Kaygan Kaya Üniversitesi tarafından sağlanan Fonlama. Biz onların anlayışlar için T. Boron III (Kaygan Kaya Üniversitesi) ve C. Haney (Pennsylvania Üniversitesi) teşekkür etmek istiyorum.

Ni-Schiff-baz Complex 1. Hidroliz <ol><li> Oda sıcaklığında 250 mL&#39;lik tabanı yuvarlak bir şişeye karıştırılarak N, N-dimetilformamid (DMF), 40 mL Ni-PBP-Schiff-baz kompleksi 1 mmol eritin. </li><li> 0.2 M sulu EDTA çözeltisi, pH 4.5, 60 mL ekleyin. </li><li> Manyetik bir karıştırma çubuğu kullanılarak ve plaka karıştırın, bir gece boyunca bir araya çözelti karıştırılır. Schiff-baz kompleksi hidrolize gibi, renk beyaz bir koyu kırmızı yönelecektir. </li><li> herhangi bir kırmızı boyama yokluğu ile gösterildiği gibi reaksiyonun tamamlanmasından sonra, bir 250 ml ayırıcı bir huniye reaksiyon aktarın. </li><li> 50 ml diklorometan ilave ayırıcı huni kapağı ve karıştırın. Bir atık behere organik yıkama boşaltın. PBP ve kalan Ni PBP-Schiff-baz kompleksi kaldırmak için bu işlem üç kez tekrarlayın. 250 mL&#39;lik yuvarlak dipli bir şişede kalan sulu tabakayı toplayın. </li></ol> Hidrolize olan Amino Asit 2. Fmoc koruma <ol><li&gt; Katı sodyum bikarbonat kullanılarak pH 7&#39;ye yukarıda tarif edilen adım 1.5 izole sulu tabaka ayarlayın. pH periyodik olarak pH test şeritleri kullanarak kontrol edin. </li><li> çözeltiye 168 mg sodyum bikarbonat (2.00 mmol, 2 eşdeğer) ilave edin ve bir manyetik karıştırma çubuğu kullanılarak karıştırıldı ve plaka karıştırın. </li><li> 10 mL&#39;lik bir şişe içinde dioksan çok az miktarda (yaklaşık 4 ya da 5 mL) içinde 337 mg Fmoc N-hidroksisüksinimit ester (1.00 mmol, 1 eşdeğer) içinde çözülür. Sulu çözeltiye Bu çözeltisini ve gece boyunca karıştırın. </li><li> Reaksiyon, gece boyunca karışmaya bırakıldıktan sonra, 1 M hidroklorik asit ile pH 2&#39;ye elde edilen çözeltiyi asitleştirmek. pH periyodik olarak pH test şeritleri kullanarak kontrol edin. </li><li> 250 mL&#39;lik bir ayırma hunisine aktarın ve reaksiyon 50 mL etil asetat ilave edin. , Ayrıcı bir huni kapağı iyice karıştırın ve 250 ml bir erlenmeyer şişesi içinde, organik faz toplanır. Organik özler birleştirerek, bu işlem iki kez daha tekrarlayın. Magnezyum Sülfat, kabaca 3 g Birleştirilen organik özler kurutulure. </li><li> Ham Fmoc-korumalı amino asit elde etmek için bir dönen buharlaştıncı kullanarak Birleştirilen organik özler konsantre edilir. </li></ol>

