The backbone structure of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein is essentially identical to its mesophilic E. coli homolog

<p>Abstract</p> <p>Background</p> <p>Comparison of experimentally determined mesophilic and thermophilic homologous protein structures is an important tool for understanding the mechanisms that contribute to thermal stability. Of particular interest are pairs of homologous structures that are structurally very similar, but differ significantly in thermal stability.</p> <p>Results</p> <p>We report the X-ray crystal structure of a <it>Thermoanaerobacter tengcongensis </it>ribose binding protein (tteRBP) determined to 1.9 Å resolution. We find that tteRBP is significantly more stable (^<it>app</it><it>T</it>_{<it>m </it>}value ~102°C) than the mesophilic <it>Escherichia coli </it>ribose binding protein (ecRBP) (^<it>app</it><it>T</it>_{<it>m </it>}value ~56°C). The tteRBP has essentially the identical backbone conformation (0.41 Å RMSD of 235/271 C_αpositions and 0.65 Å RMSD of 270/271 C_αpositions) as ecRBP. Classification of the amino acid substitutions as a function of structure therefore allows the identification of amino acids which potentially contribute to the observed thermal stability of tteRBP in the absence of large structural heterogeneities.</p> <p>Conclusion</p> <p>The near identity of backbone structures of this pair of proteins entails that the significant differences in their thermal stabilities are encoded exclusively by the identity of the amino acid side-chains. Furthermore, the degree of sequence divergence is strongly correlated with structure; with a high degree of conservation in the core progressing to increased diversity in the boundary and surface regions. Different factors that may possibly contribute to thermal stability appear to be differentially encoded in each of these regions of the protein. The tteRBP/ecRBP pair therefore offers an opportunity to dissect contributions to thermal stability by side-chains alone in the absence of large structural differences.</p

Avsikter och ambitioner med medborgarbudgetering i Göteborg

Syfte: Uppsatsen studerar två fall av medborgarbudgetering i Göteborgs stad med syftet att undersöka hur stadsdelsnämnderna avser demokratisera områdena. Teori: Teoriramen består av två idealtyper av medborgardialog som utgörs av ett idealistiskt perspektiv och ett kritiskt perspektiv. Metod: Kvalitativ textanalys och semi-strukturerade intervjuer. Resultat: Studiens resultat påvisar hur den politiska ambitionen samt syfte och genomförande i stadsdelarnas formuleringar går i linje med det idealistiska perspektivet. Däremot påvisas det hur en kritisk argumentationslinje återfinns bland de tjänstepersoner som varit delaktiga i processen.This study aims, through text analysis and semi-structured interviews, to research citizen dialogue. More specifically two cases of participatory budgeting in the city of Gothenburg taken place in Majorna-Linné and Västra Hisingen. Participatory budgeting is increasing in use within Swedish municipalities as a response to declining public democratic involvement and decreasing trust for political electives. General expectations on citizen dialogue and participatory budgeting is that trust and legitimacy will increase when citizens are given the opportunity to be involved in political decision making. Previous research on deliberative democracy and citizen dialogue shows different perspectives in how citizen dialogue often is framed. These are idealistic/normative and critical/cynical perspectives. These perspectives are used in this study and are aimed to categorize documents and interviews from both cases of participatory budgeting in the purpose to show in what ways the city districts intend to democratize society. The results show how the districts formulate the purpose and the implementation with participatory budgeting in idealistic characteristics. However, the study also shows conflicting ambitions regarding the political and operational level of the city districts. In particular public sector employees expressed arguments along the lines of the critical perspective regarding inclusion and making way for social change. Although, the political guidelines highly focused on idealistic arguments in terms of generating increased legitimacy and efficiency for political decisions. In conclusion both city districts, in spite of confliction ambitions, aim to democratize society in terms of the idealistic perspective meaning the participatory budgeting is highly process oriented and less focused on outcomes

Chromophore carbonyl twisting in fluorescent biosensors encodes direct readout of protein conformations with multicolor switching

Abstract Fluorescent labeling of proteins is a powerful tool for probing structure-function relationships with many biosensing applications. Structure-based rules for systematically designing fluorescent biosensors require understanding ligand-mediated fluorescent response mechanisms which can be challenging to establish. We installed thiol-reactive derivatives of the naphthalene-based fluorophore Prodan into bacterial periplasmic glucose-binding proteins. Glucose binding elicited paired color exchanges in the excited and ground states of these conjugates. X-ray structures and mutagenesis studies established that glucose-mediated color switching arises from steric interactions that couple protein conformational changes to twisting of the Prodan carbonyl relative to its naphthalene plane. Mutations of residues contacting the carbonyl can optimize color switching by altering fluorophore conformational equilibria in the apo and glucose-bound proteins. A commonly accepted view is that Prodan derivatives report on protein conformations via solvatochromic effects due to changes in the dielectric of their local environment. Here we show that instead Prodan carbonyl twisting controls color switching. These insights enable structure-based biosensor design by coupling ligand-mediated protein conformational changes to internal chromophore twists through specific steric interactions between fluorophore and protein

