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Backbone Brackets and Arginine Tweezers delineate Class I and Class II aminoacyl tRNA synthetases [article]

Florian Kaiser, Sebastian Bittrich, Sebastian Salentin, Christoph Leberecht, V. Joachim Haupt, Sarah Krautwurst, Michael Schroeder, Dirk Labudde
2017 bioRxiv   pre-print
Backbone Brackets and Arginine Tweezers were traced back to the proposed Protozymes and their more efficient successors, the Urzymes.  ...  The one unifying aspect of both classes is their function of binding ATP. We identified Backbone Brackets and Arginine Tweezers as most compact ATP binding motifs characteristic for each Class.  ...  Due to their 162 geometrical characteristics, we refer to the Class I and Class II motifs as Backbone Brackets and Arginine Tweezers, respectively.  ... 
doi:10.1101/198846 fatcat:adjhdoebkva2hi2hfslwcwkwva

Backbone Brackets and Arginine Tweezers delineate Class I and Class II aminoacyl tRNA synthetases

Florian Kaiser, Sebastian Bittrich, Sebastian Salentin, Christoph Leberecht, V. Joachim Haupt, Sarah Krautwurst, Michael Schroeder, Dirk Labudde, Roland L. Dunbrack
2018 PLoS Computational Biology  
Backbone Brackets and Arginine Tweezers were traced back to the proposed Protozymes and their more efficient successors, the Urzymes.  ...  While Class I binds via interactions mediated by 8 backbone hydrogen bonds, Class II uses a pair of arginine residues to establish salt 9 bridges to its ATP ligand.  ...  Due to their 162 geometrical characteristics, we refer to the Class I and Class II motifs as Backbone Brackets and Arginine Tweezers, respectively.  ... 
doi:10.1371/journal.pcbi.1006101 pmid:29659563 pmcid:PMC5919687 fatcat:vmytdp6s5nhhnpzbaxwb3inula

Characterizing the relation of functional and Early Folding Residues in protein structures using the example of aminoacyl-tRNA synthetases

Sebastian Bittrich, Michael Schroeder, Dirk Labudde, Yaakov Koby Levy
2018 PLoS ONE  
OPEN ACCESS Citation: Bittrich S, Schroeder M, Labudde D (2018) Characterizing the relation of functional and Early Folding Residues in protein structures using the example of aminoacyl-tRNA synthetases  ...  Using the two diverse superfamilies of aminoacyl-tRNA synthetases (aaRS), it is shown that the position of EFR is preserved over the course of evolution even when the corresponding sequence conservation  ...  Furthermore, the authors acknowledge scientific discussion and proofreading of the manuscript by Florian Kaiser, Christoph Leberecht, Sebastian Salentin, and Alexander Eisold.  ... 
doi:10.1371/journal.pone.0206369 fatcat:5zw4mzqbk5bqfeeaxn6of5ul4e

Characterization of Amino Acid Recognition in Aminoacyl-tRNA Synthetases [article]

Florian Kaiser, Sarah Krautwurst, Sebastian Salentin, V. Joachim Haupt, Christoph Leberecht, Sebastian Bittrich, Dirk Labudde, Michael Schroeder
2019 bioRxiv   pre-print
There are many theories on the emergence of aminoacyl-tRNA synthetases and their amino acid binding sites.  ...  For the first time, we extensively characterize and quantify the interactions between aminoacyl-tRNA synthetases and bound amino acids.  ...  Especially aromatic amino acid recognition in Class I tryptophanyl-tRNA synthetases (TrpRSs) and tyrosyl-tRNA synthetases (TyrRSs) is distinct from Class II aaRSs and forms two outgroups in the embedding  ... 
doi:10.1101/606459 fatcat:3fm3fp2d6fda5gcxubwqg6k4i4

Characterizing the relation of functional and Early Folding Residues in protein structures using the example of aminoacyl-tRNA synthetases [article]

