The Mechanism of Folding of Human Frataxin in Comparison to the Yeast Homologue - Broad Energy Barriers and the General Properties of the Transition State

The funneled energy landscape theory suggests that the folding pathway of homologous proteins should converge at the late stages of folding. In this respect, proteins displaying a broad energy landscape for folding are particularly instructive, allowing inferring both the early, intermediate and late stages of folding. In this paper we explore the folding mechanisms of human frataxin, an essential mitochondrial protein linked to the neurodegenerative disorder Friedreich's ataxia. Building upon previous studies on the yeast homologue, the folding pathway of human frataxin is thoroughly examined, revealing a mechanism implying the presence of a broad energy barrier, reminiscent of the yeast counterpart. Through an extensive site-directed mutagenesis, we employed a Φ -value analysis to map native-like contacts in the folding transition state. The presence of a broad energy barrier facilitated the exploration of such contacts in both early and late folding events. We compared results from yeast and human frataxin providing insights into the impact of native topology on the folding mechanism and elucidating the properties of the underlying free energy landscape. The findings are discussed in the context of the funneled energy landscape theory of protein folding.

Modulation of Allosteric Control and Evolution of Hemoglobin

Allostery arises when a ligand-induced change in shape of a binding site of a protein is coupled to a tertiary/quaternary conformational change with a consequent modulation of functional properties. The two-state allosteric model of Monod, Wyman and Changeux [J. Mol. Biol. 1965; 12, 88-118] is an elegant and effective theory to account for protein regulation and control. Tetrameric hemoglobin (Hb), the oxygen transporter of all vertebrates, has been for decades the ideal system to test for the validity of the MWC theory. The small ligands affecting Hb's behavior (organic phosphates, protons, bicarbonate) are produced by the red blood cell during metabolism. By binding to specific sites, these messengers make Hb sensing the environment and reacting consequently. HbI and HbIV from trout and human HbA are classical cooperative models, being similar yet different. They share many fundamental features, starting with the globin fold and the quaternary assembly, and reversible cooperative O₂ binding. Nevertheless, they differ in ligand affinity, binding of allosteric effectors, and stability of the quaternary assembly. Here, we recollect essential functional properties and correlate them to the tertiary and quaternary structures available in the protein databank to infer on the molecular basis of the evolution of oxygen transporters.

Eraldo Antonini Lectures, 1983-2019

“Can order spring from Chaos?” is the title of an extensive Report on Italian science published by NATURE on 12 May 1983 and written by Robert Walgate, the Chief European Correspondent. It is a twenty pages complete paper touching all aspects of the struggle of Italian scientists to work in the “curious amalgam of ingenuity and muddle, a reflection of the political system”. (Nature, 1983; 303: 109–128). To read it after four decades is interesting but somewhat depressing since the main problems unfolded in the paper have not been solved, starting with the largely insufficient support of fundamental curiosity driven research. At page 114 you could find a item called: ITALY’s TOP SCIENTISTS: Four in the top one thousand. The Author refers to the data reported by the ISI (Institute of Scientific Information) that took two years to scan 3,000 major journals over the period 1965–78 and covered 5 millions articles and 67 millions references. The four top Italian scientists working in Italy were: Eraldo Antonini (3127 citations), Enrico Clementi (4001), Silvio Garattini (2833), and Giorgio Giacomelli (2483); 3 out of four were 52 years old, and one 55. Antonini did not see the Report since he passed away on March 18, 1983. However the information leaked before the publication of Nature because I remember the Messaggero of Rome reporting a whole page with the ranking of the four Italians, and even a picture of Eraldo. The students of the first year Medical course, his Class, welcomed the Professor with a standing ovation. After a short time the Board of the SIB (Società Italiana di Biochimica) casted a unanimous vote in favour of the motion of President Noris Siliprandi to begin the annual Congress with an Antonini Lecture, forever. As reported below, the tradition began immediately at the Congress in Saint-Vicent, Italy, and is continuing. In this paper I report an account of the Eraldo Antonini Lectures that I attended over the years and until September 2019, a few months before the pandemics lock down.

An Outlook on the Complexity of Protein Morphogenesis in Health and Disease

The study of the mechanisms whereby proteins achieve their native functionally competent conformation has been a key issue in molecular biosciences over the last 6 decades. Nevertheless, there are several debated issues and open problems concerning some aspects of this fundamental problem. By considering the emerging complexity of the so-called “native state,” we attempt hereby to propose a personal account on some of the key topics in the field, ranging from the relationships between misfolding and diseases to the significance of protein disorder. Finally, we briefly describe the recent and exciting advances in predicting protein structures from their amino acid sequence.

