1酵母文化や蛋白発現。
注: a β 亜種展示位置 19 (Phe19) Aβ42 ペプチド (図 1 a) の 1 つ残基変異による異なる相対集計性癖。これらのペプチドの亜種は緑色蛍光タンパク質 (GFP) 集計記者 (図 1)29として機能するとタグ付けされます。
<ol><li>BY4741 親の背景 (マタ彼3Δ1ルー2Δ0に会った15Δ0 ura3Δ0)30酵母に 20 Aβ42 GFP 亜種のプラスミドを変換します。GSSGSSG リンカーによって GFP の融合 Aβ42 変異体の各プラスミドをエンコードします。プラスミッドは pESC(-URA) であり、選択可能なマーカー URA329を含んでいます。<ol>
<li>ウラシル (SC 浦) で以下のコンポーネントなし合成の完全なメディアの準備: 1.9 グラム/L の 20% (w/v) ブドウ糖の 100 mL と組み合わせて酵母窒素ウラシル、硫酸アンモニウム 5 g/L、900 mL ddH2O のも基本。</li>
		<li>変換後の酵母細胞のコロニーの SC 裏培 2% ブドウ糖 20 mL を入れ、210 rpm で攪拌下 30 ° C で一晩の文化を育てます。</li>
	</ol>
</li>
	<li>次の日、一晩かけて培養の 100 μ L 接種培 SC 裏の 5 mL に新しい酵母細胞文化を成長します。</li>
	<li>0.5 の590を OD、4 分間 3,000 x g で文化を遠心、上澄みを廃棄し、2% ラフィノース培 SC 裏の同じ容積の細胞を再懸濁します。</li>
	<li>210 rpm で 30 分間攪拌下 30 ° C で孵化させなさい。4 分間 3,000 x g で細胞を遠心分離し、上澄みを廃棄します。組換えタンパク質の発現を誘導するために 2% ガラクトースを含む新鮮な SC 裏中細胞を再懸濁します。</li>
	<li>SC 裏中 2% ガラクトースを含むタンパク質の発現を誘導する 16 時間後 4 分 3,000 × g で遠心分離によって滅菌遠心管の細胞の 1 つの mL を収穫します。 注: 最も関連性の違いは、(図 2 b) 細胞内遺伝子組換え蛋白質の分布を決定するための蛍光顕微鏡で目視できる Aβ42 GFP のバリエーションを表現する 16 h. による酵母細胞の誘導期後に発生します。</li>
</ol>2. 細胞染色
Note: 新鮮な非誘導細胞は FC 解析中に蛍光のしきい値を確立するネガティブ コントロールとして必要です。
<ol><li>16 h による酵母細胞を取るし、590 で彼らの光学密度を決定する nm (外径590).0.1 の外径590に滅菌リン酸緩衝生理食塩水 (PBS) でそれらを希釈します。<ol>
<li>リン酸緩衝生理食塩水 x 1 を次のように準備: NaCl、KCl、Na2HPO4、1.44 g 0.2 g の 8 g を追加し、KH2PO4 ddH2o. の 800 mL の 0.24 g pH 7.4 に調整後最大 1 L ddH2O のソリューションを入力塩酸フィルター 0.2 μ m のフィルターを通してバッファー。</li>
	</ol>
</li>
	<li>適切にラベル付けされた管 (12 × 75 mm 丸底ポリスチレン) を表現する細胞懸濁液を転送し、光から身を守る。彼らは非誘導し、非染め色細胞と一緒に分析の流れの cytometer でロードする準備ができていることを確認します。</li>
	<li>最終濃度 5 μ M で各サンプルに酸化ストレスのプローブ (例えば、 CellROX 深い赤) を追加し、暗闇の中で 30 分間 30 ° C で細胞をインキュベートします。</li>
	<li>インキュベーション後、1x PBS で 3 回細胞を洗浄し、FC で分析する前にバッファーの同じボリュームにそれらを再懸濁します。</li>
</ol>3. フローのフローサイトメトリー解析
注: は、GFP や酸化ストレス プローブ蛍光シグナルを検出するのに適切なレーザーとフィルターを FC セットアップを使用します。流れの cytometer GFP の検出のための 488 nm の青色レーザーと酸化ストレス プローブの蛍光性の検出の 635 nm の赤色レーザーを使用ことができます。GFP および酸化ストレス プローブの発光蛍光の買収がそれぞれ 530/30 nm BP フィルターと 660/20 BP フィルターで実行されます (表 1)。
<ol><li>新しいワークシート パネルを開くをクリックし、次の取得ドット プロットを作成します。<ol>
<li>散布プロット ツールをツールバーから選択し、作成プロット変数側散布領域 (SSC-A)、y 軸対前方の散布面積の x 軸上線形スケールで (FSC A) します。</li>
		<li>ツールバーから散布プロット ツールをクリックし、変数 FL1 エリア (FITC) x 軸対上にプロットを作成します。FL3 エリア (APC) y 軸に対数スケールで。</li>
	</ol>
</li>
	<li>楽器の設定アイコンをクリックします。[補正] タブをクリックし、すべての補正レベルを設定します。[取得] タブをクリックし、記録される 20,000 イベントの合計数を選択します。</li>
	<li>低流量を切り替える流量アイコンをクリックします。</li>
	<li>非誘導、無染色の細胞を実行を開始する [取得] タブをクリックし、人口は中央左の象限に分布するまでの前方の機器の設定および側方散乱で電圧を調整します。<ol>
<li>細胞の残骸を除くセル人口のまわりの領域 R1 を設定するポリゴンアイコンをクリックし、使用するこのゲート人口 P1 = R1 すべて蛍光ドット プロット、ヒストグラム表現 (図 3)。</li>
	</ol>
</li>
	<li>蛍光信号の PMT 電圧を調整するには、左下腹部に分布しているセルまで計測器の設定タブで、利得をチューニング、FL1 FL3 ドット プロットで無染色の細胞を実行します。</li>
	<li>GFP の蛍光を測定する誘導された細胞にサンプルを変更します。計測器の設定タブで、人口は右下の象限に分布するとき、FSC A対FL1 (FITC) のゲインを設定します。ゲート (ゲート P2) 肯定的な細胞集団を定義します。</li>
	<li>変更非誘導サンプル染色 FSC A対FL3 (APC) ドット プロット蛍光による酸化ストレスを表示するセルです。左上腹部にセル人口を分散までゲインを調整します。ゲート P3 で肯定的な細胞の集団。</li>
