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短いテトラペプチドの全原子シミュレーションによるアミノ酸のアモルファスな凝集性の洞察

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(1)Vol.2014-BIO-40 No.5 2014/12/18. ᝟ሗฎ⌮Ꮫ఍◊✲ሗ࿌ IPSJ SIG Technical Report. ▷࠸ࢸࢺࣛ࣌ࣉࢳࢻࡢ඲ཎᏊࢩ࣑࣮ࣗࣞࢩࣙࣥ࡟ࡼࡿ࢔࣑ࣀ㓟ࡢ ࢔ࣔࣝࣇ࢓ࢫ࡞ ࡞จ㞟ᛶࡢὝᐹ బ⸨㞝ኈ †1 ᮎỌᩔ †2 Ὀᆅ┿ᘯே †3 㯮⏣⿱ †1 ࢱࣥࣃࢡ㉁ࡢ⁐ゎᛶ࡟ᑐࡍࡿ࢔࣑ࣀ㓟ࡢᐤ୚ࢆㄪ࡭ࡿࡓࡵ࡟ࠊศᏊືຊᏛࢩ࣑࣮ࣗࣞࢩࣙࣥࢆ⏝࠸ࡓࠋ18 ✀㢮ࡢ࢔ ࣑ࣀ㓟ࢆ⏝࠸࡚ࠊྠ୍ࡢ࢔࣑ࣀ㓟 4 ṧᇶ࡛ᵓᡂࡉࢀࡿ࣌ࣉࢳࢻࡢࣔࢹࣝࢆసᡂࡋࠊ1 ㎶⣙ 104 ύ ࡢ❧᪉యࡢ⣔࡟ 27 ࣌ࣉࢳࢻ㓄⨨ࡋࡓࠋࡇࢀࢆึᮇᵓ㐀࡜ࡋ 100ns ࡢࢩ࣑࣮ࣗࣞࢩࣙࣥࢆ⾜ࡗࡓࠋィ⟬ࡣࠊMD-GRAPE3 ࢥࣥࣆ࣮ࣗࢱ ୖ࡛ࠊAMBER8 ࢆ⏝࠸ࠊᶆ‽ⓗ࡞ຊሙ࡛⾜ࡗࡓࠋ IࠊVࠊLࠊMࠊNࠊQࠊFࠊWࠊYࠊཬࡧ H ࠿ࡽ࡞ࡿࢸࢺࣛ࣌ࣉࢳࢻ ࡀ኱ࡁ࠸࢔ࣔࣝࣇ࢓ࢫ࡞จ㞟యࢆᙧᡂࡋࠊAࠊPࠊSࠊ࠾ࡼࡧ T ࢆྵࡴࡶࡢࡣࠊᑠࡉ࠸ࡶࡢࢆᙧᡂࡋࡓࠋDࠊEࠊKࠊ࠾ ࡼࡧ R ࡣ඲ࡃจ㞟ࡀ㉳ࡇࡽ࡞࠿ࡗࡓࠋࡇࢀࡽࡢほᐹ⤖ᯝࡣࠊBPTI ࢱࣥࣃࢡ㉁ࡢ C ᮎ➃࡟௜ຍࡉࢀࡓ 5 