This study was supported by the Astellas Foundation for Research on Metabolic Disorders (HT), the Takeda Science Foundation (HT), and by a Japan Society for the Promotion of Science Grants-in-Aid for Young Scientists (B) to HT.

1. 형질 <ol><li> 100 mm 배양 판 (2 × 106 세포 / 접시)에 HEK293 세포 종자. 배양 10 % 소 태아 혈청, 100 μg의 / ㎖ 스트렙토 마이신, 100 유닛 / ㎖의 페니실린으로 보충 된 둘 베코 변형 이글 배지에서 세포. 5 % CO 2 및 37 ℃로 가습 된 배양기에서 세포를 인큐베이션. </li><li> 다음 날, FLAG-태그 ARIP4 플라스미드의 10 μg의 제조업체의 방향 (11)에 따라 형질 전환 시약의 40 μl를 이용하여 세포를 형질. </li></ol> 2. 단백질 추출 <ol><li> 약 트랜 스펙 션 후 36 시간이 빙냉 PBS로 세포를 세척하고 스크레이퍼를 사용하여 세포를 수확. 1.5 mltube에 세포를 전송하고 4 ℃에서 2 분 동안 8,000 XG에 그것을 원심 분리기. 대기음 뜨는 배에서 세포 펠렛을 재현 탁 0.4 M KCl을 버퍼의 펠릿 볼륨 (높은 염 완충액 : 20 mM 트리스 -HCl (pH 8.0), 0.4 M KCl을5 밀리미터의 MgCl 2, 10 % 글리세롤, 0.1 % NP-40, 10 밀리미터 B-mercaptethanol, 1X 프로테아제 억제제 칵테일). 4 ℃에서 20 분 동안 혼합물을 돌립니다. </li><li> 4 ℃에서 10 분 동안 17,700 XG에서 튜브를 원심 분리기. </li><li> (새로운 2 ㎖의 튜브에 상청 (전체 세포 추출물)을 전송하고 0 M KCl을 버퍼의 초기 부피 3 배 추가 희석 완충액 : 20 mM 트리스 -HCl (pH 8.0), 5 밀리미터의 MgCl 2, 10 % 글리세롤, 0.1 % NP-40, 10 밀리미터 β 머 캅토 에탄올, 1X 프로테아제 억제제 칵테일). </li><li> 다른 원심 분리 (4 ℃에서 10 분 동안 17,700 XG)을 수행하고, 새로운 2 ML 튜브에 뜨는 (전체 세포 추출물)를 전송합니다. </li></ol> 3. 면역 침전 <ol><li> 20 mM의 트리스 : 원심 분리 (2.4) 중, (0.1M KCl을 완충액으로 두번 저염 완충액을 세척 한 다음 PBS로 안티 FLAG 비드 50 ㎕의 0.1 M 글리신 - 염산하고 1 M 트리스 - 히드로 클로라이드를 씻어 염산 (PH 8.0), 0.1 M의 KCl, 5 mM의 MgCl2를, 10 % 글리세롤, 0.1 % NP-40, 10mM (B) 머 캅토 에탄올, 1X 프로테아제 억제제 칵테일). 이 세척 공정의 원심 분리는 39 ° C에서 1 분 동안 2,000 × g으로 수행된다. </li><li> 전체 세포 추출물 FLAG 비드의 50 μL를 혼합하고 가볍게 2-4 ℃로한다 (단계 2.4의 전체 세포 추출물의 1 %는 또한 나중에 사용하기 위해 -80 ℃에서 보관한다에서 4 시간 동안 혼합물을 회전 ) 입력으로. </li><li> 마이크로 스핀 열 (중력 드롭)에 샘플을 전송합니다. (입력 및 관류 웨스턴 블롯 분석을 이용하여 양자의 단백질 수준을 확인), 1.5 ㎖의 튜브에 관류 유지 액체 질소를 사용하여 동결하고, -80 ℃에서 보관. </li><li> 국기 비즈 (중력 드롭)을 씻어 0.1 M KCl을 버퍼 (낮은 소금 버퍼)의 1 ML을 추가합니다. </li><li> 3.4 적어도 네 번 이상 (오 세척의 총) 단계를 반복합니다. </li></ol> 4. 용출 <ol><li> 1.5 ML 튜브에 열을 놓고 1 분 동안 2,000 XG에이를 원심 분리; 구슬 건조됩니다. </li><li> 하단 캡열. </li><li> 0.1 M 글리신 - 염산 (PH 2.5)의 (FLAG 구슬의 부피와 동일) 50 μl를 추가합니다. </li><li> 부드럽게 실온에서 10 분 동안 혼합물을 흔들어. </li><li> 새로운 1.5 ML 튜브에 열을 놓고 1 분 동안 2,000 XG에 그것을 원심 분리기. </li><li> 용출액을 1 M Tris-HCl (pH8.0)을 10 ㎕의 중화; 피펫 또는 와류 장치를 이용하여 잘 혼합한다. </li></ol> 5. 알킬화 및 트립신 <ol><li> 100 mM의 NH 4 HCO 3, CH 3 CN 10 μL, 혼합물에 디티 오 트레이 톨의 2 μL (112 μl의 총 부피)의 50 μl를 추가합니다. </li><li> 56 ° C에서 30 분 동안 샘플을 인큐베이션. </li><li> 실온에서 10 분 동안 샘플을 놓는다. </li><li> 요오도 아세트 아미드 시료에 333 mm의 10 μl를 첨가하고 37 ℃에서 30 분 동안 어두운 데에서 부화. </li><li> 혼합물에 트립신의 10 μL (33 NG / μL)을 추가하고 37 ° C에서 하룻밤을 품어. </li></ol><ol><li> 밤새 트립신 처리 후, LC-MS / MS 시설이나 분석 12 타사 질량 분석 실험실로 최종 제품을 수송. </li></ol>

