我々は感謝SiniがMiettinen、みんなPöllänenとたるRautavesiの技術サポートを認める。私たちは、HEKに録音機器を提供するためのツインStrepタグ、GFPとペッカEvijärviを発現する293細胞を提供するためのヘルカNurkkalaに感謝します。この作品は、フィンランド·アカデミーによって資金を供給された、数字138329、134684と258978を付与します。

ビスのStrep-Tactinのポリメタクリレート樹脂の1。架橋（スルホスクシンイミジル）スベレート（BS3） <ol><li>室温にBS3架橋剤の2ミリグラムを含む1密封されたマイクロチューブを平衡化させます。注意：BS3は、危険な物質である。保護手袋、ゴーグルを着用してください。 </li><li>再懸濁のStrep-Tactinのメタクリル樹脂（100 mMトリス - 塩酸、pH8.0の50％懸濁液、1mMのEDTA、150mMのNaCl）による簡単な激しく振盪し、すぐにピペットチップを用いてスピンカラムに懸濁液600μLを転送最後に切り落とした。 </li><li>室温で30秒間1500×gで遠心分離する。フロースルーを捨て、カラムにリン酸緩衝生理食塩水（PBS）450μlのを追加します。 </li><li>完全にPBSでトリス緩衝液を交換し、最後の遠心分離後のpHを8.0に調整のPBS 430μlに樹脂を残すように、前のステップ2を複数回繰り返します。 </li><li> 100を含むピペットチップでBS3とマイクロチューブの箔を穿刺1、超純水のL。優しく上下にピペッティングし、水中でBS3の粉末を溶解し、すぐにスピンカラムに溶液20μlを加える。架橋反応におけるBS3の最終濃度は〜1.2 mMである。 </li><li>室温で30分の列を回転させます。樹脂はBS3溶液と適切に混合されていることを確認してください。 </li><li>反応をクエンチし、3Mのトリス-HCl、pH7.5中の6μlを添加し、室温でさらに15分間、カラムを回転させる。 </li><li>室温で30秒間1500×gで遠心分離する。フロースルーを捨て、トリス450μlの中で架橋した樹脂を再懸濁トゥイーン20（TBST）で緩衝生理食塩水。遠心分離を繰り返して、手順をさらに2回洗う。最後のステップでは、TBSを450μlの樹脂を再懸濁。 </li><li>カットオフ末にピペットチップを使用して、新しいチューブに樹脂懸濁液を転送します。 TBS系の別の450μLでカラムに残った樹脂を再懸濁し、同じチューブに移す。繰り返し目もう一度チューブにカラムからの樹脂の最大転送を確保するための電子最後のステップ。 </li><li>チューブを室温で10分間放置し、過剰のTBSを除去して600μlの体積を調整してみましょう。樹脂は、そのまま使用することができます（推奨）または凍結することなく、4℃で保存することができます。 </li></ol> 2。架橋のStrep-Tactinのポリメタクリレート樹脂にツイン·Strepタグbaitタンパク質と会合した複合体の結合<ol><li> 4℃で10分間、17,000×gで、結合緩衝液中のベイトタンパク質サンプルの遠心分離機1 mlの上清を新しいチューブに移す。 </li><li> 、連鎖球菌-Tactinの樹脂に対する内因性ビオチン化タンパク質の結合を最小限に100μg/ mlのの最終濃度にアビジンを追加し、4℃で15分間回転させるには<ol><li>ステップ1.10から架橋された樹脂は4℃で長期間保管した場合、400×gでのfoでの遠心分離によって樹脂を回収4℃でR 1分、上清を廃棄し、TBST 1mlで樹脂を洗浄。遠心分離を繰り返し、洗浄は、まずTBSTで、その後TBSで2回、繰り返します。 4℃で1分間400×gでチューブを遠心分離し、過剰のTBSを削除して元のボリュームに調節してください。 </li></ol></li><li>ボルテックスにより架橋された連鎖球菌-Tactinの樹脂を再懸濁します。すぐに切断されたピペットチップを用いてベイトタンパク質試料を含むチューブに樹脂懸濁液50μlを添加し、4℃でさらに30分間回転させる</li><li>待っている間、55℃にサーモを設定し、ステップ3.1で使用するために、溶出緩衝液500μlを予熱。 </li><li> 4℃で1分間400×gで遠心分離上澄み液を捨て、あらかじめ冷却洗浄バッファー＃1の1ミリリットルで4℃で5分間ローテーター上樹脂を洗浄。遠心分離を繰り返して、手順3回洗浄する。最後のステップでは、洗浄バッファー＃2の250μlの樹脂を再懸濁。 </li><li> TR<html>新鮮なスピンカラムに樹脂懸濁液をansfer。洗浄バッファー＃2の別の250μlのチューブ内に残った樹脂を再懸濁し、同じ列に移す。 </li><li> 4℃で3分間400×gで遠心し、フロースルーを捨て、新鮮なイルカ鼻2ミリリットルチューブにカラムを移す。以下の溶出ステップにすぐに進んでください。 </li></ol>特定のタンパク質複合体の3。溶出<ol><li>ステップ2.4​​からのスピンカラムに予熱した溶出バッファー150μLを加える。 </li><li> 1,400 rpmで振とうし、55℃で5分間サーモミキサー中でインキュベートする。 </li><li>室温で1分間1500×gで遠心分離する。 </li><li>列を捨て、≤-20℃で精製された標的タンパク質を保存する</li></ol><table border="0" cellpadding="0" cellspacing="0" width="598"><tbody><tr height="20"><td colspan="2" height="20" style="height:20px;width:597px;">リン酸緩衝生理食塩水（PBS） </td></tr>0 &quot;&gt; <td height="20" style="height:20px;width:299px;">のNa 2 HPO 4 </td><td style="width:299px;"> 10 mMの</td></tr><tr height="20"><td height="20" style="height:20px;width:299px;"> KH 2 PO 4 </td><td style="width:299px;"> 2mMの</td></tr><tr height="20"><td height="20" style="height:20px;width:299px;"> NaClを</td><td style="width:299px;"> 137 mMの</td></tr><tr height="20"><td height="20" style="height:20px;width:299px;">塩化カリウム</td><td style="width:299px;"> 2.7 mMの</td></tr><tr height="20"><td colspan="2" height="20" style="height:20px;width:597px;"> （セクション1.4のpH 8.0）、特に明記しない限り、pHを7.4に調整した</td></tr><tr height="20"><td colspan="2" height="20" style="height:20px;width:597px;">トリス生理食塩水（TBS）にバッファリングされた</td></tr><tr height="20"><td height="20" style="height:20px;width:299px;">トリス-HCl、pH7.4の</td><td style="width:299px;"> 50 