c-myb 70 k N DNA C DNA 50 R1, R2, R3 DNA R2 R3 R2R3 (C/T)AAC(G/T)G DNA MBS-I ITC DNA DNA µm DNA nm DNA DNA DNA DNA DNA 1) DNA DNA S o H H C p 2) DNA D
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1 Netsu Sokutei Thermodynamic Analysis of Conformational Change Important to Protein Function Masayuki Oda (Received November 15, 2006; Accepted December 31, 2006) In the present post-genome era, although many three-dimensional structures of proteins have been determined at atomic resolution mainly by X-ray structural analysis, there remain some problems, such as dynamic properties of proteins and hydration effects, to clarify the correlation between protein structure and function. Proteins are flexible and need some conformational changes to recognize other molecules, but it is difficult to detect the dynamic properties only by static structural analyses. Thermodynamic analyses of biomolecular interactions reveal details of the energetic and dynamic features of molecular recognition processes, and complement the structural information. I have investigated several biomolecular interactions, including DNA-protein, antigen-antibody, and peptide-protein interactions, using isothermal titration and differential scanning calorimetries, together with other methods, such as NMR, X-ray, and surface plasmon resonance. Here, I focus on the thermodynamics to detect conformational changes of proteins, which is important for biomolecular function in general. X DNA MHC NMR X DSC ITC 2007 The Japan Society of Calorimetry and Thermal Analysis. 31
2 c-myb 70 k N DNA C DNA 50 R1, R2, R3 DNA R2 R3 R2R3 (C/T)AAC(G/T)G DNA MBS-I ITC DNA DNA µm DNA nm DNA DNA DNA DNA DNA 1) DNA DNA S o H H C p 2) DNA DNA Table 1 DNA c-myb R2R3 DNA NMR R2 R3 DNA Fig.1 3) R2 Table 1 Proposed mechanism of the protein-dna interaction with the characteristic features of thermodynamics and kinetics. Non-specific binding lower affinity binding long-range electrostatics entropy driven higher sensitivity of H against the ionic strength smaller negative C p faster dissociation rates Specific binding Both non-specific and specific bindings higher affinity binding specific hydrogen bonds and van der Waals contacts enthalpy driven lower sensitivity of H against the ionic strength larger negative C p slower dissociation rates conformational change of the protein and the DNA (if needed) hydration and released cations R2 Fig.1 Pro140 R3 3 N139, P140, E141 Gly Ala MBS-I N139G, P140G, P140A MBS-I N139G H P140G, P140A S o Table 2 N139G 139 R2 W134 R2 N139A 139 R3 The DNA-complexed structure of c-myb R2R3 (PDB code, 1MSE). The DNA double strands are shown by stick models. The backbone of R2R3 is shown by ribbon models, and the residue Pro140 is indicated by spacefill models. 32
3 Table 2 Thermodynamic parameters of c-myb R2R3 mutants binding to cognate DNA, MBS-I, at 20. protein n K a / M 1 G o / kj mol 1 H / kj mol 1 T S o / kj mol 1 C p / kj mol 1 K 1 wild-type N139G N139A P140G P140A E141G E141A The n value represents binding stoichiometry of DNA to protein. β R2 P140 S o DNA DNA 140 Pro G Pro Gly 5 kj mol 1 4) DNA 5) DNA IgG 150 k 2 Fig.2 (4- hydroxy-3-nitrophenyl)acetic acid NP NP 4 NP 9T7, 9T8, 9T10, 9T13 ITC Fig.2 antigen protein G protein A VL VH Fc CL CH1 CH2 CH3 CH2 CH3 CH1 V L VH S o k on k off 6) S o S o 9T7, 9T8, CL antigen protein G protein A Schematic diagram of interactions between mouse IgG1 and antigen, streptococcal protein G or staphylococcal protein A. 33
4 9T10, 9T13 7) IgG 2 IgM 10 NP NP 8,9) 10) A G Fig.2 A G 11,12) A G A Fc α chain P1 β chain P4 13) P6 Fig.3 Structure of Hb peptide covalently bound to I- E k (PDB code, 1IEA). I-E k α and β chains are shown by ribbon models, and the anchor residues of Hb peptide, Ile (P1), Phe (P4), Glu (P6), and Lys (P9), are indicated by spacefill models. MHC class II T β 2 α 2 α Fig.3 MHC class II MHC class II CLIP ph CLIP MHC class II MHC class II MHC class II I- E k Hb P9 34
