Molecular Recognition Laboratorium - Revision history

Victor Tapia: /* Technological Development of the Peptide Array Technologies */

2013-05-07T00:24:17Z

Technological Development of the Peptide Array Technologies

←Older revision		Revision as of 00:24, 7 May 2013
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	<br>		<br>
	----		----
-	~~REFERENCES~~

-	* Angenendt, P., and Glokler, J. (2004) Evaluation of antibodies and microarray coatings as a prerequisite for the generation of optimized antibody microarrays, Methods Mol Biol 264, 123-34.	+	SOURCES: For references to citations above see
-	* Angenendt, P., Glokler, J., Murphy, D., Lehrach, H., and Cahill, D. J. (2002) Toward optimized antibody microarrays: ~~a comparison of current microarray support materials, Anal Biochem 309, 253-60.~~	+	* Tapia, V.E., Ay, B., Volkmer, R., 2009. Exploring and Profiling Protein Function with Peptide Arrays, in: Marina Cretich, Chiari, M. (Eds.), Peptide Microarrays. Humana Press, Totowa, NJ, pp. 3–17.
-	* Angenendt, P., Glokler, J., Sobek, J., Lehrach, H., and Cahill, D. J. (2003) Next generation of protein microarray support materials: evaluation for protein and antibody microarray applications, J Chromatogr A 1009, 97-104.	+
-	* Daniels, S. B., Bernatowicz, M. S., Coull, J. M., and Köster, H. (1989) Membranes as solid supports for peptide synthesis., Tetrahedron Lett. 30.	+
-	* Eichler, J., Beyermann, M., and Bienert, M. (1989) Application of cellulose paper as support in simultaneous solid phase peptide synthesis., Colect. Czech. Chem. Commun. 54, 1746-52.	+
-	* Eichler, J., Bienert, M., Stierandova, A., and Lebl, M. (1991) Evaluation of cotton as a carrier for solid-phase peptide synthesis., Peptide Res. 4, 296-307.	+
-	* Ekins, R., Chu, F., and Biggart, E. (1990) Multispot, multianalyte, immunoassay, Ann Biol Clin (Paris) 48, 655-66.	+
-	* Ekins, R. P. (1989) Multi-analyte immunoassay, J Pharm Biomed Anal 7, 155-68.	+
-	* Ekins, R. P. (1998) Ligand assays: from electrophoresis to ~~miniaturized microarrays, Clin Chem 44, 2015-30.~~	+
-	* ~~El Khoury, G., Laurenceau, E., Dugas~~, V.~~, Chevolot, Y., Merieux, Y., Duclos, M. C., Souteyrand,~~ E., ~~Rigal~~, D., ~~Wallach~~, ~~J., and Cloarec, J. P. (2007) Acid deprotection of covalently immobilized peptide probes on glass slides for peptide microarrays, Conf Proc IEEE Eng Med Biol Soc 2007, 2242-6.~~	+
-	* Falsey, J. R., ~~Renil, M~~.~~, Park, S., Li, S.,~~ and ~~Lam, K. S. (2001) Peptide and small molecule microarray for high throughput cell adhesion and functional assays, Bioconjug Chem 12, 346-53.~~	+
-	* Fields, G. B., and Noble, R. L. (1990) Solid phase peptide synthesis utilizing 9-fluorenylmethoxycarbonyl amino acids, Int J Pept Protein ~~Res 35, 161-214.~~	+
-	* Fodor, S. P., Read, J. L., Pirrung, M. C., Stryer, L., Lu, A. T., and Solas, D. (1991) Light-directed, spatially addressable parallel chemical synthesis, Science 251, 767-73.	+
-	* Frank, R. (1992) Spot-synthesis: an easy technique for the positionally addressable, parallel chemical synthesis on a membrane support, Tetrahedron, 9217-32.	+
-	* Frank, R. (2002) The SPOT-synthesis technique: Synthetic peptide arrays on membrane supports--principles and applications, J. Immunol. Methods 267, 13-26.	+
-	* Frank, R., and Döring, R. (1988) Simultaneous multiple peptide synthesis under continuous flow conditions on cellulose paper disks as segmental solid supports, Tetrahedron 44, 6031-40.	+
-	* Gao, X., Pellois, J. P., Na, Y., Kim, Y., Gulari, E., and Zhou, X. (2004) High density peptide microarrays. In situ synthesis and applications, Mol Divers 8, 177-87.	+
-	*Geysen, H. M., Meloen, R. H., and Barteling, S. J. (1984) Use of peptide synthesis to probe viral antigens for epitopes to a resolution of a single amino acid, Proc Natl Acad Sci U S A 81, 3998-4002.	+
-	*Goede, A., Jaeger, I. S., and Preissner, R. (2005) SUPERFICIAL--surface mapping of proteins via structure-based peptide library design, BMC Bioinformatics 6, 223.	+
-	*Gutte, B., and Merrifield, R. B. (1969) The total synthesis of an enzyme with ~~ribonuclease A activity~~, ~~J Am Chem Soc 91, 501-2.~~	+
-	*Houseman, B. T., and Mrksich, M. (2002) Towards quantitative assays with peptide chips: ~~a surface engineering approach~~, ~~Trends Biotechnol 20, 279-81.~~	+
-	*Jonsson, U., Fagerstam, L., Ivarsson, B., Johnsson, B., Karlsson, R., Lundh, K., Lofas, S., Persson, B., Roos, H., Ronnberg, I., and et al. (1991) Real-time biospecific interaction analysis using surface plasmon resonance and a sensor chip technology, Biotechniques 11, 620-7.	+
-	*Joos, T. O., Stoll, D., and Templin, M~~. F~~. (~~2002) Miniaturised multiplexed immunoassays, Curr Opin Chem Biol 6, 76-80~~.	+
-	*Malmqvist, M. (1993) ~~Biospecific interaction analysis using biosensor technology~~, ~~Nature 361, 186-7.~~	+
-	*Merrifield, R. B. (1965) Automated synthesis of peptides, Science 150, 178-85.	+
-	*Pellois, J. P., Wang, W., and Gao, X. (2000) Peptide ~~synthesis based on t-Boc chemistry and solution photogenerated acids, J Comb Chem 2, 355-60~~.	+
-	*Pellois, ~~J. P.~~, ~~Zhou~~, X.~~, Srivannavit, O., Zhou, T., Gulari, E., and Gao, X. (2002) Individually addressable parallel peptide synthesis on microchips, Nat Biotechnol 20, 922-6~~.	+
-	*Reimer, U., Reineke, U., and Schneider-Mergener, J. (2002) Peptide arrays: from macro to micro, Curr Opin Biotechnol 13, 315-20.	+
-	*Schmidt, M., and Eichler, J. (1993) Multiple peptide synthesis using cellulose-based carriers: Synthesis of substance P - diastereoisomers and their histamine-releasing activity., Bioorg. Med. Chem. Lett. 3, 441-46.	+
-	*Schutkowski, M., Reimer, U., Panse, S., Dong, L., Lizcano, J. M., Alessi, D. R., and Schneider-Mergener, J. (2004) High-content peptide microarrays for deciphering kinase specificity and biology, Angew Chem Int Ed Engl 43, 2671-4.	+
-	*Seurynck-Servoss, S. L., Baird, C. L., Miller, K. D., Pefaur, N. B., Gonzalez, R. M., Apiyo, D. O., Engelmann, H. E., Srivastava, S., Kagan, J., Rodland, K. D., and Zangar, R. C. (2008) Immobilization strategies for single-chain antibody microarrays, Proteomics 8, 2199-210.	+
-	*Seurynck-Servoss, S. L., Baird, C. L., Rodland, K. D., and Zangar, R. C. (2007) Surface chemistries for antibody microarrays, Front Biosci 12, 3956-64.	+
-	*Seurynck-Servoss, S. L., White, A. M., Baird, C. L., Rodland, K. D., and Zangar, R. C. (2007) Evaluation of surface chemistries for antibody microarrays, Anal Biochem 371, 105-15.	+
-	*Sobek, J., Aquino, C., and Schlapbach, R. (2007) Quality considerations and selection of surface chemistry for glass-based DNA, peptide, antibody, carbohydrate, and small molecule microarrays, Methods Mol Biol 382, 17-31.	+
-	*Sobek, J., Bartscherer, K., Jacob, A., Hoheisel, J. D., and Angenendt, P. (2006) Microarray technology as a universal tool for high-throughput analysis of biological systems, Comb Chem High Throughput Screen 9, 365-80.	+
-	*Templin, M. F., Stoll, D., Schrenk, M., Traub, P. C., Vohringer, C. F., and Joos, T. O. (2002) Protein microarray technology, Drug Discov Today 7, 815-22.	+
-	*Wang, Z., and Laursen, R. A. (1992) Multiple peptide synthesis on polypropylene membranes for rapid screening of bioactive peptides., Pep. Res. 5, 275-80.	+
-	*Wenschuh, H., Volkmer-Engert, R., Schmidt, M., Schulz, M., Schneider-Mergener, J., and Reineke, U. (2000) Coherent membrane supports for parallel microsynthesis and screening of bioactive peptides, Biopolymers 55, 188-206.	+