mMの</td></tr><tr height="20"><td hei<html> GHT = &quot;20&quot;スタイル= &quot;高さ：ULは幅：299px;&quot;&gt;のNaCl </td><td style="width:299px;"> 150 mMの</td></tr><tr height="20"><td colspan="2" height="20" style="height:20px;width:597px;">トリスはトゥイーン20（TBST）で緩衝化生理食塩水</td></tr><tr height="20"><td height="20" style="height:20px;width:299px;">トリス-HCl、pH7.4の</td><td style="width:299px;"> 50 mMの</td></tr><tr height="20"><td height="20" style="height:20px;width:299px;"> NaClを</td><td style="width:299px;"> 150 mMの</td></tr><tr height="20"><td height="20" style="height:20px;width:299px;">トゥイーン20 </td><td style="width:299px;"> 0.1％（v / v）の</td></tr><tr height="20"><td colspan="2" height="20" style="height:20px;width:597px;">結合バッファー</td></tr><tr height="20"><td height="20" style="height:20px;width:299px;">トリス-HCl、pH8.0の</td><td style="width:299px;"> 25 mMの</td></tr><tr height="20"><td height="20" style="height:20px;width:299px;"> NaClを</td>X; &quot;&gt; 550 mMの</td></tr><tr height="20"><td height="20" style="height:20px;width:299px;"> NaFを</td><td style="width:299px;"> 5 mMの</td></tr><tr height="20"><td height="20" style="height:20px;width:299px;"> EDTA </td><td style="width:299px;"> 0.5 mMの</td></tr><tr height="20"><td height="20" style="height:20px;width:299px;">グリセロール</td><td style="width:299px;"> 10％（v / v）の</td></tr><tr height="20"><td height="20" style="height:20px;width:299px;"> PMSF </td><td style="width:299px;"> 0.1 mMの</td></tr><tr height="20"><td colspan="2" height="20" style="height:20px;width:597px;">洗浄バッファー＃1 </td></tr><tr height="20"><td height="20" style="height:20px;width:299px;">トリス-HCl、pH8.0の</td><td style="width:299px;"> 25 mMの</td></tr><tr height="20"><td height="20" style="height:20px;width:299px;"> NaClを</td><td style="width:299px;"> 500 mMの</td></tr><tr height="20"><td height="20" style="height:20px;width:299px;"> NaFを</<html> TD&gt; <td style="width:299px;"> 5 mMの</td></tr><tr height="20"><td height="20" style="height:20px;width:299px;"> EDTA </td><td style="width:299px;"> 0.4 mMの</td></tr><tr height="20"><td height="20" style="height:20px;width:299px;"> IGEPAL CA-630 </td><td style="width:299px;"> 0.2％（v / v）の</td></tr><tr height="20"><td height="20" style="height:20px;width:299px;">グリセロール</td><td style="width:299px;"> 5％（v / v）の</td></tr><tr height="20"><td height="20" style="height:20px;width:299px;"> PMSF </td><td style="width:299px;"> 0.1 mMの</td></tr><tr height="20"><td colspan="2" height="20" style="height:20px;width:597px;">洗浄バッファー＃2 </td></tr><tr height="20"><td height="20" style="height:20px;width:299px;">トリス-HCl、pH8.0の</td><td style="width:299px;"> 25 mMの</td></tr><tr height="20"><td height="20" style="height:20px;width:299px;"> NaClを</td><td style="width:299px;"> 150 mMの</td></tr><tr height="20">2 &quot;高さ=&quot; 20 &quot;スタイル=&quot;高さ：ULは幅：597px; &quot;&gt;溶出バッファー</td></tr><tr height="20"><td height="20" style="height:20px;width:299px;">トリス-HCl、pH8.0の</td><td style="width:299px;"> 25 mMの</td></tr><tr height="22"><td height="22" style="height:22px;width:299px;"> SDS </td><td style="width:299px;"> 1％（w / v）の</td></tr></tbody></table> 表1本研究で用いたバッファ。

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利害の対立が宣言されていません。

上記のプロトコルは、ビオチンまたは強力な変性剤を含まない任意の適切な緩衝液中の目的とそれに関連する複合体のいずれかの二Strepタグベイトタンパク質を精製するために使用することができる。プロトコルの現在のバージョンでは、結合および洗浄は、高い塩および非イオン性界面活性剤の存在下で比較的ストリンジェントな条件下で行われる。これはより少ないバックグラウンドを?...