	<li>細胞蛍光を表すヒストグラムアイコンと 2 つのヒストグラム プロットを作る。蛍光強度を表す、FL1 (FITC) GFP 蛍光を表す x 軸にあり FL3 (APC) 蛍光性を表すは、y 軸に対数目盛で P2 と P3 の人口をそれぞれ適用を確認します。 メモ: ヒストグラムのオーバーレイは、バリエーション a β を発現する細胞の蛍光プロファイルの違いを説明するために良い方法です。</li>
</ol>4. 組換え蛋白質バイオアセッテイ
<ol><li>バイオマーカ発現量を調べるには、16 時間 6 分、4,000 x g で遠心分離によるイースト文化を収穫し、-80 ° C で細胞ペレットを格納<ol>
<li>PBS の 16 h の組換え蛋白を発現する収集した細胞を再懸濁します。20 の外径590に各 Aβ42 GFP 変異体の 200 μ L の細胞懸濁液を準備します。</li>
	</ol>
</li>
	<li>総蛋白分画分析のため 20 分間 14,000 × g で遠心分離によって各変異体の 100 μ L を収穫し、酵母の換散バッファー Y の同じボリュームで細胞ペレットを再懸濁します-(50 mM トリス塩酸 pH 8.0、1 %dmso、200 mM の NaCl、1 mM EDTA を含む 10 mg/mL SB3 14 (myr あたりistyl スルホベタイン) を添加した 1 mM 特異フッ化物 (PMSF))。<ol>
<li>軽度の動揺の下で室温で 20 分間サンプルをインキュベートします。</li>
	</ol>
</li>
	<li>ブラッドフォードの試金を使用して蛋白質の抽出濃度を決定します。15% アクリルアミド SDS-PAGE の電気泳動のゲルや、100 V 60 分のポリフッ化ビニリデン (PVDF) 二フッ化膜にしみの各サンプルのタンパク質抽出物の最大 5 μ g をロードします。<ol>
<li>100 mg Coomassie ブリリアント ブルー G-250 の試薬 95% エタノール 50 mL に溶解し、85% (w/v) リン酸の 100 mL を追加ブラッドフォードを準備します。その後、染料が完全に解散したとき ddH21 L O との混合物を希釈し、使用直前のセルロース フィルター ペーパーを通してフィルターします。 注: ブラッドフォード試薬は茶色光する必要があります。</li>
		<li>ウシ血清アルブミン (BSA) ブラッドフォード試薬の 1,000 μ L 中のタンパク質の 5-100 μ g に至る標準を準備します。</li>
		<li>1-10 μ L タンパク質のブラッドフォード試薬 1 ml を抽出し、5 分間室温で混合物をインキュベートを追加します。</li>
		<li>基準及び外径595タンパク質抽出試料の吸光度を測定します。</li>
		<li>分析に標準対で得られた吸光度値でプロットを作る。蛋白質の μ g。標準曲線に基づいて、あればボリュームと、希釈を考慮したタンパク質の量から元のサンプルの濃度を決定します。</li>
	</ol>
</li>
	<li>0.1% 含有トリス緩衝生理食塩水 (TBS) x 1 と膜をすすぎトゥイーン 20 (TTBS) とブロック 1 x TTBS で 5% (w/v) 脱脂乾燥したミルクを使用しては。<ol>
<li>10 x TBS の 1 L を準備、基本トリスの 24 g と H2Oddの 900 mL の塩化ナトリウムの 88 g を溶解、7.6 に pH を調整します。DdH2O 1 L の最終巻を追加します。1 x ソリューションの ddH2o. の 9 の部分と 10 x の在庫の 1 部分をミックスします。</li>
	</ol>
</li>
	<li>一次 β-アミロイド抗体希釈 6E10 縮尺で 1 h の膜をインキュベートし、二次抗体のヤギと室温で 1 時間抗マウス IgG HRP 共役希釈 1:10, 000。</li>
	<li>Luminata 蛍光試薬 1 mL を使用して膜を開発して手順 5.2 デンシトメトリー分析によってバンドを定量化します。</li>
</ol>5. データの解析
<ol><li>FC によって得られたデータを解析する (MFI) 平均蛍光強度を表示するテーブルを作成して、対応する標準のエラーおよび/または GFP 蛍光および酸化ストレス レベルの差異 (CV) の係数と平均蛍光。<ol>
<li>インスペクターのタブと各チャネルに必要な統計データをカスタマイズするのには [統計] アイコンをクリックします。 注: 蛋白質の変形を比較すると、折り畳み式の背景または解像度指標 (RD) に蛍光値データに変換します。 <img alt="Equation 1" src="/files/ftp_upload/57470/57470eq1.jpg"> この指標で平均サンプル問題サンプルの平均蛍光、平均のコントロールは、コントロールとして使用するセルの平均蛍光あり SD は平均蛍光の標準偏差。RD 要因は MFI 値よりもより正確な指標だけでなくサンプルもデータの広がりのためのアカウントの違いを計算します。時間をかけて行ったさまざまな実験からのデータを比較する場合、この計算は具体的に関連します。RDs が計算されると、統計的検定の使用は蛋白質の変形の観察の違いの重要性を確認することをお勧め。</li>
	</ol>
</li>
	<li>タンパク質バイオアセッテイ用ウエスタンブロット ImageJ ソフトウェアを使用して組換え蛋白質のレベルを定量化します。<ol>
<li>デンシトメトリーの分析の前に開発された膜のオリジナルの raw 画像を JPEG ファイル形式とグレースケール モードに変換します。</li>
		<li>平均グレー値を [分析] メニューの設定測定セクションを調整します。</li>
		<li>ImageJ から長方形ツールをクリックし、バンドのデンシトメトリーの分析のための一貫性のあるサイズの利益 (率 ROI) の領域を定義します。作成された長方形フレーム内膜イメージの各バンドのセンターし、Ctrl + M (測定コマンド) を使用して 1 つずつ測定値を記録します。</li>
		<li>同じ ROI 領域を適用すること、各バンドに隣接したローカルのバック グラウンドを測定します。測定後、各バンドは個別から対応するローカル背景を減算します。</li>
	</ol>
</li>
</ol>