Prevalence and features of delirium in older patients admitted to rehabilitation facilities: a multicenter study

BACKGROUND

Delirium is thought to be common across various settings of care; however, still little research has been conducted in rehabilitation.

AIM

We investigated the prevalence of delirium, its features and motor subtypes in older patients admitted to rehabilitation facilities during the three editions of the "Delirium Day project".

METHODS

We conducted a cross-sectional study in which 1237 older patients (age ≥ 65 years old) admitted to 50 Italian rehabilitation wards during the three editions of the "Delirium Day project" (2015 to 2017) were included. Delirium was evaluated through the 4AT and its motor subtype with the Delirium Motor Subtype Scale.

RESULTS

Delirium was detected in 226 patients (18%), and the most recurrent motor subtype was mixed (37%), followed by hypoactive (26%), hyperactive (21%) and non-motor one (16%). In a multivariate Poisson regression model with robust variance, factors associated with delirium were: disability in basic (PR 1.48, 95%CI: 1.17-1.9, p value 0.001) and instrumental activities of daily living (PR 1.58, 95%CI: 1.08-2.32, p value 0.018), dementia (PR 2.10, 95%CI: 1.62-2.73, p value < 0.0001), typical antipsychotics (PR 1.47, 95%CI: 1.10-1.95, p value 0.008), antidepressants other than selective serotonin reuptake inhibitors (PR 1.3, 95%CI: 1.02-1.66, p value 0.035), and physical restraints (PR 2.37, 95%CI: 1.68-3.36, p value < 0.0001).

CONCLUSION

This multicenter study reports that 2 out 10 patients admitted to rehabilitations had delirium on the index day. Mixed delirium was the most prevalent subtype. Delirium was associated with unmodifiable (dementia, disability) and modifiable (physical restraints, medications) factors. Identification of these factors should prompt specific interventions aimed to prevent or mitigate delirium.

The association between low skeletal muscle mass and delirium: results from the nationwide multi-centre Italian Delirium Day 2017

Introduction

Delirium and sarcopenia are common, although underdiagnosed, geriatric syndromes. Several pathological mechanisms can link delirium and low skeletal muscle mass, but few studies have investigated their association. We aimed to investigate (1) the association between delirium and low skeletal muscle mass and (2) the possible role of calf circumference mass in finding cases with delirium.

Methods

The analyses were conducted employing the cross-sectional “Delirium Day” initiative, on patient 65 years and older admitted to acute hospital medical wards, emergency departments, rehabilitation wards, nursing homes and hospices in Italy in 2017. Delirium was diagnosed as a 4 + score at the 4-AT scale. Low skeletal muscle mass was operationally defined as calf circumference ≤ 34 cm in males and ≤ 33 cm in females. Logistic regression models were used to investigate the association between low skeletal muscle mass and delirium. The discriminative ability of calf circumference was evaluated using non-parametric ROC analyses.

Results

A sample of 1675 patients was analyzed. In total, 73.6% of participants had low skeletal muscle mass and 24.1% exhibited delirium. Low skeletal muscle mass and delirium showed an independent association (OR: 1.50; 95% CI 1.09–2.08). In the subsample of patients without a diagnosis of dementia, the inclusion of calf circumference in a model based on age and sex significantly improved its discriminative accuracy [area under the curve (AUC) 0.69 vs 0.57, p < 0.001].

Discussion and conclusion

Low muscle mass is independently associated with delirium. In patients without a previous diagnosis of dementia, calf circumference may help to better identify those who develop delirium.

Supplementary Information

The online version contains supplementary material available at 10.1007/s40520-021-01950-8.

