Name: determination of the gas-phase acidities of oligopeptides
Uploaded: 2013-06-24T12:00:00
Description: Watch this Scientific Journal Video about Determination of the Gas-phase Acidities of Oligopeptides at JoVE.com

<p class="jove_content"&gt;仕事は全米科学財団（CHE-0749737）によってサポートされていました。機器の使用量は太平洋大学の質量分析機能によって提供されていました。</p

1。試料溶液の調製<ol><li>第一のペプチドのストック溶液と1:1の体積比でメタノールと水との混合溶媒を用いて6参照酸を調製。ストック溶液は、約10 -3 Mの濃度を持っている必要があり</li><li> 1.5ミリリットルエッペンドルフチューブ中の固形ペプチド試料1mgを、CH 3を秤量し、メタノールと水との混合溶媒を1.0 mLを加え、ボルテックスを用いて混合する。 </li><li>ジフルオロ酢?...

<ol>
	<li>Forsyth, W. R., Antosiewicz, J. M., Robertson, A. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Empirical+relationships+between+protein+structure+and+carboxyl+pKa+values+in+proteins.">Empirical relationships between protein structure and carboxyl pKa values in proteins.</a> Proteins: Struct. Funct. Genet. 48 (2), 388-403 (2002).</li><li>Huyghues-Despointes, B. M. P., Scholtz, J. M., Baldwin, R. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Effect+of+a+single+aspartate+on+helix+stability+at+different+positions+in+a+neutral+alanine-based+peptide.">Effect of a single aspartate on helix stability at different positions in a neutral alanine-based peptide.</a> Protein Sci. 2 (10), 1604-1611 (1993).</li><li>Takahashi, N., Creighton, T. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=On+the+Reactivity+and+Ionization+of+the+Active+Site+Cysteine+Residues+of+Escherichia+coli+Thioredoxin.">On the Reactivity and Ionization of the Active Site Cysteine Residues of Escherichia coli Thioredoxin.</a> Biochemistry. 35 (25), 8342-8353 (1996).</li><li>Gan, Z. R., Sardana, M. K., Jacobs, J. W., Polokoff, M. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Yeast+thioltransferase+-+the+active+site+cysteines+display+differential+reactivity.">Yeast thioltransferase - the active site cysteines display differential reactivity.</a> Archives of Biochemistry and Biophysics. 282 (1), 110-115 (1990).</li><li>Philipps, B., Glockshuber, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Randomization+of+the+Entire+Active-site+Helix+alpha+1+of+the+Thiol-disulfide+Oxidoreductase+DsbA+from+Escherichia+coli.">Randomization of the Entire Active-site Helix alpha 1 of the Thiol-disulfide Oxidoreductase DsbA from Escherichia coli.</a> J. Biol. Chem. 277 (45), 43050-43057 (2002).</li><li>Joshi, H. V., Meier, M. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+effect+of+a+peptide+helix+macrodipole+on+the+pKa+of+an+Asp+side+chain+carboxylate.">The effect of a peptide helix macrodipole on the pKa of an Asp side chain carboxylate.</a> J. Am. Chem. Soc. 118, 12038-12044 (1996).</li><li>Kortemme, T., Creighton, T. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Ionization+of+cysteine+residues+at+the+termini+of+model+&#945;-helical+peptides.+Relevance+to+unusual+thiol+pKa+values+in+proteins+of+the+thioredoxin+family.">Ionization of cysteine residues at the termini of model &#945;-helical peptides. Relevance to unusual thiol pKa values in proteins of the thioredoxin family.</a> J. Mol. Biol. 253 (5), 799-812 (1995).</li><li>Gallo, E. A., Gellman, S. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Effect+of+a+C-Terminal+Cationic+Group+on+the+Competition+between+&#945;-Helical+Turn+and+&#946;-Turn+in+a+Model+Depsipeptide.">Effect of a C-Terminal Cationic Group on the Competition between &#945;-Helical Turn and &#946;-Turn in a Model Depsipeptide.</a> J. Am. Chem. Soc. 116 (25), 11560-11561 (1994).</li><li>Honig, B., Nicholls, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Classical+electrostatics+in+biology+and+chemistry.">Classical electrostatics in biology and chemistry.</a> Science. 268 (5214), 1144-1149 (1995).</li><li>Warshel, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Electrostatic+basis+of+structure-function+correlation+in+proteins.">Electrostatic basis of structure-function correlation in proteins.</a> Acc. Chem. Res. 14 (9), 284-290 (1981).</li><li>Cooks, R. G., Patrick, J. S., Kotiaho, T., McLuckey, S. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Thermochemical+determinations+by+the+kinetic+method.">Thermochemical determinations by the kinetic method.</a> Mass Spectrom. Rev. 13 (4), 287-339 (1994).</li><li>Cooks, R. G., Koskinen, J. T., Thomas, P. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+kinetic+method+of+making+thermochemical+determinations.">The kinetic method of making thermochemical determinations.</a> J. Mass Spectrom. 34 (2), 85-92 (1999).</li><li>Cheng, X., Wu, Z., Fenselau, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Collision+Energy+Dependence+of+Proton-Bound+Dimer+Dissociation:+Entropy+Effects,+Proton+Affinities,+and+Intramolecular+Hydrogen-Bonding+in+Protonated+Peptides.">Collision Energy Dependence of Proton-Bound Dimer Dissociation: Entropy Effects, Proton Affinities, and Intramolecular Hydrogen-Bonding in Protonated Peptides.