Sebastian Bittrich, Michael Schroeder, Dirk Labudde
2018 bioRxiv   pre-print
Aminoacyl-tRNA synthetases demonstrate this separation in an evolutionary context: the positions of EFR are preserved over the course of evolution and evolutionary pressure is smaller in comparison to  ...  elements and guide their respective assembly.  ...  Acknowledgments 623 The authors thank Florian Kaiser, Christoph Leberecht, Sebastian Salentin, and 624 Alexander Eisold for scientific discussions and/or proofreading the manuscript.  ... 
doi:10.1101/290627 fatcat:hhlbabvnkvhyfpnjooln4ynyta

A Generic Method for the Production of Recombinant Proteins in Escherichia coli Using a Dual Hexahistidine-Maltose-Binding Protein Affinity Tag [chapter]

Joseph E. Tropea, Scott Cherry, Sreedevi Nallamsetty, Christophe Bignon, David S. Waugh
2007 Msphere  
The MBP moiety improves the yield and enhances the solubility of the passenger protein while the His-tag facilitates its purification.  ...  The fusion protein (His 6 -MBP-passenger) is purified by immobilized metal affinity chromatography (IMAC) on nickel-nitrilotriacetic acid (Ni-NTA) resin and then cleaved in vitro with His 6 -tobacco etch  ...  Acknowledgments The Acknowledgments I thank Joanne Yeh and Matti Nikkola for helpful discussions regarding the chapter and Mark Harris for his help with the photographs.  ... 
doi:10.1007/978-1-59745-209-0_1 pmid:17272834 fatcat:3ytri6xm45fztgo5nz7i2o4ssy

Sycamore (Platanus spp) [chapter]

2008 Encyclopedia of Genetics, Genomics, Proteomics and Informatics  
IFN-γ upregulates the expression of major histocompatibility class I and class II molecules that lead to the activation of killer lymphocytes.  ...  of shortage of space): GT II: 5Ј-GCTGTGGAATGT-3Ј GT I: 5Ј-GGTGTGGAAATG-3Ј TC I and TC II: 5Ј-TCCCCAG-3Ј SPH -II: 5Ј-AAGTATGCA-3Ј SPH -I: 5Ј-Organization Gene and polypeptide map of SV40 Figure S69 .  ...  After that lower muscle regeneration occurred and loss of CD34 expression and loss of myogenic activity were observed.  ... 
doi:10.1007/978-1-4020-6754-9_16470 fatcat:vd3dng4xina5piwpaioaz25tf4

Single Strand Assimilation [chapter]

2008 Encyclopedia of Genetics, Genomics, Proteomics and Informatics  
IFN-γ upregulates the expression of major histocompatibility class I and class II molecules that lead to the activation of killer lymphocytes.  ...  of shortage of space): GT II: 5Ј-GCTGTGGAATGT-3Ј GT I: 5Ј-GGTGTGGAAATG-3Ј TC I and TC II: 5Ј-TCCCCAG-3Ј SPH -II: 5Ј-AAGTATGCA-3Ј SPH -I: 5Ј-Organization Gene and polypeptide map of SV40 Figure S69 .  ...  After that lower muscle regeneration occurred and loss of CD34 expression and loss of myogenic activity were observed.  ... 
doi:10.1007/978-1-4020-6754-9_15672 fatcat:2x2wsjganfaznnshm5kvluxr7a

A Generic Method for the Production of Recombinant Proteins in Escherichia coli Using a Dual Hexahistidine-Maltose-Binding Protein Affinity Tag [chapter]

Joseph E. Tropea, Scott Cherry, Sreedevi Nallamsetty, Christophe Bignon, David S. Waugh
Macromolecular Crystallography Protocols, Volume 1  
The MBP moiety improves the yield and enhances the solubility of the passenger protein while the His-tag facilitates its purification.  ...  The fusion protein (His 6 -MBP-passenger) is purified by immobilized metal affinity chromatography (IMAC) on nickel-nitrilotriacetic acid (Ni-NTA) resin and then cleaved in vitro with His 6 -tobacco etch  ...  Acknowledgments The Acknowledgments I thank Joanne Yeh and Matti Nikkola for helpful discussions regarding the chapter and Mark Harris for his help with the photographs.  ... 
doi:10.1385/1-59745-209-2:1 fatcat:jtu6mof445fctgkuaqclcssbbe