	</div>		</div>

Victor Tapia: /* Technological Development of the Peptide Array Technologies */

2013-05-07T00:18:06Z

Technological Development of the Peptide Array Technologies

←Older revision		Revision as of 00:18, 7 May 2013
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	<br>		<br>
	----		----
-	A_[[image:Macro_to_microarrays_of_peptides.png\|400px]] B_[[~~image~~:~~Fmoc-spotting~~.png\|400px]]	+	A_[[image:Macro_to_microarrays_of_peptides.png\|400px]] B_[[Image:Drawing.png\|400px]]

	The combination of SPOT peptide synthesis (figure A, steps 1 to 4) with <br>		The combination of SPOT peptide synthesis (figure A, steps 1 to 4) with <br>
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	peptides offers the benefit of a "chemical" purification step and <br>		peptides offers the benefit of a "chemical" purification step and <br>
	flexible array design. Additionally, the glass support is compatible <br>		flexible array design. Additionally, the glass support is compatible <br>
-	with fluorescence detection ~~(see figure B, adapted from the web)~~ and <br>	+	with fluorescence detection and <br>
	offers the possibility to miniaturize binding assays. Beyond economy, <br>		offers the possibility to miniaturize binding assays. Beyond economy, <br>
	the later point is essential for quantitative measurements at the <br>		the later point is essential for quantitative measurements at the <br>