</a> J. Am. Chem. Soc. 115 (11), 4844-4848 (1993).</li><li>Cerda, B. A., Wesdemiotis, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Li+,+Na+,+and+K++Binding+to+the+DNA+and+RNA+Nucleobases.+Bond+Energies+and+Attachment+Sites+from+the+Dissociation+of+Metal+Ion-Bound+Heterodimers.">Li+, Na+, and K+ Binding to the DNA and RNA Nucleobases. Bond Energies and Attachment Sites from the Dissociation of Metal Ion-Bound Heterodimers.</a> J. Am. Chem. Soc. 118 (47), 11884-11892 (1996).</li><li>Cooks, R. G., Wong, P. S. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Kinetic+Method+of+Making+Thermochemical+Determinations:+Advances+and+Applications.">Kinetic Method of Making Thermochemical Determinations: Advances and Applications.</a> Acc. Chem. Res. 31 (7), 379-386 (1998).</li><li>Armentrout, P. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Entropy+Measurements+and+the+Kinetic+Method:+a+Statistically+Meaningful+Approach.">Entropy Measurements and the Kinetic Method: a Statistically Meaningful Approach.</a> J. Am. Soc. Mass Spectrom. 11 (5), 371-379 (2000).</li><li>Ren, J., Tan, J. P., Harper, R. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Gas-Phase+Acidities+of+Cysteine-Polyalanine+Peptides+I:+A3,4CSH+and+HSCA3,4.">Gas-Phase Acidities of Cysteine-Polyalanine Peptides I: A3,4CSH and HSCA3,4.</a> J. Phys. Chem. A. 113 (41), 10903-10912 (2009).</li><li>Morishetti, K. K., Huang, B. D. S., Yates, J. M., Ren, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Gas-Phase+Acidities+of+Cysteine-Polyglycine+Peptides:+The+Effect+of+the+Cysteine+Position.">Gas-Phase Acidities of Cysteine-Polyglycine Peptides: The Effect of the Cysteine Position.</a> Journal of the American Society for Mass Spectrometry. 21 (4), 603-614 (2010).</li><li>Fersht, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Structure and mechanism in protein science. , (1999).</li><li>Martin, J. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Thioredoxin-a+fold+for+all+reasons.">Thioredoxin-a fold for all reasons.</a> Structure. 3 (3), 245-250 (1995).</li><li>Carvalho, A. P., Fernandes, P. A., Ramos, M. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Similarities+and+Differences+in+the+Thioredoxin+Superfamily.">Similarities and Differences in the Thioredoxin Superfamily.</a> Progress in Biophysics &amp; Molecular Biology. 91 (3), 229-248 (2006).</li><li>Bouchoux, G., Sablier, M., Berruyer-Penaud, F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Obtaining+Thermochemical+Data+by+the+Extended+Kinetic+Method.">Obtaining Thermochemical Data by the Extended Kinetic Method.</a> J. Mass Spectrom. 39 (9), 986-997 (2004).</li><li>Bouchoux, G., Desaphy, S., Bourcier, S., Malosse, C., Bimbong, R. N. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Gas-Phase+Protonation+Thermochemistry+of+Arginine.">Gas-Phase Protonation Thermochemistry of Arginine.</a> J. Phys. Chem. B. 112 (11), 3410-3419 (2008).</li><li>Bouchoux, G., Bimbong, R. N. B., Nacer, F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Gas-Phase+Protonation+Thermochemistry+of+Glutamic+Acid.">Gas-Phase Protonation Thermochemistry of Glutamic Acid.</a> J. Phys. Chem. A. 113 (24), 6666-6676 (2009).</li><li>Zheng, X., Cooks, R. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Thermochemical+Determinations+by+the+Kinetic+Method+with+Direct+Entropy+Correction.">Thermochemical Determinations by the Kinetic Method with Direct Entropy Correction.</a> J. Phys. Chem. A. 106 (42), 9939-9946 (2002).</li><li>Jones, C. M., Bernier, M., Carson, E., Colyer, K. E., Metz, R., Pawlow, A., Wischow, E. D., Webb, I., Andriole, E. J., Poutsma, J. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Gas-phase+acidities+of+the+20+protein+amino+acids.">Gas-phase acidities of the 20 protein amino acids.</a> Int. J. Mass Spectrom. 267 (1-3), 54-62 (2007).</li><li>Tan, J. P., Ren, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Determination+of+the+Gas-Phase+Acidities+of+Cysteine-Polyalanine+Peptides+Using+the+Extended+Kinetic+Method.">Determination of the Gas-Phase Acidities of Cysteine-Polyalanine Peptides Using the Extended Kinetic Method.</a> J. Am. Soc. Mass Spectrom. 18 (2), 188-194 (2007).</li><li>Harrison, A. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+gas-phase+basicities+and+proton+affinities+of+amino+acids+and+peptides.">The gas-phase basicities and proton affinities of amino acids and peptides.</a> Mass Spectrom. Rev. 16 (4), 201-217 (1997).</li><li>Gutte, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Peptides: Synthesis, Structures, and Applications. , (1995).</li><li>Barany, G., Merrifield, R. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Solid-phase+peptide+synthesis.">Solid-phase peptide synthesis.</a> The Peptides. 2, 1-284 (1979).</li><li>Chan, W. C., White, P. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Fmoc Solid Phase Peptide Synthesis: A Practical Approach. , (2000).</li></ol>

