Probing the unfolding region of ribonuclease A by site-directed mutagenesis

Conserved amino acid networks modulate discrete functional properties in an enzyme superfamily

In this work, we applied the sequence-based statistical coupling analysis approach to characterize conserved amino acid networks important for biochemical function in the pancreatic-type ribonuclease (ptRNase) superfamily. This superfamily-wide analysis indicates a decomposition of the RNase tertiary structure into spatially distributed yet physically connected networks of co-evolving amino acids, termed sectors. Comparison of this statistics-based description with new NMR experiments data shows that discrete amino acid networks, termed sectors, control the tuning of distinct functional properties in different enzyme homologs. Further, experimental characterization of evolutionarily distant sequences reveals that sequence variation at sector positions can distinguish homologs with a conserved dynamic pattern and optimal catalytic activity from those with altered dynamics and diminished catalytic activities. Taken together, these results provide important insights into the mechanistic design of the ptRNase superfamily, and presents a structural basis for evolutionary tuning of function in functionally diverse enzyme homologs.

Inactivation of immobilized trypsin under dissimilar conditions produces trypsin molecules with different structures

Bovine trypsin immobilized on glyoxyl agarose and submitted to different inactivation conditions produce different conformations.

Native state dynamics affects the folding transition of porcine pancreatic phospholipase A2

Porcine pancreatic phospholipase A2, a small and disulfide rich protein, is extremely resistant against chemically or thermally induced unfolding. Despite this marked resistance, the protein displays broad unfolding transitions resulting in comparatively low apparent thermodynamic stability. Broad unfolding transitions may result from undetected folding intermediates, residual structures in the unfolded state or an inhomogeneity of the native state. Using circular dichroism, fluorescence, and NMR spectroscopy, we ruled out the existence of stably populated folding intermediates, whereas UV absorbance measurements hinted at stable residual structures in the unfolded state. These residual structures proved, however, to have no impact on the folding parameters. Studies by limited proteolysis, CD, and NMR spectroscopy under non-denaturing conditions suggested pronounced dynamics of the protein in the native state, which as long as unrestrained by acidic pH or bound Ca(2+) ions exert considerable influence on the unfolding transition.

Stability and folding of amphibian ribonuclease A superfamily members in comparison with mammalian homologues

Comparative studies on homologous proteins can provide knowledge on how limited changes in the primary structure find their expression in large effects on catalytic activity, stability or the folding behavior. For more than half a century, members of the ribonuclease A superfamily have been the subject of a myriad of studies on protein folding and stability. Both the unfolding and refolding kinetics as well as the structure of several folding intermediates of ribonuclease A have been characterized in detail. Moreover, the RNA-degrading activity of these enzymes provides a basis for their cytotoxicity, which renders them potential tumor therapeutics. Because amphibian ribonuclease A homologues evade the human ribonuclease inhibitor, they emerged as particularly promising candidates. Interestingly, the amphibian ribonuclease A homologues investigated to date are more stable than the mammalian homologues. Nevertheless, despite the generation of numerous genetically engineered variants, knowledge of the folding of amphibian ribonuclease A homologues remains rather limited. An exception is onconase, a ribonuclease A homologue from Rana pipiens, which has been characterized in detail. This review summarizes the data on the unfolding and refolding kinetics and pathways, as well on the stability of amphibian ribonuclease A homologues compared with those of ribonuclease A, the best known member of this superfamily.

Protein prosthesis: β-peptides as reverse-turn surrogates

The introduction of non-natural modules could provide unprecedented control over folding/unfolding behavior, conformational stability, and biological function of proteins. Success requires the interrogation of candidate modules in natural contexts. Here, expressed protein ligation is used to replace a reverse turn in bovine pancreatic ribonuclease (RNase A) with a synthetic β-dipeptide: β²-homoalanine-β³-homoalanine. This segment is known to adopt an unnatural reverse-turn conformation that contains a 10-membered ring hydrogen bond, but one with a donor-acceptor pattern opposite to that in the 10-membered rings of natural reverse turns. The RNase A variant has intact enzymatic activity, but unfolds more quickly and has diminished conformational stability relative to native RNase A. These data indicate that hydrogen-bonding pattern merits careful consideration in the selection of beneficial reverse-turn surrogates.