近年では、Strepタグ技術は、プロテオミクスと構造生物学などの生物医学研究の多くの分野で広く使用されるようになった。ショートStrepタグペプチドに組換えタンパク質の融合に依存するこのタンパク質精製技術は、ストレプト-Tactinの、改良されたペプチド結合能を有するストレプトアビジンの遺伝子操作された変異体を担持するアフィニティーマトリックスの出現により成熟した図1、図2ツインStrepタグまたはSIIIタグを指定StrepタグIIの2つのコピーを含有する融合タンパク質は、組換えタンパク質のより効率的な浄化を保証する、単一のStrepタグを含有するものよりストレプ-Tactinのマトリックスに対して高い親和性を示し、そしてそれに関連付けられた結合パートナー。しかし、連鎖球菌-TactinのにツインStrepタグタンパク質の高い親和性はまた、その欠点を持っています。過剰のビオチンを有するこのようなタンパク質の競合的溶出は、標的タンパク質の収率の低下につながる、不完全であってもよい。 M鉱石効率的な代替は、SDSで溶出されていますが、プロテオーム解析を用いたアッセイ互換性がなくなり、樹脂から遊離のStrep-Tactinのとの望ましくないサンプル汚染につながる。本論文では、最初に化学架橋した後、得られる架橋樹脂からツインStrep-tag IIタグタンパク質およびそれに関連する複合体を溶出させるために、SDSを使用してのStrep-Tactinの樹脂結合型四量体を安定化させることにより、この制限を克服するための技術を提供します。したがって、十分なタンパク質収量、それによって、質量分析によるさらなる分析を可能にする、ストレプト-Tactinの試料汚染することなく達成することができる。 この方法は、表面に露出SIIIタグ3又は二Strepタグ（アミノ酸配列WSHPQFEK（GGGS）3 WSHPQFEKそれぞれSAWSHPQFEK（GGGS）2 GGSAWSHPQFEK）を有する任意の組換え融合タンパク質の精製に適している。タンパク質は、動物、植物または細菌起源のものとすることができ、全細胞のいずれかから単離することができる溶解物または濃縮された細胞小器官画。例として、ここでは、PVAに感染したベンサミアナタバコ植物の核画分からのジャガイモウイルスA（PVA）4のSIIIタグ化タンパク質のVPg -プロの精製を説明します。以前に以下の改変を、5に記載のように、核画分を単離した細胞をホルムアルデヒドで処理しなかった、酪酸ナトリウム、5 mMのフッ化ナトリウムとのすべてのバッファに置換し、完全プロテアーゼ阻害剤は、PMSFで置換し、抽出におけるトリトンX-100濃度バッファ＃2は0.3％に低下した（v / v）で（抽出緩衝液＃3）ショ糖クッションを通した遠心分離により得られた核ペレットを、予め冷却した結合緩衝液1.45中に再懸濁し、4℃で1.5時間回転SIIIタグ化ベイトタンパク質と会合した複合体（ベイトタンパク質試料）を含有する得られた核抽出物（セクション2を参照）、以下に記載されるプロトコルに従って処理した。

<table border="0" cellpadding="0" cellspacing="0" width="606">
	<tbody>
		<tr>
			<td>Bis(sulfosuccinimidyl) suberate (BS3), No-Weigh format, 8 x 2mg</td>
			<td>Pierce/Thermo Scientific</td>
			<td>21585</td>
			<td><a href="http://www.fishersci.com">www.fishersci.com CAUTION: Hazardous substance. Causes serious respiratory, skin and eye irritation. Wear protective gloves and eye protection.</a></td>
		</tr>
		<tr>
			<td>Strep-Tactin MacroPrep resin (50% suspension)</td>
			<td>IBA</td>
			<td>2-1505</td>
			<td><a href="http://www.iba-lifesciences.com/">www.iba-lifesciences.com</a></td>
		</tr>
		<tr>
			<td>Spin-X centrifuge tube filter, cellulose acetate membrane, pore size 0.45 &#956;m, non-sterile</td>
			<td>Costar (Corning)</td>
			<td>8163</td>
			<td><a href="http://www.corning.com/lifesciences/">www.corning.com/lifesciences/</a></td>
		</tr>
		<tr>
			<td>Dolphin-nose tubes</td>
			<td>Costar (Corning)</td>
			<td>3213</td>
			<td><a href="http://www.corning.com/lifesciences/">www.corning.com/lifesciences/</a></td>
		</tr>
		<tr>
			<td>Avidin&#160;</td>
			<td>IBA</td>
			<td>2-0204</td>
			<td><a href="http://www.iba-lifesciences.com/">www.iba-lifesciences.com</a></td>
		</tr>
	</tbody>
</table>

one-step purification of twin-strep-tagged proteins and their complexes on strep-tactin resin cross-linked with bis(sulfosuccinimidyl) suberate (bs3)