ペプチドの気相酸性度の測定は、主に成功した適切な基準酸の選択に依存している。理想的な基準酸は、十分に確立された気相酸性度値を有する構造的に類似の有機化合物である。基準酸は、互いに類似した構造を有するべきである。これは、セット内の基準酸のそれぞれの脱プロトン化の同様のエントロピーを確保する。基準酸は、ペプチドの酸性度に近い値を有するべきである。短いシ?...

アミノ酸残基の酸性度は、構造体に影響を与える最も重要な熱化学的性質、反応性、およびタンパク質9,19の折りたたみ展開プロセスの一つである。個々のアミノ酸残基は、しばしば、タンパク質のそれらの位置に応じて異なる有効な酸性度を示す。具体的には、活性部位に位置して残基はしばしば展示が大幅に酸性度を摂動。その一例は、酵素20,21のチオレドキシンスーパーファミリーの活性部位に存在するシステイン残基である。活性部位のシステインは、タンパク質3-5展開のものに比べて異常に酸性である。それはらせん構造が変わった酸性度に大きく貢献を有し得ることが示唆されている。特に、水溶液中2,6-8で、溶液中で行わペプチドの酸-塩基特性について鋭意実験研究がある。結果は、多くの場合、溶媒効果によって複雑にされた7。実際には、蛋白質中の活性部位のほとんどは溶媒効果は9,10最小化される内部領域の近くに配置されている。 ペプチドおよびタンパク質の固有の酸 - 塩基の特性を理解するためには、溶媒のない環境での試験を行うことが重要である。ここでは、気相酸性度の測定のための質量分析ベースの方法をご紹介します。アプローチは、拡張されたコックの運動方法と呼ばれる。この方法は、正常に、例えば気相酸性度、プロトン親和力、金属イオンアフィニティー、電子親和力およびイオン化エネルギー11-15等の各種熱特性の測定のための化学系の広い範囲に適用されている22-26。私たちは、オリゴシステインポリアラニンとシステインポリグリシンペプチド17,18,27の一連の気相酸性度を決定するためにこの方法を適用している。これらの研究は、N-末端システインpeptidことを示しているエスは、対応するC-末端のものよりも著しく酸性である。前者の高い酸性度は、おそらくチオレートアニオンが強くらせんマクロ双極子との相互作用により安定化された螺旋状の立体構造の影響によるものである。なぜならペプチドの非揮発性および熱的に不安定な性質のため、運動方法は、ペプチド28のかなり正確な酸塩基熱の量を生成するために、現時点で入手可能な最も実用的なアプローチである。 一般的なスキームと運動メソッドに関連付けられた式は、 図1に示されている。ペプチドの気相酸性度の決定は、（AH）プロトン結合型クラスターアニオンの一連の形成から始まり、[A•H•A i]が ¯（または[A¯•H +•A I¯] ¯）、¯¯と私は、ペプチドの脱プロトン化形態である質量分析計のイオンソース領域、およびそれぞれ基準酸である。基準酸は公知の気相酸性度を有する有機化合物である。基準酸は、互いに類似した構造を有するべきである（ただし、ペプチドのものと必ずしも同様）。参照核酸間の構造の類似性は、それらの間の脱プロトン化のエントロピーの類似性を保証します。プロトン結合型クラスタ 陰イオンは質量選択し、対応するモノマーのアニオンを生成する衝突誘起解離（CID）の実験を使用して衝突で活性化し、その後、解離、¯とA I¯、 図1aに示すそれぞれkおよびkの Iの速度定数、とされています。二次フラグメンテーションが無視できる場合、CIDフラグメントイオンの存在比は、[A¯] / [A iの¯]、iが k個 / kと速度定数の比の概算値を表している。全く逆activatが存在しないという仮定の下両方の解離チャネル、比率分岐CIDプロダクトイオンのためのイオン障壁はln [A¯] / [A iの ¯]、直線的気相ペプチドの酸性度（Δ 酸 H）及びそれらに相関する基準酸（Δ 酸 H i）は 、 図1bに示すように、この式で、Δ 酸 H 平均が基準酸の平均気相酸性度であり、Δ（ΔS）は （基準酸は、互いに構造的に類似している場合に一定であると仮定することができる）エントロピー用語であり、Rは一般気体定数、およびT effは 、システムの有効な温度である。効果的な温度は、衝突エネルギーを含むいくつかの実験的な変数に依存する経験的なパラメータである。 気相酸性度の値は、熱運動プロットの二組を構築することによって決定される。最初のセットはOBです。LNをプロットしtained（[A¯] / [A I¯]）Δ酸 H Iに対して- Δ 酸 H 平均 、 図4aに示すように。線形回帰は、YのX = 1 / RT EFFとインターセプトの斜面と直線の集合が得られます= - [Δ 酸 H - Δ 酸 H 平均 ] / RT EFF - Δ（ΔS）/ R。プロットの第二のセットは、 図4bに示すように、対応する斜面（X）に対する第一のセットから得られたインターセプト（Y）をプロットすることによって得られる。 Δ 酸 H 平均とΔ（ΔS）/ Rの切片-線形回帰は、Δ 酸 Hの傾きを持つ新しい行を生成します。 Δ 酸 Hの値は、勾配から得られる、エントロピー用語、Δ（ΔS）は 、から得られるインターセプト。 実験は、エレクトロスプレーイオン化（ESI）イオン源とインターフェーストリプル四重極質量分析計を用いて行われる。質量分析計の概略図を図2に示されている。 CID実験は質量が第1四重極ユニットと結合したプロトンのクラスターアニオンを選択し、それらを約0.5トルの圧力で保持される衝突室に漏れアルゴン原子との衝突を受けるようにすることによって行われる。解離生成イオンは、質量第四重極ユニットを分析する。 CIDスペクトルはすべての可能な二次のフラグメントをカバーするのに十分な幅のm / z範囲を持ついくつかの衝突エネルギーで計上される。 CIDプロダクトイオン強度は、スキャンが選択されたプロダクトイオンに焦点を当てていた選択反応モニタリング（SRM）モードでの機器を設定することによって測定される。 CID実験に対応する4つの異なる衝突エネルギー、で行われるそれぞれ1.0、1.5、2.0、2.5 eVでの重心エネルギー（E センチ ）。重心エネルギーは式を用いて計算される：E センチ = E ラボ 〔m /（M + m）は]、E 実験、実験室フレーム内の衝突エネルギーであり、mはアルゴンの質量であり、Mはプロトン結合型クラスターイオンの質量。 本稿では、モデル化合物として、オリゴペプチドアラモ3 CysNH 2（CH 3）を使用します。 C末端がアミド化されとシステイン残基のチオール基（SH）が酸性のサイトになります。適切な基準酸の選択は、気相酸性度の正常な測定のために重要である。理想的な基準酸は、構造的に類似している（相互に）十分に確立された気相酸性度値を有する有機化合物。基準酸は、ペプチドの酸性度に近い値を有するべきである。ペプチド3 CHの場合、6はカルボンハロゲン化C酸が基準酸として選択される。 6参照酸は、クロロ酢酸（MCAH）、ブロモ酢酸（MBAH）、ジフルオロ酢酸（DFAH）、ジクロロ酢酸（DCAH）、ジブロモ酢酸（DBAH）、およびトリフルオロ（TFAH）です。そのうちの二つ、DFAHとMBAHは、プロトコルを示すために使用される。

