Name: analyzing large protein complexes by structural mass spectrometry
Uploaded: 2010-06-19T17:00:00
Duration: 15 min 35 s
Description: Watch this Scientific Journal Video about Analyzing Large Protein Complexes by Structural Mass Spectrometry at JoVE.com

المؤلفان بالشكر إلى أعضاء الفريق لاستعراضها شارون حرجة ، ومساهماتها في المخطوطة. ونحن ممتنون للدعم البرامج وموراشا Bikura ، علم إسرائيل مؤسسة (المنحة رقم 378/08 و1823-1807) ، وجوزيف كوهن مينيرفا مركز للبحوث غشاء حيوي ، وبرنامج الأسرة Chais زملاء للعلماء الجديد ، إبراهيم وسونيا Rochlin المؤسسة ؛ تراست الخيرية الأسرة وولفسون ، وهيلين وميلتون ألف مركز للهيكل Kimmelman الجزيئية البيولوجية والجمعية ، وتركة شلومو وBeirzwinsky سابين ؛ Meil ​​دي بوتون Aynsley ، وكارين سيم ، المملكة المتحدة. ونحن ممتنون للتوفيق ودان Yadid ايتمار على إعطائنا عينة lectin البديل.

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الإعلان عن أي تضارب في المصالح.

وينبغي أن تعطى للحصول على الأطياف عالية الجودة الاهتمام للخطوات إعداد العينات ، والتي تتضمن تركيز العينة وتبادل العازلة. وسوف أكثر من عينات العائد المخفف اشارة منخفضة ، في حين عينات عالية التركيز ويمكن لزجة نوعا ما ، وكتلة الإبرة electrospray. وعلاوة على ذلك ، والمضافات حل مثل الأملاح ، والجلسرين والمنظفات الصناعية وايونات المعادن ، والحد من وكلاء (DTT أو β المركابتويثانول) ، وتميل إلى الانضمام إلى السطح الخارجي للبروتينات ، وتتسبب في توسيع نطاق القمم. ولذلك ، من أجل تحقيق حل جيدا قمم ، ينبغي أن تضاف هذه المكونات عند أدنى تركيز ممكن. معلمة أخرى المفتاح هو موقف nanoflow الشعرية ، نسبة إلى فوهة مطياف الكتلة. قد العثور على &quot;بقعة الحلو&quot; يمكن أن يكون تحديا للمستخدمين عديمي الخبرة ، ومع ذلك ، فإنه يؤثر بشكل كبير على نوعية الأطياف. من المهم أيضا النظر في nanoflow الشعرية قبل الشروع في الرش. حجم القطيرات هي وظيفة من قطر الحافة ، التي ينبغي أن تكون 1μm ~. قطرات صغيرة تؤدي إلى تأين أكثر كفاءة ، وبالتالي سيكون من المفيد. من المهم أيضا للتحقق من عدم وجود فقاعات هواء داخل الشعيرات الدموية التي يمكن ان تمنع تدفق ، والتي لم يتم تجريد طلاء الذهب من خلال اقتناء الشعرية ، وإذا كان الأمر كذلك ، خفض المزيد من الحافة. نضع في اعتبارنا أن كمية زائدة من عينة سيزيد من امكانية تحسين ظروف MS مثل الجهد الشعري ، الفولتية تسريع والضغط والطاقة الاصطدام. عموما ، لقد تم استخدام الإجراءات التي شرحها في بروتوكول لتحديد التركيب ، رياضيات الكيمياء والهندسة المعمارية من البروتين العديد من المجمعات (انظر استعراض 2،3،4). تحليل المجمعات الكبيرة مثل نجمة داود الحمراء في 19 الريبوسوم وcapsids الفيروس أمر غاية 20-22 ، في تحديد ملزم لالركيزة آلات جزيئية 23-25 ​​، أو توصيف شبكات التفاعل الوحيدات بمثابة 26،17،16،17،27،28 لكن بضعة أمثلة من قيمة هذا النهج.