From Kuru to Alzheimer: A personal outlook

Seventy years ago, we learned from Chris Anfinsen that the stereochemical code necessary to fold a protein is embedded into its amino acid sequence. In water, protein morphogenesis is a spontaneous reversible process leading from an ensemble of disordered structures to the ordered functionally competent protein; conforming to Aristotle's definition of substance, the synolon of matter and form. The overall process of folding is generally consistent with a two state transition between the native and the denatured protein: not only the denatured state is an ensemble of several structures, but also the native protein populates distinct functionally relevant conformational (sub)states. This two-state view should be revised, given that any globular protein can populate a peculiar third state called amyloid, characterized by an overall architecture that at variance with the native state, is by-and-large independent of the primary structure. In a nut shell, we should accept that beside the folded and unfolded states, any protein can populate a third state called amyloid which gained center stage being the hallmark of incurable neurodegenerative disorders, such as Alzheimer's and Parkinson's diseases as well as others. These fatal diseases are characterized by clear-cut clinical differences, yet display some commonalities such as the presence in the brain of amyloid deposits constituted by one misfolded protein specific for each disease. Some aspects of this complex problem are summarized here as an excursus from the prion's fibrils observed in the brain of aborigines who died of Kuru to the amyloid detectable in the cortex of Alzheimer's patients.

Control of Oxygen Affinity in Mammalian Hemoglobins: Implications for a System Biology Description of the Respiratory Properties of the Red Blood Cell

Hemoglobin and myoglobin have been considered for a long time the paradigmatic model systems for protein function, to the point of being defined the "hydrogen atom[s] of biology". Given this privileged position and the huge amount of quantitative information available on these proteins, the red blood cell might appear as the model system and"hydrogen atom" of system biology. Indeed, since the red cell's main function is O2 transport by hemoglobin, the gap between the protein and the cell may appear quite small. Yet, a surprisingly large amount of detailed biochemical information is required for the modelization of the respiratory properties of the erythrocyte. This problem is compounded if modelization aims at uncovering or explaining evolutionarily selected functional properties of hemoglobin. The foremost difficulty lies in the fact that hemoglobins having different intrinsic properties and relatively ancient evolutionary divergence may behave similarly in the complex milieu of blood, whereas very similar hemoglobins sharing a substantial sequence similarity may present important functional differences because of the mutation of a few key residues. Thus, the functional properties of hemoglobin and blood may reflect more closely the recent environmental challenges than the remote evolutionary history of the animal. We summarize in this review the case of hemoglobins from mammals, in an attempt to provide a reasoned summary of their complexity that, we hope, may be of help to scientists interested in the quantitative exploration of the evolutionary physiology of respiration. Indeed the basis of a meaningful modelization of the red cell requires a large amount of information collected in painstaking and often forgotten studies of the biochemical properties of hemoglobin carried out over more than a century.

AB0481 EFFICACY OF APREMILAST FOR THE TREATMENT OF GENITAL ULCERS ASSOCIATED WITH ACTIVE BEHÇET’S SYNDROME: A COMBINED ANALYSIS OF TWO RANDOMIZED CONTROLLED TRIALS

Background:

Behçet’s syndrome is a chronic, multi-system inflammatory disorder characterized by painful, recurrent oral ulcers (OU) and genital ulcers (GU).1The GU associated with Behçet’s syndrome can contribute to difficulties with sexual activity, walking, and sitting2; may cause scarring1; and may impair quality of life.1,2Apremilast (APR), an oral phosphodiesterase 4 inhibitor, has demonstrated efficacy in the treatment of the OU associated with Behçet’s syndrome in the phase III, randomized RELIEF study (BCT-002).3

Objectives:

To describe the efficacy of APR for the treatment of GU associated with active Behçet’s syndrome in the RELIEF study and in a pooled data analysis of RELIEF and the phase II study.

Methods:

Adult patients (≥18 years of age) with active Behçet’s syndrome and ≥3 OU at randomization or ≥2 OU at screening and randomization, without active major organ involvement, were randomized (1:1) to APR 30 mg twice daily or placebo (PBO). In RELIEF, clinical improvement in GU was assessed by evaluating the time to the first GU recurrence after loss of complete response, the mean number of GU in patients without GU at baseline, and the proportion of patients who were GU-free (complete response) at Week 12 (regardless of baseline GU status). A pooled analysis of patients in RELIEF and a randomized, phase II study4were conducted to assess achievement of GU complete response in patients with GU at baseline. In patients with GU complete response before Week 12, the median time to the first GU recurrence after loss of complete response was based on Kaplan-Meier estimates. The mean number of GU was summarized descriptively using data as observed. Between-group differences in the proportion of patients who were GU-free at Week 12 were analyzed by Cochran-Mantel-Haenszel test using non-responder imputation to handle missing data. Statistical tests were 2 sided (α=0.05).