ṧᇶࡢ࣌ࣉࢳ ࢻࢆ౑⏝ࡋࡓᡃࠎࡢ௨๓ࡢᐇ㦂ⓗ࡞⁐ゎᗘ ᐃࡢഴྥ࡟඲యⓗ࡟ἢࡗࡓࡶࡢ࡛࠶ࡗࡓࠋࡉࡽ࡟ࠊ࣐ࣝࢥࣇ≧ែࣔࢹࣝ ࢆ⏝࠸ࡓ⤫ィゎᯒ࡛ࡣࠊ஧㔞యࡀࡼࡾ኱ࡁ࡞จ㞟య࡬ࡢ᰾࡜࡞ࡿ࢜ࣜࢦ࣐࣮࡛࠶ࡿࡇ࡜ࢆᥦ᱌ࡍࡿࠋ඲య࡜ࡋ࡚ࠊࡇ ࡢ࣐ࣝࢳ࣌ࣉࢳࢻ⣔ࡢ඲ཎᏊศᏊືຊᏛࢩ࣑࣮ࣗࣞࢩࣙࣥࡣࠊᮏ㉁ⓗ࡟ᐇ㦂ⓗほᐹ࡜୍⮴ࡋ࡚࠾ࡾࠊ࣌ࣉࢳࢻࡢ⁐ゎ ᛶࡢᇶᮏⓗ࡞≉ᛶࢆ෌⌧ࡋ࡚࠸ࡓࠋ. 1. ࡣࡌࡵ࡟. ྛࣔࢹࣝ࣌ࣉࢳࢻ࡟࠾ࡅࡿࢩ࣑࣮ࣗࣞࢩࣙࣥࡢึᮇᵓ㐀ࡣࠊ.  ࢱࣥࣃࢡ㉁ࡢจ㞟ᛶཬࡧ⁐ゎᛶࡣࠊ㓝⣲ࡢ⏘ᴗⓗ࡞ᛂ⏝. ࣝ࣌ࣉࢳࢻࢆ 27 ศᏊ㓄⨨ࡋࡓࠋࡑࡋ࡚ࠊ⣙ 30,000 ಶࡢỈ. ࡸࠊ⏕໬Ꮫ◊✲࠾ࡼࡧࣂ࢖࢜་⸆ရ⏘ᴗ࡞࡝ࡢ࠸ࡃࡘ࠿ࡢ. ศᏊ࡛⣔ࢆ‶ࡓࡋࠊ⃰ᗘࢆ⣙ 40 mM ࡜ࡋࡓࠋึᮇᵓ㐀ࡢ. ศ㔝࡟࠾࠸࡚㔜せどࡉࢀ࡚࠸ࡿ[1]ࠋࡑࡢࡓࡵࠊin vivo ࠶ࡿ. సᡂࡸᐇ㝿ࡢࢩ࣑࣮ࣗࣞࢩࣙࣥࡣศᏊືຊᏛࢩ࣑࣮ࣗࣞࢩ. ࠸ࡣ in vitro ࡛ࡢจ㞟࣓࢝ࢽࢬ࣒ࡢゎ᫂ࡀᛴࡀࢀ࡚࠸ࡿࠋࡇ. ࣙࣥࢯࣇࢺ࢙࢘࢔ࣃࢵࢣ࣮ࢪ Amber 8.0 ࢆ⏝࠸ࠊ⌮໬Ꮫ◊. ࢀࡲ࡛࡟ࢱࣥࣃࢡ㉁ࡢจ㞟ᛶࠊࡲࡓࡣ⁐ゎᛶ࡟㛵ࡍࡿ◊✲. ✲ᡤࡢ MD-GRAPE3 ࢆ౑⏝ࡍࡿࡇ࡜࡟ࡼࡾ㧗㏿໬ࡀྍ⬟. ࡣᩘከࡃ⾜ࢃࢀࠊᚑ᮶࠿ࡽࡑࡢ␯ỈᛶࠊぶỈᛶࠊ⥲㟁Ⲵࡸ. ࡜࡞ࡗࡓࠋẼᅽ 1 atomࠊ ᗘ 300 K ࡢ᮲௳ࢆタᐃࡋࠊ඲ࣔ. ศᏊ⾲㠃ࡢ㟁Ⲵศᕸ࡞࡝࡟ࡼࡗ࡚Ỵࡲࡿ࡜⪃࠼ࡽࢀ࡚࠾ࡾࠊ. ࢹ࡛ࣝ 100 ࢼࣀ⛊⾜ࡗࡓࠋ0.01 