<ol>
	<li>Frydman, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Folding+of+newly+translated+proteins+in+vivo:+the+role+of+molecular+chaperones.">Folding of newly translated proteins in vivo: the role of molecular chaperones.</a> Annual Review of Biochemistry. 70, 603-647 (2001).</li><li>Hartl, F. U., Bracher, A., Hayer-Hartl, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Molecular+chaperones+in+protein+folding+and+proteostasis.">Molecular chaperones in protein folding and proteostasis.</a> Nature. 475, 324-332 (2011).</li><li>Wong, E., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Molecular+determinants+of+selective+clearance+of+protein+inclusions+by+autophagy.">Molecular determinants of selective clearance of protein inclusions by autophagy.</a> Nature Communications. 3, (2012).</li><li>Winkler, J., Tyedmers, J., Bukau, B., Mogk, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Chaperone+networks+in+protein+disaggregation+and+prion+propagation.">Chaperone networks in protein disaggregation and prion propagation.</a> Journal of Structural Biology. 179, 152-160 (2012).</li><li>Glickman, M. H., Ciechanover, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+ubiquitin-proteasome+proteolytic+pathway:+destruction+for+the+sake+of+construction.">The ubiquitin-proteasome proteolytic pathway: destruction for the sake of construction.</a> Physiological Reviews. 82, 373-428 (2002).</li><li>Dobson, C. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Getting+out+of+shape.">Getting out of shape.</a> Nature. 418, 729-730 (2002).</li><li>Chiti, F., Dobson, C. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Protein+misfolding,+functional+amyloid,+and+human+disease.">Protein misfolding, functional amyloid, and human disease.</a> Annual Review of Biochemistry. 75, 333-366 (2006).</li><li>Aguzzi, A., O'Connor, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Protein+aggregation+diseases:+pathogenicity+and+therapeutic+perspectives.">Protein aggregation diseases: pathogenicity and therapeutic perspectives.</a> Nature Reviews Drug Discovery. 9, 237-248 (2010).</li><li>Rapezzi, C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Transthyretin-related+amyloidoses+and+the+heart:+a+clinical+overview.">Transthyretin-related amyloidoses and the heart: a clinical overview.</a> Nature Reviews Cardiology. 7, 398-408 (2010).</li><li>Deas, E., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Alpha-synuclein+oligomers+interact+with+metal+ions+to+induce+oxidative+stress+and+neuronal+death+in+Parkinson's+disease.">Alpha-synuclein oligomers interact with metal ions to induce oxidative stress and neuronal death in Parkinson's disease.</a> Antioxidants &amp; Redox Signaling. 24, 376-391 (2016).</li><li>Brundin, P., Melki, R., Kopito, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Prion-like+transmission+of+protein+aggregates+in+neurodegenerative+diseases.">Prion-like transmission of protein aggregates in neurodegenerative diseases.</a> Nature Reviews Molecular Cell Biology. 11, 301-307 (2010).</li><li>Frost, B., Diamond, M. I. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Prion-like+mechanisms+in+neurodegenerative+diseases.">Prion-like mechanisms in neurodegenerative diseases.</a> Nature Reviews Neuroscience. 11, 155-159 (2009).</li><li>Arrasate, M., Mitra, S., Schweitzer, E. S., Segal, M. R., Finkbeiner, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Inclusion+body+formation+reduces+levels+of+mutant+huntingtin+and+the+risk+of+neuronal+death.">Inclusion body formation reduces levels of mutant huntingtin and the risk of neuronal death.</a> Nature. 431, 805-810 (2004).</li><li>Ross, C. A., Poirier, 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=Opinion:+what+is+the+role+of+protein+aggregation+in+neurodegeneration?.">Opinion: what is the role of protein aggregation in neurodegeneration?.</a> Nature Reviews Molecular Cell Biology. 6, 891-898 (2005).</li><li>Mishra, R., Sj&#246;lander, D., Hammarstr&#246;m, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Spectroscopic+characterization+of+diverse+amyloid+fibrils+in+vitro+by+the+fluorescent+dye+Nile+red.">Spectroscopic characterization of diverse amyloid fibrils in vitro by the fluorescent dye Nile red.</a> Molecular BioSystems. 7, 1232-1240 (2011).</li><li>Klunk, W. E., Jacob, R. F., Mason, R. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Quantifying+amyloid+by+congo+red+spectral+shift+assay.">Quantifying amyloid by congo red spectral shift assay.</a> Methods in Enzymology. 309, 285-305 (1999).</li><li>Khurana, V., Lindquist, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Modelling+neurodegeneration+in+Saccharomyces+cerevisiae:+why+cook+with+baker's+yeast?.">Modelling neurodegeneration in Saccharomyces cerevisiae: why cook with baker's yeast?.</a> Nature Reviews Neuroscience. 11, 436-449 (2010).</li><li>Tenreiro, S., Outeiro, T. F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Simple+is+good:+yeast+models+of+neurodegeneration.">Simple is good: yeast models of neurodegeneration.</a> FEMS Yeast Research. 10, 970-979 (2010).</li><li>Moosavi, B., Mousavi, B., Macreadie, I. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Yeast+model+of+amyloid-&#946;+and+Tau+aggregation+in+Alzheimer's+disease.">Yeast model of amyloid-&#946; and Tau aggregation in Alzheimer's disease.</a> Journal of Alzheimer's Disease. 47, 9-16 (2015).</li><li>Tenreiro, S., Munder, M. C., Alberti, S., Outeiro, T. F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Harnessing+the+power+of+yeast+to+unravel+the+molecular+basis+of+neurodegeneration.">Harnessing the power of yeast to unravel the molecular basis of neurodegeneration.</a> Journal of Neurochemistry. 127, 438-452 (2013).</li><li>Yang, J., Hao, X., Cao, X., Liu, B., Nystr&#246;m, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Spatial+sequestration+and+detoxification+of+huntingtin+by+the+ribosome+quality+control+complex.">Spatial sequestration and detoxification of huntingtin by the ribosome quality control complex.</a> eLife. 5, (2016).</li><li>Braun, R. J., B&#252;ttner, S., Ring, J., Kroemer, G., Madeo, F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Nervous+yeast:+modeling+neurotoxic+cell+death.">Nervous yeast: modeling neurotoxic cell death.</a> Trends in Biochemical Sciences. 35, 135-144 (2010).</li><li>Figley, M. D., Gitler, 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=Yeast+genetic+screen+reveals+novel+therapeutic+strategy+for+ALS.">Yeast genetic screen reveals novel therapeutic strategy for ALS.</a> Rare Diseases. 1, e24420 (2013).</li><li>Cooper, A. A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Alpha-synuclein+blocks+ER-Golgi+traffic+and+Rab1+rescues+neuron+loss+in+Parkinson's+models.">Alpha-synuclein blocks ER-Golgi traffic and Rab1 rescues neuron loss in Parkinson's models.</a> Science. 313, 324-328 (2006).</li><li>Johnson, B. S., McCaffery, J. M., Lindquist, S., Gitler, 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=A+yeast+TDP-43+proteinopathy+model:+exploring+the+molecular+determinants+of+TDP-43+aggregation+and+cellular+toxicity.">A yeast TDP-43 proteinopathy model: exploring the molecular determinants of TDP-43 aggregation and cellular toxicity.</a> Proceedings of the National Academy of Sciences of the United States of America. 105, 6439-6444 (2008).</li><li>Bharathi, V., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Use+of+ade1+and+ade2+mutations+for+development+of+a+versatile+red/white+color+assay+of+amyloid-induced+oxidative+stress+in+saccharomyces+cerevisiae.">Use of ade1 and ade2 mutations for development of a versatile red/white color assay of amyloid-induced oxidative stress in saccharomyces cerevisiae.</a> Yeast. 33, 607-620 (2016).</li><li>Pallar&#232;s, I., Ventura, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Advances+in+the+prediction+of+protein+aggregation+propensity.">Advances in the prediction of protein aggregation propensity.</a> Current Medicinal Chemistry. , (2017).</li><li>Villar-Piqu&#233;, A., Ventura, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Protein+aggregation+propensity+is+a+crucial+determinant+of+intracellular+inclusion+formation+and+quality+control+degradation.">Protein aggregation propensity is a crucial determinant of intracellular inclusion formation and quality control degradation.</a> Biochimica et Biophysica Acta. 1833, 2714-2724 (2013).</li><li>Navarro, S., Villar-Piqu&#233;, A., Ventura, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Selection+against+toxic+aggregation-prone+protein+sequences+in+bacteria.">Selection against toxic aggregation-prone protein sequences in bacteria.</a> Biochimica et Biophysica Acta. 1843, 866-874 (2014).</li><li>Morell, M., de Groot, N. S., Vendrell, J., Avil&#233;s, F. X., Ventura, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Linking+amyloid+protein+aggregation+and+yeast+survival.">Linking amyloid protein aggregation and yeast survival.</a> Molecular BioSystems. 7, 1121-1128 (2011).</li><li>Conchillo-Sol&#233;, O., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=AGGRESCAN:+a+server+for+the+prediction+and+evaluation+of+&amp;#34;hot+spots&amp;#34;+of+aggregation+in+polypeptides.">AGGRESCAN: a server for the prediction and evaluation of &amp;#34;hot spots&amp;#34; of aggregation in polypeptides.</a> BMC Bioinformatics. 8, 65 (2007).</li><li>Fernandez-Escamilla, A. M., Rousseau, F., Schymkowitz, J., Serrano, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Prediction+of+sequence-dependent+and+mutational+effects+on+the+aggregation+of+peptides+and+proteins.">Prediction of sequence-dependent and mutational effects on the aggregation of peptides and proteins.</a> Nature Biotechnology. 22, 1302-1306 (2004).</li><li>Renner, M., Melki, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Protein+aggregation+and+prionopathies.">Protein aggregation and prionopathies.</a> Pathologie Biologie.(Paris). 62, 162-168 (2014).</li><li>Carija, A., Navarro, S., de Groot, N. S., Ventura, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Protein+aggregation+into+insoluble+deposits+protects+from+oxidative+stress.">Protein aggregation into insoluble deposits protects from oxidative stress.</a> Redox Biology. 12, 699-711 (2017).</li></ol>