<ol>
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N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Highly+efficient+catalytic+synthesis+of+&#945;,-amino+acids+under+phase-transfer+conditions+with+a+novel+catalyst/substrate+pair.">Highly efficient catalytic synthesis of &#945;,-amino acids under phase-transfer conditions with a novel catalyst/substrate pair.</a> Angew. Chem. Int. Ed. 40 (10), 1948-1951 (2001).</li><li>Zhou, S., Wang, J., Lin, D., Zhao, F., Liu, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Enantioselective+synthesis+of+2-substituted-tetrahydroisoquinolin-1-yl+glycine+derivatives+via+oxidative+cross-dehydrogenative+coupling+of+tertiary+amines+and+chiral+nickel(II)+glycinate.">Enantioselective synthesis of 2-substituted-tetrahydroisoquinolin-1-yl glycine derivatives via oxidative cross-dehydrogenative coupling of tertiary amines and chiral nickel(II) glycinate.</a> J. Org. Chem. 78 (22), 11204-11212 (2013).</li><li>Belokon, Y. 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A., Kelly, D. E., Wolfe, A. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Large-scale+syntheses+of+Fmoc-protected+non-proteogenic+amino+acids:+useful+building+blocks+for+combinatorial+libraries.">Large-scale syntheses of Fmoc-protected non-proteogenic amino acids: useful building blocks for combinatorial libraries.</a> Org. Process Res. Dev. 5 (4), 445-449 (2001).</li><li>Cruz, L. J., Beteta, N. G., Ewenson, A., Albericio, F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=&amp;#34;One-pot&amp;#34;,+preparation+of+N-carbamate+protected+amino+acids+via+the+azide.">&amp;#34;One-pot&amp;#34;, preparation of N-carbamate protected amino acids via the azide.</a> Org Process Res. Dev. 8 (6), 920-924 (2004).</li><li>Hart, J. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Ullmann's Encyclopedia of Industrial Chemistry. , (2000).</li><li>Adamson, J. G., Blaskovich, M. A., Groenevelt, H., Lajoie, G. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Simple+and+convenient+synthesis+of+tert-butyl+ethers+of+Fmoc-serine,+Fmoc-threonine,+and+Fmoc-tyrosine.">Simple and convenient synthesis of tert-butyl ethers of Fmoc-serine, Fmoc-threonine, and Fmoc-tyrosine.</a> J. Org. Chem. 56 (10), 3447-3449 (1991).</li><li>Seyfried, M. S., Lauber, B. S., Luedtke, N. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Multiple-turnover+isotopic+labeling+of+Fmoc-+and+Boc-protected+amino+acids+with+oxygen+isotopes.">Multiple-turnover isotopic labeling of Fmoc- and Boc-protected amino acids with oxygen isotopes.</a> Org. Lett. 12 (1), 104-106 (2010).</li><li>Bonke, G., Vedel, L., Witt, M., Jaroszewski, J. W., Olsen, C. A., Franzyk, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Dimeric+building+blocks+for+solid-phase+synthesis+of+&#945;,-peptide-&#946;,-peptoid+chimeras.">Dimeric building blocks for solid-phase synthesis of &#945;,-peptide-&#946;,-peptoid chimeras.</a> Synthesis. 2008 (15), 2381-2390 (2008).</li></ol>

Yazarlar ifşa hiçbir şey yok.

Yukarıda tarif edilen protokol iki kritik adımları hafif pH koşulları ve bu izole edilmiş amino asidin daha sonra Fmoc koruma altında bir Ni-Schiff baz kompleksine bir amino asit omurgasına izole edilmesini kolaylaştırmak için yeteneği yararlıdır. İlk adım kompleksinden amino asidin salınmasını kolaylaştırmak için EDTA ihtiva eden bir DMF / su çözeltisi karıştırılarak içermektedir. Kalıntı, karmaşık ya da organik yan ürünler kolaylıkla ekstre ile temizlenebilir. Bu protokol, ikinci a?...