操作されたストレプトアビジン（のStrep-Tactinの）を有する樹脂上Strepタグ融合タンパク質のアフィニティー精製は、生理学的条件下でタンパク質複合体の単離のために広く用いられる方法となった。ツインStrepタグまたはSIIIタグを指定StrepタグIIの2つのコピーを含有する融合タンパク質は、より効率的なタンパク質精製を可能にする、単一のStrepタグを含有するものと比較してのStrep-Tactinのための高い親和性の利点を有する。しかし、この利点は、ビオチンとのツインStrepタグタンパク質の溶出は低タンパク質の回収につながる、不完全になる可能性があるという事実によって相殺される。回収率は劇的にドデシル硫酸ナトリウム（SDS）で変性溶出を使用することによって改善することができるが、これは下流のプロテオーム解析を用いたアッセイ互換性がなくなり、樹脂から遊離のStrep-Tactinの混入をサンプリングするために導く。この制限を克服するために、我々は、ストレプト-Tactinの方法により、樹脂結合型四量体を開発した第ビス（スルホスクシンイミジル）スベレート（BS3）で処理し、得られた架橋樹脂との架橋は、単一のバッチ精製段階における標的タンパク質複合体を精製するために使用される共有結合によって安定化される。ストレプト-Tactinのを汚染の不在は、質量分析による下流のタンパク質分析を可能にしながら、SDSによる効率的な溶出は、優れたタンパク質回収を確実にします。概念実証として、我々はここではウイルスに感染したNの核からSIIIタグ付きウイルスタンパク質のVPg-Proを精製するためのプロトコルを記述BS3と架橋したストレプト-Tactinのポリメタクリレート樹脂を用いてベンサミアナタバコ植物 。同じプロトコルは、目的の任意の二Strepタグタンパク質を精製し、その生理学的結合パートナーを特徴付けるために使用することができる。

精製手順を模式的に一緒に他の既存の精製方法に伴う問題の表現と、 図1に示されている。 <img alt="図1" fo:content-width="5.5in" src="/files/ftp_upload/51536/51536fig1highres.jpg" width="650" /> 図1精製手順の概略図。ワークフローは、共有結合架橋樹脂に二Strepタグベイトタンパク質と会合した複合体の結合を、BS3との架橋を介して樹?...

Watch this Scientific Journal Video about One-step Purification of Twin-Strep-tagged Proteins and Their Complexes on Strep-Tactin Resin Cross-linked With Bissulfosuccinimidyl Suberate BS3 at JoVE.com

One-step Purification of Twin-Strep-tagged Proteins and Their Complexes on Strep-Tactin Resin Cross-linked With Bissulfosuccinimidyl Suberate BS3

この方法は、ツインのStrepタグ融合タンパク質と共有結合的にビス（スルホスクシンイミジル）（BS3）で架橋された修正されたストレプトアビジン（ストレプト-Tactinの）樹脂上での具体的な複合体の効率的な精製方法が記載されている。この方法は、速い速度の利点は、良好な標的タンパク質の回収および高純度を有し、質量分析によるその後の分析に対応している。

ツイン連鎖球菌タグタンパク質とのStrep-Tactinの樹脂ビスで架橋された（スルホスクシンイミジル）スベレート（BS3）に対するそれらの複合体のいずれかの段階精製

Affinity purification of Strep-tagged fusion proteins on resins carrying an engineered streptavidin (Strep-Tactin) has become a widely used method for ...

one-step-purification-twin-strep-tagged-proteins-their-complexes-on

Research

JoVE Journal

Biology

One-step Purification of Twin-Strep-tagged Proteins and Their Complexes on Strep-Tactin Resin Cross-linked With Bis(sulfosuccinimidyl) Suberate (BS3)

18.6K ビュー.  University of Helsinki. この方法は、ツインのStrepタグ融合タンパク質と共有結合的にビス（スルホスクシンイミジル）（BS3）で架橋された修正されたストレプトアビジン（ストレプト-Tactinの）樹脂上での具体的な複合体の効率的な精製方法が記載されている。この方法は、速い速度の利点は、良好な標的タンパク質の回収および高純度を有し、質量分析によるその後の分析に?...