5 Table 3 Thermodynamic parameters for denaturation of I-E k -Hb at the denaturation temperature at ph 5.5. ph T d / T d / G / kj mol 1 H / kj mol 1 T S / kj mol I-E k β N 14) MHC class II 15,16) MHC class II I-E k Hb Hb DSC ph 17-19) ph T d ph H T d ph ph I-E k Hb H T d C p 11.1 kj mol 1 K kj mol 1 K 1 C p ph ph ph ph Table 3 C p ph MHC class II ph ph MHC class II MHC P1, P4, P6, P9 CLIP MHC class II I-A b 20) I-E k I-A b ph ph CLIP CLIP P1 Met Phe I-A b P1 I-A b -CLIP 16) I-E k Hb 19) T MHC class II 21) 1 Fc Fab 22) 35
6 特 集 2006 年度学会賞 奨励賞 ある タンパク質科学分野において熱測定が有用な基礎情 報を与えることは言うまでもないが さらに立体構造情報 との定量的評価法の確立や 溶液中で機能するタンパク質 にとって重要な水分子の寄与の解明などが今後ますます求 められる 筆者も引き続きタンパク質の熱力学解析を行い タンパク質全般 ひいては生命科学現象に通じるタンパク 質の構造機能解明に貢献したいと考えている 謝 辞 一連の上記研究は 主に生物分子工学研究所と東京理科 大学にて行い 中村春木博士 大阪大学 東 隆親博士 東 京理科大学 はじめ 多くの共同研究者や大学院生の方々 との共同研究の賜物である 最後に記して謝意を表したい 文 献 1) M. Oda, K. Furukawa, K. Ogata, A. Sarai, and H. Nakamura, J. Mol. Biol. 276, 571 (1998). 2) M. Oda, K. Furukawa, A. Sarai, and H. Nakamura, FEBS Lett. 454, 288 (1999). 3) K. Ogata, S. Morikawa, H. Nakamura, A. Sekikawa, T. Inoue, H. Kanai, A. Sarai, S. Ishii, and Y. Nishimura, Cell 79, 639 (1994). 4) B. W. Matthews, H. Nicholson, and W. J. Becktel, Proc. Natl. Acad. Sci. USA 84, 6663 (1987). 5) R. S. Spolar and M. T. Record, Science 263, 777 (1994). 6) T. Sagawa, M. Oda, M. Ishimura, K. Furukawa, and T. Azuma, Mol. Immunol. 39, 801 (2003). 7) E. T. Boder, K. S. Midelfort, and K. D. Wittrup, Proc. Natl. Acad. Sci. USA 97, (2000). 8) M. Oda and T. Azuma, Mol. Immunol. 37, 1111 (2000). 9) T. Tobita, M. Oda, and T. Azuma, Mol. Immunol. 40, 803 (2004). 10) M. Oda, S. Uchiyama, C. V. Robinson, K. Fukui, Y. Kobayashi, and T. Azuma, FEBS J. 273, 1476 (2006). 11) M. Oda, H. Morii, H. Kozono, and T. Azuma, Int. Immunol. 15, 417 (2003). 12) T. Sagawa, M. Oda, H. Morii, H. Takizawa, H. Kozono, and T. Azuma, Mol. Immunol. 42, 9 (2005). 13) Y. -M. Kim, J. Y. Pan, G. A. Korbel, V. Peperzak, 15) D. H. Fremont, W. A. Hendrickson, P. Marrack, and J. Kappler, Science 272, 1001 (1996). 16) Y. Zhu, A. Y. Rudensky, A. L. Corper, L. Teyton, and I. A. Wilson, J. Mol. Biol. 326, 1157 (2003). 17) K. Saito, A. Sarai, M. Oda, T. Azuma, and H. Kozono, J. Biol. Chem. 278, (2003). 18) K. Saito, M. Oda, A. Sarai, T. Azuma, and H. Kozono, Micro. Immunol. 48, 53 (2004). 19) K. Saito, M. Oda, A. Sarai, T. Azuma, and H. Kozono, Biochemistry 43, (2004). 20) T. Tobita, M. Oda, H. Morii, M. Kuroda, A. Yoshino, T. Azuma, and H. Kozono, Immunol. Lett. 85, 47 (2003). 21) L. J. Harris, S. B. Larson, E. Skaletsky, and A. McPherson, Immunol. Rev. 163, 35 (1998). 22) L. Bongini, D. Fanelli, F. Piazza, P. De Los Rios, S. Sandin, and U. Skoglund, Proc. Natl. Acad. Sci. USA 101, 6466 (2004). 要 旨 ポストゲノム時代において タンパク質の立体構造から の機能解明が重要課題となっている 現在 X 線結晶構造 解析などにより多くのタンパク質の立体構造が原子レベル で決定されているが 機能発現におけるタンパク質の動的 構造や水和の寄与など 未解明かつ明らかにすべき問題も 多く残されている タンパク質は柔らかい分子であり 他 分子との相互作用時には構造変化を伴う場合もある これ らの問題解明に向けて熱力学解析は重要な情報を与え 既 存の立体構造情報を相補しうる 筆者はこれまでにDNA タンパク質 抗原 抗体 ペプチド タンパク質といった 種々の生体分子間相互作用を ITC やDSC といった熱測定 を利用して解析し タンパク質の構造機能解明に取り組ん できた 本解説では タンパク質の機能発現にその立体構 造変化が重要な役割を果たしている事例を取り上げ 各熱 力学解析結果がどのような有用情報を与えるか その概要 を紹介した 織田昌幸 Masayuki Oda 京都府立大学大学院農学研究科, Graduate School of Agriculture, Kyoto Prefectural Univ., TEL&FAX , oda@kpu.ac.jp 研究テーマ タンパク質科学 趣味 スポーツ観戦 旅行 M. Boes, and H. L. Ploegh, Proc. Natl. Acad. Sci. USA 103, 3327 (2006). 14) H. Kozono, J. White, J. Clements, P. Marrack, and J. Kappler, Nature 369, 151 (1994) Netsu Sokutei 34
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