Victor Tapia: /* Modularity of WW PIDs */

2013-05-03T08:31:48Z

Modularity of WW PIDs

←Older revision		Revision as of 08:31, 3 May 2013
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	<div style="padding: 10px; color: #000; background-color: #CEF2E0; width: 600px">		<div style="padding: 10px; color: #000; background-color: #CEF2E0; width: 600px">
	The WW domain is a well-characterized protein module that mediates specific protein-protein interactions with ligands that contain short proline-rich motifs [Bork 1994; Chen 1995; Sudol 2000]. The domain is composed of 38 amino acids, it has two signature tryptophan (W) residues, and it is one of the smallest among modular protein domains. The signature tryptophan positions are spaced 20–22 amino acids apart and have important structural role. The structure is a three beta-strand meander that forms a shallow binding pocket for proline-rich ligands (reviewed in[Sudol 2005]). In general, the folding of WW domains does not require cognate ligands or co-factors. <br>		The WW domain is a well-characterized protein module that mediates specific protein-protein interactions with ligands that contain short proline-rich motifs [Bork 1994; Chen 1995; Sudol 2000]. The domain is composed of 38 amino acids, it has two signature tryptophan (W) residues, and it is one of the smallest among modular protein domains. The signature tryptophan positions are spaced 20–22 amino acids apart and have important structural role. The structure is a three beta-strand meander that forms a shallow binding pocket for proline-rich ligands (reviewed in[Sudol 2005]). In general, the folding of WW domains does not require cognate ligands or co-factors. <br>
-	~~'''MORE TEXT''' {{hide\|~~
	----		----
	There are two aspects which allow a protein motiv to be recognized as module. Firstly, '''functional modularity''': a domains ability to function independent of context, allowing transfer of function between diverse molecular systems. In the case of a WW domain, it functionally resembles the Src homology domain 3 in its recognition of proline-rich or proline-containing ligands. Based on this ligand predilection, two major and two minor groups are classified:<br>		There are two aspects which allow a protein motiv to be recognized as module. Firstly, '''functional modularity''': a domains ability to function independent of context, allowing transfer of function between diverse molecular systems. In the case of a WW domain, it functionally resembles the Src homology domain 3 in its recognition of proline-rich or proline-containing ligands. Based on this ligand predilection, two major and two minor groups are classified:<br>
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	<br>		<br>
	Secondly, '''structural modularity''': the ability of a protein motiv to be physically isolated from its protein context and yet fold into the characteristic conformation (structural autonomy). Although several WW domain structures are annotated in the Protein Database (PDB), some can only be shown to fold stabily upon ligand binding. It is a matter of controversy, if ligand binding induces the fold or if it selects a stable bounded conformation from many dynamically interchanging free conformations. This is analogous to the question whether ligand binding or folding firstly occurs. <br>		Secondly, '''structural modularity''': the ability of a protein motiv to be physically isolated from its protein context and yet fold into the characteristic conformation (structural autonomy). Although several WW domain structures are annotated in the Protein Database (PDB), some can only be shown to fold stabily upon ligand binding. It is a matter of controversy, if ligand binding induces the fold or if it selects a stable bounded conformation from many dynamically interchanging free conformations. This is analogous to the question whether ligand binding or folding firstly occurs. <br>
		+	<br>
		+	=====GOLABI-ITO-HALL SYNDROM (GIHS)=====
		+	<br>
		+	Das Gen fürs polyglutamine-tract binding Protein 1 (PQBP1), welches auf dem X-Chromosom lokalisiert ist, kodiert für ein 38 kDa Zellkernprotein das überwiegend im zentralen Nervensystem exprimiert wird. In der Literatur wird die Rolle des PQBP1 Proteins in der Entwicklung von auf Polyglutaminexpansion beruhenden Krankheiten wie z. B der spinozerebellären Ataxie Typ 1 beschrieben (Okazawa et al., 2002). Weiterhin sind Mutationen im PQBP1 Gen in mehreren X-Chromosom gebundenen Retardierungen (XLMR), wie dem Renpenning, Sutherland-Haan, Hamel, Porteous und Golabi-Ito-Hall Syndrom (GIHS), nachgewiesen worden (Ropers and Hamel, 2005). Dieser XLMR Syndrome assoziieren mit unterschiedlichen Mutationen des PQBP1 Gens, und dennoch teilen sie ähnliche klinische Merkmale.<br>
		+	<br>
		+	Die Y65C PQBP1 Mutation, die mit dem GIH Syndrom assoziiert (Lubs et al., 2006), ist einzigartig unter den bisher gemeldeten PQBP1 Mutationen. Die Läsion beeinflusst nicht die Länge des mutierten Proteins sondern betrifft eine punktuelle Position innerhalb des WW Erkennungsmodules. Mutationen, die in Erkennungsmodulen oder in ihren zugehörigen Liganden gefunden werden, beeinflussen die involvierten Proteinkomplexe und die damit verbundenen Signalwege und können zu Krankheiten führen.
		+	<br>
		+	=====Chaperon-assistierte selektive Autophagie (CASA)=====
		+	<br>
		+	CASA ist entscheidend um die Muskelaktivität unter mechanischer Spannung in Fliegen, Mäusen und Menschen (Arndt et al., 2010; Homma et al., 2006; Selcen et al., 2009) zu erhalten (Abbildung 2). Eine Beeinträchtigung der CASA verursacht schwere Muskeldystrophien und eine dilatierte Kardiomyopathie, und wurde mit der Gliedergürteldystrophie (Arimura et al., 2011; Homma et al., 2006; Sarparanta et al., 2012) in Verbindung gebracht. <br>
		+	<br>
		+	In Muskelzellen spielt BAG3 eine Schlüsselrolle wo es hoch exprimiert und überwiegend an der Z-Scheibe lokalisiert ist. Die Z-Scheibe ist ein Proteinkomplex und dient der Aktin-Verankerung in der quer-gestreiften Muskulatur. Für die Verankerung ist das Z-Scheiben-Protein Filamin wichtig, da es als verbindende Brücke zwischen Aktin und Integrinen in der sakroplasmatischen Membran wirkt. In der kontrahierenden Muskulatur wird das Filamin mechanisch stark beansprucht und häufig entfaltet und unterliegt dann einem Abbau durch CASA. Dieser Abbau wird duch BAG3 eingeleitet. <br>
		+	<br>
		+	Nach Kontraktion-induzierter Entfaltung, wird Filamin von einem Chaperon-Komplex anerkannt. Der Komplex enthält Hsc70 und HspB8 (auch als Hsp22 bekannt), die physikalisch vom CASA-induzierende Ko-Chaperon BAG3 zusammengehalten werden. Filamin wird aus der Z-Scheibe freigegeben und durch die Hsc70-assoziierte Ubiquitinligase CHIP ubiquitiniert. Es wird dann von dem autophagischen Ubiquitin Adaptor Protein p62 dem lysosomalen Verdau zugeführt, indem p62 mit Phagophorenmembranen interagiert. Der autophagische Abbau von Filamin ist eine Voraussetzung für die ordnungsmäßige Funktion von Z-Scheiben in kontrahierender, quergestreifter Muskulatur (Arndt et al., 2010). <br>
	}}		}}
	</div>		</div>