ビデオ: One-step Purification of Twin-Strep-tagged Proteins and Their Complexes on Strep-Tactin Resin Cross-linked With Bissulfosuccinimidyl Suberate BS3

Purification and Visualization of Influenza A Viral Ribonucleoprotein Complexes

The influenza A viral genome consists of eight negative-sense, single stranded RNA molecules, individually packed with multiple copies of the influenza A nucleoprotein (NP) into viral ribonulceoprotein particles (vRNPs). The influenza vRNPs are enclosed within the viral envelope. During cell entry, however, these vRNP complexes are released into the cytoplasm, where they gain access to the host nuclear transport machinery. In order to study the nuclear import of influenza vRNPs and the replication of the influenza genome, it is useful to work with isolated vRNPs so that other components of the virus do not interfere with these processes. Here, we describe a procedure to purify these vRNPs from the influenza A virus. The procedure starts with the disruption of the influenza A virion with detergents in order to release the vRNP complexes from the enveloped virion. The vRNPs are then separated from the other components of the influenza A virion on a 33-70% discontinuous glycerol gradient by velocity sedimentation. The fractions obtained from the glycerol gradient are then analyzed on via SDS-PAGE after staining with Coomassie blue. The peak fractions containing NP are then pooled together and concentrated by centrifugation. After concentration, the integrity of the vRNPs is verified by visualization of the vRNPs by transmission electron microscopy after negative staining. The glycerol gradient purification is a modification of that from Kemler et al. (1994)1, and the negative staining has been performed by Wu et al. (2007).2

The genome of the influenza A virus consists of eight separate complexes of RNA and proteins, termed viral ribonucleoprotein complexes (vRNPs). This paper describes the glycerol gradient purification and transmission electron microscopy visualization of influenza A vRNPs.

インフルエンザウイルスリボ核タンパク質複合体の精製と可視化

The influenza A viral genome consists of eight negative-sense, single stranded RNA molecules, individually packed with multiple copies of the influenza A ...

生物学

Identification of protein complexes with quantitative proteomics in S. cerevisiae

Lipids are the building blocks of cellular membranes that function as barriers and in compartmentalization of cellular processes, and recently, as important intracellular signalling molecules. However, unlike proteins, lipids are small hydrophobic molecules that traffic primarily by poorly described nonvesicular routes, which are hypothesized to occur at membrane contact sites (MCSs). MCSs are regions where the endoplasmic reticulum (ER) makes direct physical contact with a partnering organelle, e.g., plasma membrane (PM). The ER portion of ER-PM MCSs is enriched in lipid-synthesizing enzymes, suggesting that lipid synthesis is directed to these sites and implying that MCSs are important for lipid traffic. Yeast is an ideal model to study ER-PM MCSs because of their abundance, with over 1000 contacts per cell, and their conserved nature in all eukaryotes. Uncovering the proteins that constitute MCSs is critical to understanding how lipids traffic is accomplished in cells, and how they act as signaling molecules. We have found that an ER called Scs2p localize to ER-PM MCSs and is important for their formation. We are focused on uncovering the molecular partners of Scs2p. Identification of protein complexes traditionally relies on first resolving purified protein samples by gel electrophoresis, followed by in-gel digestion of protein bands and analysis of peptides by mass spectrometry. This often limits the study to a small subset of proteins. Also, protein complexes are exposed to denaturing or non-physiological conditions during the procedure. To circumvent these problems, we have implemented a large-scale quantitative proteomics technique to extract unbiased and quantified data. We use stable isotope labeling with amino acids in cell culture (SILAC) to incorporate staple isotope nuclei in proteins in an untagged control strain. Equal volumes of tagged culture and untagged, SILAC-labeled culture are mixed together and lysed by grinding in liquid nitrogen. We then carry out an affinity purification procedure to pull down protein complexes. Finally, we precipitate the protein sample, which is ready for analysis by high-performance liquid chromatography/ tandem mass spectrometry. Most importantly, proteins in the control strain are labeled by the heavy isotope and will produce a mass/ charge shift that can be quantified against the unlabeled proteins in the bait strain. Therefore, contaminants, or unspecific binding can be easily eliminated. By using this approach, we have identified several novel proteins that localize to ER-PM MCSs. Here we present a detailed description of our approach. 

Here we describe a new quantitative proteomics technique for identifying protein complexes in Saccharomyces cerevisiae. In this study, we have used the SILAC method together with affinity purification followed by tandem mass spectrometry to identify with high specificity the binding partners of an ER protein, Scs2p.

S. cerevisiaeの定量的プロテオミクスとタンパク質の複合体の同定

Lipids are the building blocks of cellular membranes that function as barriers and in compartmentalization of cellular processes, and recently, as ...

Staining of Proteins in Gels with Coomassie G-250 without Organic Solvent and Acetic Acid

In classical protein staining protocols using Coomassie Brilliant Blue (CBB), solutions with high contents of toxic and flammable organic solvents (Methanol, Ethanol or 2-Propanol) and acetic acid are used for fixation, staining and destaining of proteins in a gel after SDS-PAGE. To speed up the procedure, heating the staining solution in the microwave oven for a short time is frequently used. This usually results in evaporation of toxic or hazardous Methanol, Ethanol or 2-Propanol and a strong smell of acetic acid in the lab which should be avoided due to safety considerations. In a protocol originally published in two patent applications by E.M. Wondrak (US2001046709 (A1), US6319720 (B1)), an alternative composition of the staining solution is described in which no organic solvent or acid is used. The CBB is dissolved in bidistilled water (60-80mg of CBB G-250 per liter) and 35 mM HCl is added as the only other compound in the staining solution. The CBB staning of the gel is done after SDS-PAGE and thorough washing of the gel in bidistilled water. By heating the gel during the washing and staining steps, the process can be finished faster and no toxic or hazardous compunds are evaporating. The staining of proteins occurs already within 1 minute after heating the gel in staining solution and is fully developed after 15-30 min with a slightly blue background that is destained completely by prolonged washing of the stained gel in bidistilled water, without affecting the stained protein bands.