العينة المطلوبة : <table border="1" style=";text-align:right;direction:rtl"><tr><td> عينة </td><td> مطلب </td><td> تعليقات </td></tr><tr><td> حجم </td><td> 1-2 ميكرولتر </td><td> في شعري </td></tr><tr><td> تركيز </td><td> 1 - 20μM </td><td> في مجمع </td></tr><tr><td> العازلة </td><td> Aquanos العازلة المتطايرة مثل خلات الأمونيوم عند pH = 6-8 </td><td> عادة 5 ملم 1M </td></tr><tr><td> منظف </td><td> أدنى </td><td> مجموعات من الجزيئات تنتج المنظفات قمم واسعة والتي لم تحل </td></tr><tr><td> الغليسيرول </td><td> الحد الأدنى (حتى 5 ٪) </td><td> تلتزم nonspecifically للبروتينات ، وبالتالي لوحظ قمم واسعة </td></tr><tr><td> المذيبات العضوية </td><td> تصل إلى 50 ٪ </td><td> قد تفسد البروتينات المجمعات </td></tr><tr><td> الأحماض </td><td> تصل إلى 4 ٪ </td><td> مجمعات البروتين تفسد </td></tr><tr><td> أملاح </td><td> أدنى </td><td> adducts الملح يؤدي الى قمم واسعة النطاق والتي لم تحل </td></tr><tr><td> DTT </td><td> أدنى </td><td> 1-2 ميكرومتر يمكن أن تكون موجودة </td></tr><tr><td> عوامل مخلبية </td><td> أدنى </td><td> أكثر من 250 ميكرومتر يؤدي إلى تشكيل واسعة النطاق ناتج إضافة </td></tr></table>

analyzing large protein complexes by structural mass spectrometry

الخلايا الحية مراقبة وتنظيم العمليات البيولوجية من خلال العمل المنسق لعدد كبير من البروتينات لتجميع أنفسهم في صفيف الحيوية مجمعات متعددة البروتين ، 1. للحصول على فهم العمليات الميكانيكية الخلوية المختلفة ، لا بد من تحديد بنية البروتين مثل هذه المجمعات ، وتكشف عن كيفية تنظيمها الهيكلي يملي وظيفتها. كثير من جوانب متعددة البروتين المجمعات ، على أية حال ، من الصعب تميز ، نظرا لطبيعتها غير المتجانسة ، والهيكل غير المتماثلة ، وديناميكية. لذا ، ثمة حاجة إلى نهج جديد لدراسة مستويات عال من التنظيم البروتين. واحدة من أدوات البيولوجيا الهيكلية الناشئة عن تحليل الجزيئات المجمعات هو الطيف الكتلي (MS) 2-5. هذا الأسلوب يعطي معلومات عن تكوين البروتينات المعقدة ، رياضيات الكيمياء الوحيدات ، والبنية الهيكلية. قوة MS مستمد من حساسية عالية ، ونتيجة لذلك ، شرط العينة المنخفضة ، والتي تمكن من فحص البروتين المجمعات التي أعرب عنها في المستويات المحلية. ميزة أخرى هي سرعة التحليل ، والذي يسمح برصد ردود الفعل في الوقت الحقيقي. وعلاوة على ذلك ، يمكن للتقنية قياس الوقت نفسه خصائص السكان منفصلة تتعايش في خليط. هنا ، نحن تصف بروتوكول مفصلة لتطبيق MS الهيكلي لتحليل البروتين التجمعات الكبيرة. الإجراء يبدأ التحضير من الذهب المطلي الشعيرات الدموية لالتأين electrospray nanoflow (نيسي). ثم واصلت مع إعداد العينات ، والتأكيد على الشروط التي ينبغي أن تكون عازلة متوافق مع نيسي من جهة ، وتمكين للحفاظ على المجمعات سليمة من ناحية أخرى. نفسر ذلك الحين ، خطوة بخطوة ، وكيفية تحسين ظروف تجريبية لقياس كتلة عالية والحصول على الماجستير وجنبا إلى جنب أطياف MS. وأخيرا ، فإننا نرسم معالجة البيانات والتحليلات التي تتبع. بدلا من محاولة كل جانب من جوانب تميز المجالس البروتين ، ويدخل هذا البروتوكول الإجراءات الأساسية MS ، مما يتيح أداء التجارب MS و MS / MS على غير التساهمية المجمعات. عموما ، فإن هدفنا هو تزويد الباحثين غير ملم مع MS مجال الهيكلية ، مع العلم التجريبي من الأدوات الرئيسية.

