Full-Quantum chemical calculation of the absorption maximum of bacteriorhodopsin: a comprehensive analysis of the amino acid residues contributing to the opsin shift

スポンサーリンク

概要

• 論文の詳細を見る

• Herein, the absorption maximum of bacteriorhodopsin (bR) is calculated using our recently developed method in which the whole protein can be treated quantum mechanically at the level of INDO/S-CIS//ONIOM (B3LYP/6-31G(d,p): AMBER). The full quantum mechanical calculation is shown to reproduce the so-called opsin shift of bR with an error of less than 0.04 eV. We also apply the same calculation for 226 different bR mutants, each of which was constructed by replacing any one of the amino acid residues of the wild-type bR with Gly. This substitution makes it possible to elucidate the extent to which each amino acid contributes to the opsin shift and to estimate the inter-residue synergistic effect. It was found that one of the most important contributions to the opsin shift is the electron transfer from Tyr185 to the chromophore upon excitation. We also indicate that some aromatic (Trp86, Trp182) and polar (Ser141, Thr142) residues, located in the vicinity of the retinal polyene chain and the <symbol>b</symbol>-ionone ring, respectively, play an important role in compensating for the large blue-shift induced by both the counterion residues (Asp85, Asp212) and an internal water molecule (W402) located near the Schiff base linkage. In particular, the effect of Trp86 is comparable to that of Tyr185. In addition, Ser141 and Thr142 were found to contribute to an increase in the dipole moment of bR in the excited state. Finally, we provide a complete energy diagram for the opsin shift together with the contribution of the chromophore-protein steric interaction.

著者

• Matsuura Azuma

  Fujitsu Laboratories Ltd.

• Sato Hiroyuki

  Fujitsu Laboratories Ltd.

• Hayashi Tomohiko

  Center For Biological Resources And Informatics Tokyo Institute Of Technology

• Sakurai Minoru

  Center For Biol Res Info Tokyo Inst. Tech

• Sato Hiroyuki

  Fujitsu Laboratories, Ltd.