<table border="1">
		<tbody>
		 <tr>
			<td>Name of the reagent</td>
			<td>Company</td>
			<td>Catalogue number</td>
			<td>Comments (optional)</td>
		 </tr>
		 <tr>
			<td>Mass Spectrometer</td>
			<td>Varian</td>
			<td>1200 L and 320 L</td>
			<td></td>
		 </tr>
		 <tr>
			<td>Chloroacetic acid</td>
			<td>Sigma-Aldrich</td>
			<td>402923</td>
			<td></td>
		 </tr>
		 <tr>
			<td>Bromoacetic acid</td>
			<td>Sigma-Aldrich</td>
			<td>B56307</td>
			<td></td>
		 </tr>
		 <tr>
			<td>Difluoroacetic acid</td>
			<td>Sigma-Aldrich</td>
			<td>142859</td>
			<td></td>
		 </tr>
		 <tr>
			<td>Dichloroacetic acid</td>
			<td>Sigma-Aldrich</td>
			<td>D54702</td>
			<td></td>
		 </tr>
		 <tr>
			<td>Dibromoacetic acid</td>
			<td>Sigma-Aldrich</td>
			<td>242357</td>
			<td></td>
		 </tr>
		 <tr>
			<td>Trifluoroacetic acid</td>
			<td>Sigma-Aldrich</td>
			<td>T6508</td>
			<td></td>
		 </tr>
		</tbody>
 </table>

