The multiple forms of bovine seminal ribonuclease: structure and stability of a C-terminal swapped dimer

Deciphering the biophysical aspects of the interaction of 3,5,4'-trihydroxy-trans-stilbene with ribonuclease A: spectroscopic and computational studies

Drug-receptor interaction is an important aspect in drug action, drug discovery, and pharmacological aspects. The molecule 3,5,4'-trihydroxy-trans-stilbene known as resveratrol is a natural polyphenol and exhibits diverse biological activities. Ribonuclease A catalyses the degradation of RNA by its ribonucleolytic activity. The report presents the binding interaction of resveratrol with RNase A using experimental and theoretical techniques. Experimental studies revealed the interaction strength of 104 M-1 order with a single binding site. Resveratrol quenched the ribonuclease A fluorescence with a quenching constant of 104 M-1 range. The accessible fraction of the fluorophore was found to be 0.75 besides non-radiative energy transfer from ribonuclease A to resveratrol. The donor-acceptor distance was 2.14 nm from FRET calculations. No visible changes in the protein structure was evident from the circular dichroism studies. The interface residues involved in the interaction were obtained from docking studies. Further, the participation of the active site residues, His 12, His 119, and Lys 41 with interaction indicates the location of resveratrol near to the active site of ribonuclease A and indicates its possible potential to inhibit the ribonuclease A activity. The RMSD of less than 3 Å indicates stable conformation of protein in the complex. The protein RMSF value in the complex less than 3 Å shows no deviation of protein residues over time and thus suggests no conformational variation in the protein after binding.

Assessing Partial Inhibition of Ribonuclease A Activity by Curcumin through Fluorescence Spectroscopy and Theoretical Studies

Molecular interactions and controlled expression of enzymatic activities are fundamental to all cellular functions in an organism. The active polyphenol in turmeric known as curcumin (CCM) is known to exhibit diverse pharmacological activities. Ribonucleases (RNases) are the hydrolytic enzymes that plays important role in ribonucleic acid (RNA) metabolism. Uncontrolled and unwanted cleavage of RNA by RNases may be the cause of cell death leading to disease states. The protein ribonuclease A (RNase A) in the superfamily of RNases cleaves the RNA besides its role in different diseases like autoimmune diseases, and pancreatic disorders. Interaction of CCM with RNase A have been reported along with the possible role of CCM to inhibit the RNase A enzymatic activity. The interaction strength was found to be 104 M-1 order from spectroscopic results. Quenching of RNase A fluorescence by CCM was 104 M-1 order. Non-radiative energy transfer from RNase A (donor) to CCM (acceptor) suggested a distance of 2.42 nm between the donor-acceptor pair. Circular dichroism studies revealed no structural changes in RNase A after binding. Binding-induced conformational variation in protein was observed from synchronous fluorescence studies. Agarose gel electrophoresis revealed a partial inhibition of the RNase A activity by CCM though not significant. Molecular docking and molecular dynamics studies suggested the residues of RNase A involved in the interaction with supporting the experimental finding for the partial inhibition of the enzyme activity. This study may help in designing new CCM analogues or related structures to understand their differential inhibition of the RNase A activity.

Biological Activities of Secretory RNases: Focus on Their Oligomerization to Design Antitumor Drugs

