4-Thiaproline accelerates the slow folding phase of proteins containing cis prolines in the native state by two orders of magnitude.

The cis/trans isomerization of peptidyl-prolyl peptide bonds is often the bottleneck of the refolding reaction for proteins containing cis proline residues in the native state. Proline (Pro) analogues, especially C4-substituted fluoroprolines, have been widely used in protein engineering to enhance the thermodynamic stability of peptides and proteins and to investigate folding kinetics. 4-thiaproline (Thp) has been shown to bias the ring pucker of Pro, to increase the cis population percentage of model peptides in comparison to Pro, and to diminish the activation energy barrier for the cis/trans isomerization reaction. Despite its intriguing properties, Thp has been seldom incorporated into proteins. Moreover, the impact of Thp on the folding kinetics of globular proteins has never been reported. In this study, we show that upon incorporation of Thp at cisPro76 into the thioredoxin variant Trx1P the half-life of the refolding reaction decreased from ~2 h to ~35 s. A dramatic acceleration of the refolding rate could be observed also for the protein pseudo wild-type barstar upon replacement of cisPro48 with Thp. Quantum chemical calculations suggested that the replacement of the Cγ H2 group by a sulfur atom in the pyrrolidine ring, might lower the barrier for cis/trans rotation due to a weakened peptide bond. The protein variants retained their thermodynamic stability upon incorporation of Thp, while the catalytic and enzymatic activities of the modified Trx1P remained unchanged. Our results show that the Pro isostere Thp might accelerate the rate of the slow refolding reaction for proteins containing cis proline residues in the native state, independent from the local structural environment.

The trans-to-cis proline isomerization in E. coli Trx folding is accelerated by trans prolines.

The conserved fold of thioredoxin (Trx)-like thiol/disulfide oxidoreductases contains an invariant cis-proline residue (P76 in Escherichia coli Trx) that is essential for Trx function and that is responsible for the folding rate-limiting step. E. coli Trx contains four additional prolines, which are all in the trans conformation in the native state. Notably, a recent study revealed that replacement of all four trans prolines in Trx by alanines (Trx variant Trx1P) further slowed the rate-limiting step 25-fold, indicating that one or several of the four trans prolines accelerate the trans-to-cis transition of P76 in Trx wild-type (wt). Here, we characterized the folding kinetics of Trx variants containing cisP76 and one or several of the natural trans prolines of Trx wt with NMR spectroscopy. First, we demonstrate that the isomerization reaction in Trx1P is a pure two-state transition between two distinct tertiary structures, in which all observed NMR resonances changes follow the same first-order kinetics. Moreover, we show that trans-P68 is the critical residue responsible for the faster folding of wt Trx relative to the single-proline (P76) variant Trx1P, as the two-proline variant Trx2P(P76P68) already folds seven times faster than Trx1P. trans-P34 also accelerates trans-to-cis isomerization of P76, albeit to a smaller extent. Overall, the results demonstrate that trans prolines can significantly modulate the kinetics of rate-limiting trans-to-cis proline isomerization in protein folding. Finally, we discuss possible mechanisms of acceleration and the potential significance of a protein-internal folding acceleration mechanism for Trx in a living cell.

Protein Design with Fluoroprolines: 4,4-Difluoroproline Does Not Eliminate the Rate-Limiting Step of Thioredoxin Folding.

C4 -substituted fluoroprolines (4R)-fluoroproline ((4R)-Flp) and (4S)-fluoroproline ((4S)-Flp) have been used in protein engineering to enhance the thermodynamic stability of peptides and proteins. The electron-withdrawing effect of fluorine can bias the pucker of the pyrrolidine ring, influence the conformational preference of the preceding peptide bond, and can accelerate the cis/trans prolyl peptide bond isomerisation by diminishing its double bond character. The role of 4,4-difluoroproline (Dfp) in the acceleration of the refolding rate of globular proteins bearing a proline (Pro) residue in the cis conformation in the native state remains elusive. Moreover, the impact of Dfp on the thermodynamic stability and bioactivity of globular proteins has been seldom described. In this study, we show that the incorporation of Dfp caused a redox state dependent and position dependent destabilisation of the thioredoxin (Trx) fold, while the catalytic activities of the modified proteins remained unchanged. The Pro to Dfp substitution at the conserved cisPro76 in the thioredoxin variant Trx1P did not elicited acceleration of the rate-limiting trans-to-cis isomerization of the Ile75-Pro76 peptide bond. Our results show that pucker preferences in the context of a tertiary structure could play a major role in protein folding, thus overtaking the rules determined for cis/trans isomerisation barriers determined in model peptides.