Victor Tapia: /* Technological Development of the Peptide Array Technologies */

2013-03-07T12:45:19Z

Technological Development of the Peptide Array Technologies

←Older revision		Revision as of 12:45, 7 March 2013
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	A_[[image:Macro_to_microarrays_of_peptides.png\|400px]] B_[[image:Fmoc-spotting.png\|400px]]		A_[[image:Macro_to_microarrays_of_peptides.png\|400px]] B_[[image:Fmoc-spotting.png\|400px]]

-	~~'''PEPTIDE ARRAYS '''~~ The combination of SPOT peptide synthesis (figure A, steps 1 to 4) with <br>	+	The combination of SPOT peptide synthesis (figure A, steps 1 to 4) with <br>
	appropriate immobilization techniques on glass supports (figure A, steps <br>		appropriate immobilization techniques on glass supports (figure A, steps <br>
	5 and 6) is wide spread. The SPOT technology provides low-scale but <br>		5 and 6) is wide spread. The SPOT technology provides low-scale but <br>

Victor Tapia: /* Technological Development of the Peptide Array Technologies */

2013-03-07T12:25:42Z

Technological Development of the Peptide Array Technologies

←Older revision		Revision as of 12:25, 7 March 2013
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	===Technological Development of the Peptide Array Technologies===		===Technological Development of the Peptide Array Technologies===
	by ''Victor Tapia'' <br>		by ''Victor Tapia'' <br>
-	~~FIGURE {{hide\|~~	+	<br>
	----		----
	A_[[image:Macro_to_microarrays_of_peptides.png\|400px]] B_[[image:Fmoc-spotting.png\|400px]]		A_[[image:Macro_to_microarrays_of_peptides.png\|400px]] B_[[image:Fmoc-spotting.png\|400px]]
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	----		----
	<br>		<br>
-	}}
	<div style="padding: 10px; color: #000; background-color: #CEF2E0; width: 600px">		<div style="padding: 10px; color: #000; background-color: #CEF2E0; width: 600px">
	The basic point of this technology is the simultaneous display of a <br>		The basic point of this technology is the simultaneous display of a <br>
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	bimolecular interaction assays can be carried out under homogeneous <br>		bimolecular interaction assays can be carried out under homogeneous <br>
	conditions. <br>		conditions. <br>
-	~~MORE {{hide\|~~	+	<br>
	----		----
	PEPTIDE ARRAYS IN THE ADVANCEMENT OF PEPTIDE SYNTHESIS<br>		PEPTIDE ARRAYS IN THE ADVANCEMENT OF PEPTIDE SYNTHESIS<br>
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	under development [Goede, et al., 2005]. <br>		under development [Goede, et al., 2005]. <br>
	<br>		<br>
		+	----
	PEPTIDE ARRAYS IN THE ADVANCEMENT OF BINDING ASSAY SYSTEMS <br>		PEPTIDE ARRAYS IN THE ADVANCEMENT OF BINDING ASSAY SYSTEMS <br>
	<br>		<br>
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	* to 2000-4000 peptides in 1.5 cm2, in the case of microarrays generated by digital photolithography [El Khoury, et al., 2007; Gao, et al., 2004; Pellois, et al., 2000; Pellois, et al., 2002].		* to 2000-4000 peptides in 1.5 cm2, in the case of microarrays generated by digital photolithography [El Khoury, et al., 2007; Gao, et al., 2004; Pellois, et al., 2000; Pellois, et al., 2002].
	<br>		<br>
		+	----
	SUPPORT MATERIALS <br>		SUPPORT MATERIALS <br>
	<br>		<br>
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	Seurynck-Servoss, et al., 2007; Seurynck-Servoss, et al., 2007; Sobek, <br>		Seurynck-Servoss, et al., 2007; Seurynck-Servoss, et al., 2007; Sobek, <br>
	et al., 2007; Sobek, et al., 2006; Wenschuh, et al., 2000]. <br>		et al., 2007; Sobek, et al., 2006; Wenschuh, et al., 2000]. <br>
-	}}	+	<br>
-		+
-	~~REFERENCES {{hide\|~~	+
	----		----
		+	REFERENCES
		+
	* Angenendt, P., and Glokler, J. (2004) Evaluation of antibodies and microarray coatings as a prerequisite for the generation of optimized antibody microarrays, Methods Mol Biol 264, 123-34.		* Angenendt, P., and Glokler, J. (2004) Evaluation of antibodies and microarray coatings as a prerequisite for the generation of optimized antibody microarrays, Methods Mol Biol 264, 123-34.
	* Angenendt, P., Glokler, J., Murphy, D., Lehrach, H., and Cahill, D. J. (2002) Toward optimized antibody microarrays: a comparison of current microarray support materials, Anal Biochem 309, 253-60.		* Angenendt, P., Glokler, J., Murphy, D., Lehrach, H., and Cahill, D. J. (2002) Toward optimized antibody microarrays: a comparison of current microarray support materials, Anal Biochem 309, 253-60.
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	*Wenschuh, H., Volkmer-Engert, R., Schmidt, M., Schulz, M., Schneider-Mergener, J., and Reineke, U. (2000) Coherent membrane supports for parallel microsynthesis and screening of bioactive peptides, Biopolymers 55, 188-206.		*Wenschuh, H., Volkmer-Engert, R., Schmidt, M., Schulz, M., Schneider-Mergener, J., and Reineke, U. (2000) Coherent membrane supports for parallel microsynthesis and screening of bioactive peptides, Biopolymers 55, 188-206.