A short protocol for protein staining with Coomassie Brilliant Blue (CBB) G-250 in polyacrylamide gels is described without using organic solvents or acetic acid as in the classical staining procedures with CBB.

クーマシー有機溶媒および酢酸のないG - 250でゲル中のタンパク質の染色

In classical protein staining protocols using Coomassie Brilliant Blue (CBB), solutions with high contents of toxic and flammable organic solvents ...

Genetic Studies of Human DNA Repair Proteins Using Yeast as a Model System 

Understanding the roles of human DNA repair proteins in genetic pathways is a formidable challenge to many researchers. Genetic studies in mammalian systems have been limited due to the lack of readily available tools including defined mutant genetic cell lines, regulatory expression systems, and appropriate selectable markers. To circumvent these difficulties, model genetic systems in lower eukaryotes have become an attractive choice for the study of functionally conserved DNA repair proteins and pathways. We have developed a model yeast system to study the poorly defined genetic functions of the Werner syndrome helicase-nuclease (WRN) in nucleic acid metabolism. Cellular phenotypes associated with defined genetic mutant backgrounds can be investigated to clarify the cellular and molecular functions of WRN through its catalytic activities and protein interactions. The human WRN gene and associated variants, cloned into DNA plasmids for expression in yeast, can be placed under the control of a regulatory plasmid element. The expression construct can then be transformed into the appropriate yeast mutant background, and genetic function assayed by a variety of methodologies. Using this approach, we determined that WRN, like its related RecQ family members BLM and Sgs1, operates in a Top3-dependent pathway that is likely to be important for genomic stability. This is described in our recent publication [1] at <a href="http://www.impactaging.com">www.impactaging.com</a>. Detailed methods of specific assays for genetic complementation studies in yeast are provided in this paper.

Genetic Studies of Human DNA Repair Proteins Using Yeast as a Model System

Genetic studies in yeast can be employed to investigate the molecular and cellular functions of human genes in cellular DNA metabolism. Methods are described for the genetic characterization of the human WRN gene product defective in the premature aging disorder Werner syndrome in functionally conserved pathways using yeast as a tractable model system.

人間のDNA修復タンパク質の遺伝的研究は、モデルシステムとして酵母を使用

Understanding the roles of human DNA repair proteins in genetic pathways is a formidable challenge to many researchers.  Genetic studies in mammalian ...

One-step Metabolomics: Carbohydrates, Organic and Amino Acids Quantified in a Single Procedure

Every infant born in the US is now screened for up to 42 rare genetic disorders called "inborn errors of metabolism". The screening method is based on tandem mass spectrometry and quantifies acylcarnitines as a screen for organic acidemias and also measures amino acids. All states also perform enzymatic testing for carbohydrate disorders such as galactosemia. Because the results can be non-specific, follow-up testing of positive results is required using a more definitive method. The present report describes the "urease" method of sample preparation for inborn error screening. Crystalline urease enzyme is used to remove urea from body fluids which permits most other water-soluble metabolites to be dehydrated and derivatized for gas chromatography in a single procedure. Dehydration by evaporation in a nitrogen stream is facilitated by adding acetonitrile and methylene chloride. Then, trimethylsilylation takes place in the presence of a unique catalyst, triethylammonium trifluoroacetate. Automated injection and chromatography is followed by macro-driven custom quantification of 192 metabolites and semi-quantification of every major component using specialized libraries of mass spectra of TMS derivatized biological compounds. The analysis may be performed on the widely-used Chemstation platform using the macros and libraries available from the author. In our laboratory, over 16,000 patient samples have been analyzed using the method with a diagnostic yield of about 17%--that is, 17% of the samples results reveal findings that should be acted upon by the ordering physician. Included in these are over 180 confirmed inborn errors, of which about 38% could not have been diagnosed using previous methods.

The urease method of sample preparation for GC/MS analysis of intermediary metabolites is presented by its inventor. The method allows one-step follow-up of newborn screening for inborn errors by tandem mass spectrometry by quantifying carbohydrates, organic and amino acids all in a single process.

ワンステップのメタボロミクス：炭水化物、1つの手続きが定量化された有機とアミノ酸

Every infant born in the US is now screened for up to 42 rare genetic disorders called "inborn errors of metabolism". The screening method is based on ...

Preparation, Purification, and Characterization of Lanthanide Complexes for Use as Contrast Agents for Magnetic Resonance Imaging

Polyaminopolycarboxylate-based ligands are commonly used to chelate lanthanide ions, and the resulting complexes are 
useful as contrast agents for magnetic resonance imaging (MRI). Many commercially available ligands are especially useful because they contain 
functional groups that allow for fast, high-purity, and high-yielding conjugation to macromolecules and biomolecules via amine-reactive 
activated esters and isothiocyanate groups or thiol-reactive maleimides. While metalation of these ligands is considered common 
knowledge in the field of bioconjugation chemistry, subtle differences in metalation procedures must be taken into account when 
selecting metal starting materials. Furthermore, multiple options for purification and characterization exist, and selection of the most 
effective procedure partially depends on the selection of starting materials. These subtle differences are often neglected in published 
protocols. Here, our goal is to demonstrate common methods for metalation, purification, and characterization of lanthanide complexes 
that can be used as contrast agents for MRI (Figure 1). We expect that this publication will enable biomedical scientists to incorporate 
lanthanide complexation reactions into their repertoire of commonly used reactions by easing the selection of starting materials and 
purification methods.