Watch this Scientific Journal Video about Analyzing Large Protein Complexes by Structural Mass Spectrometry at JoVE.com

Analyzing Large Protein Complexes by Structural Mass Spectrometry

وقد أثبتت الطيف الكتلي ليكون أداة قيمة لتحليل البروتين المجمعات الكبيرة. هذا الأسلوب يتيح نظرة ثاقبة لتكوين العمارة ، رياضيات الكيمياء والشاملة متعددة الوحيدات التجمعات. هنا ، وصفنا ، وخطوة بخطوة ، وكيفية إجراء تحليل الطيف الكتلي الهيكلي ، وتوصيف البنى الجزيئات.

تحليل البروتين المجمعات الكبيرة التي الطيف الكتلي الإنشائية

Living cells control and regulate their biological processes through the coordinated action of a large number of proteins that assemble themselves into an ...

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MALDI Sample Preparation: the Ultra Thin Layer Method

This video demonstrates the preparation of an ultra-thin matrix/analyte layer for analyzing peptides and proteins by Matrix-Assisted Laser Desorption Ionization Mass Spectrometry (MALDI-MS) 1,2. The ultra-thin layer method involves the production of a substrate layer of matrix crystals (alpha-cyano-4-hydroxycinnamic acid) on the sample plate, which serves as a seeding ground for subsequent crystallization of a matrix/analyte mixture. Advantages of the ultra-thin layer method over other sample deposition approaches (e.g. dried droplet) are that it provides (i) greater tolerance to impurities such as salts and detergents, (ii) better resolution, and (iii) higher spatial uniformity. This method is especially useful for the accurate mass determination of proteins. The protocol was initially developed and optimized for the analysis of membrane proteins and used to successfully analyze ion channels, metabolite transporters, and receptors, containing between 2 and 12 transmembrane domains 2. Since the original publication, it has also shown to be equally useful for the analysis of soluble proteins. Indeed, we have used it for a large number of proteins having a wide range of properties, including those with molecular masses as high as 380 kDa 3. It is currently our method of choice for the molecular mass analysis of all proteins. The described procedure consistently produces high-quality spectra, and it is sensitive, robust, and easy to implement.

This video demonstrates the preparation of an ultra-thin matrix/analyte layer for analyzing peptides and proteins by Matrix-Assisted Laser Desorption Ionization Mass Spectrometry (MALDI-MS).

MALDI تحضير العينة : الترا أسلوب طبقة رقيقة

This video demonstrates the preparation of an ultra-thin matrix/analyte layer for analyzing peptides and proteins by Matrix-Assisted Laser Desorption ...

T-wave Ion Mobility-mass Spectrometry: Basic Experimental Procedures for Protein Complex Analysis

Ion mobility (IM) is a method that measures the time taken for an ion to travel through a pressurized cell under the influence of a weak electric field. The speed by which the ions traverse the drift region depends on their size: large ions will experience a greater number of collisions with the background inert gas (usually N2) and thus travel more slowly through the IM device than those ions that comprise a smaller cross-section. In general, the time it takes for the ions to migrate though the dense gas phase separates them, according to their collision cross-section (&Omega;). 
Recently, IM spectrometry was coupled with mass spectrometry and a traveling-wave (T-wave) Synapt ion mobility mass spectrometer (IM-MS) was released. Integrating mass spectrometry with ion mobility enables an extra dimension of sample separation and definition, yielding a three-dimensional spectrum (mass to charge, intensity, and drift time). This separation technique allows the spectral overlap to decrease, and enables resolution of heterogeneous complexes with very similar mass, or mass-to-charge ratios, but different drift times. Moreover, the drift time measurements provide an important layer of structural information, as &Omega; is related to the overall shape and topology of the ion. The correlation between the measured drift time values and &Omega; is calculated using a calibration curve generated from calibrant proteins with defined cross-sections1.
The power of the IM-MS approach lies in its ability to define the subunit packing and overall shape of protein assemblies at micromolar concentrations, and near-physiological conditions1. Several recent IM studies of both individual proteins2,3 and non-covalent protein complexes4-9, successfully demonstrated that protein quaternary structure is maintained in the gas phase, and highlighted the potential of this approach in the study of protein assemblies of unknown geometry. Here, we provide a detailed description of IMS-MS analysis of protein complexes using the Synapt (Quadrupole-Ion Mobility-Time-of-Flight) HDMS instrument (Waters Ltd; the only commercial IM-MS instrument currently available)10. We describe the basic optimization steps, the calibration of collision cross-sections, and methods for data processing and interpretation. The final step of the protocol discusses methods for calculating theoretical &Omega; values. Overall, the protocol does not attempt to cover every aspect of IM-MS characterization of protein assemblies; rather, its goal is to introduce the practical aspects of the method to new researchers in the field.