Ribonucleases (RNases) are a large number of enzymes gathered into different bacterial or eukaryotic superfamilies. Bovine pancreatic RNase A, bovine seminal BS-RNase, human pancreatic RNase 1, angiogenin (RNase 5), and amphibian onconase belong to the pancreatic type superfamily, while binase and barnase are in the bacterial RNase N1/T1 family. In physiological conditions, most RNases secreted in the extracellular space counteract the undesired effects of extracellular RNAs and become protective against infections. Instead, if they enter the cell, RNases can digest intracellular RNAs, becoming cytotoxic and having advantageous effects against malignant cells. Their biological activities have been investigated either in vitro, toward a number of different cancer cell lines, or in some cases in vivo to test their potential therapeutic use. However, immunogenicity or other undesired effects have sometimes been associated with their action. Nevertheless, the use of RNases in therapy remains an appealing strategy against some still incurable tumors, such as mesothelioma, melanoma, or pancreatic cancer. The RNase inhibitor (RI) present inside almost all cells is the most efficacious sentry to counteract the ribonucleolytic action against intracellular RNAs because it forms a tight, irreversible and enzymatically inactive complex with many monomeric RNases. Therefore, dimerization or multimerization could represent a useful strategy for RNases to exert a remarkable cytotoxic activity by evading the interaction with RI by steric hindrance. Indeed, the majority of the mentioned RNases can hetero-dimerize with antibody derivatives, or even homo-dimerize or multimerize, spontaneously or artificially. This can occur through weak interactions or upon introducing covalent bonds. Immuno-RNases, in particular, are fusion proteins representing promising drugs by combining high target specificity with easy delivery in tumors. The results concerning the biological features of many RNases reported in the literature are described and discussed in this review. Furthermore, the activities displayed by some RNases forming oligomeric complexes, the mechanisms driving toward these supramolecular structures, and the biological rebounds connected are analyzed. These aspects are offered with the perspective to suggest possible efficacious therapeutic applications for RNases oligomeric derivatives that could contemporarily lack, or strongly reduce, immunogenicity and other undesired side-effects.

Species-specific and collection method-dependent differences in endometrial susceptibility to seminal plasma-induced RNA degradation

This study aimed to determine the effect of bull seminal plasma (SP) and sperm on endometrial function. Bovine endometrial explants were incubated with: ejaculated sperm with or without SP, epididymal sperm, or SP alone. Neither ejaculated nor epididymal sperm induced differential expression of IL1A, IL1B, IL6, IL8, PTGES2, TNFA, and LIF. Interestingly, SP had a detrimental effect on endometrial RNA integrity. Addition of an RNase inactivation reagent to SP blocked this effect, evidencing a role for a SP-RNase. Because bulls deposit the ejaculate in the vagina, we hypothesized that the bovine endometrium is more sensitive to SP-RNase than vaginal and cervical tissues (which come into contact with SP during mating), or to endometrium from intrauterine ejaculators (such as the horse). In addition, due to differences in SP-RNase abundance depending on SP collection method (i.e., with an artificial vagina, AV, or by electroejaculation, EE), this effect was also tested. Bull SP, collected by AV, degrades RNA of mare endometrium, and bovine vagina, cervix and endometrium. However, stallion SP or bull SP collected by EE did not elicit this effect. Thus, results do not support a role for SP in modulating endometrial function to establish pregnancy in cattle.

Structure, stability and aggregation propensity of a Ribonuclease A-Onconase chimera

Structural roles of loop regions are frequently overlooked in proteins. Nevertheless, they may be key players in the definition of protein topology and in the self-assembly processes occurring through domain swapping. We here investigate the effects on structure and stability of replacing the loop connecting the last two β-strands of RNase A with the corresponding region of the more thermostable Onconase. The crystal structure of this chimeric variant (RNaseA-ONC) shows that its terminal loop size better adheres to the topological rules for the design of stabilized proteins, proposed by Baker and coworkers [43]. Indeed, RNaseA-ONC displays a thermal stability close to that of RNase A, despite the lack of Pro at position 114, which, due to its propensity to favor a cis peptide bond, has been identified as an important stabilizing factor of the native protein. Accordingly, RNaseA-ONC is significantly more stable than RNase A variants lacking Pro114; RNaseA-ONC also displays a higher propensity to form oligomers in native conditions when compared to either RNase A or Onconase. This finding demonstrates that modifications of terminal loops should to be carefully controlled in terms of size and sequence to avoid unwanted and/or potentially harmful aggregation processes.