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The authors have nothing to disclose.

효율적인 형질 감염 프로토콜이 성공적인 결과를 얻는 것이 필수적이다. 따라서, 우리는 면역 FLAG 태그가 단백질 수준을 결정하는 웨스턴 블롯 분석을 사용하는 것이 좋습니다. 이 단계는 IP가 성공적으로 수행되었는지, 그들의 관심 단백질이 제대로 또한, 과발현되어 있는지 확인하려면 사용자 수 있습니다. FLAG 태그가 단백질 수준은 질량 분광 분석에 앞서 확인하여야한다. ...

단백질 - 단백질 상호 작용은 다양한 생물학적 기능에 중요한 역할을한다. 따라서, 이러한 상호 작용은 신호 전달에 연루되어왔다 세포막 단백질 수송; 세포의 신진 대사; 및 DNA 복제, DNA 손상 복구, 재조합 및 전사 1, 2, 3, 4 등 여러 핵 프로세스. 이러한 상호 작용에 관여하는 단백질을 확인하는 것은이 세포 과정에 대한 우리의 이해를 증진하는 것이 중요하다. 면역 침전 (IP)는 단백질 - 단백질 상호 작용을 분석하는데 사용되는 검증 된 기술이다. 공동 - 면역 침전 된 단백질의 동정을 용이하게하기 위하여, 질량 분석계는 종종 이용 5, 6, 7, 8,9. 항체와 단백질 복합체의 공지 부재 타겟팅함으로써, 단백질 복합체를 분리하고,이어서 질량 분광 분석을 통해 그 미지의 컴포넌트를 식별 할 수있다. ARIP4 (안드로겐 수용체 상호 작용하는 단백질 4), 전사 coregulator은 활성화 또는 상황에 의존적으로 9, 10 년 대상 발기인을 억제하기 위해 핵 수용체 단백질과 상호 작용한다. 더 이러한 핵 인자를 지배하는 전사 조절 메커니즘을 이해하기 위해 정화하고, LC-MS / MS 시스템을 사용하여 ARIP4 상호 작용 단백질을 확인하는 포괄적 인 방법을 설명한다.