病気の広い範囲は、携帯電話預金6,7,8,33への誤って折りたたまれたタンパク質の蓄積にリンクされます。アカウント タンパク質濃度を考慮していない、計算のアプローチを使用してこれらの病気の発症を引き起こす分子メカニズムを解明するため多くの努力がなされたまたは体外に近づく?...

プロテオステイシスはセルのフィットネスと老化のプロセスの基本的な決定要因です。ネットワーク、正しいリフォールディング conformers の誤って折りたたまれたタンパク質のシャペロンおよびその対象となるタンパク質がいくつか保存されているメカニズム1 を確保することを目的と高度な品質管理によって細胞の蛋白質の恒常性を維持します。 ,2,3,4,5。多数の調査では、発症および人間の病気の広い範囲とのプロテオステイシス、タンパクにつながる障害の進行の間のリンクをサポートします。例えば、タンパク質の堆積物の存在の多くの神経変性疾患、アルツハイマー病、パーキンソン病などとハンチントン病6,7、8、病理学的特徴であります。prionogenic 病と非変性アミロイドーシス9。それは、凝集反応の初期のオリゴマーと protofibrillar のアセンブリが混雑した細胞環境の10の他の蛋白質と異常な相互作用を確立する細胞毒性の主な成分エリシターであることが示唆されています。また、その毒性効果11,12を伝播する、細胞間タンパク質介在物 (PI) を送信できます。したがって、それは、PI の形成可能性があります確かに危険な集約された種の存在を処理または主要な副作用のない蓄積があるなどこのセルに特定の場所に制限する解毒機構を構成するかもしれない13,14。
標準的な体外生化学的アプローチは、凝集反応およびそのプロパティ15,16種に重要な洞察を提供しています。しかし、これらの試金で使用される条件は、細胞内で発生する明確に異なると、したがって、その生理学的な妥当性を質問します。タンパク質品質管理、オートファジーは、細胞の酸化還元状態の17,18真核生物19,20,21 の規制など携帯電話経路の注目すべき保全のため ,22,23, 出芽酵母酵母(出芽酵母) 蛋白質の集合の分子決定要因を研究する特権を持つ単純な細胞モデルとして浮上しています。関連する生物学的環境24,25,26で関連付けられた細胞毒性影響。
タンパク質凝集傾向は、本質的に主なシーケンスでエンコード機能です。識別と集計推進の力の評価に基づくアミロイド様構造の形成を予測できるため、ポリペプチド27の地域。しかし、タンパク質の体外集計プロパティを予測するバイオインフォマティクス アルゴリズムの成功にもかかわらずこれらの性癖が生体内で細胞毒性影響に変換する方法を予測には程遠いです。体系的に特定の蛋白質の集合の状態とその関連付けられている細胞の損傷間のリンクに対応する研究はこの計算の制限を回避するために役立つことがあります。この接続は、単一の残渣でのみが異なるが、凝集体内性癖28の連続した範囲を表示するアミロイド β ペプチド Aβ42 の亜種の大規模なセットを利用して、本研究で扱われます。特に、酵母細胞の凝集を起こしやすい蛋白質によって誘発される酸化的損傷の会計構造の種を識別するために FC ベースのアプローチを説明します。方法論は、シンプルさ、高処理能力と正確な定量的測定など多くの利点を提供します。このアプローチでは、PI プレイ酸化ストレスに対する保護の役割を確認可能。