We demonstrate the metalation, purification, and characterization of lanthanide complexes. The complexes described here can be conjugated to macromolecules to enable tracking of these molecules using magnetic resonance imaging.

磁気共鳴イメージングのための準備、精製、および造影剤として使用するための希土類錯体のキャラクタリゼーション

Polyaminopolycarboxylate-based ligands are commonly used to chelate lanthanide ions, and the resulting complexes are 
useful as contrast agents for ...

Identification of Protein Complexes in Escherichia coli using Sequential Peptide Affinity Purification in Combination with Tandem Mass Spectrometry

Since most cellular processes are mediated by macromolecular assemblies, the systematic identification of protein-protein interactions (PPI) and the identification of the subunit composition of multi-protein complexes can provide insight into gene function and enhance understanding of biological systems1, 2. Physical interactions can be mapped with high confidence vialarge-scale isolation and characterization of endogenous protein complexes under near-physiological conditions based on affinity purification of chromosomally-tagged proteins in combination with mass spectrometry (APMS). This approach has been successfully applied in evolutionarily diverse organisms, including yeast, flies, worms, mammalian cells, and bacteria1-6. In particular, we have generated a carboxy-terminal Sequential Peptide Affinity (SPA) dual tagging system for affinity-purifying native protein complexes from cultured gram-negative Escherichia coli, using genetically-tractable host laboratory strains that are well-suited for genome-wide investigations of the fundamental biology and conserved processes of prokaryotes1, 2, 7. Our SPA-tagging system is analogous to the tandem affinity purification method developed originally for yeast8, 9, and consists of a calmodulin binding peptide (CBP) followed by the cleavage site for the highly specific tobacco etch virus (TEV) protease and three copies of the FLAG epitope (3X FLAG), allowing for two consecutive rounds of affinity enrichment. After cassette amplification, sequence-specific linear PCR products encoding the SPA-tag and a selectable marker are integrated and expressed in frame as carboxy-terminal fusions in a DY330 background that is induced to transiently express a highly efficient heterologous bacteriophage lambda recombination system10. Subsequent dual-step purification using calmodulin and anti-FLAG affinity beads enables the highly selective and efficient recovery of even low abundance protein complexes from large-scale cultures. Tandem mass spectrometry is then used to identify the stably co-purifying proteins with high sensitivity (low nanogram detection limits).
Here, we describe detailed step-by-step procedures we commonly use for systematic protein tagging, purification and mass spectrometry-based analysis of soluble protein complexes from E. coli, which can be scaled up and potentially tailored to other bacterial species, including certain opportunistic pathogens that are amenable to recombineering. The resulting physical interactions can often reveal interesting unexpected components and connections suggesting novel mechanistic links. Integration of the PPI data with alternate molecular association data such as genetic (gene-gene) interactions and genomic-context (GC) predictions can facilitate elucidation of the global molecular organization of multi-protein complexes within biological pathways. The networks generated for E. coli can be used to gain insight into the functional architecture of orthologous gene products in other microbes for which functional annotations are currently lacking.

Identification of Protein Complexes in Escherichia coli using Sequential Peptide Affinity Purification in Combination with Tandem Mass Spectrometry

Affinity purification of tagged proteins in combination with mass spectrometry (APMS) is a powerful method for the systematic mapping of protein interaction networks and for investigating the mechanistic basis of biological processes. Here, we describe an optimized sequential peptide affinity (SPA) APMS procedure developed for the bacterium Escherichia coli that can be used to isolate and characterize stable multi-protein complexes to near homogeneity even starting from low copy numbers per cell.

のタンパク質複合体の同定<em&gt;大腸菌</em&gt;タンデム質量分析との組み合わせでシーケンシャルペプチドアフィニティ精製を用いた

Since most cellular processes are mediated by macromolecular assemblies, the systematic identification of protein-protein interactions (PPI) and the ...

Formulations for Freeze-drying of Bacteria and Their Influence on Cell Survival

Cellular water can be removed to reversibly inactivate microorganisms to facilitate storage. One such method of removal is freeze-drying, which is considered a gentle dehydration method. To facilitate cell survival during drying, the cells are often formulated beforehand. The formulation forms a matrix that embeds the cells and protects them from various harmful stresses imposed on the cells during freezing and drying. We present here a general method to evaluate the survival rate of cells after freeze-drying and we illustrate it by comparing the results obtained with four different formulations: the disaccharide sucrose, the sucrose derived polymer Ficoll PM400, and the respective polysaccharides hydroxyethyl cellulose (HEC) and hydroxypropyl methyl cellulose (HPMC), on two strains of bacteria, P. putida KT2440 and A. chlorophenolicus A6. In this work we illustrate how to prepare formulations for freeze-drying and how to investigate the mechanisms of cell survival after rehydration by characterizing the formulation using of differential scanning calorimetry (DSC), surface tension measurements, X-ray analysis, and electron microscopy and relating those data to survival rates. The polymers were chosen to get a monomeric structure of the respective polysaccharide resembling sucrose to a varying degrees. Using this method setup we showed that polymers can support cell survival as effectively as disaccharides if certain physical properties of the formulation are controlled1.

