4e0b\u306e\u3088\u3046\u306bpulling\u306e\u305f\u3081\u306e\u8a18\u8ff0\u3092\u52a0\u3048\u3066COM-pulling\u30b7\u30df\u30e5\u30ec\u30fc\u30b7\u30e7\u30f3\u3092\u5b9f\u884c\u3057\u307e\u3057\u305f\u3002<\/p>\n

    ; Pull code\npull                    = yes\npull_ncoords            = 1         ; \u53cd\u5fdc\u5ea7\u6a19\u306f1\u3064\u3060\u3051\npull_ngroups            = 2         ; 2\u3064\u306e\u30b0\u30eb\u30fc\u30d7\u3067\u53cd\u5fdc\u5ea7\u6a19\u3092\u5b9a\u7fa9\npull_group1_name        = TPA       ; \u30ea\u30ac\u30f3\u30c9\npull_group2_name        = MEMB      ; \u8102\u8cea\u4e8c\u91cd\u819c\u5168\u4f53\npull_coord1_type        = umbrella  ; harmonic potential\npull_coord1_geometry    = distance  ; \u8ddd\u96e2\u3092\u5909\u5316\u3055\u305b\u308b\npull_coord1_dim         = N N Y     ; Z\u8ef8\u306b\u6cbf\u3063\u3066pull\u3059\u308b\npull_coord1_groups      = 1 2       \npull_coord1_start       = yes       ; define initial COM distance > 0\npull_coord1_rate        = -0.00025     ; -0.00025 nm per ps = -0.25 nm\uff082.5 \u212b\uff09per ns. \npull_coord1_k           = 1000      ; kJ mol^-1 nm^-2\n<\/pre>\n
    \u7d50\u679c<\/h3>\n
    \u6c34\u4e2d\u3067\u306f\u4e38\u307e\u3063\u3066\u3044\u305fTPA\u306e\u5074\u9396\u304c\u819c\u4e2d\u3067\u306f\u4f38\u3073\u305f\u306e\u304c\u5370\u8c61\u7684\u3067\u3057\u305f\u3002\u30c8\u30e9\u30b8\u30a7\u30af\u30c8\u30ea\u304b\u3089\u521d\u671f\u5ea7\u6a19\u3092\u53d6\u3063\u3066\u3001\u53cd\u5fdc\u5ea7\u6a19\u3092\u56fa\u5b9a\u3057\u3066\u305d\u308c\u305e\u308cMD\u30b7\u30df\u30e5\u30ec\u30fc\u30b7\u30e7\u30f3\u3092\u3057\u305f\u5f8c\uff08\u30a2\u30f3\u30d6\u30ec\u30e9\u30b5\u30f3\u30d7\u30ea\u30f3\u30b0\uff09\u3001WHAM\uff08weighted histogram analysis method\uff09\u6cd5\u3067\u89e3\u6790\u3059\u308b\u3053\u3068\u3067\u53cd\u5fdc\u5ea7\u6a19\u4e0a\u306ePMF\uff08potential of mean force\uff09\u66f2\u7dda\uff08\u53cd\u5fdc\u5ea7\u6a19\u306b\u6cbf\u3063\u3066\u81ea\u7531\u30a8\u30cd\u30eb\u30ae\u30fc\u3092\u30d7\u30ed\u30c3\u30c8\u3057\u305f\u3082\u306e\uff09\u3092\u5f97\u308b\u3053\u3068\u304c\u3067\u304d\u308b\u305d\u3046\u3067\u3059\u3002<\/p>\n
    \u753b\u50cf<\/h4>\n
    \u6a59\u8272\u306e\u7403\u306f\u30ea\u30f3\u8102\u8cea\u306e\u30ea\u30f3\u539f\u5b50\u3092\u8868\u308f\u3059\u3002<\/p>\n
    \u6700\u521d<\/p>\n
    \"\"<\/p>\n
    \u6700\u5f8c<\/p>\n
    \"\"<\/p>\n
    \u52d5\u753b<\/h4>\n
    https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2020\/03\/movie.mp4<\/a><\/video><\/div>\n
    \uff08\u4e86\uff09<\/p>\n","protected":false},"excerpt":{"rendered":"
    \u7814\u7a76\u5ba4\u5185\u30e1\u30e2 \u74b0\u5883: CentOS 7, GROMACS 2 …<\/p>\n","protected":false},"author":1,"featured_media":2347,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"om_disable_all_campaigns":false,"_uag_custom_page_level_css":"","_monsterinsights_skip_tracking":false,"_monsterinsights_sitenote_active":false,"_monsterinsights_sitenote_note":"","_monsterinsights_sitenote_category":0,"_uf_show_specific_survey":0,"_uf_disable_surveys":false,"_locale":"","_original_post":"","footnotes":""},"categories":[5],"tags":[],"class_list":["post-2337","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-5","ja"],"aioseo_notices":[],"aioseo_head":"\n\t\t\n\t\n\t\n\t\n\t\n\t\n\t\t\n\t\t\n\t\t\n\t\t\n\t\t\n\t\t\n\t\t\n\t\t\n\t\t\n\t\t\n\t\t\n\t\t\n\t\t\n\t\t\n\t\t\n\t\t\n\t\t