determination of the gas-phase acidities of oligopeptides

折り畳まれたタンパク質中の異なる位置にあるアミノ酸残基は、しばしば、酸性度の異なる程度を示す。例えば、ヘリックスのN-末端またはその近傍に位置するシステイン残基は、しばしば、C-末端1-6または近くよりも酸性である。ペプチドの酸-塩基特性について鋭意実験研究は、水溶液6-8特に、凝縮相中で実施されてきたが、結果がしばしば溶媒効果7によって複雑になる。実際には、タンパク質中の活性部位のほとんどは、溶媒効果は9,10を最小化された内部領域の近くに位置しています。ペプチドおよびタンパク質の固有の酸 - 塩基の特性を理解するためには、溶媒のない環境で研究を行うことが重要である。 私たちは、気相中オリゴペプチドの酸性度を測定するための手法を提案する。私たちは、システイン含有オリゴペプチド、アラモ3 CysNHを使用<subのモデル化合物として&gt; 2（CH 3）。測定は、十分に確立された拡張厨運動方法（ 図1）は 11-16に基づいています。実験は、エレクトロスプレーイオン化（ESI）イオン源（ 図2）とインターフェーストリプル四重極質量分析計を用いて行われる。各ペプチド試料について、いくつかの基準酸が選択される。基準酸は公知の気相酸性度と構造的に類似の有機化合物である。ペプチドおよび基準酸の混合物の溶液を質量分析計に導入され、そしてペプチド基準酸の気相に結合したプロトンアニオン性クラスターが形成される。プロトン結合型クラスタは、質量分離し、その後、衝突誘起解離（CID）の実験を介して、断片化されている。得られたフラグメントイオンの存在量は、酸性度及びクラスターイオン解離速度との関係を使用して分析される。ペプチドの気相酸性度は、その後obtaiある熱運動プロット17,18の線形回帰によってNED。 方法は、有機化合物、アミノ酸及びその誘導体、オリゴヌクレオチド、およびオリゴペプチドを含む分子系の様々に適用することができる。異なる配座異性体について計算これらの値を実験的に測定された気相酸性度を比較することによって、酸性度にコンフォメーションの効果を評価することができる。

<ol><li> CIDブラケット実験は、選択された基準のアミノ酸に比べペプチドの相対的な酸性度に関する情報を提供します。二つの基準酸、DFAHとMBAHを有するペプチド（CH 3）の2つの代表的CIDスペクトルは、 図3に示されている。 図3aにペプチドイオンのイオンの存在量は、（ピーク高さ）DFA¯よりも弱くなり、 図3bに、ペプチドイオンのイオン豊富MBAと¯よりも強い。 2?...

Watch this Scientific Journal Video about Determination of the Gas-phase Acidities of Oligopeptides at JoVE.com

Determination of the Gas-phase Acidities of Oligopeptides

システイン含有オリゴペプチドの気相酸性度の判定について説明する。実験は三連四重極質量分析計を用いて行われる。ペプチドの相対的な酸性度は、衝突誘起解離実験を用いて測定し、定量的な酸性度は、拡張コック運動手法を用いて決定される。

オリゴペプチドの気相酸性度の決定

Amino acid residues located at different positions in folded proteins often exhibit different degrees of acidities. For example, a cysteine residue ...

determination-of-the-gas-phase-acidities-of-oligopeptides

Research

JoVE Journal

Chemistry

Rapid High Throughput Amylose Determination in Freeze Dried Potato Tuber Samples

This protocol describes a high through put colorimetric method that relies on the formation of a complex between iodine and chains of glucose molecules in starch. Iodine forms complexes with both amylose and long chains within amylopectin. After the addition of iodine to a starch sample, the maximum absorption of amylose and amylopectin occurs at 620 and 550 nm, respectively. The amylose/amylopectin ratio can be estimated from the ratio of the 620 and 550 nm absorbance values and comparing them to a standard curve in which specific known concentrations are plotted against absorption values. This high throughput, inexpensive method is reliable and reproducible, allowing the evaluation of large populations of potato clones.&#160;

凍結乾燥したジャガイモ塊茎のサンプルの急速なハイスループットアミロース決定

This protocol describes a high through put colorimetric method that relies on the formation of a complex between iodine and chains of glucose molecules in ...

化学

Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D 1H NMR

Copper (I) binding by metallochaperone transport proteins prevents copper oxidation and release of the toxic ions that may participate in harmful redox reactions. The Cu (I) complex of the peptide model of a Cu (I) binding metallochaperone protein, which includes the sequence MTCSGCSRPG (underlined is conserved), was determined in solution under inert conditions by NMR spectroscopy.
NMR is a widely accepted technique for the determination of solution structures of proteins and peptides. Due to difficulty in crystallization to provide single crystals suitable for X-ray crystallography, the NMR technique is extremely valuable, especially as it provides information on the solution state rather than the solid state. Herein we describe all steps that are required for full three-dimensional structure determinations by NMR. The protocol includes sample preparation in an NMR tube, 1D and 2D data collection and processing, peak assignment and integration, molecular mechanics calculations, and structure analysis. Importantly, the analysis was first conducted without any preset metal-ligand bonds, to assure a reliable structure determination in an unbiased manner.

Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D 1H NMR

The NMR-solution structure of a metallochaperone model peptide with Cu (I) was determined, and a detailed protocol from sample preparation and 1D and 2D data collection to a three-dimensional structure is described.

Copper (I) binding by metallochaperone transport proteins prevents copper oxidation and release of the toxic ions that may participate in harmful redox ...

