Name: creating and applying a reference to facilitate the discussion and classification of proteins in a diverse group
Uploaded: 2017-08-16T14:00:00
Description: Watch this Scientific Journal Video about Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group at JoVE.com

Igangværende tardigrade antimikrobielle peptid forskning er støttet af murene finansiering fra Midwestern Universitet Office of Research og sponsorerede programmer (ORSP). ORSP spillede ingen rolle i undersøgelse design, dataindsamling, analyse, fortolkning eller manuskript forberedelse.

1. afgøre definerer funktionerne i gruppen Protein af interesse <ol><li>Consult tidligere publikationer til at afgøre, om der er enighed om de funktioner, der er nødvendige for at blive betragtet som en del af gruppen. Vær opmærksom på eventuelle uoverensstemmelser eller forskelle i opfattelse mellem forskningsgrupper, og omfatter egenskaber, der kan tjene til at adskille en undergruppe af en anden.</li>
	<li>Hvis tidligere litteratur ikke omhandler definerende karakteristik, bruge sekvenser, der betragtes som r...

<ol>
	<li>Matsuyama, K., Natori, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Purification+of+Three+Antibacterial+Proteins+from+the+Culture+Medium+of+NIH-Sape-4,+an+Embryonic+Cell+Line+of+Sarcophaga+peregrina.">Purification of Three Antibacterial Proteins from the Culture Medium of NIH-Sape-4, an Embryonic Cell Line of Sarcophaga peregrina.</a> J Biol Chem. 263 (32), 17112-17116 (1988).</li><li>Lambert, J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Insect+immunity:+Isolation+from+immune+blood+of+the+dipteran+Phormia+terranovae.+of+two+insect+antibacterial+peptides+with+sequence+homology+to+rabbit+lung+macrophage+bactericidal+peptides.">Insect immunity: Isolation from immune blood of the dipteran Phormia terranovae. of two insect antibacterial peptides with sequence homology to rabbit lung macrophage bactericidal peptides.</a> PNAS. 86 (262-266), (1989).</li><li>Dimarcq, J. -. L., Bulet, P., Hetru, C., Hoffmann, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cysteine-rich+antimicrobial+peptides+in+invertebrates.">Cysteine-rich antimicrobial peptides in invertebrates.</a> Biopolymers. 47, 465-477 (1998).</li><li>Shafee, T. M. A., Lay, F. T., Hulett, M. D., Anderson, M. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+Defensins+Consist+of+Two+Independent,+Convergent+Protein+Superfamilies.">The Defensins Consist of Two Independent, Convergent Protein Superfamilies.</a> Mol Biol Evol. 33 (9), 2345-2356 (2016).</li><li>Zhu, S., Gao, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Nematode-derived+drosomycin-type+antifungal+peptdies+provide+evidence+for+plant-to-ecdysozoan+horizontal+transfer+of+a+disease+resistance+gene.">Nematode-derived drosomycin-type antifungal peptdies provide evidence for plant-to-ecdysozoan horizontal transfer of a disease resistance gene.</a> Nat Commun. 5, (2014).</li><li>Zhu, S., Gao, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Evolutionary+origin+of+b-defensins.">Evolutionary origin of b-defensins.</a> Dev. Comp. Immunol. 39, 79-84 (2013).</li><li>Bonmatin, J. -. M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Two-dimensional+1H+NMR+study+of+recombinant+insect+defensin+A+in+water:+Resonance+assignments,+secondary+structure+and+global+folding.">Two-dimensional 1H NMR study of recombinant insect defensin A in water: Resonance assignments, secondary structure and global folding.</a> J Biomol NMR. 2 (3), 235-256 (1992).</li><li>Cornet, B., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Refined+three-dimensional+solution+structure+of+insect+defensin+A.">Refined three-dimensional solution structure of insect defensin A.</a> Structure. 3 (5), 435-448 (1995).</li><li>Murzin, A. G., Brenner, S. E., Hubbard, T., Chothia, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=SCOP:+a+structural+classification+of+proteins+database+for+the+investigations+of+sequences+and+structures.">SCOP: a structural classification of proteins database for the investigations of sequences and structures.</a> J Mol Biol. 247, 536-540 (1995).