Ion mobility-mass spectrometry is an emerging gas-phase technology that separates ions, based on their collision cross-section and mass. The method provides three-dimensional information on the overall topology and shape of protein complexes. Here, we outline a basic procedure for instrument setting and optimization, calibration of drift times, and data interpretation.

تي موجة ايون التنقل الكتلة الطيفي : الإجراءات التجريبية الأساسية لتحليل البروتين مجمع

Ion mobility (IM) is a method that measures the time taken for an ion to travel through a pressurized cell under the influence of a weak electric field. ...

Atmospheric-pressure Molecular Imaging of Biological Tissues and Biofilms by LAESI Mass Spectrometry

Ambient ionization methods in mass spectrometry allow analytical investigations to be performed directly on a tissue or biofilm under native-like experimental conditions. Laser ablation electrospray ionization (LAESI) is one such development and is particularly well-suited for the investigation of water-containing specimens. LAESI utilizes a mid-infrared laser beam (2.94 &mu;m wavelength) to excite the water molecules of the sample. When the ablation fluence threshold is exceeded, the sample material is expelled in the form of particulate matter and these projectiles travel to tens of millimeters above the sample surface. In LAESI, this ablation plume is intercepted by highly charged droplets to capture a fraction of the ejected sample material and convert its chemical constituents into gas-phase ions. A mass spectrometer equipped with an atmospheric-pressure ion source interface is employed to analyze and record the composition of the released ions originating from the probed area (pixel) of the sample. A systematic interrogation over an array of pixels opens a way for molecular imaging in the microprobe analysis mode. A unique aspect of LAESI mass spectrometric imaging is depth profiling that, in combination with lateral imaging, enables three-dimensional (3D) molecular imaging. With current lateral and depth resolutions of ~100 &mu;m and ~40 &mu;m, respectively, LAESI mass spectrometric imaging helps to explore the molecular structure of biological tissues. Herein, we review the major elements of a LAESI system and provide guidelines for a successful imaging experiment.

Laser ablation electrospray ionization (LAESI) is an atmospheric-pressure ion source for mass spectrometry. In the imaging mode, a mid-infrared laser probes the distributions of molecules across a tissue section or a biofilm. This technique presents a new approach for diverse bioanalytical studies carried out under native experimental conditions.

الضغط الجوي التصوير الجزيئي من الأنسجة البيولوجية والأغشية الحيوية التي LAESI طيف الكتلة

Ambient ionization methods in mass spectrometry allow analytical investigations to be performed directly on a tissue or biofilm under native-like ...