From Constructs to Crystals &#8211; Towards Structure Determination of &#946;-barrel Outer Membrane Proteins

Membrane proteins serve important functions in cells such as nutrient transport, motility, signaling, survival and virulence, yet constitute only ~1% percent of known structures. There are two types of membrane proteins, &#945;-helical and &#946;-barrel. While &#945;-helical membrane proteins can be found in nearly all cellular membranes, &#946;-barrel membrane proteins can only be found in the outer membranes of mitochondria, chloroplasts, and Gram-negative bacteria. One common bottleneck in structural studies of membrane proteins in general is getting enough pure sample for analysis. In hopes of assisting those interested in solving the structure of their favorite &#946;-barrel outer membrane protein (OMP), general protocols are presented for the production of target &#946;-barrel OMPs at levels useful for structure determination by either X-ray crystallography and/or NMR spectroscopy. Here, we outline construct design for both native expression and for expression into inclusion bodies, purification using an affinity tag, and crystallization using detergent screening, bicelle, and lipidic cubic phase techniques. These protocols have been tested and found to work for most OMPs from Gram-negative bacteria; however, there are some targets, particularly for mitochondria and chloroplasts that may require other methods for expression and purification. As such, the methods here should be applicable for most projects that involve OMPs from Gram-negative bacteria, yet the expression levels and amount of purified sample will vary depending on the target OMP.

From Constructs to Crystals &amp;#8211; Towards Structure Determination of &amp;#946;-barrel Outer Membrane Proteins

&#946;-barrel outer membrane proteins (OMPs) serve many functions within the outer membranes of Gram-negative bacteria, mitochondria, and chloroplasts. Here, we hope to alleviate a known bottleneck in structural studies by presenting protocols for the production of &#946;-barrel OMPs in sufficient quantities for structure determination by X-ray crystallography or NMR spectroscopy.

βバレル外膜タンパク質の構造決意を目指して - 構築物から結晶へ

Membrane proteins serve important functions in cells such as nutrient transport, motility, signaling, survival and virulence, yet constitute only ~1% ...

Determination of Carbonyl Functional Groups in Bio-oils by Potentiometric Titration: The Faix Method

Carbonyl compounds present in bio-oils are known to be responsible for bio-oil property changes upon storage and during upgrading. Specifically, carbonyls cause an increase in viscosity (often referred to as &#39;aging&#39;) during storage of bio-oils. As such, carbonyl content has previously been used as a method of tracking bio-oil aging and condensation reactions with less variability than viscosity measurements. Additionally, carbonyls are also responsible for coke formation in bio-oil upgrading processes. Given the importance of carbonyls in bio-oils, accurate analytical methods for their quantification are very important for the bio-oil community. Potentiometric titration methods based on carbonyl oximation have long been used for the determination of carbonyl content in pyrolysis bio-oils. Here, we present a modification of the traditional carbonyl oximation procedures that results in less reaction time, smaller sample size, higher precision, and more accurate carbonyl determinations. While traditional carbonyl oximation methods occur at room temperature, the Faix method presented here occurs at an elevated temperature of 80 &#176;C.

Here we present a potentiometric titration technique for accurately quantifying carbonyl compounds in pyrolysis bio-oils.

Faix方法：電位差滴定法によりバイオ油中のカルボニル官能基の決意

Carbonyl compounds present in bio-oils are known to be responsible for bio-oil property changes upon storage and during upgrading. Specifically, carbonyls ...

Determination of Thermodynamic Properties of Alkaline Earth-liquid Metal Alloys Using the Electromotive Force Technique

A novel electrochemical cell based on a CaF2 solid-state electrolyte has been developed to measure the electromotive force (emf) of binary alkaline earth-liquid metal alloys as functions of both composition and temperature in order to acquire thermodynamic data. The cell consists of a chemically stable solid-state CaF2-AF2 electrolyte (where A is the alkaline-earth element such as Ca, Sr, or Ba), with binary A-B alloy (where B is the liquid metal such as Bi or Sb) working electrodes, and a pure A metal reference electrode. Emf data are collected over a temperature range of 723 K to 1,123 K in 25 K increments for multiple alloy compositions per experiment and the results are analyzed to yield activity values, phase transition temperatures, and partial molar entropies/enthalpies for each composition.

This protocol describes the measurement of the electromotive force of alkaline-earth elements in liquid metal alloys at high temperatures (723-1,123 K) to determine their thermodynamic properties, including activity, partial molar entropy, partial molar enthalpy, and phase transition temperatures, over a wide composition range.

起電力法を用いたアルカリ土類液体金属合金の熱力学的性質の測定

A novel electrochemical cell based on a CaF2 solid-state electrolyte has been developed to measure the electromotive force (emf) of binary alkaline ...