Onconase dimerization through 3D domain swapping: structural investigations and increase in the apoptotic effect in cancer cells

Onconase® (ONC), a protein extracted from the oocytes of the Rana pipiens frog, is a monomeric member of the secretory 'pancreatic-type' RNase superfamily. Interestingly, ONC is the only monomeric ribonuclease endowed with a high cytotoxic activity. In contrast with other monomeric RNases, ONC displays a high cytotoxic activity. In this work, we found that ONC spontaneously forms dimeric traces and that the dimer amount increases about four times after lyophilization from acetic acid solutions. Differently from RNase A (bovine pancreatic ribonuclease) and the bovine seminal ribonuclease, which produce N- and C-terminal domain-swapped conformers, ONC forms only one dimer, here named ONC-D. Cross-linking with divinylsulfone reveals that this dimer forms through the three-dimensional domain swapping of its N-termini, being the C-terminus blocked by a disulfide bond. Also, a homology model is proposed for ONC-D, starting from the well-known structure of RNase A N-swapped dimer and taking into account the results obtained from spectroscopic and stability analyses. Finally, we show that ONC is more cytotoxic and exerts a higher apoptotic effect in its dimeric rather than in its monomeric form, either when administered alone or when accompanied by the chemotherapeutic drug gemcitabine. These results suggest new promising implications in cancer treatment.

Extensive deamidation of RNase A inhibits its oligomerization through 3D domain swapping

Bovine pancreatic ribonuclease A (RNase A) is the monomeric prototype of the so-called secretory 'pancreatic-type' RNase super-family. Like the naturally domain-swapped dimeric bovine seminal variant, BS-RNase, and its glycosylated RNase B isoform, RNase A forms N- and C-terminal 3D domain-swapped oligomers after lyophilization from acid solutions, or if subjected to thermal denaturation at high protein concentration. All mentioned RNases can undergo deamidation at Asn67, forming Asp or isoAsp derivatives that modify the protein net charge and consequently its enzymatic activity. In addition, deamidation slightly affects RNase B self-association through the 3D domain swapping (3D-DS) mechanism. We report here the influence of extensive deamidation on RNase A tendency to oligomerize through 3D-DS. In particular, deamidation of Asn67 alone slightly decreases the propensity of the protein to oligomerize, with the Asp derivative being less affected than the isoAsp one. Contrarily, the additional Asp and/or isoAsp conversion of residues other than N67 almost nullifies RNase A oligomerization capability. In addition, Gln deamidation, although less kinetically favorable, may affect RNase A self-association. Using 2D and 3D NMR we identified the Asn/Gln residues most prone to undergo deamidation. Together with CD spectroscopy, NMR also indicates that poly-deamidated RNase A generally maintains its native tertiary structure. Again, we investigated in silico the effect of the residues undergoing deamidation on RNase A dimers structures. Finally, the effect of deamidation on RNase A oligomerization is discussed in comparison with studies on deamidation-prone proteins involved in amyloid formation.

Abundance of RNase4 and RNase5 mRNA and protein in host defence related tissues and secretions in cattle

Members of the RNaseA family are present in various tissues and secretions but their function is not well understood. Some of the RNases are proposed to participate in host defence. RNase4 and RNase5 are present in cows' milk and have antimicrobial activity. However, their presence in many tissues and secretions has not been characterised. We hypothesised that these two RNases are present in a range of tissues and secretions where they could contribute to host defence. We therefore, determined the relative abundance of RNase4 and RNase5 mRNA as well as protein levels in a range of host defence related and other tissues as well as a range of secretions in cattle, using real time PCR and western blotting. The two RNases were found to be expressed in liver, lung, pancreas, mammary gland, placenta, endometrium, small intestine, seminal vesicle, salivary gland, kidney, spleen, lymph node, skin as well as testes. Corresponding proteins were also detected in many of the above tissues, as well as in seminal fluid, mammary secretions and saliva. This study provides evidence for the presence of RNase4 and RNase5 in a range of tissues and secretions, as well as some major organs in cattle. The data are consistent with the idea that these proteins could contribute to host defence in these locations. This work contributes to growing body of data suggesting that these proteins contribute to the physiology of the organism in a more complex way than acting merely as digestive enzymes.

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RNase4 and RNase5 are present in several tissues and secretions in cattle.

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mRNA and protein levels of the RNases correlate in various tissues analysed.

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The RNases could contribute to host defence in these tissues and secretions.