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>Yeast cells BY4741&#160;</td>
			<td>ATCC</td>
			<td>201388</td>
			<td>Genotype: MATa his3&#916;1 leu2&#916;0 met15&#916;0 ura3&#916;0</td>
		</tr>
		<tr>
			<td>pESC(-Ura) plasmid&#160;</td>
			<td>Agilent Genomics</td>
			<td>217454</td>
			<td>Yeast expression plasmid with a Gal promotor. Selectable marker URA3</td>
		</tr>
		<tr>
			<td>Yeast Synthetic Drop-out Medium Supplements</td>
			<td>Sigma</td>
			<td>Y1501</td>
			<td>Powder</td>
		</tr>
		<tr>
			<td>Yeast Nitrogen Base Without Amino Acids</td>
			<td>Sigma</td>
			<td>Y0626</td>
			<td>Powder</td>
		</tr>
		<tr>
			<td>Raffinose</td>
			<td>Sigma</td>
			<td>R7630</td>
			<td>Powder</td>
		</tr>
		<tr>
			<td>Glucose</td>
			<td>Sigma</td>
			<td>G7021</td>
			<td>Powder</td>
		</tr>
		<tr>
			<td>Galactose</td>
			<td>Sigma</td>
			<td>G0750</td>
			<td>Powder</td>
		</tr>
		<tr>
			<td>Phosphate Buffered Saline (PBS)</td>
			<td>Fisher Scientific</td>
			<td>BP3991&#160;</td>
			<td>Solution 10X</td>
		</tr>
		<tr>
			<td>CellROX Deep Red Reagent&#160;</td>
			<td>Life Technologies</td>
			<td>C10422</td>
			<td>Free radical cell-permeant fluorescent sensor, non-fluorescent while in a reduced state, and exhibits bright fluorescence upon oxidation by reactive oxygen species (ROS), with absorption/emission maxima at 644/665 nm.&#160;</td>
		</tr>
		<tr>
			<td>Y-PER protein extraction reagent&#160;</td>
			<td>Thermo Scientific</td>
			<td>78990</td>
			<td>Liquid cell lysis buffer</td>
		</tr>
		<tr>
			<td>Acrylamide/Bis-acrylamide</td>
			<td>Sigma</td>
			<td>A6050</td>
			<td>Solution</td>
		</tr>
		<tr>
			<td>Bradford dye reagent</td>
			<td>Bio-Rad&#160;</td>
			<td>5000205</td>
			<td>Dye reagent for one-step determination of protein concentration</td>
		</tr>
		<tr>
			<td>&#946;-amyloid antibody 6E10&#160;</td>
			<td>BioLegend</td>
			<td>803001</td>
			<td>Mouse IgG1. The epitope lies within amino acids 3-8 of beta amyloid (EFRHDS).</td>
		</tr>
		<tr>
			<td>Goat anti-mouse IgG-HRP conjugate&#160;</td>
			<td>Bio-Rad</td>
			<td>1721011</td>
			<td></td>
		</tr>
		<tr>
			<td>Membrane Immobilon-P, PVDF</td>
			<td>Millipore</td>
			<td>IPVH00010</td>
			<td></td>
		</tr>
		<tr>
			<td>Luminata forte</td>
			<td>Merk</td>
			<td>WBLUF0100</td>
			<td>Premixed, ready to use chemiluminescent HRP detection reagent</td>
		</tr>
		<tr>
			<td>Phenylmethanesulfonyl fluoride solution (PMSF)</td>
			<td>Sigma</td>
			<td>93482</td>
			<td>Protease inhibitor. Dissolved at 0.1 M in ethanol</td>
		</tr>
		<tr>
			<td>FACSCanto flow cytometer&#160;</td>
			<td>BD Biosciences</td>
			<td>657338</td>
			<td>Equipped with a 488&#160;nm blue laser for the detection of GFP, and 635&#160;nm red laser / 530/30 nm BP filter and 660/20 BP filter</td>
		</tr>
		<tr>
			<td>Mini Trans-Blot Electrophoresis Transfer cell</td>
			<td>Bio-Rad</td>
			<td>1703930</td>
			<td>Protein transference system</td>
		</tr>
		<tr>
			<td>Mini-PROTEAN Tetra Handcast Systems</td>
			<td>Bio-Rad</td>
			<td>1658000FC</td>
			<td>Electrophoresis system</td>
		</tr>
	</tbody>
</table>

evaluation of the impact of protein aggregation on cellular oxidative stress in yeast

タンパク質のフォールディングとアミロイドの立体構造に集約は、発症といくつかの神経変性疾患の進行に関連しています。しかし、少し情報はまだどのように不溶性タンパク質について集計はその毒性で生体を発揮します。細菌や酵母などの単純な原核生物と真核生物のモデル生物は、細胞内アミロイド線維形成、集計の伝達、および毒性の背後にあるメカニズムの私達の現在の理解に大きく貢献しています。このプロトコルでは、酵母の使用は、タンパク質凝集体の形成と細胞の酸化ストレスに与える影響との関係を分析するモデルとして記述されます。メソッドは、フローサイトメトリー (FC) を使用して、式から生じる細胞の酸化損傷の定量化とアミロイド蛋白質の細胞内の可溶性/集計状態の検出を兼ね備えています。この方法は、簡単、迅速、かつ定量的です。研究は、彼らのそれぞれの組み込み集計性癖とアミロイド β ペプチド亜種の大規模なセットによって引き起こされる細胞の酸化ストレスを関連付けることによってテクニックを示しています。

このプロトコルでは、Phe19 がすべて天然蛋白質構成アミノ酸28変異されてどこ Aβ42 ペプチドの 20 個の商品のコレクションを使用する方法について説明します。これらの蛋白質の集計の理論的な性癖は、2 つの異なるバイオ情報アルゴリズム (AGGRESCAN とタンゴ31,32) を使用して分析できます。両方のケースで?...