<table><tbody><tr><td>Lipofectamine 2000 Transfection Reagent</td><td>Thermo Fisher Scientific</td><td>11668019</td><td></td></tr><tr><td>Protease Inhibitor Cocktail (EDTA free) (100x)</td><td>nacalai tesque</td><td>03969-21</td><td></td></tr><tr><td>ANTI-FLAG M2 Affinity Gel</td><td>Sigma-Aldrich</td><td>A2220</td><td></td></tr><tr><td>Micro Bio-Spin Columns</td><td>BIO-RAD</td><td>732-6204</td><td></td></tr></tbody></table>

a protein preparation method for the high-throughput identification of proteins interacting with a nuclear cofactor using lc-ms/ms analysis

Transcriptional coregulators are vital to the efficient transcriptional regulation of nuclear chromatin structure. Coregulators play a variety of roles in regulating transcription. These include the direct interaction with transcription factors, the covalent modification of histones and other proteins, and the occasional chromatin conformation alteration. Accordingly, establishing relatively quick methods for identifying proteins that interact within this network is crucial to enhancing our understanding of the underlying regulatory mechanisms. LC-MS/MS-mediated protein binding partner identification is a validated technique used to analyze protein-protein interactions. By immunoprecipitating a previously-identified member of a protein complex with an antibody (occasionally with an antibody for a tagged protein), it is possible to identify its unknown protein interactions via mass spectrometry analysis. Here, we present a method of protein preparation for the LC-MS/MS-mediated high-throughput identification of protein interactions involving nuclear cofactors and their binding partners. This method allows for a better understanding of the transcriptional regulatory mechanisms of the targeted nuclear factors.

우리는 강한 신호 ARIP4 약 160 KDa의뿐 모의 샘플 제어 및 몇몇 다른 미지의 단백질의 것과 (도 1)을 확인 하였다. LC-MS / MS 분석은 펩티드 복합체 ARIP4 FLAG 비드 (표 1)의 분획 내의 잠재적 인 펩티드 공동 인자를 모두 식별. P62 (Sequestosome1)는 공지 ARIP4 공동 인자 (11)는이 시스템 (11)의 유효성을 확인하는 분석 (표...

Watch this Scientific Journal Video about A Protein Preparation Method for the High-throughput Identification of Proteins Interacting with a Nuclear Cofactor Using LC-MS/MS Analysis at JoVE.com

A Protein Preparation Method for the High-throughput Identification of Proteins Interacting with a Nuclear Cofactor Using LC-MS/MS Analysis

우리는 LC-MS / MS 시스템을 사용 coregulatory 상호 작용 단백질의 정제 방법을 확립 하였다.

LC-MS / MS 분석을 이용하여 핵 공동 인자와 상호 작용 단백질의 높은 처리량 식별 단백질 제조 방법

Transcriptional coregulators are vital to the efficient transcriptional regulation of nuclear chromatin structure. Coregulators play a variety of roles in ...

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Biochemistry

8.3K 조회수.  Osaka University.  우리는 LC-MS / MS 시스템을 사용 coregulatory 상호 작용 단백질의 정제 방법을 확립 하였다. 

비디오: A Protein Preparation Method for the High-throughput Identification of Proteins Interacting with a Nuclear Cofactor Using LC-MS/MS Analysis

Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions

Noncoding RNAs play important roles in several nuclear processes, including regulating gene expression, chromatin structure, and DNA repair. In most cases, the action of noncoding RNAs is mediated by proteins whose functions are in turn regulated by these interactions with noncoding RNAs. Consistent with this, a growing number of proteins involved in nuclear functions have been reported to bind RNA and in a few cases the RNA-binding regions of these proteins have been mapped, often through laborious, candidate-based methods.
Here, we report a detailed protocol to perform a high-throughput, proteome-wide unbiased identification of RNA-binding proteins and their RNA-binding regions. The methodology relies on the incorporation of a photoreactive uridine analog in the cellular RNA, followed by UV-mediated protein-RNA crosslinking, and mass spectrometry analyses to reveal RNA-crosslinked peptides within the proteome. Although we describe the procedure for mouse embryonic stem cells, the protocol should be easily adapted to a variety of cultured cells.