</li><li>Sillitoe, I., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=CATH:+comprehensive+structural+and+functional+annotations+for+genome+sequences.">CATH: comprehensive structural and functional annotations for genome sequences.</a> Nucleic Acids Res. 43, 376-381 (2015).</li><li>Lam, S. D., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Gene3D:+expanding+the+utility+of+domain+assignments.">Gene3D: expanding the utility of domain assignments.</a> Nucleic Acids Res. 44, 404-409 (2016).</li><li>Tarr, D. E. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Establishing+a+reference+array+for+the+CS-ab+superfamily+of+defensive+peptides.">Establishing a reference array for the CS-ab superfamily of defensive peptides.</a> BMC Res Notes. 9, 490 (2016).</li><li>Shafee, T. M. A., Robinson, A. J., van der Weerden, N., Anderson, M. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Structural+homology+guided+alignment+of+cysteine+rich+proteins.">Structural homology guided alignment of cysteine rich proteins.</a> SpringerPlus. 5 (27), (2016).</li><li>Altschul, S. F., Gish, W., Miller, W., Myers, E. W., Lipman, D. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Basic+Local+Alignment+Search+Tool.">Basic Local Alignment Search Tool.</a> J Mol Biol. 215 (3), 403-410 (1990).</li><li>Duckert, P., Brunak, S., Blom, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Prediction+of+proprotein+convertase+cleavage+sites.">Prediction of proprotein convertase cleavage sites.</a> Protein Eng Des Sel. 17 (1), 107-112 (2004).</li><li>Petersen, T. N., Brunak, S., von Heijne, G., Nielsen, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=SignalP+4.0:discriminating+signal+peptides+from+transmembrane+regions.">SignalP 4.0:discriminating signal peptides from transmembrane regions.</a> Nat Methods. 8, 785-786 (2011).</li><li>Kobayashi, Y., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+cysteine-stabilized+a-helix:+A+common+structural+motif+of+ion-channel+blocking+neurotoxic+peptides.">The cysteine-stabilized a-helix: A common structural motif of ion-channel blocking neurotoxic peptides.</a> Biopolymers. 31, 1213-1220 (1991).</li><li>Gao, B., del Carmen Rodriguez, M., Lanz-Mendoza, H., Zhu, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=AdDLP,+a+bacterial+defensin-like+peptide,+exhibits+anti-Plasmodium.+activity.">AdDLP, a bacterial defensin-like peptide, exhibits anti-Plasmodium. activity.</a> Biochem Biophys Res Commun. 387, 393-398 (2009).</li><li>Tamura, K., Stecher, G., Peterson, D., Filipski, A., Kumar, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=MEGA6:+Molecular+Evolutionary+Genetics+Analysis.">MEGA6: Molecular Evolutionary Genetics Analysis.</a> Mol Biol Evol. 30 (12), 2725-2729 (2013).</li><li>Edgar, R. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=MUSCLE:+multiple+sequence+alignment+with+high+accuracy+and+high+throughput.">MUSCLE: multiple sequence alignment with high accuracy and high throughput.</a> Nucleic Acids Res. 32 (5), 1792-1797 (2004).</li><li>Ronquist, F., Huelsenbeck, J. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=MrBayes+3:+Bayesian+phylogenetic+inference+under+mixed+models.">MrBayes 3: Bayesian phylogenetic inference under mixed models.</a> Bioinformatics. 19 (12), 1572-1574 (2003).</li><li>Altschul, S. F., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Gapped+BLAST+and+PSI-BLAST:+a+new+generation+of+protein+database+search+programs.">Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.</a> Nucleic Acids Res. 25 (17), 3389-3402 (1997).</li><li>Zhang, Z., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Protein+sequence+similarity+searches+using+patterns+as+seeds.">Protein sequence similarity searches using patterns as seeds.</a> Nucleic Acids Res. 26 (17), 3986-3990 (1998).</li></ol>

Kriterier til at navngive et protein inden for en gruppe skal være klart, men det er ikke altid tilfældet. Sekvenser, der har CS-αβ fold har været studeret i mange laboratorier ved hjælp af en række forskellige organismer, hvilket resulterer i forskellige systemer i nomenklatur, samt forskellige niveauer af karakterisering. Forsøger at indføre en helt ny nomenklatur er ikke rimeligt og ville resultere i en stor forvirring, når consulting tidligere litteratur. Reference nummerering system kan bruges ud over navn...

