Oligomerization of Ribonuclease A

Human RNase 1 can extensively oligomerize through 3D domain swapping thanks to the crucial contribution of its C-terminus

Human ribonuclease (RNase) 1 and bovine RNase A are the proto-types of the secretory "pancreatic-type" (pt)-RNase super-family. RNase A can oligomerize through the 3D domain swapping (DS) mechanism upon acetic acid (HAc) lyophilisation, producing enzymatically active oligomeric conformers by swapping both N- and C-termini. Also some RNase 1 mutants were found to self-associate through 3D-DS, however forming only N-swapped dimers. Notably, enzymatically active dimers and larger oligomers of wt-RNase 1 were collected here, in higher amount than RNase A, from HAc lyophilisation. In particular, RNase 1 self-associates through the 3D-DS of its N-terminus and, at a higher extent, of the C-terminus. Since RNase 1 is four-residues longer than RNase A, we further analyzed its oligomerization tendency in a mutant lacking the last four residues. The C-terminus role has been investigated also in amphibian onconase (ONC®), a pt-RNase that can form only a N-swapped dimer, since its C-terminus, that is three-residues longer than RNase A, is locked by a disulfide bond. While ONC mutants designed to unlock or cut this constraint were almost unable to dimerize, the RNase 1 mutant self-associated at a higher extent than the wt, suggesting a specific role of the C-terminus in the oligomerization of different RNases. Overall, RNase 1 reaches here the highest ability, among pt-RNases, to extensively self-associate through 3D-DS, paving the way for new investigations on the structural and biological properties of its oligomers.

Slow Evolution toward “Super-Aggregation” of the Oligomers Formed through the Swapping of RNase A N-Termini: A Wish for Amyloidosis?

Natively monomeric RNase A can oligomerize upon lyophilization from 40% acetic acid solutions or when it is heated at high concentrations in various solvents. In this way, it produces many dimeric or oligomeric conformers through the three-dimensional domain swapping (3D-DS) mechanism involving both RNase A N- or/and C-termini. Here, we found many of these oligomers evolving toward not negligible amounts of large derivatives after being stored for up to 15 months at 4 °C in phosphate buffer. We call these species super-aggregates (SAs). Notably, SAs do not originate from native RNase A monomer or from oligomers characterized by the exclusive presence of the C-terminus swapping of the enzyme subunits as well. Instead, the swapping of at least two subunits’ N-termini is mandatory to produce them. Through immunoblotting, SAs are confirmed to derive from RNase A even if they retain only low ribonucleolytic activity. Then, their interaction registered with Thioflavin-T (ThT), in addition to TEM analyses, indicate SAs are large and circular but not “amyloid-like” derivatives. This confirms that RNase A acts as an “auto-chaperone”, although it displays many amyloid-prone short segments, including the 16–22 loop included in its N-terminus. Therefore, we hypothesize the opening of RNase A N-terminus, and hence its oligomerization through 3D-DS, may represent a preliminary step favoring massive RNase A aggregation. Interestingly, this process is slow and requires low temperatures to limit the concomitant oligomers’ dissociation to the native monomer. These data and the hypothesis proposed are discussed in the light of protein aggregation in general, and of possible future applications to contrast amyloidosis.

Supramolecular Organization As a Factor of Ribonuclease Cytotoxicity

One of the approaches used to eliminate tumor cells is directed destruction/modification of their RNA molecules. In this regard, ribonucleases (RNases) possess a therapeutic potential that remains largely unexplored. It is believed that the biological effects of secreted RNases, namely their antitumor and antiviral properties, derive from their catalytic activity. However, a number of recent studies have challenged the notion that the activity of RNases in the manifestation of selective cytotoxicity towards cancer cells is exclusively an enzymatic one. In this review, we have analyzed available data on the cytotoxic effects of secreted RNases, which are not associated with their catalytic activity, and we have provided evidence that the most important factor in the selective apoptosis-inducing action of RNases is the structural organization of these enzymes, which determines how they interact with cell components. The new idea on the preponderant role of non-catalytic interactions between RNases and cancer cells in the manifestation of selective cytotoxicity will contribute to the development of antitumor RNase-based drugs.