Direct Analysis of Single Cells by Mass Spectrometry at Atmospheric Pressure

Analysis of biochemicals in single cells is important for understanding cell metabolism, cell cycle, adaptation, disease states, etc. Even the same cell types exhibit heterogeneous biochemical makeup depending on their physiological conditions and interactions with the environment. Conventional methods of mass spectrometry (MS) used for the analysis of biomolecules in single cells rely on extensive sample preparation. Removing the cells from their natural environment and extensive sample processing could lead to changes in the cellular composition. Ambient ionization methods enable the analysis of samples in their native environment and without extensive sample preparation.1 The techniques based on the mid infrared (mid-IR) laser ablation of biological materials at 2.94 &mu;m wavelength utilize the sudden excitation of water that results in phase explosion.2 Ambient ionization techniques based on mid-IR laser radiation, such as laser ablation electrospray ionization (LAESI) and atmospheric pressure infrared matrix-assisted laser desorption ionization (AP IR-MALDI), have successfully demonstrated the ability to directly analyze water-rich tissues and biofluids at atmospheric pressure.3-11 In LAESI the mid-IR laser ablation plume that mostly consists of neutral particulate matter from the sample coalesces with highly charged electrospray droplets to produce ions. Recently, mid-IR ablation of single cells was performed by delivering the mid-IR radiation through an etched fiber. The plume generated from this ablation was postionized by an electrospray enabling the analysis of diverse metabolites in single cells by LAESI-MS.12 This article describes the detailed protocol for single cell analysis using LAESI-MS. The presented video demonstrates the analysis of a single epidermal cell from the skin of an Allium cepa bulb. The schematic of the system is shown in Figure 1. A representative example of single cell ablation and a LAESI mass spectrum from the cell are provided in Figure 2.

Single cell analysis is performed by mass spectrometry on plant and animal cells at atmospheric pressure by using a sharpened optical fiber to sample the cells for laser ablation electrospray ionization (LAESI) mass spectrometry.

التحليل المباشر للخلايا واحدة بواسطة الطيف الكتلي في الضغط الجوي

Analysis of biochemicals in single cells is important for understanding cell metabolism, cell cycle, adaptation, disease states, etc. Even the same cell ...

Profiling Thiol Redox Proteome Using Isotope Tagging Mass Spectrometry

Pseudomonas syringae pv. tomato strain DC3000 not only causes bacterial speck disease in Solanum lycopersicum but also on Brassica species, as well as on Arabidopsis thaliana, a genetically tractable host plant1,2. The accumulation of reactive oxygen species (ROS) in cotyledons inoculated with DC3000 indicates a role of ROS in modulating necrotic cell death during bacterial speck disease of tomato3. Hydrogen peroxide, a component of ROS, is produced after inoculation of tomato plants with Pseudomonas3. Hydrogen peroxide can be detected using a histochemical stain 3'-3' diaminobenzidine (DAB)4. DAB staining reacts with hydrogen peroxide to produce a brown stain on the leaf tissue4. ROS has a regulatory role of the cellular redox environment, which can change the redox status of certain proteins5. Cysteine is an important amino acid sensitive to redox changes. Under mild oxidation, reversible oxidation of cysteine sulfhydryl groups serves as redox sensors and signal transducers that regulate a variety of physiological processes6,7. Tandem mass tag (TMT) reagents enable concurrent identification and multiplexed quantitation of proteins in different samples using tandem mass spectrometry8,9. The cysteine-reactive TMT (cysTMT) reagents enable selective labeling and relative quantitation of cysteine-containing peptides from up to six biological samples. Each isobaric cysTMT tag has the same nominal parent mass and is composed of a sulfhydryl-reactive group, a MS-neutral spacer arm and an MS/MS reporter10. After labeling, the samples were subject to protease digestion. The cysteine-labeled peptides were enriched using a resin containing anti-TMT antibody. During MS/MS analysis, a series of reporter ions (i.e., 126-131 Da) emerge in the low mass region, providing information on relative quantitation. The workflow is effective for reducing sample complexity, improving dynamic range and studying cysteine modifications. Here we present redox proteomic analysis of the Pst DC3000 treated tomato (Rio Grande) leaves using cysTMT technology. This high-throughput method has the potential to be applied to studying other redox-regulated physiological processes.

Reactive oxygen species level is elevated when cells encounter stress conditions. Here we show the example of 3'-3' diaminobenzidine staining as well as cysTMT labeling and mass spectrometry to profile the redox proteome in Pseudomonas syringae treated tomato leaves.

التنميط بروتيوم الأكسدة والاختزال ثيول استخدام الطيف النظائر كتلة توصيف

Pseudomonas syringae pv. tomato strain DC3000 not only causes bacterial speck disease in Solanum lycopersicum but also on Brassica species, as well as on ...

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.