ࢼࣀ⛊ࡈ࡜࡟ฟຊࡉࢀࡿᗙ. ࡇࢀࡽࡣ඲࡚࢔࣑ࣀ㓟ࡢ✀㢮࡟ࡼࡿᛶ㉁࡛࠶ࡿࠋࡲࡓࠊࡇ. ᶆࢹ࣮ࢱࡸ࢚ࢿࣝࢠ࣮ࢹ࣮ࢱ࠿ࡽゎᯒࢆ⾜ࡗࡓࠋ1 ࡘࡢࣔ. ⣔ࡢ኱ࡁࡉࡀ 1 ㎶⣙ 104 ύ ࡢ❧᪉యࡢෆ࡟ࠊྠ୍ࡢࣔࢹ. ࢀࡽࡢᅉᏊ࡜ࢱࣥࣃࢡ㉁ࡢจ㞟ᛶࠊ⁐ゎᛶࡢᐃ㔞ⓗ࡞㛵ಀ. ࢹࣝࢆ 100 ࢼࣀ⛊⤊࠼ࡿࡢ࡟ࠊ8 core ౑⏝ࡋࠊ6 ࣨ᭶ࡢィ. ࡣࠊࡲࡔゎ᫂ࡉࢀ࡚࠸࡞࠸ࠋᮏ◊✲࡛⏝࠸ࡓศᏊືຊᏛࢩ. ⟬㔞ࢆᚲせ࡜ࡋࡓࠋ. ࣑࣮ࣗࣞࢩࣙࣥࡣ୍⯡ⓗ࡟ศᏊจ㞟యࡢ⇕ຊᏛ㔞ࡸ᫬㛫౫ Ꮡᛶ࡟㛵ࡍࡿᵝࠎ࡞≀⌮㔞ࢆศᏊ࡛ࣞ࣋ࣝィ⟬࡛ࡁࠊ࣓࢝. 2.2 ࢡࣛࢫࢱ࣮ᐃ⩏. ࢽࢬ࣒ࢆ⿬௜ࡅࡿᙺ๭࡛⏝࠸ࡽࢀࡿሙྜࡀከ࠸ࠋࡋ࠿ࡋࠊ.  ඲࡚ࡢ࣌ࣉࢳࢻ㛫࡟࠾ࡅࡿ඲ཎᏊ㛫ࡢ㊥㞳ࢆィ⟬ࡋࠊ2. ⌧ᅾࠊจ㞟ࡢࢩ࣑࣮ࣗࣞࢩࣙࣥࡣ࢔࣑ࣟ࢖ࢻᙧᡂࡢゎᯒࡀ. ᮏࡢ࣌ࣉࢳࢻ㛫ࡢ࠸ࡎࢀ࠿ࡢཎᏊ㛫㊥㞳ࡀࠊࡑࢀࡽࡢཎᏊ. ୰ᚰ࡛ࠊ࢔ࣔࣝࣇ࢓ࢫ࡞จ㞟ࡢゎᯒ࡟↔Ⅼࢆ⤠ࡗࡓࢩ࣑ࣗ. ࡢࣇ࢓ࣥࢹ࣮ࣝ࣡ࣝࢫ༙ᚄࡢ෇ෆ࡟཰ࡲࡗ࡚࠸ࡿሙྜ࡟ࠊ. ࣮ࣞࢩࣙࣥࡣᴟࡵ࡚ᑡ࡞࠸ࠋࡑࡇ࡛ᮏ◊✲࡛ࡣศᏊືຊᏛ. ࣌ࣉࢳࢻྠኈࡀจ㞟ࢆᙧᡂࡋ࡚࠸ࡿ࡜ぢ࡞ࡋࡓࠋ௒ᅇࡢ◊. ࢩ࣑࣮ࣗࣞࢩࣙࣥࢆ⏝࠸࡚࢔࣑ࣀ㓟ࡢ✀㢮࡟ࡼࡿᛶ㉁ࡢ㐪. ✲࡛ࡣ༙ᚄࡢ෇ෆ࡟㸯ࡘ࡛ࡶཎᏊྠኈࡢ㊥㞳ࡀ⣡ࡲࡗ࡚࠸. ࠸ࡀจ㞟࡟ཬࡰࡍᙳ㡪ࢆศᏊ࡛ࣞ࣋ࣝゎᯒࡍࡿࡇ࡜ࢆ┠ⓗ. ࡿሙྜ࡟࣌ࣉࢳࢻྠኈࡀ⤖ࡧࡘ࠸࡚࠸ࡿ࡜௬ᐃࡋࠊ」ᩘࡢ. ࡜ࡋࡓࠋ. ࣌ࣉࢳࢻࡀ⤖ࡧࡘ࠸ࡓ≧ែࡢ㞟ྜయࢆࢡࣛࢫࢱ࣮࡜࿧ࡪࡇ ࡜࡟ࡋࡓࠋࡲࡓࠊࡑࡢ᫬࡟ྵࡲࢀ࡚࠸ࡿ࣌ࣉࢳࢻࡢᩘࢆࢡ. 2. ᡭἲ. ࣛࢫࢱ࣮ࢧ࢖ࢬ࡜ᐃ⩏ࡋࡓࠋ. 2.1 MD ࢩ࣑࣮ࣗࣞࢩࣙࣥ  ࢢࣜࢩࣥ࡜ࢩࢫࢸ࢖ࣥࢆ㝖࠸ࡓ 18 ✀㢮ࡢ࢔࣑ࣀ㓟ࢆ⏝. 