関連論文

• 2P421 Cellular States of Dried Polypedirum Vanderplanki as Studied by Temperature-Controlled Fourier Transform Infrared Spectroscopy(46. Water and bio-molecule,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)
• 2P-038 リガンド-タンパク質問の結合自由エネルギーに対するマルチフィジクス的計算手法の比較および評価(蛋白質・構造機能相関(2),第46回日本生物物理学会年会)
• 1P260 Fragment molecular orbital calculation of the absorption maxima of bacteriorhodopsin and pharaonis phoborhodopsin(Photobiology:Vision & Photoreception,The 48th Annual Meeting of the Biophysical Society of Japan)
• 3P095 親水性結合部位を有したタンパク質-リガンド間の結合自由ネルギーにおける水和エントロピーの寄与(蛋白質-計測・解析の方法論,第48回日本生物物理学会年会)
• 1P267 全原子量子化学計算によるレチナータンパク質及びGFPの吸収波長の解析(光生物-視覚・光受容,第48回日本生物物理学会年会)
• 2P-289 タンパク質の金属結合部位に関する電子波動関数の解析(生命情報科学・構造ゲノミクス,第46回日本生物物理学会年会)
• 3P077 Refinement of Modeled Protein Structure by Replica Exchange Molecular Dynamics and Hydration Entropy based Scoring Function(Protein: Property,The 48th Annual Meeting of the Biophysical Society of Japan)
• 2P-055 水のエントロピーに焦点を置いたタンパク質-リガンド間結合能の新規計算手法(蛋白質-物性(安定性,折れたたみなど),第47回日本生物物理学会年会)
• 1P-108 トレハロースの水和構造と抗酸化作用に関する計算機シミュレーション(水・水和/電解質,第47回日本生物物理学会年会)
• 2P407 Molecular Dynamics Study on the interaction between trehalose and a lipid bilayer system(46. Water and bio-molecule,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)
• Effects of Trehalose on the Swelling Behavior of Hydrogel : Visualization of the Preferential Hydration of Disaccharides
• 2P-215 シロイヌナズナ青色光受容体・フォトトロピン2の光シグナル伝達に対するアルギニン427の関与(光生物-視覚・光受容,第47回日本生物物理学会年会)
• 1P-066 気相状態でのグループ3LEAタンパク質及びそのモデルペプチドのレプリカ交換分子動力学計算(蛋白質・構造機能相関(1),第46回日本生物物理学会年会)
• Selectively Aligned Polymer Film Growth on Obliquely Evaporated SiO_2 Pattern by Chemical Vapor Deposition
• 1P263 Molecular Dynamics study on the mechanical difference in the LOV2-kinase domain interaction between photol and photo2(Photobiology:Vision & Photoreception,The 48th Annual Meeting of the Biophysical Society of Japan)
• Interaction between Trehalose and Alkaline-Earth Metal Ions
• 2P120 The effect of trehalose on the aggregation of β-amyloid(31. Protein folding and misfolding (II),Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)
• 2P-036 分子動力学計算によるABCトランスポーターSav1866の薬剤輸送機構の研究(蛋白質・構造機能相関(2),第46回日本生物物理学会年会)
• 2P406 Molecular Dynamics Simulation on the Glassy States of Trehalose and Neotrehalose(46. Water and bio-molecule,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)
• 3P-081 コンピュータシミュレーションによるABCトランスポーター・Sav1866の薬剤排出機構の解明(膜蛋白質,第47回日本生物物理学会年会)
• 2P336 Molecular dynamics simulations of the Gln1029Leu mutant of phy3 LOV2 domain in the dark and S390 states(42. Sensory signal transduction,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)
• 2P335 Molecular dynamics study on the structure of the FAD binding site of some BLUF proteins(42. Sensory signal transduction,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)
• 2P337 Computational study on the photochemical reactivities of Adiantum Phy3-LOV1 and LOV2. Role of Phe1010 located near FMN in LOV2.(42. Sensory signal transduction,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)
• Full-Quantum chemical calculation of the absorption maximum of bacteriorhodopsin: a comprehensive analysis of the amino acid residues contributing to the opsin shift
• A scoring function based on solvation thermodynamics for protein structure prediction
• 2P331 The activation mechanism of rhodopsin as studied by MD simulation for a constitutively active mutant E113Q/M257Y(42. Sensory signal transduction,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)
• 2PT185 The chroride ion uptake mechanism in pharaonis halorhodopisin as studied by the energy representation method(The 50th Annual Meeting of the Biophysical Society of Japan)
• 2F1400 全原子量子化学計算によるレチナールタンパク質の吸収波長制御機構の解析(光生物-視覚,光受容II,口頭発表,日本生物物理学会第50回年会(2012年度))
• 3PT160 ABCトランスポーターのヌクレオチド結合ドメインに対するATP結合自由エネルギー計算(日本生物物理学会第50回年会(2012年度))
• 1PT162 リゾチームの乾燥誘導凝集に対するG3LEAタンパク質及びモデルペプチドの抑制効果(日本生物物理学会第50回年会(2012年度))
• 2PT125 基質及び阻害剤によって誘起されるABCトランスポーターABCB1の構造・ダイナミクス変化(日本生物物理学会第50回年会(2012年度))
• 3G0912 Effects of model peptides for late embryogenesis abundant (LEA) proteins on the thermal properties of liposomes(Biological& Artificial Membranes:Structure & Property,Oral Presentation)
• 2P405 Molecular dynamics simulation study on the interaction between trehalose and unsaturated bonds in aqueous medium(46. Water and bio-molecule,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)
• 1P039 分子動力学シミュレーションで探るセルラーゼTrCel7Aの基質取り込みのメカニズム(01B. 蛋白質:構造機能相関,ポスター,日本生物物理学会年会第51回(2013年度))

もっと見る 閉じる

スポンサーリンク