The Native Monomer of Bacillus Pumilus Ribonuclease Does Not Exist Extracellularly

Supported by crystallography studies, secreted ribonuclease of Bacillus pumilus (binase) has long been considered to be monomeric in form. Recent evidence obtained using native polyacrylamide gel electrophoresis and size-exclusion chromatography suggests that binase is in fact dimeric. To eliminate ambiguity and contradictions in the data we have measured conformational changes, hypochromic effect, and hydrodynamic radius of binase. The immutability of binase secondary structure upon transition from low to high protein concentration was registered, suggesting the binase dimerization immediately after translocation through the cell membrane and leading to detection of binase dimers only in the culture fluid regardless of ribonuclease concentration. Our results made it necessary to take a fresh look at the binase stability and cytotoxicity towards virus-infected or tumor cells.

Crystallographic studies on protein misfolding: Domain swapping and amyloid formation in the SH3 domain

Oligomerization by 3D domain swapping is found in a variety of proteins of diverse size, fold and function. In the early 1960s this phenomenon was postulated for the oligomers of ribonuclease A, but it was not until the 1990s that X-ray diffraction provided the first experimental evidence of this special manner of oligomerization. Nowadays, structural information has allowed the identification of these swapped oligomers in over one hundred proteins. Although the functional relevance of this phenomenon is not clear, this alternative folding of protomers into intertwined oligomers has been related to amyloid formation. Studies on proteins that develop 3D domain swapping might provide some clues on the early stages of amyloid formation. The SH3 domain is a small modular domain that has been used as a model to study the basis of protein folding. Among SH3 domains, the c-Src-SH3 domain emerges as a helpful model to study 3D domain swapping and amyloid formation.

Change in structure and ligand binding properties of hyperstable cytochrome c555 from Aquifex aeolicus by domain swapping

Cytochrome c555 from hyperthermophilic bacteria Aquifex aeolicus (AA cyt c555 ) is a hyperstable protein belonging to the cyt c protein family, which possesses a unique long 310 -α-310 helix containing the heme-ligating Met61. Herein, we show that AA cyt c555 forms dimers by swapping the region containing the extra 310 -α-310 helix and C-terminal α-helix. The asymmetric unit of the crystal of dimeric AA cyt c555 contained two dimer structures, where the structure of the hinge region (Val53-Lys57) was different among all four protomers. Dimeric AA cyt c555 dissociated to monomers at 92 ± 1°C according to DSC measurements, showing that the dimer was thermostable. According to CD measurements, the secondary structures of dimeric AA cyt c555 were maintained at pH 2.2-11.0. CN(-) and CO bound to dimeric AA cyt c555 in the ferric and ferrous states, respectively, owing to the flexibility of the hinge region close to Met61 in the dimer, whereas these ligands did not bind to the monomer under the same conditions. In addition, CN(-) and CO bound to the oxidized and reduced dimer at neutral pH and a wide range of pH (pH 2.2-11.0), respectively, in a wide range of temperature (25-85°C), owing to the thermostability and pH tolerance of the dimer. These results show that the ligand binding character of hyperstable AA cyt c555 changes upon dimerization by domain swapping.

Ribonucleases as antiviral agents

Many ribonucleases (RNases) are able to inhibit the reproduction of viruses in infected cell cultures and laboratory animals, but the molecular mechanisms of their antiviral activity remain unclear. The review discusses the well-known RNases that possess established antiviral effects, including both intracellular RNases (RNase L, MCPIP1 protein, and eosinophil-associated RNases) and exogenous RNases (RNase A, BS-RNase, onconase, binase, and synthetic RNases). Attention is paid to two important, but not always obligatory, aspects of molecules of RNases that have antiviral properties, i.e., catalytic activity and ability to dimerize. The hypothetic scheme of virus elimination by exogenous RNases that reflects possible types of interaction of viruses and RNases with a cell is proposed. The evidence for RNases as classical components of immune defense and thus perspective agents for the development of new antiviral therapeutics is proposed.