Doğada bulunan yirmi doğal olarak meydana gelen amino asitler aşağıdaki farklı doğal olmayan amino asitler (UAA) &#39;ın yatak yan zincirleri geniş bir uygulama aralığı içinde faydalı oldukları bulunmuştur. Bu, UAA &#39;s sentezi, ancak, yan zincirlerin yapı ve amino asit omurgasına stereokimyasına bağlı olarak zor olabilir. Bir nikel Schiff baz kompleksine bağlamında glisin CH bond aktivasyon a, β-diamino asitler 1 ve 2 ya da heterosiklik yan zincirler fluorinatlı UAA en yatak içeren amino asit türevlerinin çeşitli üretmek için kullanılmıştır. 3 Doğal olmayan yan zincirler eklenmesinden sonra, UAA en tipik haliyle hidroklorik asit 4 geri akış ile Schiff baz kompleksine çıkarılır ve daha sonra iyon değişimi kromatografisi kullanılarak izole edilir işlevselleştirilmiş. genellikle verimli olsa da, bu protokol bir üretirKatı faz peptit sentezi ile (SPPS) içinde kullanım için uygun olabilir amino asitlik. SPPS doğası bozulmamış bu koruyucu gruplarla UAA en izolasyonunu önler asit-labil yan zincir koruma gruplarının varlığını ve tipik Ni-Schiff bazı ayrışma koşulları güçlü asidik doğası gerektirir. Bildiğimiz kadarıyla, tek alternatif ayrıştırma yöntemi bildirilmiştir: etilendiamintetraasetik asit (EDTA) ve hidrazin kullanılması, yüksek sıcaklıklarda, kendilerini bazı yan zincir gibi ftalimitler gibi koruma grupları için uygun olmayabilir 5 koşullar, bu. <img alt="Şekil 1" src="/files/ftp_upload/55677/55677fig1.jpg" /> Şekil 1: Ni2 +, PBP ve Glisin (Giy) Ni PBP-Gly sentezi. <a href="http://ecsource.jove.com/files/ftp_upload/55677/55677fig1large.jpg" target="_blank">Bu rakamın büyük halini görmek için buraya tıklayın.</a> </a&gt; Burada, Ni-PBP-Gly (Şekil 1), bir Ni-Schiff baz kompleksine hidrolizi için bir yöntem sunulmaktadır. Ni2 +, glisin ve piridin-2-karboksilik asit (2-benzoil-fenil) -amid (PBP), 6 türetilmiş Bu kompleks, UAA en çeşitli sentezi için yararlı bir platform olduğu gösterilmiştir ve kolay bir edilmiştir erişilebilen iki aşamalı bir sentetik yol kullanılarak. Bu kompleksin 7 sentezi literatürde-konmuşturlar yüksek verimde olan. 6 Sonuçlarımız, aşağıda tarif edilen UAA en taşıyan asit kararsız yan zincir koruma grupları ile kullanım için uygun olan nötr pH koşulları hafif asidik EDTA kullanılarak hidroliz şartları uygulanabilirliğini göstermektedir. Hidrolizi takiben, elde edilen sulu çözelti, izole edilebilir ve Fmoc-korumalı amino asit elde standart Fmoc koruma koşullarında (Şekil 2) hemen tabi tutuldu. Şekil 2: Hidroliz ve Ni-PBP-Gly İzole bir şekilde bir Amino Asit Fmoc-koruma. Reaksiyon koşulları: i. EDTA (12 eşdeğer), pH 4.5; ii. pH 7&#39;ye etil asetat yıkama ve ayarlanması; iii. Fmoc-OSu (1 eşdeğer), NaHCO 3 (2 eşdeğ) eklenir. <a href="http://ecsource.jove.com/files/ftp_upload/55677/55677fig2large.jpg" target="_blank">Bu rakamın büyük halini görmek için buraya tıklayın.</a>