3. ⤖ᯝࠊ⪃ᐹ. ࠸࡚ࠊྠ୍ࡢ࢔࣑ࣀ㓟 4 ṧᇶ࡛ᵓᡂࡉࢀࡿ࣌ࣉࢳࢻࡢࣔࢹ. 3.1 ࢡࣛࢫࢱ࣮ゎᯒ. ࣝࢆసᡂࡋࡓࠋഃ㙐ࡢ㐪࠸࡟ࡼࡿ⤖ᯝࢆヲ⣽࡟ゎᯒࡍࡿࡓ.  ྛ᫬㛫࡟࠾࠸࡚ࢡࣛࢫࢱ࣮ࢧ࢖ࢬࡢᖹᆒ㸦Mean Cluster. ࡵࠊ඲࡚ࡢࣔࢹࣝ࣌ࣉࢳࢻ࡟࠾࠸࡚ࠊC ᮎ➃ࢆ N-࣓ࢳࣝ. Size㸧ࢆࢢࣛࣇ໬ࡋࡓ࡜ࡇࢁࠊI, V, L, N, Q, F, M, H, W, Y ࡣࠊ. ໬ࠊN ᮎ➃ࢆ࢔ࢭࢳࣝ໬ࡋࠊ୺㙐㟁Ⲵࡢᙳ㡪ࢆ࡞ࡃࡋࡓࠋ. 23㹼27 ࡢ኱ࡁ࡞ࢡࣛࢫࢱ࣮ࢆᙧᡂࡋ࡚࠸ࡓࠋ୍᪉ࠊE, D, R,. †1 ᮾி㎰ᕤ኱Ꮫ࣭ᕤ࣭⏕࿨ᕤ   Department of Biotechnology and Life Sciences/Graduate School of Engineering    †2 ⏘ᴗᢏ⾡⥲ྜ◊✲ᡤࠊ๰⸆ศᏊࣉࣟࣇ࢓࢖ࣜࣥࢢ◊✲ࢭࣥࢱ࣮   Molecular Profiling Research Center for Drug Discovery, AIST. †3 ⌮◊ࠊ⏕࿨ࢩࢫࢸ࣒◊✲ࢭࣥࢱ࣮   Quantitative Biology Center, RIKEN. ⓒ 2014 Information Processing Society of Japan. 1.