-	}}
	</div>		</div>
	<br>		<br>
		+
	===Messsystemanalyse von Peptidarray Techniken===		===Messsystemanalyse von Peptidarray Techniken===
	by ''Victor Tapia'' <br>		by ''Victor Tapia'' <br>

Victor Tapia at 12:09, 7 March 2013

2013-03-07T12:09:24Z

←Older revision		Revision as of 12:09, 7 March 2013
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-	~~<div style="padding: 10px; color: #ffffff; background-color: #000; width: 600px">~~
	[[Image:MolRec-Logo.jpg\|600px]]		[[Image:MolRec-Logo.jpg\|600px]]
		+	<div style="padding: 10px; color: #000; background-color: #CEF2E0; width: 600px">
		+


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	CHARITÉ - UNIVERSITÄTSMEDIZIN BERLIN<br>		CHARITÉ - UNIVERSITÄTSMEDIZIN BERLIN<br>
	{{hide\|		{{hide\|
-	[[Image:Molrec placeholder.png\|~~167px~~\|right]]	+	[[Image:Molrec placeholder.png\|112px\|right]]
	Hessische Str. 3-4		Hessische Str. 3-4
	D-10115 Berlin, Germany		D-10115 Berlin, Germany
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	</div><br>		</div><br>
	==Group Leader==		==Group Leader==
-	<div style="padding: 10px; color: #~~ffffff~~; background-color: #~~000~~; width: 600px">	+	<div style="padding: 10px; color: #000; background-color: #CEF2E0; width: 600px">
	Rudolf Volkmer {{hide\|		Rudolf Volkmer {{hide\|
-	[[Image:Molrec placeholder.png\|~~130px~~\|right]]	+	[[Image:Molrec placeholder.png\|112px\|right]]
	Tel.: +49 30 450 524 267		Tel.: +49 30 450 524 267
	Fax: +49 30 450 524 942		Fax: +49 30 450 524 942
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	==Group Members==		==Group Members==
-	<div style="padding: 10px; color: #~~ffffff~~; background-color: #~~000~~; width: 600px">	+	<div style="padding: 10px; color: #000; background-color: #CEF2E0; width: 600px">
	*Annette Hayungs - Secretary {{hide\|		*Annette Hayungs - Secretary {{hide\|
-	[[Image:Molrec placeholder.png\|~~130px~~\|right]]	+	[[Image:Molrec placeholder.png\|112px\|right]]
	Tel.: +49 30 450 524 092		Tel.: +49 30 450 524 092
	Fax: +49 30 450 524 942		Fax: +49 30 450 524 942
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	}}		}}
	*Ines Kretzschmar - CTA {{hide\|		*Ines Kretzschmar - CTA {{hide\|
-	[[Image:Molrec placeholder.png\|~~130px~~\|right]]	+	[[Image:Molrec placeholder.png\|112px\|right]]
	Tel.: +49 30 450 524 253		Tel.: +49 30 450 524 253
	Fax: +49 30 450 524 942		Fax: +49 30 450 524 942
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	}}		}}
	*Christiane Landgraf - CTA {{hide\|		*Christiane Landgraf - CTA {{hide\|
-	[[Image:Molrec placeholder.png\|~~130px~~\|right]]	+	[[Image:Molrec placeholder.png\|112px\|right]]
	Tel.: +49 30 450 524 253		Tel.: +49 30 450 524 253
	Fax: +49 30 450 524 942		Fax: +49 30 450 524 942
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	}}		}}
	*Judith Müller - Doktorandin {{hide\|		*Judith Müller - Doktorandin {{hide\|
-	[[Image:Molrec placeholder.png\|~~130px~~\|right]]	+	[[Image:Molrec placeholder.png\|112px\|right]]
	Tel.: +49 30 450 524 046		Tel.: +49 30 450 524 046
	Fax: +49 30 450 524 942		Fax: +49 30 450 524 942
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	}}		}}
	*Livia Otte - Postdoc {{hide\|		*Livia Otte - Postdoc {{hide\|
-	[[Image:Molrec placeholder.png\|~~130px~~\|right]]	+	[[Image:Molrec placeholder.png\|112px\|right]]
	Tel.: +49 30 450 524 146		Tel.: +49 30 450 524 146
	Fax: +49 30 450 524 942		Fax: +49 30 450 524 942
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	}}		}}
	*Rolf-Dietrich Stigler - IT- u. Sicherheitsbeauftragter {{hide\|		*Rolf-Dietrich Stigler - IT- u. Sicherheitsbeauftragter {{hide\|
-	[[Image:Molrec placeholder.png\|~~130px~~\|right]]	+	[[Image:Molrec placeholder.png\|112px\|right]]
	Tel.: +49 30 450 524 268		Tel.: +49 30 450 524 268
	Fax: +49 30 450 524 942		Fax: +49 30 450 524 942
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	}}		}}
	*[http://openwetware.org/wiki/User:Victor_Tapia Víctor Tapia] - Doktorand {{hide\|		*[http://openwetware.org/wiki/User:Victor_Tapia Víctor Tapia] - Doktorand {{hide\|
-	[[Image:Molrec placeholder.png\|~~130px~~\|right]]	+	[[Image:Molrec placeholder.png\|112px\|right]]
	ACTUALLY SEARCHING FOR A NEW POSITION		ACTUALLY SEARCHING FOR A NEW POSITION
	Email: ve.tapia.m@gmail.com		Email: ve.tapia.m@gmail.com
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	}}		}}
	*Lars Vouillème - Doktorand {{hide\|		*Lars Vouillème - Doktorand {{hide\|
-	[[Image:Molrec placeholder.png\|~~130px~~\|right]]	+	[[Image:Molrec placeholder.png\|112px\|right]]
	Tel.: +49 30 450 524 254		Tel.: +49 30 450 524 254
	Fax: +49 30 450 524 942		Fax: +49 30 450 524 942
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	<br>		<br>
	}}		}}
-	<div style="padding: 10px; color: #~~ffffff~~; background-color: #~~000~~; width: 600px">	+	<div style="padding: 10px; color: #000; background-color: #CEF2E0; width: 600px">
	The basic point of this technology is the simultaneous display of a <br>		The basic point of this technology is the simultaneous display of a <br>
	systematic collection of peptides on a planar support, on which numerous <br>		systematic collection of peptides on a planar support, on which numerous <br>
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	by ''Victor Tapia'' <br>		by ''Victor Tapia'' <br>