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>Ni-PBP-Gly</td>
			<td></td>
			<td></td>
			<td>Synthesized from published protocol</td>
		</tr>
		<tr>
			<td>DMF</td>
			<td>Fisher</td>
			<td>D119-4</td>
			<td></td>
		</tr>
		<tr>
			<td>EDTA</td>
			<td>Fisher</td>
			<td>S311-100</td>
			<td></td>
		</tr>
		<tr>
			<td>Dichloromethane</td>
			<td>Acros</td>
			<td>AC610050040</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium Bicarbonate</td>
			<td>Fisher</td>
			<td>S233-500</td>
			<td></td>
		</tr>
		<tr>
			<td>Fmoc-OSu</td>
			<td>Chem-Impex</td>
			<td>&#34;00147&#34;</td>
			<td></td>
		</tr>
		<tr>
			<td>Dioxane</td>
			<td>Fisher</td>
			<td>D111-500</td>
			<td></td>
		</tr>
		<tr>
			<td>Hydrochloric Acid</td>
			<td>Fisher</td>
			<td>A144-500</td>
			<td></td>
		</tr>
		<tr>
			<td>Ethyl Acetate</td>
			<td>Acros</td>
			<td>AC610060040</td>
			<td></td>
		</tr>
		<tr>
			<td>Magnesium Sulfate</td>
			<td>Fisher</td>
			<td>M65-500</td>
			<td></td>
		</tr>
		<tr>
			<td>ZEOPrep 60ECO Silica Gel</td>
			<td>ZEOChem</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Hexanes</td>
			<td>Fisher</td>
			<td>3200250.650.443</td>
			<td></td>
		</tr>
		<tr>
			<td>Chromatography Column</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>pH Test Strips</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Rotary Evaporator</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>250 mL Separatory Funnel</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>250 mL Round Bottom Flask</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Stir Bar</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Stir Plate</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
	</tbody>
</table>

hydrolysis of a ni-schiff-base complex using conditions suitable for retention of acid-labile protecting groups

Doğal olmayan amino asitler, doğada yaygın şekilde görülmeyen yan zincir işlevsellikleri ihtiva eden bir amino asit, giderek sentetik peptid dizileri bulunur. Bazı doğal olmayan amino asitlerin sentezi genellikle nikel katyon ile stabilize edilmiş bir Schiff-baz içeren bir ön-madde kullanımını içerir. Doğal olmayan yan zincirler, bu Schiff-baz kompleksi içinde bulunan bir amino asit omurgası üzerinde monte edilebilir. Elde edilen doğal olmayan amino asit, daha sonra, tipik olarak kuvvetli asitli çözelti içinde geri akış kullanılarak, Schiff-baz bu kompleks ile hidrolizi ile izole edilebilir. doğal olmayan amino asitler mikrodalga destekli bir katı-faz peptid sentezi kullanılmak için bu yüksek derecede asidik koşullar asit kararsız yan zincir koruma grupları, gerekli kaldırabilir. Bu çalışmada, etkin bir hidroliz ve bir Ni-Schiff baz kompleksine izole edilen bir amino asidin daha sonra Fmoc koruma sunmaktadır. Bu çalışmada sunulan Hidroliz koşulları asit-labil s tutma için uygun olanide-zincir koruma gruplarını ve doğal olmayan amino asit çeşitli substratlar için adapte edilebilir.

Bu sert pH koşullarında gerek kalmadan Schiff-baz etkin bir sulu hidroliz izin verebilir Ni PBP-Gly kompleksinden Ni + 2 &#39;nin bu kaldırılmasını hipotezini kurduk. EDTA, ucuz ve iyi incelenmiş şelatlayıcı madde olduğu için, 10 biz Ni PBP-Gly bir çözeltiye EDTA ilavesi ve böylece kompleksin hidrolizi teşvik Ni + 2 iyonlarının çelasyonunu kolaylaştırmak varsaydık. <p class="jove_content" fo:keep-together.within-page...

Watch this Scientific Journal Video about Hydrolysis of a Ni-Schiff-Base Complex Using Conditions Suitable for Retention of Acid-labile Protecting Groups at JoVE.com

Hydrolysis of a Ni-Schiff-Base Complex Using Conditions Suitable for Retention of Acid-labile Protecting Groups

Burada, etkili bir hidroliz ve bir Ni-Schiff-baz kompleksi izole edilen bir amino asidin daha sonra Fmoc koruma sunmaktadır. asit-labil yan zincir koruma gruplarının tutma gerekli olduğunda burada sunulan Hidroliz koşulları kullanılmak üzere uygundur. Bu teknik, doğal olmayan amino asit çeşitli substratlar için adapte edilebilir.