(2) Vol.2014-BIO-40 No.5 2014/12/18. ᝟ሗฎ⌮Ꮫ఍◊✲ሗ࿌ IPSJ SIG Technical Report K ࡟࠾࠸࡚ࡣ࡯࡜ࢇ࡝ࡢ࣌ࣉࢳࢻࡀࢡࣛࢫࢱ࣮ࢆᙧᡂࡋ࡚. ᅇࡢィ⟬ࡢ್࡜ࡢẚ㍑ࢆ⾜ࡗࡓࠋᖹᆒࢡࣛࢫࢱ࣮ࢧ࢖ࢬࡢ. ࠸࡞࠿ࡗࡓࠋࡲࡓࠊT, A, P, S ࡟࠾࠸࡚ࡣ୍㒊኱ࡁ࡞ࢡࣛࢫ. ࢹ࣮ࢱ࠿ࡽࠊ80~100ns ࡢ㛫࡛ᖹᆒࢆྲྀࡗࡓࡶࡢࢆィ⟬ࡢ್. ࢱ࣮ࢆᙧᡂࡋ࡚࠸ࡓࠋࡇࢀࡽࡢࡇ࡜࠿ࡽ㟁Ⲵࡢ᭷↓ࡸぶỈ. ࡜ࡋࡓࠋ. ᛶࠊ␯Ỉᛶ࡜࠸ࡗࡓᛶ㉁ࡀࢡࣛࢫࢱ࣮ᙧᡂ࡟ᙳ㡪ࢆཬࡰࡋ ࡚࠸ࡿࡇ࡜ࡀ♧၀ࡉࢀࡓࠋ(ᅗ 1). ᅗ 3 ᐇ㦂ⓗ࡞⁐ゎᛶࡢ್࡜ࡢẚ㍑ ᅗ 1 ྛ࢔࣑ࣀ㓟ࣔࢹࣝ࡟࠾ࡅࡿᖹᆒࢡࣛࢫࢱ࣮ࢧ࢖ࢬ. ୖグࡢ Hydropathy ࡜ Hydrophobicity ࡟࠾࠸࡚≉࡟㧗࠸┦ 㛵ࡀぢࡽࢀࡓࠋࡑࡢ௚ࡢᐇ㦂ⓗ࡞್࡟ᑐࡋ࡚ࡶࠊ␯Ỉᛶ࢔. 3.2 ࣐ࣝࢥࣇ≧ែࣔࢹࣝ࡟ࡼࡿゎᯒ. ࣑ࣀ㓟ࡸぶỈᛶ࢔࣑ࣀ㓟࡞࡝ࠊ㒊ศⓗ࡟┦㛵ࡀぢࡽࢀࡓࠋ. จ㞟ࡢ࣓࢝ࢽࢬ࣒ࡢึᮇẁ㝵ࢆㄪ࡭ࡿࡓࡵ࡟ࠊࢡࣛࢫࢱ. ࡇࡢ⤖ᯝࡣࠊ༢࡟ᮏィ⟬ࡢᣦ᦬ࢆ⿬௜ࡅࡿࡇ࡜࡟ຍ࠼ࠊ࢔. ࣮ᙧᡂࡀ☜ㄆ࡛ࡁࡓ࢔࣑ࣀ㓟࡟ࡘ࠸࡚࣐ࣝࢥࣇ≧ែࣔࢹࣝ. ࣑ࣀ㓟ࡢ⁐ゎᛶࡀᶆ‽ⓗ࡞ MD ࢩ࣑࣮ࣗࣞࢩࣙࣥࢆ⏝࠸࡚. ࢆ⏝࠸࡚ゎᯒࢆ⾜ࡗࡓࠋ0~20ns ࡢࢹ࣮ࢱࢆ౑⏝ࡋ≧ែ㑄⛣. ෌⌧ࡉࢀࡓࡇ࡜ࡣ⯆࿡῝࠸ࡇ࡜࡛࠶ࡿࠋ. ☜⋡ࢆィ⟬ࡋࠊ༢㔞యࡀ 100㸣ࡢึᮇศᕸ࡛ࢫࢸࢵࣉẖ࡟ ከ㔞యࡢ๭ྜࢆィ⟬ࡋࡓࠋ. 4. ࠾ࢃࡾ࡟  ࢩ࣑࣮ࣗࣞࢩࣙࣥࢆ⏝࠸࡚ぶỈᛶࡸ␯Ỉᛶࠊ㟁Ⲵࠊഃ㙐 ࡢ኱ࡁࡉ࡜࠸ࡗࡓ࢔࣑ࣀ㓟ࡢ≉ᚩ࡟ࡼࡿ࣌ࣉࢳࢻࡢจ㞟ᛶ ࡢ㐪࠸ࢆࠊࢡࣛࢫࢱ࣮ࡢᙧᡂ࡜࠸࠺ศᏊࣞ࣋ࣝࡢゎᯒ࡛☜ ㄆ࡛ࡁࡓࠋࡲࡓࠊ࣐ࣝࢥࣇࣔࢹࣝࢆ⏝࠸ࡓゎᯒ࡟ࡼࡾ 2~4 