Et protein navn bør afspejle karakteristika og forholdet til andre proteiner. Desværre navne tildeles generelt på tidspunktet for opdagelse, og forskningen fortsætter og forståelse af en større sammenhæng kan ændre. Dette kan føre til flere navne, hvis et protein blev selvstændigt identificeret af mere end én lab, at ændringer i nomenklatur eller i de kendetegn, menes at være endelige, når du tildeler navnet og navnet ikke længere tilstrækkelig differentiering af protein fra andre.
Hvirvelløse defensins give et godt eksempel på degeneration i nomenklatur og klassificering. De første hvirvelløse defensins blev rapporteret fra insekter, og det navn "insekt defensin" blev foreslået baseret på den opfattede homologi til pattedyr defensins1,2. Sigt defensin bruges stadig, selv om det er nu klart, at hvirvelløse og pattedyr defensins deler ikke en fælles forfader3,4. Afhængigt af arten, kan en hvirvelløse "defensin" har seks eller otte cysteines, (der udgør tre eller fire disulfid obligationer) og en række antimikrobielle aktiviteter. At komplicere situationen, proteiner med samme egenskaber som defensins ikke er altid kaldt "defensins," som den for nylig påviste cremycins fra Caenorhabditis remanei5. Derudover er hvirvelløse store defensins mere tilbøjelige til at være evolutionært relateret til hvirveldyr β-defensins end til andre hvirvelløse defensins6. Trods dette stole forskere undertiden på den navnet "defensin" ved fastlæggelsen af, hvilke sekvenser bør inkluderes i analyserne.
Strukturelle undersøgelser afslørede ligheden mellem insekt defensins og scorpion toksiner7og CS-αβ fold blev senere etableret som den strukturelle kendetegn for insekt defensins8. Denne fold definerer scorpion toksin-lignende (CS-αβ) superfamilien i strukturelle klassificering af proteiner (SCOP) database9, som i øjeblikket omfatter fem familier: insekt defensins, kortkædede scorpion toksiner, langkædede scorpion toksiner, MGD-1 (fra en bløddyr), og plante defensins. Denne superfamilien er synonymt med den seneste beskrevet cis-defensins4 og superfamilien 3.30.30.10 i CATH-genet 3D database10,11. Undersøgelser fra en række af hvirvelløse taxa, planter og svampe vis at navnene på proteiner, der indeholder denne fold ikke klart er relateret til cystein nummer eller limning mønster, antimikrobiel aktivitet eller evolutionær historie12.
Manglen sammenhæng og klare kriterier gør det udfordrende at navngive og klassificere nyligt identificerede sekvenser i denne superfamilien. En væsentlig hindring for sammenligning af proteiner i denne superfamilien er, at cysteines er nummereret med hensyn til hver enkelt sekvens (den første cystein i hver sekvens er C1) med ingen måde at tage højde for den strukturelle rolle. Det betyder, at kun sekvenser med det samme antal cysteines kan sammenlignes. Der er lille sekvens bevarelse end cysteines danner CS-αβ-fold, hvilket vanskeliggør linjeføringer og fylogenetiske analyser. Ved at udvikle et nummersystem, der prioriterer strukturelle træk, kan superfamilien sekvenser mere nemt sammenlignet og justeret. Bevarede funktioner, som de definerer undergrupper, kan visualiseres hurtigt, og nye sekvenser mere let kan placeres i den relevante kontekst.
Dette papir bruger regneark software (fx Excel) til at generere en reference nummerering system for CS-αβ superfamilien. Det viser hvordan dette tydeliggør sammenligninger mellem sekvenser og gælder det nye CS-αβ sekvenser identificeret fra Biogeografi. Bruger CS-αβ superfamilien som et eksempel, var protokollen skrevet at yde vejledning, når du bruger sekvenser af interesse; Det er dog ikke beregnet til at være specifik for denne superfamilien eller cystein-rige sekvenser. Denne metode vil sandsynligvis være mest nyttig for grupper af proteiner, der har været forsket uafhængigt i divergerende taxa og/eller har lille samlede sekvens homologi, med diskrete egenskaber, der ikke kan genkendes nemt af Molekylær analyse software. Denne metode kræver nogle på forhånd beslutninger om vigtige funktioner, så det vil være af begrænset nytte, hvis ingen vigtige funktioner er blevet identificeret. Det primære mål er at vise, hvordan en simpel visualisering af sekvens relationer kan opnås. Dette kan så bruges til at informere sequence alignment og analyse, men hvis justering og analyse er de primære mål, en stregkode metode ville være et egnet alternativ, som har mere kapacitet til automatisering13. Den nuværende metode viser funktionerne af hver peptid i en lineær form, så det ikke vil være nyttigt for den direkte visualisering af 3D-struktur.