Koruma Grupları aside dayanıksız Saklanmasına için uygun bir Ni-Schiff-Base hidrolizi Kompleksi kullanma Koşullar

Unnatural amino acids, amino acids containing side-chain functionalities not commonly seen in nature, are increasingly found in synthetic peptide ...

hydrolysis-ni-schiff-base-complex-using-conditions-suitable-for

Research

JoVE Journal

Biochemistry

9.6K Görüntüleme.  Slippery Rock University.  Burada, etkili bir hidroliz ve bir Ni-Schiff-baz kompleksi izole edilen bir amino asidin daha sonra Fmoc koruma sunmaktadır. asit-labil yan zincir koruma gruplarının tutma gerekli olduğunda burada sunulan Hidroliz koşulları kullanılmak üzere uygundur. Bu teknik, doğal olmayan amino asit çeşitli substratlar için adapte edilebilir. 

Video: Hydrolysis of a Ni-Schiff-Base Complex Using Conditions Suitable for Retention of Acid-labile Protecting Groups

Protein Complex Affinity Capture from Cryomilled Mammalian Cells

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

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

Cryomilled memeli hücrelerinden protein kompleksi olan ele geçirme kapasitesini

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

Biyokimya

A Method for Measuring Metabolism in Sorted Subpopulations of Complex Cell Communities Using Stable Isotope Tracing

Mammalian cell types exhibit specialized metabolism, and there is ample evidence that various co-existing cell types engage in metabolic cooperation. Moreover, even cultures of a single cell type may contain cells in distinct metabolic states, such as resting or cycling cells. Methods for measuring metabolic activities of such subpopulations are valuable tools for understanding cellular metabolism. Complex cell populations are most commonly separated using a cell sorter, and subpopulations isolated by this method can be analyzed by metabolomics methods. However, a problem with this approach is that the cell sorting procedure subjects cells to stresses that may distort their metabolism.
To overcome these issues, we reasoned that the mass isotopomer distributions (MIDs) of metabolites from cells cultured with stable isotope-labeled nutrients are likely to be more stable than absolute metabolite concentrations, because MIDs are formed over longer time scales and should be less affected by short-term exposure to cell sorting conditions. Here, we describe a method based on this principle, combining cell sorting with liquid chromatography-high resolution mass spectrometry (LC-HRMS). The procedure involves analyzing three types of samples: (1) metabolite extracts obtained directly from the complex population; (2) extracts of "mock sorted" cells passed through the cell sorter instrument without gating any specific population; and (3) extracts of the actual sorted populations. The mock sorted cells are compared against direct extraction to verify that MIDs are indeed not altered by the cell sorting procedure itself, prior to analyzing the actual sorted populations. We show example results from HeLa cells sorted according to cell cycle phase, revealing changes in nucleotide metabolism.

This article describes a method for studying cellular metabolism in complex communities of multiple cell types, using a combination of stable isotope tracing, cell sorting to isolate specific cell types, and mass spectrometry.

Kararlı İzotop izlemeyi kullanma Kompleks Hücre Toplulukları Sıralama alt popülasyonlar Metabolizma Ölçme Bir Yöntem

Mammalian cell types exhibit specialized metabolism, and there is ample evidence that various co-existing cell types engage in metabolic cooperation. ...

Preparation of Giant Vesicles Encapsulating Microspheres by Centrifugation of a Water-in-oil Emulsion

The constructive biology and the synthetic biology approach to creating artificial life involve the bottom-up assembly of biological or nonbiological materials. Such approaches have received considerable attention in research on the boundary between living and nonliving matter and have been used to construct artificial cells over the past two decades. In particular, Giant Vesicles (GVs) have often been used as artificial cell membranes. In this paper, we describe the preparation of GVs encapsulating highly packed microspheres as a model of cells containing highly condensed biomolecules. The GVs were prepared by means of a simple water-in-oil emulsion centrifugation method. Specifically, a homogenizer was used to emulsify an aqueous solution containing the materials to be encapsulated and an oil containing dissolved phospholipids, and the resulting emulsion was layered carefully on the surface of another aqueous solution. The layered system was then centrifuged to generate the GVs. This powerful method was used to encapsulate materials ranging from small molecules to microspheres.

