large and spatially proximal paratopes, minimal newly exposed SASA upon terminal trimming, and a. Binding function is evaluated against several molecular targets to determine which proteins evolve specific binding variants. This simple yet versatile model system can help elucidate the molecular interactions implicated in MLOs and pave ways to a new type of biomimetic materials. Protein scaffold libraries consisting of millions of unique variants are expressed with diversified binding interfaces. We report the structure of a Lig-E type DNA ligase bound to the nicked DNA-adenylate reaction intermediate, confirming that complete encirclement is unnecessary for substrate. Moreover, the droplets formed are capable of recruiting proteins and RNAs and providing a favorable environment for a biochemical reaction with highly enriched components, thereby mimicking the function of natural MLOs. In the present study, we have used a structure-guided mutagenesis approach to investigate the role of conserved regions in the Lig E proteins with respect to DNA binding. Hybrids undergo LLPS into micron-sized liquid droplets resembling LLPS in vitro and in living cells. ( a) The mevalonate pathway was placed under expression. There is a striking parallel with the structure of a mini-Glu-zincin, which represents the minimum structure of a Glu-zincin (a metallopeptidase in which the third zinc ligand is a glutamic acid). we have used a structure-guided mutagenesis approach to investigate the role of conserved regions in the Lig E proteins with respect to DNA binding. Figure 3: Synthetic scaffolds built from modular protein-protein interaction domains provide modular control over metabolic pathway flux. It contains the minimum structural features of a member of this protein superfamily, and can be described as a 'mini- zincin'. Here, we report the first design of synthetic hybrids consisting of short oligopeptides of fewer than 10 residues as "stickers" and dextran as a "spacer" to recapitulate the characteristics of IDPs, as exemplified by the multivalent FUS protein. DNA Binding With a Minimal Scaffold: Structure-Function Analysis of Lig E DNA Ligases Nucleic Acids Res. The advantages include smaller size and a more robust, single-domain structural framework with a defined binding surface amenable to mutation. Genetic engineering is generally applied to reconstruct IDPs harboring over 100 amino acid residues. Engineered small non-antibody protein scaffolds are a promising alternative to antibodies and are especially attractive for use in protein therapeutics and diagnostics. Liquid-liquid phase separation (LLPS) is an emerging and universal mechanism for intracellular organization, particularly, by forming membraneless organelles (MLOs) hosting intrinsically disordered proteins (IDPs) as scaffolds.
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