ࡢᑠࡉ࡞ࢡࣛࢫࢱ࣮ࡀึᮇࡢẁ㝵࡛⵳✚ࡉࢀࠊࡑࡢᚋࡼࡾ ኱ࡁ࡞ࢡࣛࢫࢱ࣮࡬㑄⛣ࡋ࡚࠸ࡃࡇ࡜ࡀ♧၀ࡉࢀࡓࠋᐇ㦂 ⓗ࡞⁐ゎᛶࡢ್ࡢẚ㍑࠿ࡽࡶࠊ࠸ࡃࡘ࠿ࡢࣃ࣓࣮ࣛࢱ࣮࡜ ࡣ㧗࠸┦㛵ࡀぢࡽࢀࡓࡓࡵࠊࢩ࣑࣮ࣗࣞࢩࣙࣥ࡟ࡼࡿ࣓࢝ ࢽࢬ࣒ゎ᫂ࡀ࢔࣑ࣀ㓟ࡢ㐪࠸࡟ࡼࡿจ㞟ᛶࡢゎᯒ࡜࠸࠺ࢸ ࣮࣐࡟ᑐࡋ࡚ࡶ᭷ຠ࡛࠶ࡿࡇ࡜ࡀ♧ࡉࢀࡓࠋ. ᅗ 2 ≧ែ㑄⛣☜⋡࡟ࡼࡗ࡚ィ⟬ࡉࢀࡓከ㔞యࡢ๭ྜ. ㅰ㎡ ᮏ◊✲ࡢィ⟬⤖ᯝࡣࠊRIKEN Integrated Cluster of Clusters.  ⤖ᯝࡼࡾࠊ2mer ࡢࡼ࠺࡞ᑠࡉ࡞ࢡࣛࢫࢱ࣮ࡀ⵳✚ࡉࢀࠊ. (RICC) ࢩࢫࢸ࣒ࢆ฼⏝ࡋ࡚ᚓࡽࢀࡓࠋ. ࡑࢀࡀࡼࡾ኱ࡁ࡞ࢡࣛࢫࢱ࣮ࢆᙧᡂࡋ࡚࠸ࡃࡇ࡜ࡀほᐹࡉ ࢀࡓࠋࡇࡢ⤖ᯝࡣࠊᡃࠎࡢࢩ࣑࣮ࣗࣞࢩࣙࣥࢩࢫࢸ࣒ୗ࡟ ࠾ࡅࡿึᮇẁ㝵࡟࠾࠸࡚㔜せ࡞ᙺ๭ࢆᯝࡓࡋ࡚࠸ࡿ࡜⪃࠼ ࡽࢀࡿࠋ. ཧ⪃ᩥ⊩ 1) Fowler, S.B., et al., Rational design of aggregation resistant bioactive peptides: reengineering human calcitonin. Proceedings of the National Academy of Sciences of the United States of America, 2005. 102(29): p. 10105-10.. 3.3 ᐇ㦂ⓗ࡞⁐ゎᛶࡢ್࡜ࡢẚ㍑  ಶࠎࡢ࢔࣑ࣀ㓟ࡢ≉ᚩ࡜࣏ࣜ࣌ࣉࢳࢻࡢ⁐ゎᛶࡢ㛫ࡢ㛵 ಀࢆㄪ࡭ࡿࡓࡵ࡟ࠊ࠸ࡃࡘ࠿ࡢ࢔࣑ࣀ㓟ࡢᐇ㦂ⓗ࡞್࡜௒. ⓒ 2014 Information Processing Society of Japan. 2.

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