تحديد بروتين في مجمعات<em&gt; كولاي</em&gt; استخدام المتعاقبة تنقية تقارب الببتيد في تركيبة مع جنبا إلى جنب الطيف الكتلي

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

A Protocol for the Identification of Protein-protein Interactions Based on 15N Metabolic Labeling, Immunoprecipitation, Quantitative Mass Spectrometry and Affinity Modulation

Protein-protein interactions are fundamental for many biological processes in the cell. Therefore, their characterization plays an important role in current research and a plethora of methods for their investigation is available1. Protein-protein interactions often are highly dynamic and may depend on subcellular localization, post-translational modifications and the local protein environment2. Therefore, they should be investigated in their natural environment, for which co-immunoprecipitation approaches are the method of choice3. Co-precipitated interaction partners are identified either by immunoblotting in a targeted approach, or by mass spectrometry (LC-MS/MS) in an untargeted way. The latter strategy often is adversely affected by a large number of false positive discoveries, mainly derived from the high sensitivity of modern mass spectrometers that confidently detect traces of unspecifically precipitating proteins. A recent approach to overcome this problem is based on the idea that reduced amounts of specific interaction partners will co-precipitate with a given target protein whose cellular concentration is reduced by RNAi, while the amounts of unspecifically precipitating proteins should be unaffected. This approach, termed QUICK for QUantitative Immunoprecipitation Combined with Knockdown4, employs Stable Isotope Labeling of Amino acids in Cell culture (SILAC)5 and MS to quantify the amounts of proteins immunoprecipitated from wild-type and knock-down strains. Proteins found in a 1:1 ratio can be considered as contaminants, those enriched in precipitates from the wild type as specific interaction partners of the target protein. Although innovative, QUICK bears some limitations: first, SILAC is cost-intensive and limited to organisms that ideally are auxotrophic for arginine and/or lysine. Moreover, when heavy arginine is fed, arginine-to-proline interconversion results in additional mass shifts for each proline in a peptide and slightly dilutes heavy with light arginine, which makes quantification more tedious and less accurate5,6. Second, QUICK requires that antibodies are titrated such that they do not become saturated with target protein in extracts from knock-down mutants.
Here we introduce a modified QUICK protocol which overcomes the abovementioned limitations of QUICK by replacing SILAC for 15N metabolic labeling and by replacing RNAi-mediated knock-down for affinity modulation of protein-protein interactions. We demonstrate the applicability of this protocol using the unicellular green alga Chlamydomonas reinhardtii as model organism and the chloroplast HSP70B chaperone as target protein7 (Figure 1). HSP70s are known to interact with specific co-chaperones and substrates only in the ADP state8. We exploit this property as a means to verify the specific interaction of HSP70B with its nucleotide exchange factor CGE19.

A Protocol for the Identification of Protein-protein Interactions Based on 15N Metabolic Labeling, Immunoprecipitation, Quantitative Mass Spectrometry and Affinity Modulation

We present a variation of the QUICK (QUantitative Immunoprecipitation Combined with Knockdown) approach that was introduced previously to distinguish between true and false protein-protein interactions. Our approach is based on 15N metabolic labeling, the modulation of affinities of protein-protein interactions by the presence/absence of ATP, immunoprecipitation, and quantitative mass spectrometry.

بروتوكول لتحديد البروتين البروتين التفاعلات على أساس<sup&gt; 15</sup&gt; N صفها الأيض، مناعي، الكمي والتحوير الطيف الكتلي الانجذاب

Protein-protein interactions are fundamental for many biological processes in the cell. Therefore, their characterization plays an important role in ...

Protein Purification-free Method of Binding Affinity Determination by Microscale Thermophoresis

Quantitative characterization of protein interactions is essential in practically any field of life sciences, particularly drug discovery. Most of currently available methods of KD determination require access to purified protein of interest, generation of which can be time-consuming and expensive. We have developed a protocol that allows for determination of binding affinity by microscale thermophoresis (MST) without purification of the target protein from cell lysates. The method involves overexpression of the GFP-fused protein and cell lysis in non-denaturing conditions. Application of the method to STAT3-GFP transiently expressed in HEK293 cells allowed to determine for the first time the affinity of the well-studied transcription factor to oligonucleotides with different sequences. The protocol is straightforward and can have a variety of application for studying interactions of proteins with small molecules, peptides, DNA, RNA, and proteins.