We describe a protocol to identify RNA-binding proteins and map their RNA-binding regions in live cells using UV-mediated photocrosslinking and mass spectrometry.

질량 분석 기반 식별 RNA 바인딩 영역에 대 한 샘플 준비

Noncoding RNAs play important roles in several nuclear processes, including regulating gene expression, chromatin structure, and DNA repair. In most ...

연구

생화학

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.

온-막 소화 기술을 사용한 단백질-단백질 상호 작용의 평가

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

Label-Free Immunoprecipitation Mass Spectrometry Workflow for Large-scale Nuclear Interactome Profiling

Immunoaffinity purification mass spectrometry (IP-MS) has emerged as a robust quantitative method of identifying protein-protein interactions. This publication presents a complete interaction proteomics workflow designed for identifying low abundance protein-protein interactions from the nucleus that could also be applied to other subcellular compartments. This workflow includes subcellular fractionation, immunoprecipitation, sample preparation, offline cleanup, single-shot label-free mass spectrometry, and downstream computational analysis and data visualization. Our protocol is optimized for detecting compartmentalized, low abundance interactions that are difficult to identify from whole cell lysates (e.g., transcription factor interactions in the nucleus) by immunoprecipitation of endogenous proteins from fractionated subcellular compartments. The sample preparation pipeline outlined here provides detailed instructions for the preparation of HeLa cell nuclear extract, immunoaffinity purification of endogenous bait protein, and quantitative mass spectrometry analysis. We also discuss methodological considerations for performing large-scale immunoprecipitation in mass spectrometry-based interaction profiling experiments and provide guidelines for evaluating data quality to distinguish true positive protein interactions from nonspecific interactions. This approach is demonstrated here by investigating the nuclear interactome of the CMGC kinase, DYRK1A, a low abundance protein kinase with poorly defined interactions within the nucleus.

Described is a proteomics workflow for identifying protein interaction partners from a nuclear subcellular fraction using immunoaffinity enrichment of a given protein of interest and label-free mass spectrometry. The workflow includes subcellular fractionation, immunoprecipitation, filter aided sample preparation, offline cleanup, mass spectrometry, and a downstream bioinformatics pipeline.

대규모 핵 상호 작용 프로파일링을 위한 라벨 없는 면역 침전 질량 분광 워크플로우

Immunoaffinity purification mass spectrometry (IP-MS) has emerged as a robust quantitative method of identifying protein-protein interactions. This ...

Microsampling in Targeted Mass Spectrometry-Based Protein Analysis of Low-Abundance Proteins

This paper presents a protocol with detailed descriptions for efficient sample cleanup of low-abundance proteins from dried samples. This is performed using bead-based proteolysis prior to proteotypic peptide affinity-capture and liquid chromatography tandem mass spectrometry (LC-MS/MS) determination. The procedure can be applied to both conventional dried samples using paper cards (e.g., dried blood spots [DBSs] and dried serum spots [DSSs]), as well as samples collected with newer sampling methods such as volumetric absorptive microsampling (VAMS). In addition to describing this procedure, the preparation of both trypsin beads and antibody-coated beads is presented in a step-by-step manner in this work. The advantages of the presented procedure are time-efficient proteolysis using beads and selective robust cleanup using peptide affinity-capture. The current procedure describes the determination of the low-abundance small-cell lung cancer (SCLC) biomarker, progastrin-releasing peptide (ProGRP), in dried serum (both DSSs and VAMS). Detailed procedures for bead preparation make it easier to implement the workflow in new applications or other laboratories. It is demonstrated that the results may be dependent on the sampling material; for the present project, higher signal intensities were seen for samples collected using VAMS compared to DSSs.

A protocol is presented for the determination of low-abundance biomarkers from dried serum samples exemplified with the biomarker progastrin-releasing peptide (ProGRP). Antibody-coated magnetic beads are used for the selective cleanup and enrichment of a proteotypic ProGRP peptide. The captured peptide is subsequently analyzed by liquid chromatography-tandem mass spectrometry.