Giant vesicles containing highly packed micrometer-sized components are useful cell models. The water-in-oil emulsion centrifugation method is a simple, powerful tool for the preparation of giant vesicles with encapsulated materials.

bir su-içinde-yağ emülsiyonu santrifüj Dev veziküller Kapsüllenen Mikrokürelerin hazırlanması

The constructive biology and the synthetic biology approach to creating artificial life involve the bottom-up assembly of biological or nonbiological ...

A Modified Yeast-one Hybrid System for Heteromeric Protein Complex-DNA Interaction Studies

Over the years, the yeast one-hybrid assay has proven to be an important technique for the identification and validation of physical interactions between proteins such as transcription factors (TFs) and their DNA target. The method presented here utilizes the underlying concept of the Y1H but is modified further to study and validate protein complexes binding to their target DNA. Hence, it is referred to as the modified yeast one-hybrid (Y1.5H) assay. This assay is cost effective and can be easily performed in a regular laboratory setting. Albeit using a heterologous system, the described method could be a valuable tool to test and validate the heteromeric protein complex binding to their DNA target(s) for functional genomics in any system of study, especially plant genomics.

The modified yeast one-hybrid assay described here is an extension of the classical yeast one-hybrid (Y1H) assay to study and validate the heteromeric protein complex-DNA interaction in a heterologous system for any functional genomics study.

Heteromerik Protein Kompleksi-DNA Etkileşim Çalışmaları İçin Modifiye Maya-Bir Hibrid Sistem

Over the years, the yeast one-hybrid assay has proven to be an important technique for the identification and validation of physical interactions between ...

Biochemical and Structural Characterization of the Carbohydrate Transport Substrate-binding-protein SP0092

Development of new antimicrobials and vaccines for Streptococcus pneumoniae (pneumococcus) are necessary to halt the rapid rise in multiple resistant strains. Carbohydrate substrate binding proteins (SBPs) represent viable targets for the development of protein-based vaccines and new antimicrobials because of their extracellular localization and the centrality of carbohydrate import for pneumococcal metabolism, respectively. Described here is a rationalized integrated protocol to carry out a comprehensive characterization of SP0092, which can be extended to other carbohydrate SBPs from the pneumococcus and other bacteria. This procedure can aid the structure-based design of inhibitors for this class of proteins. Presented in the first part of this manuscript are protocols for biochemical analysis by thermal shift assay, multi angle light scattering (MALS), and size exclusion chromatography (SEC), which optimize the stability and homogeneity of the sample directed to crystallization trials and so enhance the probability of success. The second part of this procedure describes the characterization of the SBP crystals using a tunable wavelength anomalous diffraction synchrotron beamline, and data collection protocols for measuring data that can be used to resolve the crystallized protein structure.

A streamlined protocol for performing an extensive biochemical and structural characterization of a carbohydrate substrate binding protein from Streptococcus pneumoniae is presented.

Karbonhidrat taşıma substrat-bağlayıcı-protein SP0092 biyokimyasal ve yapısal karakterizasyonu

Development of new antimicrobials and vaccines for Streptococcus pneumoniae (pneumococcus) are necessary to halt the rapid rise in multiple resistant ...

Toeprinting Analysis of Translation Initiation Complex Formation on Mammalian mRNAs

Translation initiation is the rate-limiting step of protein synthesis and represents a key point at which cells regulate their protein output. Regulation of protein synthesis is the key to cellular stress-response, and dysregulation is central to many disease states, such as cancer. For instance, although cellular stress leads to the inhibition of global translation by attenuating cap-dependent initiation, certain stress-response proteins are selectively translated in a cap-independent manner. Discreet RNA regulatory elements, such as cellular internal ribosome entry sites (IRESes), allow for the translation of these specific mRNAs. Identification of such mRNAs, and the characterization of their regulatory mechanisms, have been a key area in molecular biology. Toeprinting is a method for the study of RNA structure and function as it pertains to translation initiation. The goal of toeprinting is to assess the ability of in vitro transcribed RNA to form stable complexes with ribosomes under a variety of conditions, in order to determine which sequences, structural elements, or accessory factors are involved in ribosome binding&#8212;a pre-cursor for efficient translation initiation. Alongside other techniques, such as western analysis and polysome profiling, toeprinting allows for a robust characterization of mechanisms for the regulation of translation initiation.