Mapping the stability clusters in bovine pancreatic ribonuclease A

In the present work, we have thermodynamically characterized the thermally induced unfolding of 20 variants of bovine pancreatic ribonuclease A (RNase A) to experimentally describe the residues and the regions that are critical for the stability of the enzyme. The achieved results, complemented with previous studies by our group, allowed us to define the significance of the two hydrophobic nuclei present in the RNase A structure, as well as the contribution of the participating residues within each nucleus, to the global enzyme stability. We propose a structural model for the major and the minor hydrophobic nuclei of RNase A. The major nucleus is composite and located in the cavity delimited by alpha-helices 1 and 3, and the beta-sheet that is formed by strands 2, 3, 5, and 6. It consists of a central tight packed part constituted by residues Phe8, Met13, Val54, Val57, Ile106, Val108, and Phe120. This central part is surrounded by a layer formed by residues Val63, Tyr73, Met79, Ile107, Val116, and Val118. The minor nucleus, although less complex, is also constituted by a tight packing that involves the side chains of residues Tyr25, Met29, Met30, Leu35, Phe46, and Tyr97, which fill the cavity that originates the beta-sheet formed by beta-strands 1, 4, and 5 together with alpha-helix2.

Kinetic and thermodynamic stability of bacterial intracellular aggregates

Protein aggregation is related to many human disorders and constitutes a major bottleneck in protein production. However, little is known about the conformational properties of in vivo formed aggregates and how they relate to the specific polypeptides embedded in them. Here, we show that the kinetic and thermodynamic stability of the inclusion bodies formed by the Abeta42 Alzheimer peptide and its Asp19 alloform differ significantly and correlate with their amyloidogenic propensity and solubility inside the cell. Our results indicate that the nature of the polypeptide chain determines the specific conformational properties of intracellular aggregates. This implies that different protein inclusions impose dissimilar challenges to the cellular quality-control machinery.

Pressure as a tool to study protein-unfolding/refolding processes: The case of ribonuclease A

This paper gives an overview of the application of high-pressure to study the folding/unfolding processes of proteins using Ribonuclease A as a model protein. A particular focus is the study of pressure-equilibrium unfolding and folding kinetics using variants and the information obtained by comparing these with the wild-type enzyme.

Contribution of Structural Peculiarities of Onconase to Its High Stability and Folding Kinetics

Onconase (ONC) from Rana pipiens is the smallest member of the ribonuclease A (RNase A) superfamily. Despite a tertiary structure similar to RNase A, ONC is distinguished by an extremely high thermodynamic stability. In the present paper we have probed the significance of three structural regions, which exhibit structural peculiarities in comparison to RNase A, for the stability of ONC to temperature and guanidine hydrochloride induced denaturation: (i) the N-terminal pyroglutamate residue, (ii) the hydrophobic cluster between helix I and the first beta-sheet, and (iii) the C-terminal disulfide bond. For this purpose, the enzyme variants <E1E-, <E1P-, F28T-, F28A-, F36Y-, and C87A/C104A-ONC were produced and studied in equilibrium and kinetic measurements. The destabilizing influence of the mutations strongly depended on the modified structural region. The exchanges of the N-terminal pyroglutamate (<E1E- and <E1P-ONC) had the smallest impact (DeltaDeltaG([D])50% = 4.2 and 7.0 kJ mol(-)(1)), while interferences in the hydrophobic cluster (F28T-, F28A-, and F36Y-ONC) had larger effects (DeltaDeltaG([D])50% = 22.2, 20.9, and 19.5 kJ mol(-)(1)). The removal of the C-terminal disulfide bond (C87A/C104A-ONC) showed the largest influence on stability (DeltaDeltaG([D])50% = 32.0 kJ mol(-)(1)). As concluded from the comparison of DeltaDeltaG([D])50% and DeltaDeltaG++(U)[D]50%, all destabilization effects were exclusively caused by increased unfolding rate constants except for C87A/C104A-ONC, where unfolding as well as folding was impacted. Of all amino acid residues investigated, Phe28, which is unique for ONC among the ribonucleases, had the greatest importance for rate of unfolding. Our data on the folding and unfolding kinetics indicate that the strong stabilization of ONC in comparison to RNase A is caused by a dramatic deceleration of the unfolding reaction.