Watch this Scientific Journal Video about Evaluation of the Impact of Protein Aggregation on Cellular Oxidative Stress in Yeast at JoVE.com

Evaluation of the Impact of Protein Aggregation on Cellular Oxidative Stress in Yeast

酵母細胞の酸化ストレスに対するタンパク質凝集の影響の評価

蛋白質の集合は、細胞の酸化ストレスを引き出します。このプロトコルでは、アミロイド蛋白質の細胞内の状態およびフローサイトメトリーを使用して、それらに関連付けられている酸化ストレスを監視する方法について説明します。アミロイド β ペプチドの水溶性で集計しやすい亜種の挙動を調べるためのアプローチが使用されます。

Protein misfolding and aggregation into amyloid conformations have been related to the onset and progression of several neurodegenerative diseases. ...

evaluation-impact-protein-aggregation-on-cellular-oxidative-stress

Research

JoVE Journal

Biochemistry

7.2K ビュー.  Universitat Autònoma de Barcelona. 蛋白質の集合は、細胞の酸化ストレスを引き出します。このプロトコルでは、アミロイド蛋白質の細胞内の状態およびフローサイトメトリーを使用して、それらに関連付けられている酸化ストレスを監視する方法について説明します。アミロイド β ペプチドの水溶性で集計しやすい亜種の挙動を調べるためのアプローチが使用されます。

ビデオ: Evaluation of the Impact of Protein Aggregation on Cellular Oxidative Stress in Yeast

Protein Complex Affinity Capture from Cryomilled Mammalian Cells

Affinity capture is an effective technique for isolating endogenous protein complexes for further study. When used in conjunction with an antibody, this technique is also frequently referred to as immunoprecipitation. Affinity capture can be applied in a bench-scale and in a high-throughput context. When coupled with protein mass spectrometry, affinity capture has proven to be a workhorse of interactome analysis. Although there are potentially many ways to execute the numerous steps involved, the following protocols implement our favored methods. Two features are distinctive: the use of cryomilled cell powder to produce cell extracts, and antibody-coupled paramagnetic beads as the affinity medium. In many cases, we have obtained superior results to those obtained with more conventional affinity capture practices. Cryomilling avoids numerous problems associated with other forms of cell breakage. It provides efficient breakage of the material, while avoiding denaturation issues associated with heating or foaming. It retains the native protein concentration up to the point of extraction, mitigating macromolecular dissociation. It reduces the time extracted proteins spend in solution, limiting deleterious enzymatic activities, and it may reduce the non-specific adsorption of proteins by the affinity medium. Micron-scale magnetic affinity media have become more commonplace over the last several years, increasingly replacing the traditional agarose- and Sepharose-based media. Primary benefits of magnetic media include typically lower non-specific protein adsorption; no size exclusion limit because protein complex binding occurs on the bead surface rather than within pores; and ease of manipulation and handling using magnets.

Here we describe protocols to disrupt mammalian cells by solid-state milling at a cryogenic temperature, produce a cell extract from the resulting cell powder, and isolate protein complexes of interest by affinity capture upon antibody-coupled micron-scale paramagnetic beads.

Cryomilled哺乳動物細胞からのタンパク質複合体の親和性のキャプチャ

Affinity capture is an effective technique for isolating endogenous protein complexes for further study. When used in conjunction with an antibody, this ...

生化学

Time-resolved ElectroSpray Ionization Hydrogen-deuterium Exchange Mass Spectrometry for Studying Protein Structure and Dynamics

Intrinsically disordered proteins (IDPs) have long been a challenge to structural biologists due to their lack of stable secondary structure elements. Hydrogen-Deuterium Exchange (HDX) measured at rapid time scales is uniquely suited to detect structures and hydrogen bonding networks that are briefly populated, allowing for the characterization of transient conformers in native ensembles. Coupling of HDX to mass spectrometry offers several key advantages, including high sensitivity, low sample consumption and no restriction on protein size. This technique has advanced greatly in the last several decades, including the ability to monitor HDX labeling times on the millisecond time scale. In addition, by incorporating the HDX workflow onto a microfluidic platform housing an acidic protease microreactor, we are able to localize dynamic properties at the peptide level. In this study, Time-Resolved ElectroSpray Ionization Mass Spectrometry (TRESI-MS) coupled to HDX was used to provide a detailed picture of residual structure in the tau protein, as well as the conformational shifts induced upon hyperphosphorylation.

Conformational flexibility plays a critical role in protein function. Herein, we describe the use of time-resolved electrospray ionization mass spectrometry coupled to hydrogen-deuterium exchange for probing the rapid structural changes that drive function in ordered and disordered proteins.

時間分解エレクトロスプレーイオン化水素 - 重水素交換質量分析タンパク質の構造とダイナミクスを学ぶために

Intrinsically disordered proteins (IDPs) have long been a challenge to structural biologists due to their lack of stable secondary structure elements. ...

A Simple Method for High Throughput Chemical Screening in Caenorhabditis Elegans

Caenorhabditis elegans is a useful organism for testing chemical effects on physiology. Whole organism small molecule screens offer significant advantages for identifying biologically active chemical structures that can modify complex phenotypes such as lifespan. Described here is a simple protocol for producing hundreds of 96-well culture plates with fairly consistent numbers of C. elegans in each well. Next, we specified how to use these cultures to screen thousands of chemicals for effects on the lifespan of the nematode C. elegans. This protocol makes use of temperature sensitive sterile strains, agar plate conditions, and simple animal handling to facilitate the rapid and high throughput production of synchronized animal cultures for screening.