Structural and functional relationships of natural and artificial dimeric bovine ribonucleases: new scaffolds for potential antitumor drugs

Protein aggregation via 3D domain swapping is a complex mechanism which can lead to the acquisition of new biological, benign or also malignant functions, such as amyloid deposits. In this context, RNase A represents a fascinating model system, since by dislocating different polypeptide chain regions, it forms many diverse oligomers. No other protein displays such a large number of different quaternary structures. Here we report a comparative structural analysis between natural and artificial RNase A dimers and bovine seminal ribonuclease, a natively dimeric RNase with antitumor activity, with the aim to design RNase A derivatives with improved pharmacological potential.

Different 3D domain-swapped oligomeric cyanovirin-N structures suggest trapped folding intermediates

Although it has long been established that the amino acid sequence encodes the fold of a protein, how individual proteins arrive at their final conformation is still difficult to predict, especially for oligomeric structures. Here, we present a comprehensive characterization of oligomeric species of cyanovirin-N that all are formed by a polypeptide chain with the identical amino acid sequence. Structures of the oligomers were determined by X-ray crystallography, and each one exhibits 3D domain swapping. One unique 3D domain-swapped structure is observed for the trimer, while for both dimer and tetramer, two different 3D domain-swapped structures were obtained. In addition to the previously identified hinge-loop region of the 3D domain-swapped dimer, which resides between strands β5 and β6 in the middle of the polypeptide sequence, another hinge-loop region is observed between strands β7 and β8 in the structures. Plasticity in these two regions allows for variability in dihedral angles and concomitant differences in chain conformation that results in the differently 3D domain-swapped multimers. Based on all of the different structures, we propose possible folding pathways for this protein. Altogether, our results illuminate the amazing ability of cyanovirin-N to proceed down different folding paths and provide general insights into oligomer formation via 3D domain swapping.

Dynamic oligomeric properties

This chapter provides a foundation for further research into the relationship between dynamic oligomeric properties and functional diversity. The structural basis that underlies the conformational sub-states of the GAPDH oligomer is discussed. The issue of protein stability is given a thorough analysis, since it is well-established that the primary strategy for protein oligomerization is to stabilize conformation. Several factors that affect oligomerization are described, including chemical modification by synthetic reagents. The effects of native substrates and coenzymes are also discussed. The curious feature of chloride ions having a de-stabilizing effect on native GAPDH structure is described. Additionally, the role of adenine dinucleotides in tetramer-dimer equilibrium dynamics is suggested to be a major part of the physiological regulation of GAPDH structure and function. This chapter also contends that a vast amount of useful information can come from comparative analyses of diverse species, particularly regarding protein stability and subunit-subunit interaction. Lastly, the concept of domain exchange is introduced as a means of understanding the stabilization of dynamic oligomers, suggesting that inter-subunit contacts may also be a way of masking docking sites to other proteins.

Double domain swapping in bovine seminal RNase: formation of distinct N- and C-swapped tetramers and multimers with increasing biological activities

Bovine seminal (BS) RNase, the unique natively dimeric member of the RNase super-family, represents a special case not only for its additional biological actions but also for the singular features of 3D domain swapping. The native enzyme is indeed a mixture of two isoforms: M = M, a dimer held together by two inter-subunit disulfide bonds, and MxM, 70% of the total, which, besides the two mentioned disulfides, is additionally stabilized by the swapping of its N-termini.

When lyophilized from 40% acetic acid, BS-RNase oligomerizes as the super-family proto-type RNase A does. In this paper, we induced BS-RNase self-association and analyzed the multimers by size-exclusion chromatography, cross-linking, electrophoresis, mutagenesis, dynamic light scattering, molecular modelling. Finally, we evaluated their enzymatic and cytotoxic activities.