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			<td height="42" style="width:216px;height:42px;">BLAST webpage</td>
			<td style="width:71px;"></td>
			<td style="width:119px;"></td>
			<td style="width:167px;">https://blast.ncbi.nlm.nih.gov/Blast.cgi</td>
		</tr>
		<tr height="21">
			<td height="21" style="width:216px;height:21px;">EditSeq (Lasergene suite)</td>
			<td style="width:71px;">DNASTAR</td>
			<td style="width:119px;"></td>
			<td style="width:167px;">https://www.dnastar.com/t-allproducts.aspx</td>
		</tr>
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			<td height="21" style="width:216px;height:21px;">Excel 2013</td>
			<td style="width:71px;">Microsoft</td>
			<td style="width:119px;"></td>
			<td style="width:167px;"></td>
		</tr>
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			<td height="63" style="width:216px;height:63px;">FigTree</td>
			<td style="width:71px;"></td>
			<td style="width:119px;"></td>
			<td style="width:167px;">&#160;http://tree.bio.ed.ac.uk/software/figtree/</td>
		</tr>
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			<td height="21" style="width:216px;height:21px;">MEGA</td>
			<td style="width:71px;"></td>
			<td style="width:119px;"></td>
			<td>www.megasoftware.net</td>
		</tr>
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			<td height="42" style="width:216px;height:42px;">MrBayes</td>
			<td style="width:71px;"></td>
			<td style="width:119px;"></td>
			<td style="width:167px;">http://mrbayes.sourceforge.net/</td>
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			<td height="42" style="width:216px;height:42px;">SCOP database</td>
			<td style="width:71px;"></td>
			<td style="width:119px;"></td>
			<td style="width:167px;">http://scop.mrc-lmb.cam.ac.uk/scop/</td>
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creating and applying a reference to facilitate the discussion and classification of proteins in a diverse group

Relaterede proteiner, der er blevet undersøgt i forskellige laboratorier ved hjælp af varierende organismer kan mangle et ensartet system af nomenklatur og klassificering, hvilket gør det vanskeligt at diskutere gruppen som helhed og at placere nye sekvenser i den relevante kontekst. Udvikle en reference, der prioriterer vigtigt sekvens funktioner relateret til struktur og/eller aktivitet kan bruges ud over etablerede navne til at tilføje nogle sammenhæng til en forskelligartet gruppe af proteiner. Dette papir bruger cystein-stabiliseret alpha-helix (CS-αβ) superfamilien som et eksempel til at vise hvordan en reference, der er genereret i regneark software kan afklare forholdet mellem eksisterende proteiner i superfamilien, samt lette tilføjelsen af nye sekvenser. Det viser også, hvordan henvisningen kan bidrage til at forfine sekvens alignments genereret i almindeligt anvendte software, som påvirker gyldigheden af fylogenetiske analyser. Brug af en henvisning vil sandsynligvis være mest nyttige for protein grupper, der omfatter meget forskellige sekvenser fra et bredt spektrum af taxa, med funktioner, der ikke er tilstrækkeligt fanget af molekylære analyser.

