PspF-binding domain PspA1-144 and the PspA·F complex: New insights into the coiled-coil-dependent regulation of AAA+ proteins.

Phage shock protein A (PspA) belongs to the highy conserved PspA/IM30 family and is a key component of the stress inducible Psp system in Escherichia coli. One of its central roles is the regulatory interaction with the transcriptional activator of this system, the σ(54) enhancer-binding protein PspF, a member of the AAA+ protein family. The PspA/F regulatory system has been intensively studied and serves as a paradigm for AAA+ enzyme regulation by trans-acting factors. However, the molecular mechanism of how exactly PspA controls the activity of PspF and hence σ(54) -dependent expression of the psp genes is still unclear. To approach this question, we identified the minimal PspF-interacting domain of PspA, solved its structure, determined its affinity to PspF and the dissociation kinetics, identified residues that are potentially important for PspF regulation and analyzed effects of their mutation on PspF in vivo and in vitro. Our data indicate that several characteristics of AAA+ regulation in the PspA·F complex resemble those of the AAA+ unfoldase ClpB, with both proteins being regulated by a structurally highly conserved coiled-coil domain. The convergent evolution of both regulatory domains points to a general mechanism to control AAA+ activity for divergent physiologic tasks via coiled-coil domains.

N-terminal protein modification by substrate-activated reverse proteolysis.

Although site-specific incorporation of artificial functionalities into proteins is an important tool in both basic and applied research, it can be a major challenge to protein chemists. Enzymatic protein modification is an attractive goal due to the inherent regio- and stereoselectivity of enzymes, yet their specificity remains a problem. As a result of the intrinsic reversibility of enzymatic reactions, proteinases can in principle catalyze ligation reactions. While this makes them attractive tools for site-specific protein bioconjugation, competing hydrolysis reactions limits their general use. Here we describe the design and application of a highly specific trypsin variant for the selective modification of N-terminal residues of diverse proteins with various reagents. The modification proceeds quantitatively under native (aqueous) conditions. We show that the variant has a disordered zymogen-like activation domain, effectively suppressing the hydrolysis reaction, which is converted to an active conformation in the presence of appropriate substrates.

Probing selected structural regions in the secreted phospholipase A2 from Arabidopsis thaliana for their impact on stability and activity.

In contrast to the well characterized secreted phospholipases A2 (sPLA2) from animals, their homologues from plants have been less explored. Their production in purified form is more difficult, and no data on their stability are known. In the present paper, different variants of the sPLA2 isoform α from Arabidopsis thaliana (AtPLA2α) were designed using a new homology model with the aim to probe the impact of regions that are assumed to be important for stability and catalysis. Moreover tryptophan residues were introduced in critical regions to enable stability studies by fluorescence spectroscopy. The variants were expressed in Escherichia coli and the purified enzymes were analyzed to get first insights into the peculiarities of structure stability and structure activity relationships in plant sPLA2s in comparison with the well-characterized homologous enzymes from bee venom and porcine pancreas. Stability data of the AtPLA2 variants obtained by fluorescence or CD measurements of the reversible unfolding by guanidine hydrochloride and urea showed that all enzyme variants are less stable than the enzymes from animal sources although a similar tertiary core structure can be assumed based on molecular modeling. More extended loop structures at the N-terminus in AtPLA2α are suggested to be the main reasons for the much lower thermodynamic stabilities and cooperativities of the transition curves. Modifications in the N-terminal region (insertion, deletion, substitution by a Trp residue) exhibited a strong positive effect on activity whereas amino acid exchanges in other regions of the protein such as the Ca(2+)-binding loop and the loop connecting the two central helices were deleterious with respect to activity.

Significant stabilization of ribonuclease A by additive effects.

Among the strategies that employ genetic engineering to stabilize proteins, the introduction of disulfide bonds has proven to be a very potential approach. As, however, the replacement of amino acid residues by cysteines and the subsequent formation of the covalent bond can result in a severe deformation of the parental protein structure, the stabilization effect is strongly context dependent. Alternatively, the introduction of charged amino acid residues at the surface, which may result in the formation of extra ionic interactions or hydrogen bonds, provide propitious means for protein stabilization. The generation of an extra disulfide bond between residues 4 and 118 in ribonuclease A had resulted in a stabilization by 6 °C or 7 kJ mol(-1), which was mainly caused by a deceleration of the unfolding reaction [Pecher, P. & Arnold, U. (2009) Biophys Chem, 141, 21-28]. Here, Asp83 was replaced by Glu resulting in a comparable stabilization. Moreover, combination of both mutations led to an additive effect and the resulting ribonuclease A variant (T(m) ~ 76 °C, ΔG° ~ 53 kJ mol(-1)) is the most stable ribonuclease A variant described so far. The analysis of the crystal structure of A4C/D83E/V118C-ribonuclease A reveals the formation of a salt bridge between the γ-carboxyl group of Glu83 and the ε-amino group of Lys104.