Several BS-RNase domain-swapped oligomers were detected, including two tetramers, one exchanging only the N-termini, the other being either N- or C-swapped. The C-swapping event, confirmed by results on a BS-K113N mutant, has been firstly seen in BS-RNase here, and probably stabilizes also multimers larger than tetramers.

Interestingly, all BS-RNase oligomers are more enzymatically active than the native dimer and, above all, they display a cytotoxic activity that definitely increases with the molecular weight of the multimers. This latter feature, to date unknown for BS-RNase, suggests again that the self-association of RNases strongly modulates their biological and potentially therapeutic properties.

RNase A oligomerization through 3D domain swapping is favoured by a residue located far from the swapping domains

Bovine pancreatic ribonuclease A forms 3D domain-swapped oligomers by lyophilization from 40% acetic acid solutions or if subjected to various thermally-induced denaturation procedures. Considering that the intrinsic swapping propensity of bovine seminal RNase, the only member of the pancreatic-type RNase super-family that is dimeric in nature, is decreased from 70 to 30% if Arg80 is substituted by Ser (the corresponding residue in native RNase A), we introduced the opposite mutation in position 80 of the pancreatic enzyme. Our aim was to detect if the RNase A tendency to aggregate through domain swapping could increase. Aggregation of the S80R-RNase A mutant was induced either through the 'classic' acetic acid lyophilization, or through a thermally-induced method. The results indicate that the S80R mutant aggregates to a higher extent than the native protein, and that the increase occurs especially through N-terminal swapping. Additional investigations on the dimeric and multimeric species formed indicate that the S80R mutation increases their stability against regression to monomer, and does not significantly change their structural and functional features.

Eosinophil cationic protein aggregation: identification of an N-terminus amyloid prone region

Eosinophil cationic protein (ECP) is an antimicrobial protein belonging to the superfamily of RNase A. ECP exhibits a broad spectrum of action against bacteria and, at higher concentrations, displays cytotoxic activity to eukaryotic cells. Recently, a powerful aggregation activity for lipid vesicles and for the gram-negative E. coli specie has also been related to the protein toxicity. Here we present the amyloid-like aggregation capacity of ECP. This is the first report of amyloid aggregation in a native nonengineered ribonuclease. The ECP aggregates are able to bind the amyloid-diagnostic dyes Thioflavin T and Congo Red and display a protofibril morphology when observed under electronic microscopy. We have also identified an N-terminus hydrophobic patch (residues 8-16) that is required for the amyloid aggregation process. A single substitution, I13A, breaks the aggregation prone sequence and abolishes the amyloid aggregation ability. Moreover, the corresponding R1N19 peptide is able to reproduce the protein amyloid-like aggregation behavior. The results may provide new clues on the protein antimicrobial mechanism and its toxicity to the host tissues in inflammation processes.

Domain swapping in materials design

Peptide self-assembly can be used as a bottom-up approach to material fabrication. Although many different types of materials can be prepared from peptides, hydrogels are perhaps one of the most common. Gels typically result from the self-assembly of peptides into fibrillar networks. Controlling the structural morphology of these fibrils and the networks they form allows direct control over a given material's bulk properties. However, exerting this control is extremely difficult as the mechanistic rules that govern peptide self-assembly are far from being established. Conversely, several amyloidogenic proteins have been shown to self-assemble into fibrils using a mechanism known as domain swapping. Here, discrete units of secondary structure or even whole domains are exchanged (swapped) among discrete proteins during self-assembly to form extended networks with precise structural control. This review discusses several common mechanistic variations of domain swapping using naturally occurring proteins as examples. The possibility of using these principles to design peptides capable of controlled assembly and fibril formation leading to materials with targeted properties is explored.