Results:

A total of 207 patients were randomized and received ≥1 dose of study medication (APR: n=104; PBO: n=103). In all, 17 patients in the APR group and 17 in the PBO group had GU at baseline, with mean GU counts of 2.9 (APR) and 2.6 (PBO). Among patients with GU at baseline in RELIEF, 12/17 (70.6% [APR]) and 7/17 (41.2% [PBO]) achieved GU complete response at Week 12 (P=0.110). The median time to first GU recurrence in these patients occurred earlier with PBO (6.1 weeks) vs. APR (not calculable). In the pooled analysis of RELIEF and the phase II study, a significantly greater proportion of patients with GU at baseline achieved GU complete response at Week 12 with APR vs. PBO (21/27 [77.8%] vs. 9/23 [39.1%];P=0.011) (Figure 1). The proportion of patients who were GU-free was significantly greater with APR (92/104 [88.5%]) vs. PBO (72/101 [71.3%]), regardless of baseline number of GU (P=0.002) (Figure 2).

Conclusion:

The number of patients with GU was low, but the totality of the data shows a favorable trend in the treatment effect of APR on GU. Greater proportions of APR-treated patients were GU-free at Week 12 vs. patients receiving PBO, and the time to the first GU recurrence occurred earlier with PBO vs. APR.

References:

[1]Kokturk A. Patholog Res Int. 2012;2012:690390. 2. Senusi A, et al. Orphanet J Rare Dis. 2015;10:117. 3. Hatemi G, et al. N Engl J Med. 2019;381:1918-1928. 4. Hatemi G, et al. N Engl J Med. 2015;372:1510-1518.

Disclosure of Interests:

Gulen Hatemi Grant/research support from: BMS, Celgene Corporation, Silk Road Therapeutics – grant/research support, Consultant of: Bayer, Eli Lilly – consultant, Speakers bureau: AbbVie, Mustafa Nevzat, Novartis, UCB – speaker, Alfred Mahr Consultant of: Celgene, Speakers bureau: Roche, Chugai, Mitsuhiro Takeno Speakers bureau: Esai, Tanabe-Mitsubishi – speaker; Celgene Corporation – advisory board, Doyoung Kim: None declared, Melike Melikoglu: None declared, Sue Cheng Employee of: Amgen Inc. – employment; Celgene Corporation – employment at the time of study conduct, Shannon McCue Employee of: Amgen Inc. – employment; Celgene Corporation – employment at the time of study conduct, Sven Richter Employee of: Amgen Inc. – employment; Celgene Corporation – employment at the time of study conduct, Michele Brunori Employee of: Amgen Inc. – employment; Celgene Corporation – employment at the time of study conduct, Maria Paris Employee of: Amgen Inc. – employment; Celgene Corporation – employment at the time of study conduct, Mindy Chen Employee of: Amgen Inc. – employment; Celgene Corporation – employment at the time of the conduct, Yusuf Yazici Consultant of: BMS, Celgene Corporation, Genentech, Sanofi – consultant, Consultant of: BMS, Celgene Corporation, Genentech, Sanofi – consultant

OP0028 EFFICACY OF APREMILAST FOR THE PAIN OF ORAL ULCERS ASSOCIATED WITH ACTIVE BEHÇET’S SYNDROME: 12-WEEK RESULTS FROM THE RANDOMIZED, PHASE III RELIEF STUDY

Background:

Oral ulcers (OU) associated with Behçet’s syndrome are often painful, may interfere with the ability to eat and can negatively affect quality of life.1,2Apremilast (APR), an oral phosphodiesterase 4 inhibitor, demonstrated efficacy in the treatment of OU associated with Behçet’s syndrome in a phase III, multicenter, randomized, double-blind, placebo (PBO)-controlled study (RELIEF; BCT-002).3

Objectives:

To describe the efficacy of APR treatment in improving OU pain associated with Behçet’s syndrome in RELIEF.