-	<div style="padding: 10px; color: #~~ffffff~~; background-color: #~~000~~; width: 600px">	+	<div style="padding: 10px; color: #000; background-color: #CEF2E0; width: 600px">
	Mit dem Ziel die Affinitätsvorhersagbarkeit von Peptidarray-orientierten Bindunsstudien zu analyzieren, wurde die CB4 1 Epitope Bibliothek definiert, welche auf ein Repertoire von 26 verschiedene Liganden für das CB4-1 Antikörper besteht. Es handelt sich hierbei haupsächlich um Sequenz- und Mimika¬varianten des natürlichen Epitopes von CB4-1 (? p24 von HIV 1). Die Eignung dieser Proben für das oben erklärtes Ziel beruhrt auf das vorhandene Affinitätsprofil, das jedes Peptid mit einzeln gemessenen KD Werte assoziiert. <br>		Mit dem Ziel die Affinitätsvorhersagbarkeit von Peptidarray-orientierten Bindunsstudien zu analyzieren, wurde die CB4 1 Epitope Bibliothek definiert, welche auf ein Repertoire von 26 verschiedene Liganden für das CB4-1 Antikörper besteht. Es handelt sich hierbei haupsächlich um Sequenz- und Mimika¬varianten des natürlichen Epitopes von CB4-1 (? p24 von HIV 1). Die Eignung dieser Proben für das oben erklärtes Ziel beruhrt auf das vorhandene Affinitätsprofil, das jedes Peptid mit einzeln gemessenen KD Werte assoziiert. <br>
	<br>		<br>
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	}}		}}
	====Protein Interaction Domains====		====Protein Interaction Domains====
-	<div style="padding: 10px; color: #~~ffffff~~; background-color: #~~000~~; width: 600px">	+	<div style="padding: 10px; color: #000; background-color: #CEF2E0; width: 600px">
	The organisation of living systems is a complex network of molecular interactions. Proteins are a central component of the network as they may bind to other proteins as well as to phospholipids, nucleic acids and small molecules to interconnect the diverse physiological functions of the cell. In the background of these observations, the existence of a molecular recognition code for cellular organisation is very suggestive. <br>		The organisation of living systems is a complex network of molecular interactions. Proteins are a central component of the network as they may bind to other proteins as well as to phospholipids, nucleic acids and small molecules to interconnect the diverse physiological functions of the cell. In the background of these observations, the existence of a molecular recognition code for cellular organisation is very suggestive. <br>
	Structural analysis of functional protein complexes suggests at least two classes of protein-protein interactions. In the first class, the so called surface/surface interactions, complementary rigid surfaces link the interacting partners. Under these circumstances, the residues involved in each interacting surface only come together upon protein folding. The second class consists on asymmetric or surface/string interactions, where a protein domain (folding module of moderate size that may resemble a pocket on the protein’s surface) docks a short lineal peptide motive (a peptide ligand) on the partner protein. While surface/surface interactions cannot be inferred because the primary structure is not linearly involved, the binding determinants of a protein interaction domain (PID) may be mapped to short peptides matching the sequence of the ligand peptide. The importance of these recognition domains in the formation of protein complexes by binding to short lineal peptides was firstly demonstrated in the late 1980s and early 1990s [Sadowski 1986 Dec; Mayer 1993; Ren 1993].<br>		Structural analysis of functional protein complexes suggests at least two classes of protein-protein interactions. In the first class, the so called surface/surface interactions, complementary rigid surfaces link the interacting partners. Under these circumstances, the residues involved in each interacting surface only come together upon protein folding. The second class consists on asymmetric or surface/string interactions, where a protein domain (folding module of moderate size that may resemble a pocket on the protein’s surface) docks a short lineal peptide motive (a peptide ligand) on the partner protein. While surface/surface interactions cannot be inferred because the primary structure is not linearly involved, the binding determinants of a protein interaction domain (PID) may be mapped to short peptides matching the sequence of the ligand peptide. The importance of these recognition domains in the formation of protein complexes by binding to short lineal peptides was firstly demonstrated in the late 1980s and early 1990s [Sadowski 1986 Dec; Mayer 1993; Ren 1993].<br>
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	====Modularity of WW PIDs====		====Modularity of WW PIDs====
-	<div style="padding: 10px; color: #~~ffffff~~; background-color: #~~000~~; width: 600px">	+	<div style="padding: 10px; color: #000; background-color: #CEF2E0; width: 600px">
	The WW domain is a well-characterized protein module that mediates specific protein-protein interactions with ligands that contain short proline-rich motifs [Bork 1994; Chen 1995; Sudol 2000]. The domain is composed of 38 amino acids, it has two signature tryptophan (W) residues, and it is one of the smallest among modular protein domains. The signature tryptophan positions are spaced 20–22 amino acids apart and have important structural role. The structure is a three beta-strand meander that forms a shallow binding pocket for proline-rich ligands (reviewed in[Sudol 2005]). In general, the folding of WW domains does not require cognate ligands or co-factors. <br>		The WW domain is a well-characterized protein module that mediates specific protein-protein interactions with ligands that contain short proline-rich motifs [Bork 1994; Chen 1995; Sudol 2000]. The domain is composed of 38 amino acids, it has two signature tryptophan (W) residues, and it is one of the smallest among modular protein domains. The signature tryptophan positions are spaced 20–22 amino acids apart and have important structural role. The structure is a three beta-strand meander that forms a shallow binding pocket for proline-rich ligands (reviewed in[Sudol 2005]). In general, the folding of WW domains does not require cognate ligands or co-factors. <br>
	'''MORE TEXT''' {{hide\|		'''MORE TEXT''' {{hide\|
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	====From Promiscuous Recognition Events to Mutually Exclusive Cellular Responses====		====From Promiscuous Recognition Events to Mutually Exclusive Cellular Responses====
-	<div style="padding: 10px; color: #~~ffffff~~; background-color: #~~000~~; width: 600px">	+	<div style="padding: 10px; color: #000; background-color: #CEF2E0; width: 600px">
	The elucidation of functional pathways of signal transduction, biochemical function or gene regulation, is firstly addressed in proteomics by deriving interaction networks depicting ideally all interactions in the cell. Several attempts have been done in this direction on different model organisms and with varied methods, including co-purification by affinity chromatography [Gavin 2002; Ho 2002; Bouwmeester 2004], yeast two-hybrid [Uetz 2000; Ito 2001], phage display, peptide array technologies [Landgraf 2004], etc. A comparison of datasets derived by individual methods demonstrates that different methods have different potential. <br>		The elucidation of functional pathways of signal transduction, biochemical function or gene regulation, is firstly addressed in proteomics by deriving interaction networks depicting ideally all interactions in the cell. Several attempts have been done in this direction on different model organisms and with varied methods, including co-purification by affinity chromatography [Gavin 2002; Ho 2002; Bouwmeester 2004], yeast two-hybrid [Uetz 2000; Ito 2001], phage display, peptide array technologies [Landgraf 2004], etc. A comparison of datasets derived by individual methods demonstrates that different methods have different potential. <br>
	'''MORE TEXT''' {{hide\|		'''MORE TEXT''' {{hide\|
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	== Who's visiting ==		== Who's visiting ==
-	<div style="padding: 10px; color: #~~ffffff~~; background-color: #~~000~~; width: 600px">	+	<div style="padding: 10px; color: #000; background-color: #CEF2E0; width: 600px">
	start on 18 Mar 2010		start on 18 Mar 2010