Freeze-drying is often an easy and convenient way to obtain dry products of viable bacterial cells. An issue of the process is cell survival. We detail here a procedure to investigate how cell survival during freeze-drying is influenced by the properties of the formulation used.

細菌の凍結乾燥と細胞の生存への影響のための処方

Cellular water can be removed to reversibly inactivate microorganisms to facilitate storage. One such method of removal is freeze-drying, which is ...

High-throughput Purification of Affinity-tagged Recombinant Proteins

X-ray crystallography is the method of choice for obtaining a detailed view of the structure of proteins. Such studies need to be complemented by further biochemical analyses to obtain detailed insights into structure/function relationships. Advances in oligonucleotide- and gene synthesis technology make large-scale mutagenesis strategies increasingly feasible, including the substitution of target residues by all 19 other amino acids. Gain- or loss-of-function phenotypes then allow systematic conclusions to be drawn, such as the contribution of particular residues to catalytic activity, protein stability and/or protein-protein interaction specificity.
In order to attribute the different phenotypes to the nature of the mutation - rather than to fluctuating experimental conditions - it is vital to purify and analyse the proteins in a controlled and reproducible manner. High-throughput strategies and the automation of manual protocols on robotic liquid-handling platforms have created opportunities to perform such complex molecular biological procedures with little human intervention and minimal error rates1-5.
Here, we present a general method for the purification of His-tagged recombinant proteins in a high-throughput manner. In a recent study, we applied this method to a detailed structure-function investigation of TFIIB, a component of the basal transcription machinery. TFIIB is indispensable for promoter-directed transcription in vitro and is essential for the recruitment of RNA polymerase into a preinitiation complex6-8. TFIIB contains a flexible linker domain that penetrates the active site cleft of RNA polymerase9-11. This linker domain confers two biochemically quantifiable activities on TFIIB, namely (i) the stimulation of the catalytic activity during the 'abortive' stage of transcript initiation, and (ii) an additional contribution to the specific recruitment of RNA polymerase into the preinitiation complex4,5,12 . We exploited the high-throughput purification method to generate single, double and triple substitution and deletions mutations within the TFIIB linker and to subsequently analyse them in functional assays for their stimulation effect on the catalytic activity of RNA polymerase4. Altogether, we generated, purified and analysed 381 mutants - a task which would have been time-consuming and laborious to perform manually. We produced and assayed the proteins in multiplicates which allowed us to appreciate any experimental variations and gave us a clear idea of the reproducibility of our results.
This method serves as a generic protocol for the purification of His-tagged proteins and has been successfully used to purify other recombinant proteins. It is currently optimised for the purification of 24 proteins but can be adapted to purify up to 96 proteins.

We describe a method for the affinity-tagged purification of recombinant proteins using liquid-handling robotics. This method is generally applicable to the small-scale purification of soluble His-tagged proteins in a high-throughput format.

アフィニティータグ組換えタンパク質のハイスループット精製

X-ray crystallography is the method of choice for obtaining a detailed view of the structure of proteins. Such studies need to be complemented by further ...

Purification of Transcripts and Metabolites from Drosophila Heads

For the last decade, we have tried to understand the molecular and cellular mechanisms of neuronal degeneration using Drosophila as a model organism. Although fruit flies provide obvious experimental advantages, research on neurodegenerative diseases has mostly relied on traditional techniques, including genetic interaction, histology, immunofluorescence, and protein biochemistry. These techniques are effective for mechanistic, hypothesis-driven studies, which lead to a detailed understanding of the role of single genes in well-defined biological problems. However, neurodegenerative diseases are highly complex and affect multiple cellular organelles and processes over time. The advent of new technologies and the omics age provides a unique opportunity to understand the global cellular perturbations underlying complex diseases. Flexible model organisms such as Drosophila are ideal for adapting these new technologies because of their strong annotation and high tractability. One challenge with these small animals, though, is the purification of enough informational molecules (DNA, mRNA, protein, metabolites) from highly relevant tissues such as fly brains. Other challenges consist of collecting large numbers of flies for experimental replicates (critical for statistical robustness) and developing consistent procedures for the purification of high-quality biological material. Here, we describe the procedures for collecting thousands of fly heads and the extraction of transcripts and metabolites to understand how global changes in gene expression and metabolism contribute to neurodegenerative diseases. These procedures are easily scalable and can be applied to the study of proteomic and epigenomic contributions to disease.

Purification of Transcripts and Metabolites from Drosophila Heads

We describe here the procedures for the extraction and purification of mRNA and metabolites from Drosophila heads. We are applying these techniques to better understand the cellular perturbations underlying neuronal degeneration. These methodologies can be easily scaled and adapted for other "omic" projects.

転写産物および代謝物からの精製<em&gt;ショウジョウバエ</em&gt;ヘッド

For the last decade, we have tried to understand the molecular and cellular mechanisms of neuronal degeneration using Drosophila as a model organism. ...