표적 질량분석법 기반 단백질 분석의 마이크로샘플링 저농도 단백질

This paper presents a protocol with detailed descriptions for efficient sample cleanup of low-abundance proteins from dried samples. This is performed ...

화학

Profiling of Methyltransferases and Other S-adenosyl-L-homocysteine-binding Proteins by Capture Compound Mass Spectrometry (CCMS)

There is a variety of approaches to reduce the complexity of the proteome on the basis of functional small molecule-protein interactions such as affinity chromatography 1 or Activity Based Protein Profiling 2. Trifunctional Capture Compounds (CCs, Figure 1A) 3 are the basis for a generic approach, in which the initial equilibrium-driven interaction between a small molecule probe (the selectivity function, here S-adenosyl-L-homocysteine, SAH, Figure 1A) and target proteins is irreversibly fixed upon photo-crosslinking between an independent photo-activable reactivity function (here a phenylazide) of the CC and the surface of the target proteins. The sorting function (here biotin) serves to isolate the CC - protein conjugates from complex biological mixtures with the help of a solid phase (here streptavidin magnetic beads). Two configurations of the experiments are possible: "off-bead" 4 or the presently described "on-bead" configuration (Figure 1B). The selectivity function may be virtually any small molecule of interest (substrates, inhibitors, drug molecules).
S-Adenosyl-L-methionine (SAM, Figure 1A) is probably, second to ATP, the most widely used cofactor in nature 5, 6. It is used as the major methyl group donor in all living organisms with the chemical reaction being catalyzed by SAM-dependent methyltransferases (MTases), which methylate DNA 7, RNA 8, proteins 9, or small molecules 10. Given the crucial role of methylation reactions in diverse physiological scenarios (gene regulation, epigenetics, metabolism), the profiling of MTases can be expected to become of similar importance in functional proteomics as the profiling of kinases. Analytical tools for their profiling, however, have not been available. We recently introduced a CC with SAH as selectivity group to fill this technological gap (Figure 1A).
SAH, the product of SAM after methyl transfer, is a known general MTase product inhibitor 11. For this reason and because the natural cofactor SAM is used by further enzymes transferring other parts of the cofactor or initiating radical reactions as well as because of its chemical instability 12, SAH is an ideal selectivity function for a CC to target MTases. Here, we report the utility of the SAH-CC and CCMS by profiling MTases and other SAH-binding proteins from the strain DH5&alpha; of Escherichia coli (E. coli), one of the best-characterized prokaryotes, which has served as the preferred model organism in countless biochemical, biological, and biotechnological studies. Photo-activated crosslinking enhances yield and sensitivity of the experiment, and the specificity can be readily tested for in competition experiments using an excess of free SAH.

Profiling of Methyltransferases and Other S-adenosyl-L-homocysteine-binding Proteins by Capture Compound Mass Spectrometry CCMS

Capture Compounds are trifunctional small molecules to reduce the complexity of the proteome by functional reversible small molecule-protein interaction followed by photo-crosslinking and purification. Here we use a Capture Compound with S-adenosyl-L-homocysteine-binding as selectivity function to isolate methyltransferases from an Escherichia coli whole cell lysate and identify them by MS.

Methyltransferases의 프로 파일링 및 기타 S - adenosyl - L</sub캡처 컴파 운드 질량 분광법 (CCMS)에서> - 호모 시스테인 결합 단백질

There is a variety of approaches to reduce the complexity of the proteome on the basis of functional small molecule-protein interactions such as affinity ...

생물학

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.

을 바탕으로 단백질 - 단백질 상호 작용의 확인에 프로토콜<sup&gt; 15</sup&gt; N 신진 대사 라벨링, Immunoprecipitation, 수량 질량 분석법 및 선호도 변조

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

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.

multiprotein의 단지의 비교 분석을위한 새로운 접근 방식을 기반으로<sup&gt; 15</sup&gt; N 대사 라벨링 및 정량 질량 분석

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

Identification of Protein Interaction Partners in Mammalian Cells Using SILAC-immunoprecipitation Quantitative Proteomics