Elucidation of the ribonuclease A aggregation process mediated by 3D domain swapping: a computational approach reveals possible new multimeric structures

By lyophilization from 40% acetic acid solutions, bovine pancreatic ribonuclease A forms several three-dimensional (3D) domain-swapped oligomers: dimers, trimers, tetramers, pentamers, hexamers, and traces of high-order oligomers, purifiable by cation-exchange chromatography. Each oligomeric species consists of at least two conformers displaying different basicity density, and/or exposure of positive charges. The structures of the two dimers and one trimer have been solved. Plausible models have been proposed for a second RNase A trimer and four tetramers, but not all the models are certainly assignable to the tetramers purified. Further studies have also been made on the pentameric and hexameric species, again without reaching structurally clear-cut results. This work is focused on the detailed modeling of the tetrameric RNase A species, using four different approaches to possibly clarify unknown structural aspects. The results obtained do not confirm the validity of one tetrameric model previously proposed, but allow the proposal of a novel tetrameric structure displaying new interfaces that are absent in the other known conformers. New details concerning other tetrameric structures are also described. RNase A multimers larger than tetramers, i.e., pentamers, hexamers, octamers, nonamers, up to dodecamers, are also modeled, with the proposal of novel domain-swapped structures, and the confirmation of what had previously been inferred. Finally, the propensity of RNase A to possibly form high-order supramolecular multimers is analyzed starting from the large number of domain-swapped RNase A conformers modeled.

Oligomerization of ribonuclease A under reducing conditions

By lyophilization from 40% acetic acid solutions, bovine ribonuclease A forms well characterized, three-dimensional domain-swapped oligomers: dimers, trimers, tetramers, and higher order multimers. Each oligomeric species consists of at least two conformers. Identical oligomers also form by thermally-inducing the oligomerization of highly concentrated RNase A dissolved in fluids endowed with various denaturing power. Now, our question is: which might the influence of a reducing agent be on RNase A oligomerization, i.e., of conditions that decrease the stability of the protein and increase the mobility of its swapping domains? To address this question, we carried out experiments of RNase A oligomerization in the presence of increasing concentrations of dithiothreitol (DTT) under the two experimental conditions mentioned above. Results indicate that RNase A oligomers similar to those previously known form anyhow, but with a change of their relative proportions. The amounts of dimers and trimers decrease by increasing the concentration of DTT, while the yields of two tetramers remarkably increase. Moreover, in the presence of DTT RNase A forms labile and probably unstructured aggregates that can possibly drive the protein towards precipitation when the reducing agent's concentration increases. Taken together, these results point out once again (i) the important role of the 3D domain swapping mechanism in protein oligomerization, and (ii) the importance of the native structure of RNase A (and of proteins in general) in preventing an uncontrolled aggregation and precipitation in a reducing and highly crowded environment like that existing in a living cell.

Increase of RNase a N-terminus polarity or C-terminus apolarity changes the two domains' propensity to swap and form the two dimeric conformers of the protein

Do the polarities of the N-terminus or the apolarity of the C-terminus of bovine RNase A influence the relative yields of its two 3D domain-swapped dimeric conformers, the N-dimer and C-dimer? We have addressed this question by substituting Ala-4 or Ala-5 with serine (A4S and A5S mutants) or Ser-123 with alanine (S123A mutant) through site-directed mutagenesis. Both the polarity of the N-terminus and the apolarity of the C-terminus of RNase A were, therefore, increased. CD spectra revealed no significant differences between the secondary structures of the mutants and native RNase A. According to thermal denaturation analyses, the A4S and A5S mutants are less stable, and the S123A mutant is more stable than wild type RNase A. By subjecting the mutants under mild or drastic denaturing conditions, side-by-side with native and recombinant RNase A, to a thermally induced oligomerization procedure, the following results were obtained. (i) The N-terminal mutants showed a higher propensity, with respect to the native protein, to form N-dimers under mild unfolding conditions. (ii) The C-terminal mutant showed a higher propensity to form the C-dimer under severely unfolding conditions. These results are discussed in light of the relative stabilities of the various RNase A species under different environmental conditions, and we conclude that the hydrophilic or hydrophobic character of the RNase N-terminus or C-terminus can be an important variable governing the oligomerization of RNase A and possibly other proteins through the 3D domain-swapping mechanism.