Grupper af sekvenser i CS-αβ superfamilien rapporteret i litteraturen er vist i figur 4. Cystein bindinger baseret på nummerering for hver sekvens foreslår fem grundlæggende grupper (tabel 1, midterste kolonne). Gruppe 1 har seks cysteines, der fra tre disulfid obligationer og indeholder sekvenser fra insekter, arachnids, bløddyr, nematoder og svampe. Gruppe 2, 3 og 4 har 8 cysteines, der danner fire disulfid obligationer. Gruppe 2 omfa...

Watch this Scientific Journal Video about Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group at JoVE.com

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

At oprette og anvende en Reference for at lette drøftelserne og klassificering af proteiner i en forskelligartet gruppe

Målet med denne protokol er at udvikle en reference for divergerende proteiner i en gruppe, der mangler sammenhængende kriterier for nomenklatur og klassificering. Denne henvisning vil lette analyser og diskussion af gruppen som helhed og kan anvendes som supplement etablerede navne.

Related proteins that have been studied in different labs using varying organisms may lack a uniform system of nomenclature and classification, making it ...

The overall goal of this procedure is to use standard spreadsheet software to develop a reference for divergent proteins in a group that lacks coherent criteria for nomenclature and classification. This method can help clarify relationships between related proteins that have confusing or inconsistent nomenclature, such as the cysteine-stabilized alpha-beta superfamily of defensive peptides that includes invertebrate defenses. The main advantage of this technique is that it provides a simple visual representation of the proteins of interest.To begin, identify the defining characteristics of the protein group of interest. For example, the CS alpha-beta fold in the solution structure of insect defense and aid from phormia terraenovae defines the CS alpha-beta superfamily. This fold also includes a smaller motif called the cysteine-stabilized helix, which is identified by CXXXC upstream of a CXC.The four cysteines form two disulfide bonds. To complete the CS alpha-beta motif, a third disulfide bond is formed by an additional pair of cysteines. Ultimately it is critical to know at least some important features related to the structure or function of the protein.Without this, there is no basis for generating a reference. Now, enter these defining features into a spreadsheet. Use columns for the conserved features and to represent the spaces between these features.Keep the columns wide enough to fit numbers, and give them a consistent width. In the rows, describe the sequences. To indicate a sequence as a feature, fill in the feature box with color, using the fill function.Then, to indicate the spacing between the features, enter the number of amino acids in the box between. Now, add representative sequences that have been previously established as members of the group based on structural databases and published results. As needed, add features that are likely to define a subgroup of sequences, such as an extra cysteine.If features are missing from a given sequence, leave the box unfilled and combine it with boxes representing intervening amino acids. To do this, us the Merge and Center function. Once representative sequences have been entered, identify groups of clearly related sequences.Then, summarize the characteristics of these groups. When the number of amino acids between features varies, use a hyphen to indicate a range or slashes to indicate a few specific numbers. As needed, creatively annotate features that may be relevant or aren't common enough to include in the reference.For example, since cysteines are important in the superfamily, the presence of additional cysteines can be labeled. Sometimes, when adding newly identified sequences to the spreadsheet, the sequences of one species fall into several different groups of the superfamily, such as for tardigrades. Once completed, the rows of the spreadsheet can then be sorted to highlight variation within a species, or variation in between taxonomic groups.This demonstration uses the freely available MEGA 6 software. However, other software can be used similarly. To start a new alignment, select Edit/Build Alignment under the Align tab.Then select Create a new alignment, in the box that appears and click OK.Then select Protein. Now, select Insert Sequence from File, in the Edit menu, to import the sequences. The sequences must be in FASTA format.Background colors reflecting different amino acid types are shown by default and can be turned off with a toggle, under the Display menu. Once all the sequences are entered, click the flexing arm icon and then Align Protein to align the sequences using the muscle algorithm. If the message, Nothing selected for alignment.Select all? pops up, choose OK.Some parameters can be changed in the pop-up window, but for this demonstration, the defaults will suffice. Now, check the alignment based on the important features of the protein superfamily.The top bar shows an asterisk in any position in which the amino acid is completely conserved. The initial alignment identifies three of the four conserved cysteines. One sequence is clearly misaligned.To fix a misaligned sequence, highlight the dashes and press the Delete key without accidentally deleting amino acids. Then, move the amino acids into their proper alignment by adding spaces. After aligning the sequence manually, note that the last cysteine of the CXXXC motif is conserved throughout the alignment.Manual adjustment is often necessary to prioritize the most important features of the sequences. The spreadsheet alignment of the previously established CS alpha-beta superfamily revealed five basic patterns of bond formation. The newly identified tardigrade sequences fell into the complete spectrum of these patterns.Next, phylogenetic analyses were used to examine how this group of proteins may have evolved. However, the sequences are generally short and highly divergent. Thus, the resulting trees were poorly resolved and offered little insight.The multiple sequence alignment was optimized using the reference, but there was still poor resolution in the maximum likelihood analysis and in the Bayesian phylogenetic analysis. Most clades had only low levels of support. However, five small groups were supported in at least one of the two trees.Sequences with different cysteine numbers within a taxonomical group may be more closely related than sequences with the same pattern from different groups. After watching this video, you should have a good understanding of how to use spreadsheet software to generate a simple visualization of important protein characteristics. While attempting this procedure, it's important to remember that determining the most relevant characteristics for the group of proteins is often an iterative process, and revision of the reference will likely be necessary.New sequences can always be added to a spreadsheet, and it is easy to have multiple versions allowing for new features to be added that may be useful for classification and analysis. Although the spreadsheet alignment allows easy visualization of structural and functional features, other methods like phylogenetic analysis can be performed to provide additional insight into evolutionary relationships.