High Flexibility of RNaseH2 Catalytic Activity with Respect to Non-Canonical DNA Structures.

Ribonucleotides misincorporated in the human genome are the most abundant DNA lesions. The 2'-hydroxyl group makes them prone to spontaneous hydrolysis, potentially resulting in strand breaks. Moreover, their presence may decrease the rate of DNA replication causing replicative fork stalling and collapse. Ribonucleotide removal is initiated by Ribonuclease H2 (RNase H2), the key player in Ribonucleotide Excision Repair (RER). Its absence leads to embryonic lethality in mice, while mutations decreasing its activity cause Aicardi-Goutières syndrome. DNA geometry can be altered by DNA lesions or by peculiar sequences forming secondary structures, like G-quadruplex (G4) and trinucleotide repeats (TNR) hairpins, which significantly differ from canonical B-form. Ribonucleotides pairing to lesioned nucleotides, or incorporated within non-B DNA structures could avoid RNase H2 recognition, potentially contributing to genome instability. In this work, we investigate the ability of RNase H2 to process misincorporated ribonucleotides in a panel of DNA substrates showing different geometrical features. RNase H2 proved to be a flexible enzyme, recognizing as a substrate the majority of the constructs we generated. However, some geometrical features and non-canonical DNA structures severely impaired its activity, suggesting a relevant role of misincorporated ribonucleotides in the physiological instability of specific DNA sequences.

The Antibacterial Drug Candidate SBC3 is a Potent Inhibitor of Bacterial Thioredoxin Reductase.

Antibiotic resistance is a growing problem for public health and associated with increasing economic costs and mortality rates. Silver and silver-related compounds have been used for centuries due to their antimicrobial properties. In this work, we show that 1,3-dibenzyl-4,5-diphenyl-imidazol-2-ylidene silver(I) acetate/NHC*-Ag-OAc (SBC3) is a reversible, high affinity inhibitor of E. coli thioredoxin reductase (TrxR; Ki =10.8±1.2 nM). Minimal inhibition concentration (MIC) tests with different E. coli and P. aeruginosa strains demonstrated that SBC3 can efficiently inhibit bacterial cell growth, especially in combination with established antibiotics like gentamicin. Our results show that SBC3 is a promising antibiotic drug candidate targeting bacterial TrxR.

The emotional and social burden of heart failure: integrating physicians', patients', and caregivers' perspectives through narrative medicine.

BACKGROUND: The The Roadmap Using Story Telling project used a narrative medicine (NM) framework to assess the perspectives of people with heart failure (HF), their informal caregivers and HF specialists of the impact of HF on the daily life of patients and their carers. METHODS: Italian HF specialists participated on a voluntary basis, completing their own narratives, and inviting patients and their caregivers to write anonymously about their experiences, all on a dedicated online platform. The narratives were analyzed according to standard NM methodology. RESULTS: 82 narratives were collected from patients, 61 from caregivers, and 104 from HF specialists. Analysis of the three points of view revealed the extent of the burden of illness on the entire family, particularly that of the caregiver. The impact was mainly experienced as emotional and social limitations in patients' and their caregivers' daily lives. The analysis of all three points of view highlighted a strong difference between how HF is perceived by patients, caregivers, and HF specialists. CONCLUSIONS: This NM project illustrates the complex issues of living with HF and gave insights to integrate three different perspectives into the HF pathway of care.

Use of narrative medicine to identify key factors for effective doctor-patient relationships in severe asthma.