Toeprinting aims to measure the ability of in vitro transcribed RNA to form translation initiation complexes with ribosomes under a variety of conditions. This protocol describes a method for toeprinting mammalian RNA and can be used to study both cap-dependent and IRES-driven translation.

Çeviri başlatma karmaşık oluşumu memeli mRNA'ların Toeprinting analizi

Translation initiation is the rate-limiting step of protein synthesis and represents a key point at which cells regulate their protein output. Regulation ...

Medium Preparation for the Cultivation of Microorganisms under Strictly Anaerobic/Anoxic Conditions

In contrast to aerobic organisms, strictly anaerobic microorganisms require the absence of oxygen and usually a low redox potential to initiate growth. As oxygen is ubiquitous in air, retaining O2-free conditions during all steps of cultivation is challenging but a prerequisite for anaerobic culturing. The protocol presented here demonstrates the successful cultivation of an anaerobic mixed culture derived from a biogas plant using a simple and inexpensive method. A precise description of the entire anoxic culturing process is given including media preparation, filling of cultivation flasks, supplementation with redox indicator and reducing agents to provide low redox potentials as well as exchanging the headspace to keep media free from oxygen. Furthermore, a detailed overview of aseptically inoculating gas tight serum flasks (by using sterile syringes and needles) and suitable incubation conditions is provided. The present protocol further deals with gas and liquid sampling for subsequent analyses regarding gas composition and volatile fatty acid concentrations using gas chromatography (GC) and high performance liquid chromatography (HPLC), respectively, and the calculation of biogas and methane yield considering the ideal gas law.

As obligate anaerobic organisms are unable to grow upon oxygen exposure, the use of anaerobic culturing techniques is indispensable. Here, we demonstrate a simple and effective method to cultivate a mixed culture derived from a biogas plant from media preparation to gas and volatile fatty acid quantification.

Kesinlikle Anaerobik/Anoksik Koşullarda Mikroorganizmaların Yetiştirilmesi için Orta Hazırlık

In contrast to aerobic organisms, strictly anaerobic microorganisms require the absence of oxygen and usually a low redox potential to initiate growth. As ...

Crystallization and Structural Determination of an Enzyme:Substrate Complex by Serial Crystallography in a Versatile Microfluidic Chip

The preparation of well diffracting crystals and their handling before their X-ray analysis are two critical steps of biocrystallographic studies. We describe a versatile microfluidic chip that enables the production of crystals by the efficient method of counter-diffusion. The convection-free environment provided by the microfluidic channels is ideal for crystal growth and useful to diffuse a substrate into the active site of the crystalline enzyme. Here we applied this approach to the CCA-adding enzyme of the psychrophilic bacterium Planococcus halocryophilus in the presented example. After crystallization and substrate diffusion/soaking, the crystal structure of the enzyme:substrate complex was determined at room temperature by serial crystallography and the analysis of multiple crystals directly inside the chip. The whole procedure preserves the genuine diffraction properties of the samples because it requires no crystal handling.

A versatile microfluidic device is described that enables the crystallization of an enzyme using the counter-diffusion method, the introduction of a substrate in the crystals by soaking, and the 3D structure determination of the enzyme:substrate complex by a serial analysis of crystals inside the chip at room temperature.

Çok Yönlü Bir Mikroakışkan Çipte Seri Kristalografi ile Bir Enzim:Substrat Kompleksinin Kristalizasyonu ve Yapısal Belirlenmesi

The preparation of well diffracting crystals and their handling before their X-ray analysis are two critical steps of biocrystallographic studies. We ...

