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Additional file 14. A table with description of strains and plasmids generated and used in this study and graphical representation of over-expressed operons/genes

Modulation of Coiled-Coil Dimer Stability through Surface Residues while Preserving Pairing Specificity

The coiled-coil dimer is a widespread protein structural motif and, due to its designability, represents an attractive building block for assembling modular nanostructures. The specificity of coiled-coil dimer pairing is mainly based on hydrophobic and electrostatic interactions between residues at positions a, d, e, and g of the heptad repeat. Binding affinity, on the other hand, can also be affected by surface residues that face away from the dimerization interface. Here we show how design of the local helical propensity of interacting peptides can be used to tune the stabilities of coiled-coil dimers over a wide range. By designing intramolecular charge pairs, regions of high local helical propensity can be engineered to form trigger sequences, and dimer stability is adjusted without changing the peptide length or any of the directly interacting residues. This general principle is demonstrated by a change in thermal stability by more than 30 °C as a result of only two mutations outside the binding interface. The same approach was successfully used to modulate the stabilities in an orthogonal set of coiled-coils without affecting their binding preferences. The stability effects of local helical propensity and peptide charge are well described by a simple linear model, which should help improve current coiled-coil stability prediction algorithms. Our findings enable tuning the stabilities of coiled-coil-based building modules match a diverse range of applications in synthetic biology and nanomaterials

Energetic Basis of Uncoupling Folding from Binding for an Intrinsically Disordered Protein

Intrinsically disordered proteins (IDPs) are proteins that lack a unique three-dimensional structure in their native state. Many have, however, been found to fold into a defined structure when interacting with specific binding partners. The energetic implications of such behavior have been widely discussed, yet experimental thermodynamic data is scarce. We present here a thorough thermodynamic and structural study of the binding of an IDP (antitoxin CcdA) to its molecular target (gyrase poison CcdB). We show that the binding-coupled folding of CcdA is driven by a combination of specific intramolecular interactions that favor the final folded structure and a less specific set of intermolecular contacts that provide a desolvation entropy boost. The folded structure of the bound IDP appears to be defined largely by its own amino acid sequence, with the binding partner functioning more as a facilitator than a mold to conform to. On the other hand, specific intermolecular interactions do increase the binding affinity up to the picomolar range. Overall, this study shows how an IDP can achieve very strong and structurally well-defined binding and it provides significant insight into the molecular forces that enable such binding properties

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Additional file 8. Results of the 2-D PAGE experiments: representation of 2-D gels of WT and HP strain in different time points (t1-t4), comparison of 2-D images between HP and WT in t1 and t2

MOESM2 of Integrated omics approaches provide strategies for rapid erythromycin yield increase in Saccharopolyspora erythraea

Additional file 2. An integrated table of all obtained genomic, transcriptomic and proteomic data as well as data obtained and published in previous studies (Peano et al., 2012; Marcellin et al., 2013, Li et al., 2011)

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Additional file 4. A table for validation of microarray data by qPCR

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Additional file 12. Figures representing western blot analyses of constitutively over-expressed ilvB1 gene and mms operon (mmsOp)

CC-protein-origami

Dataset includes:<p><strong>Topologies-circular-permutations-TCO.xlsx</strong> – List of topologies and circular permutations in file</p><p><strong>CC-protein-origami.fasta</strong> – List of all the design sequences in fasta format.</p><p><strong>all-atom-models.zip</strong> – representative models generated by CoCoPOD, including the models with best fit to SAXS data</p><p><strong>SAXS-data.zip</strong> – SAXS scattering curves of constructs presented in the main article. electron-reconstruction – negative stain density reconstructions.</p><p><b>electron-reconstruction.zip</b> - contains the reconstituted electron microscopy densities in mrc format.<br></p><p><b>Supplementary Source Code.zip </b>– contains the source code of CoCoPOD and all needed files for installation. <b> </b><strong> </strong><br></p><p><br></p