Victor Tapia: /* Protein Interaction Domains */

2013-03-07T11:18:29Z

Protein Interaction Domains

←Older revision		Revision as of 11:18, 7 March 2013
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	<div style="padding: 10px; color: #ffffff; background-color: #000; width: 600px">		<div style="padding: 10px; color: #ffffff; background-color: #000; width: 600px">
	The organisation of living systems is a complex network of molecular interactions. Proteins are a central component of the network as they may bind to other proteins as well as to phospholipids, nucleic acids and small molecules to interconnect the diverse physiological functions of the cell. In the background of these observations, the existence of a molecular recognition code for cellular organisation is very suggestive. <br>		The organisation of living systems is a complex network of molecular interactions. Proteins are a central component of the network as they may bind to other proteins as well as to phospholipids, nucleic acids and small molecules to interconnect the diverse physiological functions of the cell. In the background of these observations, the existence of a molecular recognition code for cellular organisation is very suggestive. <br>
-	~~'''MORE TEXT''' {{hide\|~~
-	~~----~~
	Structural analysis of functional protein complexes suggests at least two classes of protein-protein interactions. In the first class, the so called surface/surface interactions, complementary rigid surfaces link the interacting partners. Under these circumstances, the residues involved in each interacting surface only come together upon protein folding. The second class consists on asymmetric or surface/string interactions, where a protein domain (folding module of moderate size that may resemble a pocket on the protein’s surface) docks a short lineal peptide motive (a peptide ligand) on the partner protein. While surface/surface interactions cannot be inferred because the primary structure is not linearly involved, the binding determinants of a protein interaction domain (PID) may be mapped to short peptides matching the sequence of the ligand peptide. The importance of these recognition domains in the formation of protein complexes by binding to short lineal peptides was firstly demonstrated in the late 1980s and early 1990s [Sadowski 1986 Dec; Mayer 1993; Ren 1993].<br>		Structural analysis of functional protein complexes suggests at least two classes of protein-protein interactions. In the first class, the so called surface/surface interactions, complementary rigid surfaces link the interacting partners. Under these circumstances, the residues involved in each interacting surface only come together upon protein folding. The second class consists on asymmetric or surface/string interactions, where a protein domain (folding module of moderate size that may resemble a pocket on the protein’s surface) docks a short lineal peptide motive (a peptide ligand) on the partner protein. While surface/surface interactions cannot be inferred because the primary structure is not linearly involved, the binding determinants of a protein interaction domain (PID) may be mapped to short peptides matching the sequence of the ligand peptide. The importance of these recognition domains in the formation of protein complexes by binding to short lineal peptides was firstly demonstrated in the late 1980s and early 1990s [Sadowski 1986 Dec; Mayer 1993; Ren 1993].<br>
	<br>		<br>
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	<br>		<br>
	In this era of extensive genome sequencing, many PIDs have been discovered. The interaction partners — and, therefore, the functions of many proteins ― may be determined by identifying the critical binding sites for family members through evolutionary tracing [Lichtarge 1996 Mar 29] or mapping protein-protein interactions using functional protein arrays [Phizicky 2003 Mar 13]. Many of the PIDs in proteins can be grouped into families that show clear evidence of their evolution from a common ancestor, and genome sequences from Saccharomyces cerevisiae to Homo sapiens reveal large numbers of proteins that contain one or more common domain.		In this era of extensive genome sequencing, many PIDs have been discovered. The interaction partners — and, therefore, the functions of many proteins ― may be determined by identifying the critical binding sites for family members through evolutionary tracing [Lichtarge 1996 Mar 29] or mapping protein-protein interactions using functional protein arrays [Phizicky 2003 Mar 13]. Many of the PIDs in proteins can be grouped into families that show clear evidence of their evolution from a common ancestor, and genome sequences from Saccharomyces cerevisiae to Homo sapiens reveal large numbers of proteins that contain one or more common domain.
-	}}	+
	</div>		</div>
	<br>		<br>