Quantitative proteomics combined with immuno-affinity purification, SILAC immunoprecipitation, represent a powerful means for the discovery of novel protein:protein interactions. By allowing the accurate relative quantification of protein abundance in both control and test samples, true interactions may be easily distinguished from experimental contaminants. Low affinity interactions can be preserved through the use of less-stringent buffer conditions and remain readily identifiable. This protocol discusses the labeling of tissue culture cells with stable isotope labeled amino acids, transfection and immunoprecipitation of an affinity tagged protein of interest, followed by the preparation for submission to a mass spectrometry facility. This protocol then discusses how to analyze and interpret the data returned from the mass spectrometer in order to identify cellular partners interacting with a protein of interest. As an example this technique is applied to identify proteins binding to the eukaryotic translation initiation factors: eIF4AI and eIF4AII.

SILAC immunoprecipitation experiments represent a powerful means for discovering novel protein:protein interactions. By allowing the accurate relative quantification of protein abundance in both control and test samples, true interactions may be easily distinguished from experimental contaminants, and low affinity interactions preserved through use of less-stringent buffer conditions.

SILAC - 면역 정량 프로테오믹스를 사용하여 포유 동물 세포에있는 단백질 상호 작용 파트너의 식별

Quantitative proteomics combined with immuno-affinity purification, SILAC immunoprecipitation, represent a powerful means for the discovery of novel ...

Characterization of Neuronal Lysosome Interactome with Proximity Labeling Proteomics

Lysosomes frequently communicate with a variety of biomolecules to achieve the degradation and other diverse cellular functions. Lysosomes are critical to human brain function, as neurons are postmitotic and rely heavily on the autophagy-lysosome pathway to maintain cellular homeostasis. Despite advancements in the understanding of various lysosomal functions, capturing the highly dynamic communications between lysosomes and other cellular components is technically challenging, particularly in a high-throughput fashion. Here, a detailed protocol is provided for the recently published endogenous (knock-in) lysosome proximity labeling proteomic method in human induced pluripotent stem cell (hiPSC)-derived neurons. 
Both lysosomal membrane proteins and proteins surrounding lysosomes within a 10-20 nm radius can be confidently identified and accurately quantified in live human neurons. Each step of the protocol is described in detail, i.e., hiPSC-neuron culture, proximity labeling, neuron harvest, fluorescence microscopy, biotinylated protein enrichment, protein digestion, LC-MS analysis, and data analysis. In summary, this unique endogenous lysosomal proximity labeling proteomics method provides a high-throughput and robust analytical tool to study the highly dynamic lysosomal activities in live human neurons.

A neuronal lysosome proximity labeling proteomics protocol is described here to characterize the dynamic lysosomal microenvironment in human induced pluripotent stem cell-derived neurons. Lysosomal membrane proteins and proteins that interact with lysosomes (stably or transiently) can be accurately quantified in this method with excellent intracellular spatial resolution in live human neurons.

뉴런 리소좀 상호작용과 근접 라벨링 단백질체학의 특성 분석

Lysosomes frequently communicate with a variety of biomolecules to achieve the degradation and other diverse cellular functions. Lysosomes are critical to ...

신경과학

Identification of MyoD Interactome Using Tandem Affinity Purification Coupled to Mass Spectrometry

Skeletal muscle terminal differentiation starts with the commitment of pluripotent mesodermal precursor cells to myoblasts. These cells have still the ability to proliferate or they can differentiate and fuse into multinucleated myotubes, which maturate further to form myofibers. Skeletal muscle terminal differentiation is orchestrated by the coordinated action of various transcription factors, in particular the members of the Muscle Regulatory Factors or MRFs (MyoD, Myogenin, Myf5, and MRF4), also called the myogenic bHLH transcription factors family. These factors cooperate with chromatin-remodeling complexes within elaborate transcriptional regulatory network to achieve skeletal myogenesis. In this, MyoD is considered the master myogenic transcription factor in triggering muscle terminal differentiation. This notion is strengthened by the ability of MyoD to convert non-muscle cells into skeletal muscle cells. Here we describe an approach used to identify MyoD protein partners in an exhaustive manner in order to elucidate the different factors involved in skeletal muscle terminal differentiation. The long-term aim is to understand the epigenetic mechanisms involved in the regulation of skeletal muscle genes, i.e., MyoD targets. MyoD partners are identified by using Tandem Affinity Purification (TAP-Tag) from a heterologous system coupled to mass spectrometry (MS) characterization, followed by validation of the role of relevant partners during skeletal muscle terminal differentiation. Aberrant forms of myogenic factors, or their aberrant regulation, are associated with a number of muscle disorders: congenital myasthenia, myotonic dystrophy, rhabdomyosarcoma and defects in muscle regeneration. As such, myogenic factors provide a pool of potential therapeutic targets in muscle disorders, both with regard to mechanisms that cause disease itself and regenerative mechanisms that can improve disease treatment. Thus, the detailed understanding of the intermolecular interactions and the genetic programs controlled by the myogenic factors is essential for the rational design of efficient therapies.