Microscale thermophoresis (MST) can be widely used for determination of binding affinity without purification of the target protein from cell lysates. The protocol involves overexpression of the GFP-fused protein, cell lysis in non-denaturing conditions, and detection of MST signal in the presence of varying concentrations of the ligand.

البروتين طريقة خالية من تنقية تجليد تحديد الانجذاب من قبل Thermophoresis الميكروسكيل

Quantitative characterization of protein  interactions is essential in practically any field of life sciences,  particularly drug discovery. Most of ...

A New Approach for the Comparative Analysis of Multiprotein Complexes Based on 15N Metabolic Labeling and Quantitative Mass Spectrometry

The introduced protocol provides a tool for the analysis of multiprotein complexes in the thylakoid membrane, by revealing insights into complex composition under different conditions. In this protocol the approach is demonstrated by comparing the composition of the protein complex responsible for cyclic electron flow (CEF) in Chlamydomonas reinhardtii, isolated from genetically different strains. The procedure comprises the isolation of thylakoid membranes, followed by their separation into multiprotein complexes by sucrose density gradient centrifugation, SDS-PAGE, immunodetection and comparative, quantitative mass spectrometry (MS) based on differential metabolic labeling (14N/15N) of the analyzed strains. Detergent solubilized thylakoid membranes are loaded on sucrose density gradients at equal chlorophyll concentration. After ultracentrifugation, the gradients are separated into fractions, which are analyzed by mass-spectrometry based on equal volume. This approach allows the investigation of the composition within the gradient fractions and moreover to analyze the migration behavior of different proteins, especially focusing on ANR1, CAS, and PGRL1. Furthermore, this method is demonstrated by confirming the results with immunoblotting and additionally by supporting the findings from previous studies (the identification and PSI-dependent migration of proteins that were previously described to be part of the CEF-supercomplex such as PGRL1, FNR, and cyt f). Notably, this approach is applicable to address a broad range of questions for which this protocol can be adopted and e.g. used for comparative analyses of multiprotein complex composition isolated from distinct environmental conditions.

A New Approach for the Comparative Analysis of Multiprotein Complexes Based on 15N Metabolic Labeling and Quantitative Mass Spectrometry

The described comparative, quantitative proteomic approach aims at obtaining insights into the composition of multiprotein complexes&#160;under different conditions and is demonstrated by comparing genetically different strains. For quantitative analysis equal volumes of different fractions from a sucrose density gradient are mixed and analyzed by mass spectrometry.

نهج جديد لتحليل مقارن لMultiprotein مجمعات بناء على<sup&gt; 15</sup&gt; N الأيض وصفها والكمية الطيف الكتلي

The introduced protocol provides a tool for the analysis of multiprotein complexes in the thylakoid membrane, by revealing insights into complex ...

Selected Reaction Monitoring Mass Spectrometry for Absolute Protein Quantification

Absolute quantification of target proteins within complex biological samples is critical to a wide range of research and clinical applications. This protocol provides step-by-step instructions for the development and application of quantitative assays using selected reaction monitoring (SRM) mass spectrometry (MS). First, likely quantotypic target peptides are identified based on numerous criteria. This includes identifying proteotypic peptides, avoiding sites of posttranslational modification, and analyzing the uniqueness of the target peptide to the target protein. Next, crude external peptide standards are synthesized and used to develop SRM assays, and the resulting assays are used to perform qualitative analyses of the biological samples. Finally, purified, quantified, heavy isotope labeled internal peptide standards are prepared and used to perform isotope dilution series SRM assays. Analysis of all of the resulting MS data is presented. This protocol was used to accurately assay the absolute abundance of proteins of the chemotaxis signaling pathway within RAW 264.7 cells (a mouse monocyte/macrophage cell line). The quantification of Gi2 (a heterotrimeric G-protein &#945;-subunit) is described in detail.

This protocol describes how to perform absolute quantification assays of target proteins within complex biological samples using selected reaction monitoring. It was used to accurately quantify proteins of the mouse macrophage chemotaxis signaling pathway. Target peptide selection, assay development, and qualitative and quantitative assays are described in detail.

رد الفعل المحدد رصد الطيف الكتلي لالمطلق البروتين الكمي

Absolute quantification of target proteins within complex biological samples is critical to a wide range of research and clinical applications. This ...