Victor Tapia: /* Group Members */

2012-02-28T12:24:15Z

Group Members

←Older revision		Revision as of 12:24, 28 February 2012
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	==Group Members==		==Group Members==
	<div style="padding: 10px; color: #ffffff; background-color: #000; width: 600px">		<div style="padding: 10px; color: #ffffff; background-color: #000; width: 600px">
-	*Bernhard Aÿ, Postdoc {{hide\|
-	~~[[Image:Molrec placeholder.png\|130px\|right]]~~
-	~~Tel.: +49 30 450 524 254~~
-	~~Fax: +49 30 450 524 942~~
-	~~E-Mail: bernhard.giese(at)charite.de~~
-
-
-	}}
-	*Prisca Boisguérin, Postdoc {{hide\|
-	~~[[Image:Molrec placeholder.png\|130px\|right]]~~
-	~~Tel.: +49 30 450 524 254~~
-	~~Fax: +49 30 450 524 942~~
-	~~E-Mail: prisca.boisguerin(at)charite.de~~
-
-
-	}}
-	*Zerrin Fidan, Doktorandin {{hide\|
-	~~[[Image:Molrec placeholder.png\|130px\|right]]~~
-	~~Tel.: +49 30 450 524 285~~
-	~~Fax: +49 30 450 524 942~~
-	~~E-Mail: zerrin.fidan(at)charite.de~~
-
-
-	}}
	*Annette Hayungs - Secretary {{hide\|		*Annette Hayungs - Secretary {{hide\|
	[[Image:Molrec placeholder.png\|130px\|right]]		[[Image:Molrec placeholder.png\|130px\|right]]
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	Fax: +49 30 450 524 942		Fax: +49 30 450 524 942
	E-Mail: annette.hayungs(at)charite.de		E-Mail: annette.hayungs(at)charite.de
-
-
-	}}
-	*Marc Hovestädt - Doktorand {{hide\|
-	~~[[Image:Molrec placeholder.png\|130px\|right]]~~
-	~~Tel.: +49 30 450 524 254~~
-	~~Fax: +49 30 450 524 942~~
-	~~E-Mail: marc.hovestaedt(at)charite.de~~


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	Fax: +49 30 450 524 942		Fax: +49 30 450 524 942
	E-Mail: chl(at)charite.de		E-Mail: chl(at)charite.de
-
-
-	}}
-	*[http://openwetware.org/wiki/User:Carsten_C._Mahrenholz Carsten Mahrenholz] - Doktorand {{hide\|
-	~~[[Image:Molrec placeholder.png\|130px\|right]]~~
-	~~Tel.: +49 30 450 524 278~~
-	~~Fax: +49 30 450 524 942~~
-	~~E-Mail: carsten.mahrenholz(at)charite.de~~

Victor Tapia: /* Group Members */

2012-02-28T12:22:11Z

Group Members

←Older revision		Revision as of 12:22, 28 February 2012
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	*[http://openwetware.org/wiki/User:Victor_Tapia Víctor Tapia] - Doktorand {{hide\|		*[http://openwetware.org/wiki/User:Victor_Tapia Víctor Tapia] - Doktorand {{hide\|
	[[Image:Molrec placeholder.png\|130px\|right]]		[[Image:Molrec placeholder.png\|130px\|right]]
-	~~Tel.: +49 30 450 524 046~~	+	ACTUALLY SEARCHING FOR A NEW POSITION
-	~~Fax~~: ~~+49 30 450 524 942~~	+	Email: ve.tapia.m@gmail.com
-	~~E-Mail: victor~~.tapia~~(at)charite~~.de	+

Victor Tapia: /* Messsystemanalyse von Peptidarray Techniken */

2012-01-28T01:03:52Z

Messsystemanalyse von Peptidarray Techniken

←Older revision		Revision as of 01:03, 28 January 2012
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	===Messsystemanalyse von Peptidarray Techniken===		===Messsystemanalyse von Peptidarray Techniken===
	by ''Victor Tapia'' <br>		by ''Victor Tapia'' <br>
-	~~FIGURE {{hide\|~~
-	~~----~~
-	~~[[Image:Mikroarray Messsystem.png\|600px]]~~
-	~~Abbildung 1. Schematischer Überblick der eingesetzten Strategie zur Analyse der Affinitätsvorhersagbarkeit. Panel A zeigt die <br>~~
-	~~Aufgaben mit denen Ist-Bestimmungswerte erzielt worden sind. Diese Aufgaben wurden vom Autor im Rahmen der gegenwärtigen Arbeit <br>~~
-	~~durchgeführt (siehe Materialen & Methoden und [Tapia 2007]). Panel B stellen Aufgaben dar, die im Rahmen früheren Arbeiten vom Autor <br>~~
-	~~durgeführt wurden. Eine ausführliche Beschreibung der Durchfuhrung und Ergebnisse dieser letzten Arbeiten sind im [Tapia 2004; <br>~~
-	~~Weiser 2005] veröffentlich worden. Die in beiden Panele mit 1 bis 3 beschriffteten Aufgaben kennzeichnen die wessentliche <br>~~
-	~~Unterschiede der jewieligen Messsysteme: Peptid Synthese (1), kovalente Kopplung an die Trägeroberfläche des Messsystems (2), und <br>~~
-	~~die Bindungsstudie an sich (3). <br>~~
-	~~<br>~~
-	~~----~~
-	}}

	<div style="padding: 10px; color: #ffffff; background-color: #000; width: 600px">		<div style="padding: 10px; color: #ffffff; background-color: #000; width: 600px">