Complementation of Splicing Activity by a Galectin-3 - U1 snRNP Complex on Beads

Classic depletion-reconstitution experiments indicate that galectin-3 is a required splicing factor in nuclear extracts. The mechanism of incorporation of galectin-3 into the splicing pathway is addressed in this paper. Sedimentation of HeLa cell nuclear extracts on 12%-32% glycerol gradients yields fractions enriched in an endogenous ~10S particle that contains galectin-3 and U1 snRNP. We now describe a protocol to deplete nuclear extracts of U1 snRNP with concomitant loss of splicing activity. Splicing activity in the U1-depleted extract can be reconstituted by the galectin-3 - U1 snRNP particle trapped on agarose beads covalently coupled with anti-galectin-3 antibodies. The results indicate that the galectin-3 - U1 snRNP - pre-mRNA ternary complex is a functional E complex leading to intermediates and products of the splicing reaction and that galectin-3 enters the splicing pathway through its association with U1 snRNP. The scheme of using complexes affinity- or immuno-selected on beads to reconstitute splicing activity in extracts depleted of a specific splicing factor may be generally applicable to other systems.

This article describes the experimental procedures for (a) depletion of U1 snRNP from nuclear extracts, with concomitant loss of splicing activity; and (b) reconstitution of splicing activity in the U1-depleted extract by galectin-3 - U1 snRNP particles bound to beads covalently coupled with anti-galectin-3 antibodies.

Boncuklar Üzerinde Galectin-3 - U1 snRNP Kompleksi ile Birleştirme Etkinliğinin Tamamlayıcısı

Classic depletion-reconstitution experiments indicate that galectin-3 is a required splicing factor in nuclear extracts. The mechanism of incorporation of ...

RIBO-seq in Bacteria: a Sample Collection and Library Preparation Protocol for NGS Sequencing

The ribosome profiling technique (RIBO-seq) is currently the most effective tool for studying the process of protein synthesis in vivo. The advantage of this method, in comparison to other approaches, is its ability to monitor translation by precisely mapping the position and number of ribosomes on a mRNA transcript.
In this article, we describe the consecutive stages of sample collection and preparation for RIBO-seq method in bacteria, highlighting the details relevant to the planning and execution of the experiment.
Since the RIBO-seq relies on intact ribosomes and related mRNAs, the key step is rapid inhibition of translation and adequate disintegration of cells. Thus, we suggest filtration and flash-freezing in liquid nitrogen for cell harvesting with an optional pretreatment with chloramphenicol to arrest translation in bacteria. For the disintegration, we propose grinding frozen cells with mortar and pestle in the presence of aluminum oxide to mechanically disrupt the cell wall. In this protocol, sucrose cushion or a sucrose gradient ultracentrifugation for monosome purification is not required. Instead, mRNA separation using polyacrylamide gel electrophoresis (PAGE) followed by the ribosomal footprint excision (28-30 nt band) is applied and provides satisfactory results. This largely simplifies the method as well as reduces the time and equipment requirements for the procedure. For library preparation, we recommend using the commercially available small RNA kit for Illumina sequencing from New England Biolabs, following manufacturer&#39;s guidelines with some degree of optimization.
The resulting cDNA libraries present appropriate quantity and quality required for next generation sequencing (NGS). Sequencing of the libraries prepared according to the described protocol results in 2 to 10 mln uniquely mapped reads per sample providing sufficient data for comprehensive bioinformatic analysis. The protocol we present is quick and relatively easy and can be performed with standard laboratory equipment.

Here we describe the stages of sample collection and preparation for RIBO-seq in bacteria. Sequencing of the libraries prepared according to these guidelines results in sufficient data for comprehensive bioinformatic analysis. The protocol we present is simple, uses standard laboratory equipment and takes seven days from lysis to obtaining libraries.

Bakterilerde RIBO-seq: NGS Dizilimi için Örnek Toplama ve Kütüphane Hazırlama Protokolü

The ribosome profiling technique (RIBO-seq) is currently the most effective tool for studying the process of protein synthesis in vivo. The advantage of ...