A Simple Method for High Throughput Chemical Screening in Caenorhabditis Elegans

Here we describe a simple protocol for rapidly producing hundreds of nematode growth media agar, 96-well culture plates with consistent numbers of Caenorhhabditis elegans per well. These cultures are useful for the phenotypic screening of whole organisms. We focus here on using these cultures to screen chemicals for pro-longevity effects.

カエノラブディティス ・ エレガンスにおけるハイスループット化合物スクリーニングのための簡単な方法

Caenorhabditis elegans is a useful organism for testing chemical effects on physiology. Whole organism small molecule screens offer significant advantages ...

A Yeast 2-Hybrid Screen in Batch to Compare Protein Interactions

Screening for protein-protein interactions using the yeast 2-hybrid assay has long been an effective tool, but its use has largely been limited to the discovery of high-affinity interactors that are highly enriched in the library of interacting candidates. In a traditional format, the yeast 2-hybrid assay can yield too many colonies to analyze when conducted at low stringency where low affinity interactors might be found. Moreover, without a comprehensive and complete interrogation of the same library against different bait plasmids, a comparative analysis cannot be achieved. Although some of these problems can be addressed using arrayed prey libraries, the cost and infrastructure required to operate such screens can be prohibitive. As an alternative, we have adapted the yeast 2-hybrid assay to simultaneously uncover dozens of transient and static protein interactions within a single screen utilizing a strategy termed DEEPN (Dynamic Enrichment for Evaluation of Protein Networks), which incorporates high-throughput DNA sequencing and computation to follow the evolution of a population of plasmids that encode interacting partners. Here, we describe customized reagents and protocols that allow a DEEPN screen to be executed easily and cost-effectively.

Batch processing of yeast 2-hybrid screens allows for direct comparison of the interaction profiles of multiple bait proteins with a highly complex set of prey fusion proteins. Here, we describe refined methods, new reagents, and how to implement their use for such screens.

蛋白質の相互作用を比較するバッチの酵母 2 ハイブリッド スクリーン

Screening for protein-protein interactions using the yeast 2-hybrid assay has long been an effective tool, but its use has largely been limited to the ...

In Vitro Reconstitution of Self-Organizing Protein Patterns on Supported Lipid Bilayers

Many aspects of the fundamental spatiotemporal organization of cells are governed by reaction-diffusion type systems. In vitro reconstitution of such systems allows for detailed studies of their underlying mechanisms which would not be feasible in vivo. Here, we provide a protocol for the in vitro reconstitution of the MinCDE system of Escherichia coli, which positions the cell division septum in the cell middle. The assay is designed to supply only the components necessary for self-organization, namely a membrane, the two proteins MinD and MinE and energy in the form of ATP. We therefore fabricate an open reaction chamber on a coverslip, on which a supported lipid bilayer is formed. The open design of the chamber allows for optimal preparation of the lipid bilayer and controlled manipulation of the bulk content. The two proteins, MinD and MinE, as well as ATP, are then added into the bulk volume above the membrane. Imaging is possible by many optical microscopies, as the design supports confocal, wide-field and TIRF microscopy alike. In a variation of the protocol, the lipid bilayer is formed on a patterned support, on cell-shaped PDMS microstructures, instead of glass. Lowering the bulk solution to the rim of these compartments encloses the reaction in a smaller compartment and provides boundaries that allow mimicking of in vivo oscillatory behavior. Taken together, we describe protocols to reconstitute the MinCDE system both with and without spatial confinement, allowing researchers to precisely control all aspects influencing pattern formation, such as concentration ranges and addition of other factors or proteins, and to systematically increase system complexity in a relatively simple experimental setup.

In Vitro Reconstitution of Self-Organizing Protein Patterns on Supported Lipid Bilayers

We provide a protocol for in vitro self-organization assays of MinD and MinE on a supported lipid bilayer in an open chamber. Additionally, we describe how to enclose the assay in lipid-clad PDMS microcompartments to mimic in vivo conditions by reaction confinement.

体外自己組織化人工脂質膜上のタンパク質パターンの再構成

Many aspects of the fundamental spatiotemporal organization of cells are governed by reaction-diffusion type systems. In vitro reconstitution of such ...

Covalent Immobilization of Proteins for the Single Molecule Force Spectroscopy

In recent years, atomic force microscopy (AFM) based single molecule force spectroscopy (SMFS) extended our understanding of molecular properties and functions. It gave us the opportunity to explore a multiplicity of biophysical mechanisms, e.g., how bacterial adhesins bind to host surface receptors in more detail. Among other factors, the success of SMFS experiments depends on the functional and native immobilization of the biomolecules of interest on solid surfaces and AFM tips. Here, we describe a straightforward protocol for the covalent coupling of proteins to silicon surfaces using silane-PEG-carboxyls and the well-established N-hydroxysuccinimid/1-ethyl-3-(3-dimethyl-aminopropyl)carbodiimid (EDC/NHS) chemistry in order to explore the interaction of pilus-1 adhesin RrgA from the Gram-positive bacterium Streptococcus pneumoniae (S. pneumoniae) with the extracellular matrix protein fibronectin (Fn). Our results show that the surface functionalization leads to a homogenous distribution of Fn on the glass surface and to an appropriate concentration of RrgA on the AFM cantilever tip, apparent by the target value of up to 20% of interaction events during SMFS measurements and revealed that RrgA binds to Fn with a mean force of 52 pN. The protocol can be adjusted to couple via site specific free thiol groups. This results in a predefined protein or molecule orientation and is suitable for other biophysical applications besides the SMFS.

This protocol describes the covalent immobilization of proteins with a heterobifunctional silane coupling agent to silicon-oxide surfaces designed for the atomic force microscopy based single molecule force spectroscopy which is exemplified by the interaction of RrgA (pilus-1 tip adhesin of S. pneumoniae) with fibronectin.

力の単一分子分光法のための蛋白質の共有結合固定

In recent years, atomic force microscopy (AFM) based single molecule force spectroscopy (SMFS) extended our understanding of molecular properties and ...