BACKGROUND: In this project the authors use a narrative medicine (NM) approach to assess the promotion of trust in the relationship between physicians and their asthma patients. METHODS: Following a NM educational course for physicians, a research was carried out in which at least 5 written narratives (parallel charts) for each participating physician were collected and qualitatively analysed according to Bury's classification and the Grounded Theory. RESULTS: The results of this study were of speculative and clinical interest. In particular, 66 participants wrote 314 narratives (246 on adult and 68 on paediatric patients). As a result of applying the NM approach, when the relationships remained problematic, many physicians wrote with a moral style about their adult (67%), and paediatric patients (33%) - especially in cases of asthmatic children's or adolescents' overprotective or absent families (40%) -. On the contrary, physicians who were able to listen to their patients with empathy (35%) made more shared decisions with patients, even with those they initially had a bad relationship. The used words of welcome, interest and acceptance were promoting patients' trust that lead to restoring their activities in 45% of cases, according to physicians self-reporting. CONCLUSIONS: These approaches of NM are useful in daily clinical practice, with the goal of improving the quality of life (QOL) of patients with severe asthma, even in cases in which the doctor-patient relationship isn't initially good.

Functional analyses of ancestral thioredoxins provide insights into their evolutionary history.

Thioredoxin (Trx) is a conserved, cytosolic reductase in all known organisms. The enzyme receives two electrons from NADPH via thioredoxin reductase (TrxR) and passes them on to multiple cellular reductases via disulfide exchange. Despite the ubiquity of thioredoxins in all taxa, little is known about the functions of resurrected ancestral thioredoxins in the context of a modern mesophilic organism. Here, we report on functional in vitro and in vivo analyses of seven resurrected Precambrian thioredoxins, dating back 1-4 billion years, in the Escherichia coli cytoplasm. Using synthetic gene constructs for recombinant expression of the ancestral enzymes, along with thermodynamic and kinetic assays, we show that all ancestral thioredoxins, as today's thioredoxins, exhibit strongly reducing redox potentials, suggesting that thioredoxins served as catalysts of cellular reduction reactions from the beginning of evolution, even before the oxygen catastrophe. A detailed, quantitative characterization of their interactions with the electron donor TrxR from Escherichia coli and the electron acceptor methionine sulfoxide reductase, also from E. coli, strongly hinted that thioredoxins and thioredoxin reductases co-evolved and that the promiscuity of thioredoxins toward downstream electron acceptors was maintained during evolution. In summary, our findings suggest that thioredoxins evolved high specificity for their sole electron donor TrxR while maintaining promiscuity to their multiple electron acceptors.

Narrative medicine in metastatic prostate cancer reveals ways to improve patient awareness & quality of care.

AIM: To describe the journey of patients with metastatic castration-resistant prostate cancer (mCRPC) in treatment with radium-223. METHODS: A multiperspective analysis was performed using narrative medicine in four Italian centers. RESULTS: The substantial impact of mCRPC on quality of life through all phases of the disease was described. After an initial lack of awareness of the disease or denial of its effects, symptoms of pain, fatigue and side effects often led to sadness, fear and loneliness. The majority underwent radium-223 therapy positively, restoring their quality of life and routine activities. CONCLUSION: Using narrative medicine, the importance of a patient-centered approach in the pathway of care for patients with mCRPC through all the stages of the disease was highlighted.

Narrative medicine educational project to improve the care of patients with chronic obstructive pulmonary disease.

Chronic obstructive pulmonary disease (COPD) is characterised by a progressive loss of pulmonary function. Often patients do not adhere to inhaled therapies and this leads clinicians to switch treatments in order to improve control of the symptoms. Narrative medicine is a useful approach that helps healthcare professionals to think over the doctor-patient relationship and how patients live with their disease. The aim of this training project was to teach pulmonologists the basics of narrative medicine: to carefully listen to patients and to practice reflective writing in their relationship with them. Training on narrative medicine and parallel charts was provided through a webinar and a weekly newsletter. Across 362 narratives, written by 74 Italian pulmonologists, 92% of patients had activity limitations at their first visit. The main factor influencing the effectiveness and adherence to therapy was a positive doctor-patient relationship; indeed, if such relationship is difficult, only 21% of patients are able to resume all their activities. After learning the narrative approach, clinicians became aware of the need to spend more time listening to patients, to reflect through writing and to understand more deeply the motivations that lead people towards adherence to new therapies.