The backbone structure of the thermophilic ribose binding protein is essentially identical to its mesophilic homolog-3

S 55–61, 2/residues 117–126, 3/residues 149–156). (B) Close-up view of the polar binding pocket residues in tteRBP (blue) and ecRBP (magenta). Ribose is shown in gray. Critical residues involved in ribose binding are indicated (where the tteRBP and ecRBP numbering are different, the former is given first). (C) Close-up view of the non-polar binding pocket amino acids of tteRBP (blue) and ecRBP (magenta). (D) Structural differences in the Cα positions of the aligned models of ecRBP and tteRBP generated by LSQMAN [60]. Dashed and dotted lines indicate the RMSD of 235/271 and 270/271 of the Cα atoms respectively of the aligned structures. The N- and C- terminal residues are indicated with a solid line. Loops and turns are indicated (asterisk), or loops (underlined asterisk) in the binding pocket region.<p><b>Copyright information:</b></p><p>Taken from "The backbone structure of the thermophilic ribose binding protein is essentially identical to its mesophilic homolog"</p><p>http://www.biomedcentral.com/1472-6807/8/20</p><p>BMC Structural Biology 2008;8():20-20.</p><p>Published online 28 Mar 2008</p><p>PMCID:PMC2315655.</p><p></p

The backbone structure of the thermophilic ribose binding protein is essentially identical to its mesophilic homolog-5

underlined, amino acids that are conserved but not identical are in bold type (charge inversions are scored as non-conservative here). Core, boundary or surface classification of amino acids is shown below the aligned residues.<p><b>Copyright information:</b></p><p>Taken from "The backbone structure of the thermophilic ribose binding protein is essentially identical to its mesophilic homolog"</p><p>http://www.biomedcentral.com/1472-6807/8/20</p><p>BMC Structural Biology 2008;8():20-20.</p><p>Published online 28 Mar 2008</p><p>PMCID:PMC2315655.</p><p></p

The backbone structure of the thermophilic ribose binding protein is essentially identical to its mesophilic homolog-2

Ted.<p><b>Copyright information:</b></p><p>Taken from "The backbone structure of the thermophilic ribose binding protein is essentially identical to its mesophilic homolog"</p><p>http://www.biomedcentral.com/1472-6807/8/20</p><p>BMC Structural Biology 2008;8():20-20.</p><p>Published online 28 Mar 2008</p><p>PMCID:PMC2315655.</p><p></p

The backbone structure of the thermophilic ribose binding protein is essentially identical to its mesophilic homolog-6

S). Thermal denaturation of ecRBP in the absence (open circle) or presence of 1 mM ribose (black circles). Solid lines in (A) are fit to a two-state model [31, 32] which takes into account the native and denatured baseline slopes. (B) Extrapolated of tteRBP in the absence (open squares) or presence of 1 mM ribose (black squares) obtained from a series of thermal melting curves at different GdCl concentrations. Solid lines represent linear fits to the observations.<p><b>Copyright information:</b></p><p>Taken from "The backbone structure of the thermophilic ribose binding protein is essentially identical to its mesophilic homolog"</p><p>http://www.biomedcentral.com/1472-6807/8/20</p><p>BMC Structural Biology 2008;8():20-20.</p><p>Published online 28 Mar 2008</p><p>PMCID:PMC2315655.</p><p></p

The backbone structure of the thermophilic ribose binding protein is essentially identical to its mesophilic homolog-0

underlined, amino acids that are conserved but not identical are in bold type (charge inversions are scored as non-conservative here). Core, boundary or surface classification of amino acids is shown below the aligned residues.<p><b>Copyright information:</b></p><p>Taken from "The backbone structure of the thermophilic ribose binding protein is essentially identical to its mesophilic homolog"</p><p>http://www.biomedcentral.com/1472-6807/8/20</p><p>BMC Structural Biology 2008;8():20-20.</p><p>Published online 28 Mar 2008</p><p>PMCID:PMC2315655.</p><p></p

The backbone structure of the thermophilic ribose binding protein is essentially identical to its mesophilic homolog-1

S). Thermal denaturation of ecRBP in the absence (open circle) or presence of 1 mM ribose (black circles). Solid lines in (A) are fit to a two-state model [31, 32] which takes into account the native and denatured baseline slopes. (B) Extrapolated of tteRBP in the absence (open squares) or presence of 1 mM ribose (black squares) obtained from a series of thermal melting curves at different GdCl concentrations. Solid lines represent linear fits to the observations.<p><b>Copyright information:</b></p><p>Taken from "The backbone structure of the thermophilic ribose binding protein is essentially identical to its mesophilic homolog"</p><p>http://www.biomedcentral.com/1472-6807/8/20</p><p>BMC Structural Biology 2008;8():20-20.</p><p>Published online 28 Mar 2008</p><p>PMCID:PMC2315655.</p><p></p