Analysis of Protein Folding, Transport, and Degradation in Living Cells by Radioactive Pulse Chase

Radioactive pulse-chase labeling is a powerful tool for studying the conformational maturation, the transport to their functional cellular location, and the degradation of target proteins in live cells. By using short (pulse) radiolabeling times (&lt;30 min) and tightly controlled chase times, it is possible to label only a small fraction of the total protein pool and follow its folding. When combined with nonreducing/reducing SDS-polyacrylamide gel electrophoresis (SDS-PAGE) and immunoprecipitation with (conformation-specific) antibodies, folding processes can be examined in great detail. This system has been used to analyze the folding of proteins with a huge variation in properties such as soluble proteins, single and multi-pass transmembrane proteins, heavily N- and O-glycosylated proteins, and proteins with and without extensive disulfide bonding. Pulse-chase methods are the basis of kinetic studies into a range of additional features, including co- and posttranslational modifications, oligomerization, and polymerization, essentially allowing the analysis of a protein from birth to death. Pulse-chase studies on protein folding are complementary with other biochemical and biophysical methods for studying proteins in vitro by providing increased temporal resolution and physiological information. The methods as described within this paper are adapted easily to study the folding of almost any protein that can be expressed in mammalian or insect-cell systems.

Here we describe a protocol for a general pulse-chase method that allows the kinetic analysis of folding, transport, and degradation of proteins to be followed in live cells.

タンパク質の折り畳み、トランスポート、および放射性パルス追跡による生体細胞の劣化の解析

Radioactive pulse-chase labeling is a powerful tool for studying the conformational maturation, the transport to their functional cellular location, and ...

Evaluation of Protein&#8211;Protein Interactions using an On-Membrane Digestion Technique

Numerous intracellular proteins physically interact in accordance with their intracellular and extracellular circumstances. Indeed, cellular functions largely depend on intracellular protein&#8211;protein interactions. Therefore, research regarding these interactions is indispensable to facilitating the understanding of physiologic processes. Co-precipitation of associated proteins, followed by mass spectrometry (MS) analysis, enables the identification of novel protein interactions. In this study, we have provided details of the novel technique of immunoprecipitation-liquid chromatography (LC)-MS/MS analysis combined with on-membrane digestion for the analysis of protein&#8211;protein interactions. This technique is suitable for crude immunoprecipitants and can improve the throughput of proteomic analyses. Tagged recombinant proteins were precipitated using specific antibodies; next, immunoprecipitants blotted onto polyvinylidene difluoride membrane pieces were subjected to reductive alkylation. Following trypsinization, the digested protein residues were analyzed using LC-MS/MS. Using this technique, we were able to identify several candidate associated proteins. Thus, this method is convenient and useful for the characterization of novel protein&#8211;protein interactions.

Here, we present a protocol for an on-membrane digestion technique for the preparation of samples for mass spectrometry. This technique facilitates the convenient analysis of protein&#8211;protein interactions.

膜上消化技術を用いてのタンパク質・タンパク質相互作用の評価

Numerous intracellular proteins physically interact in accordance with their intracellular and extracellular circumstances. Indeed, cellular functions ...

Examining the Dynamics of Cellular Adhesion and Spreading of Epithelial Cells on Fibronectin During Oxidative Stress

The adhesion and spreading of cells onto the extracellular matrix (ECM) are essential cellular processes during organismal development and for the homeostasis of adult tissues. Interestingly, oxidative stress can alter these processes, thus contributing to the pathophysiology of diseases such as metastatic cancer. Therefore, understanding the mechanism(s) of how cells attach and spread on the ECM during perturbations in redox status can provide insight into normal and disease states. Described below is a step-wise protocol that utilizes an immunofluorescence-based assay to specifically quantify cell adhesion and spreading of immortalized fibroblast cells on fibronectin (FN) in vitro. Briefly, anchorage-dependent cells are held in suspension and exposed to the ATM kinase inhibitor Ku55933 to induce oxidative stress. Cells are then plated on FN-coated surface and allowed to attach for predetermined periods of time. Cells that remain attached are fixed and labeled with fluorescence-based antibody markers of adhesion (e.g., paxillin) and spreading (e.g., F-actin). Data acquisition and analysis are performed using commonly available laboratory equipment, including an epifluorescence microscope and freely available Fiji software. This procedure is highly versatile and can be modified for a variety of cell lines, ECM proteins, or inhibitors in order to examine a broad range of biological questions.

This method is useful for quantifying the early dynamics of cellular adhesion and spreading of anchorage-dependent cells onto the fibronectin. Furthermore, this assay can be used to investigate the effects of altered redox homeostasis on cell spreading and/or cell adhesion-related intracellular signaling pathways.

酸化ストレス中のフィブロネクチン上皮細胞の細胞接着と広がりのダイナミクスを調べる

The adhesion and spreading of cells onto the extracellular matrix (ECM) are essential cellular processes during organismal development and for the ...

Assessment of Submitochondrial Protein Localization in Budding Yeast Saccharomyces cerevisiae

Despite recent advances in the characterization of yeast mitochondrial proteome, the submitochondrial localization of a significant number of proteins remains elusive. Here, we describe a robust and effective method for determining the suborganellar localization of yeast mitochondrial proteins, which is considered a fundamental step during mitochondrial protein function elucidation. This method involves an initial step that consists of obtaining highly pure intact mitochondria. These mitochondrial preparations are then subjected to a subfractionation protocol consisting of hypotonic shock (swelling) and incubation with proteinase K (protease). During swelling, the outer mitochondrial membrane is selectively disrupted, allowing the proteinase K to digest proteins of the intermembrane space compartment. In parallel, to obtain information about the topology of membrane proteins, the mitochondrial preparations are initially sonicated, and then subjected to alkaline extraction with sodium carbonate. Finally, after centrifugation, the pellet and supernatant fractions from these different treatments are analyzed by SDS-PAGE and western blot. The submitochondrial localization as well as the membrane topology of the protein of interest is obtained by comparing its western blot profile with known standards.

Assessment of Submitochondrial Protein Localization in Budding Yeast Saccharomyces cerevisiae

Despite recent advances, many yeast mitochondrial proteins still remain with their functions completely unknown. This protocol provides a simple and reliable method to determine the submitochondrial localization of proteins, which has been fundamental for the elucidation of their molecular functions.

出芽酵母サッカロミセスセレビシエにおけるサブソキアドタンパク質の局在化の評価

Despite recent advances in the characterization of yeast mitochondrial proteome, the submitochondrial localization of a significant number of proteins ...