Incorporation of styrene enhances recognition of ribonuclease A by molecularly imprinted polymers

Ribonuclease A (RNase A) is an RNA-cleaving enzyme characterized by its high conformational stability and strong catalytic activity. This enzyme is ubiquitous in living organisms and is difficult to inactivate. In polymerase chain reaction (PCR) RNase activity is removed by adding inhibitors. Molecularly imprinted polymers (MIPs) with high selectivity, high stability, low cost and facile synthesis could prove useful in extraction of target molecules, such as RNase A, from reaction mixtures. In this investigation, MIPs were synthesized from the monomers styrene and polyethyleneglycol 400 dimethacrylate (PEG400DMA) in several different ratios. Styrene as a functional monomer gave MIPs with a higher affinity for RNase A than other functional monomers tested, according to both enzyme-linked immnuosorbent assay (ELISA) and isothermal titration calorimetry (ITC). The optimum volume ratio of styrene/PEG400DMA was 20/100 at 25 degrees C, and this ratio maximized the rebinding efficiency of RNase A to MIPs. Isothermal titration calorimetry was also used, and could be useful to design the composition of molecularly imprinted polymers for various target molecules.

Deposition diseases and 3D domain swapping

Protein aggregation is a feature of both normal cellular assemblies and pathological protein depositions. Although the limited order of aggregates has often impeded their structural characterization, 3D domain swapping has been implicated in the formation of several protein aggregates. Here, we review known structures displaying 3D domain swapping in the context of amyloid and related fibrils, prion proteins, and macroscopic aggregates, and we discuss the possible involvement of domain swapping in protein deposition diseases.

Tandemization Endows Bovine Pancreatic Ribonuclease with Cytotoxic Activity

Due to their ability to degrade RNA, selected members of the bovine pancreatic ribonuclease A (RNase A) superfamily are potent cytotoxins. These cytotoxic ribonucleases enter the cytosol of target cells, where they degrade cellular RNA and cause cell death. The cytotoxic activity of most RNases, however, is abolished by the cytosolic ribonuclease inhibitor (RI). Consequently, the development of RNase derivatives with the ability to evade RI binding is a desirable goal. In this study, tandem enzymes consisting of two RNase A units that are bound covalently via a peptide linker were generated by gene duplication. As deduced from the crystal structure of the RNase A.RI complex, one RNase A unit of the tandem enzyme can still be bound by RI. The other unit, however, should remain unbound because of steric hindrance. This free RNase A unit is expected to maintain its activity and to act as a cytotoxic agent. The study of the influence of the linker sequence on the conformation and stability of these constructs revealed that tandemization has only minor effects on the activity and stability of the constructs in comparison to monomeric RNase A. Relative activity was decreased by 10-50% and the melting temperature was decreased by less than 2.5 K. Furthermore, the cytotoxic potency of the RNase A tandem enzymes was investigated. Despite an in vitro inhibition by RI, tandemization was found to endow RNase A with remarkable cytotoxic activity. While monomeric RNase A is not cytotoxic, IC(50) values of the RNase A tandem variants decreased to 70.3-12.9 microM. These findings might establish the development of a new class of chemotherapeutic agents based on pancreatic ribonucleases.

Formation, structure, and dissociation of the ribonuclease S three-dimensional domain-swapped dimer

Post-translational events, such as proteolysis, are believed to play essential roles in amyloid formation in vivo. Ribonuclease A forms oligomers by the three-dimensional domain-swapping mechanism. Here, we demonstrate the ability of ribonuclease S, a proteolytically cleaved form of ribonuclease A, to oligomerize efficiently. This unexpected capacity has been investigated to study the effect of proteolysis on oligomerization and amyloid formation. The yield of the RNase S dimer was found to be significantly higher than that of RNase A dimers, which suggests that proteolysis can activate oligomerization via the three-dimensional domain-swapping mechanism. Characterization by chromatography, enzymatic assays, and NMR spectroscopy indicate that the structure of the RNase S dimer is similar to that of the RNase A C-dimer. The RNase S dimer dissociates much more readily than the RNase A C-dimer does. By measuring the dissociation rate as a function of temperature, the activation enthalpy and entropy for RNase S dimer dissociation were found to resemble those for the release of the small fragment (S-peptide) from monomeric RNase S. Excess S-peptide strongly slows RNase S dimer dissociation. These results strongly suggest that S-peptide release is the rate-limiting step of RNase S dimer dissociation.