Disentangling High Strength Copolymer Aramid Fibers to Enable the Determination of Their Mechanical Properties

Traditionally, soft body armor has been made from poly(p-phenylene terephthalamide) (PPTA) and ultra-high molecular weight polyethylene. However, to diversify the fiber choices in the United States body armor market, copolymer fibers based on the combination of 5-amino-2-(p-aminophenyl) benzimidazole (PBIA) and the more conventional PPTA were introduced. Little is known regarding the long-term stability of these fibers, but as condensation polymers, they are expected to have potential sensitivity to moisture and humidity. Therefore, characterizing the strength of the materials and understanding their vulnerability to environmental conditions is important for evaluating their use lifetime in safety applications. Ballistic resistance and other critical structural properties of these fibers are predicated on their strength. To accurately determine the strength of the individual fibers, it is necessary to disentangle them from the yarn without introducing any damage. Three aramid-based copolymer fibers were selected for the study. The fibers were washed with acetone followed by methanol to remove an organic coating that held the individual fibers in each yarn bundle together. This coating makes it difficult to separate single fibers from the yarn bundle for mechanical testing without damaging the fibers and affecting their strength. After washing, fourier transform infrared (FTIR) spectroscopy was performed on both washed and unwashed samples and the results were compared. This experiment has shown that there are no significant variations in the spectra of poly(p-phenylene-benzimidazole-terephthalamide-co-p-phenylene terephthalamide) (PBIA-co-PPTA1) and PBIA-co-PPTA3 after washing, and only a small variation in intensity for PBIA. This indicates that the acetone and methanol rinses are not adversely affecting the fibers and causing chemical degradation. Additionally, single fiber tensile testing was performed on the washed fibers to characterize their initial tensile strength and strain to failure, and compare those to other reported values. Iterative procedural development was necessary to find a successful method for performing tensile testing on these fibers.

The primary goal of the study is to develop a protocol to prepare consistent specimens for accurate mechanical testing of high strength copolymer aramid fibers, by removing a coating and disentangling the individual fiber strands without introducing significant chemical or physical degradation.

その力学的特性の測定を可能にする高強度共重合体のアラミド繊維を disentangling

Traditionally, soft body armor has been made from poly(p-phenylene terephthalamide) (PPTA) and ultra-high molecular weight polyethylene. However, to ...

Synthesis and Structure Determination of &#181;-Conotoxin PIIIA Isomers with Different Disulfide Connectivities

Peptides with a high number of cysteines are usually influenced regarding the three-dimensional structure by their disulfide connectivity. It is thus highly important to avoid undesired disulfide bond formation during peptide synthesis, because it may result in a completely different peptide structure, and consequently altered bioactivity. However, the correct formation of multiple disulfide bonds in a peptide is difficult to obtain by using standard self-folding methods such as conventional buffer oxidation protocols, because several disulfide connectivities can be formed. This protocol represents an advanced strategy required for the targeted synthesis of multiple disulfide-bridged peptides which cannot be synthesized via buffer oxidation in high quality and quantity. The study demonstrates the application of a distinct protecting group strategy for the synthesis of all possible 3-disulfide-bonded peptide isomers of &#181;-conotoxin PIIIA in a targeted way. The peptides are prepared by Fmoc-based solid phase peptide synthesis using a protecting group strategy for defined disulfide bond formation. The respective pairs of cysteines are protected with trityl (Trt), acetamidomethyl (Acm), and tert-butyl (tBu) protecting groups to make sure that during every oxidation step only the required cysteines are deprotected and linked. In addition to the targeted synthesis, a combination of several analytical methods is used to clarify the correct folding and generation of the desired peptide structures. The comparison of the different 3-disulfide-bonded isomers indicates the importance of accurate determination and knowledge of the disulfide connectivity for the calculation of the three-dimensional structure and for interpretation of the biological activity of the peptide isomers. The analytical characterization includes the exact disulfide bond elucidation via tandem mass spectrometry (MS/MS) analysis which is performed with partially reduced and alkylated derivatives of the intact peptide isomer produced by an adapted protocol. Furthermore, the peptide structures are determined using 2D nuclear magnetic resonance (NMR) experiments and the knowledge obtained from MS/MS analysis.

Synthesis and Structure Determination of &amp;#181;-Conotoxin PIIIA Isomers with Different Disulfide Connectivities

Cysteine-rich peptides fold into distinct three-dimensional structures depending on their disulfide connectivity. Targeted synthesis of individual disulfide isomers is required when buffer oxidation does not lead to the desired disulfide connectivity. The protocol deals with the selective synthesis of 3-disulfide-bonded peptides and their structural analysis using NMR and MS/MS studies.

合成と異なる二硫化接続と μ-コノトキシン PIIIA 異性体の構造決定

Peptides with a high number of cysteines are usually influenced regarding the three-dimensional structure by their disulfide connectivity. It is thus ...