MyoD is a myogenic transcription factor with a strong capacity to induce myogenic transdifferentiation of many fully differentiated non-muscle cell lines. The epigenetic mechanisms involved in this transdifferentiation are largely unknown. Here we describe a double-affinity purification method followed by mass spectrometry to exhaustively characterize MyoD partners.

탠덤 선호도 정화를 사용하여 MyoD 상호 작용 체의 식별 질량 분석에 결합

Skeletal muscle terminal differentiation starts with the commitment of pluripotent mesodermal precursor cells to myoblasts. These cells have still the ...

LC-MS / MS 분석을 이용하여 핵 공동 인자와 상호 작용 단백질의 높은 처리량 식별 단백질 제조 방법

요약

더 많은 비디오 탐색

이 비디오의 챕터

질량 분석 기반 식별 RNA 바인딩 영역에 대 한 샘플 준비

온-막 소화 기술을 사용한 단백질-단백질 상호 작용의 평가

대규모 핵 상호 작용 프로파일링을 위한 라벨 없는 면역 침전 질량 분광 워크플로우

표적 질량분석법 기반 단백질 분석의 마이크로샘플링 저농도 단백질

Methyltransferases의 프로 파일링 및 기타 S - adenosyl -_{L - 호모 시스테인 결합 단백질}

을 바탕으로 단백질 - 단백질 상호 작용의 확인에 프로토콜

multiprotein의 단지의 비교 분석을위한 새로운 접근 방식을 기반으로

SILAC - 면역 정량 프로테오믹스를 사용하여 포유 동물 세포에있는 단백질 상호 작용 파트너의 식별

뉴런 리소좀 상호작용과 근접 라벨링 단백질체학의 특성 분석

탠덤 선호도 정화를 사용하여 MyoD 상호 작용 체의 식별 질량 분석에 결합

LC-MS / MS 분석을 이용하여 핵 공동 인자와 상호 작용 단백질의 높은 처리량 식별 단백질 제조 방법

요약

더 많은 비디오 탐색

이 비디오의 챕터

질량 분석 기반 식별 RNA 바인딩 영역에 대 한 샘플 준비

온-막 소화 기술을 사용한 단백질-단백질 상호 작용의 평가

대규모 핵 상호 작용 프로파일링을 위한 라벨 없는 면역 침전 질량 분광 워크플로우

표적 질량분석법 기반 단백질 분석의 마이크로샘플링 저농도 단백질

Methyltransferases의 프로 파일링 및 기타 S - adenosyl - L - 호모 시스테인 결합 단백질

을 바탕으로 단백질 - 단백질 상호 작용의 확인에 프로토콜

multiprotein의 단지의 비교 분석을위한 새로운 접근 방식을 기반으로

SILAC - 면역 정량 프로테오믹스를 사용하여 포유 동물 세포에있는 단백질 상호 작용 파트너의 식별

뉴런 리소좀 상호작용과 근접 라벨링 단백질체학의 특성 분석

탠덤 선호도 정화를 사용하여 MyoD 상호 작용 체의 식별 질량 분석에 결합

Methyltransferases의 프로 파일링 및 기타 S - adenosyl -_{L - 호모 시스테인 결합 단백질}