Hydralazine Inhibits Rapid Acrolein-Induced Protein Oligomerization: Role of Aldehyde Scavenging and Adduct Trapping in Cross-Link Blocking and Cytoprotection

Hydralazine strongly suppresses the toxicity of acrolein, a reactive aldehyde that contributes to numerous health disorders. At least two mechanisms may underlie the cytoprotection, both of which involve the nucleophilic hydrazine possessed by hydralazine. Under the simplest scenario, hydralazine directly scavenges free acrolein, decreasing intracellular acrolein availability and thereby suppressing macromolecular adduction. In a second "adduct-trapping" mechanism, the drug forms hydrazones with acrolein-derived Michael adducts in cell proteins, preventing secondary reactions of adducted proteins that may trigger cell death. To identify the most important mechanism, we explored these two pathways in mouse hepatocytes poisoned with the acrolein precursor allyl alcohol. Intense concentration-dependent adduct-trapping in cell proteins accompanied the suppression of toxicity by hydralazine. However, protective concentrations of hydralazine did not alter extracellular free acrolein levels, cellular glutathione loss, or protein carbonylation, suggesting that the cytoprotection is not due to minimization of intracellular acrolein availability. To explore ways whereby adduct-trapping might confer cytoprotection, the effect of hydralazine on acrolein-induced protein cross-linking was examined. Using bovine pancreas ribonuclease A as a model protein, acrolein caused rapid time- and concentration-dependent cross-linking, with dimerized protein detectable within 45 min of commencing protein modification. Lysine adduction in monomeric protein preceded the appearance of oligomers, whereas reductive methylation of protein amine groups abolished both adduction and oligomerization. Hydralazine inhibited cross-linking if added 30 min after commencing acrolein exposure but was ineffective if added after a 90-min delay. Adduct-trapping closely accompanied the inhibition of cross-linking by hydralazine. These findings suggest that cross-link blocking may contribute to hydralazine cytoprotection.

Three-dimensional domain-swapped oligomers of ribonuclease A: identification of a fifth tetramer, pentamers and hexamers, and detection of trace heptameric, octameric and nonameric species

By lyophilization from 40% acetic acid solutions, bovine pancreatic Ribonuclease A forms three-dimensional domain-swapped dimers, trimers, and tetramers that can be separated by cation-exchange chromatography. Each oligomeric species consists of at least two conformers, one less basic, one more basic. The structures of the two dimers and one trimer have been solved. Plausible models have been proposed for a second RNase A trimer and four tetramers. This work is focused on the characterization of the largest oligomers which compose small peaks that have always appeared in chromatograms of RNase A. These higher order oligomers were collected by repeated cation-exchange chromatographies. On the basis of (a) gel filtrations through analytical Superdex 75 and 200; (b) gel electrophoreses under non-denaturing conditions, (c) cross-linking with divynilsulfone followed by analyses with SDS-PAGE and mass spectrometry, (d) enzymatic activity assays, and (e) analyses of the products of spontaneous dissociation of the oligomers, we could identify three-dimensional domain-swapped pentamers and hexamers, and one additional tetrameric conformer. For the latter we propose a cyclic model (C(TT)). Moreover, we advance a linear model (NCNC(P)) for one pentamer, and three possible cyclic models (with a C-trimer as the main component) for one hexamer. The experimental evidence also indicates the existence of heptameric, octameric and nonameric species.