Ion Mobility-Mass Spectrometry Techniques for Determining the Structure and Mechanisms of Metal Ion Recognition and Redox Activity of Metal Binding Oligopeptides

Electrospray ionization (ESI) can transfer an aqueous-phase peptide or peptide complex to the gas-phase while conserving its mass, overall charge, metal-binding interactions, and conformational shape. Coupling ESI with ion mobility-mass spectrometry (IM-MS) provides an instrumental technique that allows for simultaneous measurement of a peptide&#8217;s mass-to-charge (m/z) and collision cross section (CCS) that relate to its stoichiometry, protonation state, and conformational shape. The overall charge of a peptide complex is controlled by the protonation of 1) the peptide&#8217;s acidic and basic sites and 2) the oxidation state of the metal ion(s). Therefore, the overall charge state of a complex is a function of the pH of the solution that affects the peptides metal ion binding affinity. For ESI-IM-MS analyses, peptide and metal ions solutions are prepared from aqueous-only solutions, with the pH adjusted with dilute aqueous acetic acid or ammonium hydroxide. This allows for pH dependence and metal ion selectivity to be determined for a specific peptide. Furthermore, the m/z and CCS of a peptide complex can be used with B3LYP/LanL2DZ molecular modeling to discern binding sites of the metal ion coordination and tertiary structure of the complex. The results show how ESI-IM-MS can characterize the selective chelating performance of a set of alternative methanobactin peptides and compare them to the copper-binding peptide methanobactin.

Ion mobility-mass spectrometry and molecular modeling techniques can characterize the selective metal chelating performance of designed metal-binding peptides and the copper-binding peptide methanobactin. Developing new classes of metal chelating peptides will help lead to therapeutics for diseases associated with metal ion misbalance.

金属イオン認識の構造とメカニズムを決定するイオン移動質量分析技術と金属結合オリゴペプチドの酸化還元活性

Electrospray ionization (ESI) can transfer an aqueous-phase peptide or peptide complex to the gas-phase while conserving its mass, overall charge, ...

Determination of the Photoisomerization Quantum Yield of a Hydrazone Photoswitch

Photoswitching organic molecules that undergo light-driven structural transformations are key components to construct adaptive molecular systems, and they are utilized in a wide variety of applications. In most studies employing photoswitches, several important photophysical properties such as maximum wavelengths of absorption and emission, molar attenuation coefficient, fluorescence lifetime, and photoisomerization quantum yield are carefully determined to investigate their electronic states and transition processes. However, measurement of the photoisomerization quantum yield, the efficiency of photoisomerization with respect to the absorbed photons, in a typical laboratory setting is often complicated and prone to error because it requires the implementation of rigorous spectroscopic measurements and calculations based on an appropriate integration method. This article introduces a set of procedures to measure the photoisomerization quantum yield of a bistable photoswitch using a photochromic hydrazone. We anticipate that this article will be a useful guide for the investigation of bistable photoswitches that are being increasingly developed.

Photoisomerization quantum yield is a fundamental photophysical property that should be accurately determined in the investigation of newly developed photoswitches. Here, we describe a set of procedures to measure the photoisomerization quantum yield of a photochromic hydrazone as a model bistable photoswitch.

ヒドラゾンフォトスイッチの光異性化量子収率の決定

Photoswitching organic molecules that undergo light-driven structural transformations are key components to construct adaptive molecular systems, and they ...

QuEChERS メソッドと CG-MS/MS を使用したアボカド中の農薬の分析

Determination of 45 Pesticides in Avocado Varieties by the QuEChERS Method and Gas Chromatography-Tandem Mass Spectrometry

Gas chromatography (GC) tandem mass spectrometry (MS/MS) stands as a preeminent analytical instrument extensively employed for the surveillance of pesticide residues in food. Nevertheless, these methods are vulnerable to matrix effects (MEs), which can potentially affect accurate quantification depending on the specific combination of analyte and matrix. Among the various strategies to mitigate MEs, matrix-matched calibration represents the prevailing approach in pesticide residue applications due to its cost-effectiveness and straightforward implementation. In this study, a total of 45 representative pesticides were analyzed in three different varieties of avocado (i.e., Criollo, Hass, and Lorena) using the Quick-Easy-Cheap-Effective-Rugged-Safe (QuEChERS) method with ammonium formate and GC-MS/MS. 
For this purpose, 5 g of the avocado sample was extracted with 10 mL of acetonitrile, and then 2.5 g of ammonium formate was added to induce phase separation. Subsequently, the supernatant underwent a cleanup process via dispersive solid-phase extraction employing 150 mg of anhydrous MgSO4, 50 mg of primary-secondary amine, 50 mg of octadecylsilane, 10 mg of graphitized carbon black, and 60 mg of a zirconium oxide-based sorbent (Z-Sep+). The GC-MS/MS analysis was successfully performed in less than 25 min. Rigorous validation experiments were carried out to assess the performance of the method. The examination of a matrix-matched calibration curve for each variety of avocado revealed that the ME remained relatively consistent and less than 20% (considered as a soft ME) for most pesticide/variety combinations. Furthermore, the method&#180;s limits of quantification were lower than 5 &#181;g/kg for all three varieties. Finally, the recovery values for most pesticides fell within the acceptable range of 70-120%, with relative standard deviation values below 20%.

QuEChERS 法とギ酸アンモニウムを用いた農薬分析用アボカドサンプル調製(英語)

The present protocol describes the analysis of multiclass pesticide residues in avocado varieties using the Quick-Easy-Cheap-Effective-Rugged-Safe (QuEChERS) method with ammonium formate, followed by gas chromatography-tandem mass spectrometry.