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The Modified Hole Board - Measuring Behavior, Cognition and Social Interaction in Mice and Rats

Den modificerede Hole Board - Måling Behavior, Erkendelse og social interaktion hos mus og rotter

This protocol describes the modified hole board (mHB), which combines features from a traditional hole board and open field and is designed to measure ...

Applying Stereotactic Injection Technique to Study Genetic Effects on Animal Behaviors

Anvendelse af Stereotaktisk injektionsteknik at studere genetiske virkninger på Animal Behaviors

Stereotactic injection is a useful technique to deliver high titer lentiviruses to targeted brain areas in mice. Lentiviruses can either overexpress or ...

The Social Dimension of Stress: Experimental Manipulations of Social Support and Social Identity in the Trier Social Stress Test

Den sociale dimension af stress: Eksperimentelle manipulationer af social støtte og social identitet i Trier Social stresstesten

In many situations humans are influenced by the behavior of other people and their relationships with them. For example, in stressful situations ...

Psychophysical Tracking Method to Measure Taste Preferences in Children and Adults

Psykofysiske Tracking metode til at måle smagspræferencer hos børn og voksne

The Monell two-series, forced-choice, paired-comparison tracking method provides a reliable measure of sweet taste preferences from childhood to ...

Behavioral Disturbances: An Innovative Approach to Monitor the Modulatory Effects of a Nutraceutical Diet

Adfærdsforstyrrelser: en innovativ tilgang til at overvåge Modulerende Virkninger af en Nutraceutical kost

In dogs, diets are often used to modulate behavioral disturbances related to chronic anxiety and stress caused by intense and restless activity. However, ...

Using a Virtual Store As a Research Tool to Investigate Consumer In-store Behavior

Brug af en virtuel butik som et forskningsværktøj til at undersøge forbrugernes i butiksadfærd

People&#39;s responses to products and/or choice environments are crucial to understanding in-store consumer behaviors. Currently, there are various ...

Using the FishSim Animation Toolchain to Investigate Fish Behavior: A Case Study on Mate-Choice Copying In Sailfin Mollies

Using the FishSim Animation Toolchain to Investigate Fish Behavior: A Case Study on Mate-Choice Copying In Sailfin Mollies

Ved hjælp af FishSim Animation Toolchain at undersøge fisk adfærd: en Case Study om Mate-valg kopiering i Sailfin jensoehrberg

Over the last decade, employing computer animations for animal behavior research has increased due to its ability to non-invasively manipulate the ...

Applying an eMASS Customization Program as a Research Tool to Evaluate Consumer Benefits

Anvendelse af et eMASS tilpasnings program som et forskningsværktøj til at evaluere fordele for forbrugerne

As many scholars and practitioners study personalization and relationship marketing, it is important to provide personalization such as mass customization ...