Methods:

Patients were randomized (1:1) to APR 30 mg twice daily (APR 30 BID) or PBO twice daily for a 12-week PBO-controlled phase, followed by a 52-week active treatment extension. Eligible patients were ≥18 years of age and had active Behçet’s syndrome with ≥3 OU at randomization or ≥2 OU at screening and randomization and without active major organ involvement. Clinical improvement in OU was evaluated by the area under the curve for the number of OU through Week 12 (AUCWk0-12; primary efficacy endpoint) and by assessments of OU number. Patient-reported OU pain was evaluated by the 100-mm visual analogue scale (VAS). The statistical tests were 2-sided (α=0.05). The proportions of patients achieving the minimal clinically important difference (MCID) and higher rates of improvement, defined as ≥10-mm,4≥30-mm (3-fold MCID), ≥50-mm (5-fold MCID) improvements in OU pain VAS scores, respectively, were analyzed through Week 12. An ANCOVA model was used to analyze the primary endpoint and assessments of OU number and OU pain (VAS). The proportion of patients achieving improvement in OU pain VAS scores at Week 12 were summarized descriptively.

Results:

A total of 207 patients were randomized and received ≥1 dose of study medication (APR: n=104; PBO: n=103). At baseline, the mean (SD) number of OU was 4.2 (3.7) in the APR 30 BID group and 3.9 (2.7) in the PBO group, and the mean (SD) OU pain VAS scores were 61.2 (27.6) and 60.8 (26.9), respectively. At Week 12, significantly greater improvements were observed with APR 30 BID vs. PBO in AUCWk0-12(least-squares [LS] mean [SE]: 129.5 [15.9] vs. 222.1 [15.9];P<0.0001), number of OU (LS mean [SE]: 1.1 [0.2] vs. 2.0 [0.3];P=0.0003) and OU pain VAS scores (LS mean [SE] change from baseline: −40.7 [3.3] vs. −15.9 [3.3];P<0.0001). The proportion of patients who achieved the MCID of ≥10-mm improvement in OU pain VAS scores at Week 12 was greater with APR 30 BID vs. PBO; this pattern was also observed for the higher 3- and 5-fold improvements in MCID (Figure 1). Greater proportions of APR 30 BID vs. PBO patients achieved ≥10-mm and ≥30-mm improvements in OU pain VAS scores over 12 weeks. Notably, greater achievement of ≥50-mm improvement in OU pain VAS scores was observed with APR 30 BID vs. PBO as early as Week 1 and maintained up to Week 12 (Figure 2).

Conclusion:

For patients with active Behçet’s syndrome, APR 30 BID provided significantly greater improvements vs. PBO in OU number and OU pain at Week 12, including the greater proportion of patients achieving MCID and 3- and 5-fold MCID of OU pain in the APR 30 BID group vs. the PBO group. These results indicate a clinically meaningful treatment effect of APR 30 BID on the OU associated with Behçet’s syndrome.

References:

[1]Kokturk A.Patholog Res Int. 2012;2012:690390.

[2]Hatemi G, et al.Ann Rheum Dis. 2008;67:1656-1662.

[3]Hatemi G, et al.N Engl J Med. 2019;381:1918-1928. 4. Dworkin RH, et al.J Pain. 2008;9:105-121.

Disclosure of Interests:

Gulen Hatemi Grant/research support from: BMS, Celgene Corporation, Silk Road Therapeutics – grant/research support, Consultant of: Bayer, Eli Lilly – consultant, Speakers bureau: AbbVie, Mustafa Nevzat, Novartis, UCB – speaker, Alfred Mahr Consultant of: Celgene, Speakers bureau: Roche, Chugai, Mitsuhiro Takeno Speakers bureau: Esai, Tanabe-Mitsubishi – speaker; Celgene Corporation – advisory board, Doyoung Kim: None declared, Melike Melikoglu: None declared, Sue Cheng Employee of: Amgen Inc. – employment; Celgene Corporation – employment at the time of study conduct, Shannon McCue Employee of: Amgen Inc. – employment; Celgene Corporation – employment at the time of study conduct, Sven Richter Employee of: Amgen Inc. – employment; Celgene Corporation – employment at the time of study conduct, Michele Brunori Employee of: Amgen Inc. – employment; Celgene Corporation – employment at the time of study conduct, Maria Paris Employee of: Amgen Inc. – employment; Celgene Corporation – employment at the time of study conduct, Mindy Chen Employee of: Amgen Inc. – employment; Celgene Corporation – employment at the time of the conduct, Yusuf Yazici Consultant of: BMS, Celgene Corporation, Genentech, Sanofi – consultant, Consultant of: BMS, Celgene Corporation, Genentech, Sanofi – consultant

FRI0352 PROBABILITY OF ACHIEVING LOW DISEASE ACTIVITY OR REMISSION WITH APREMILAST TREATMENT AMONG DMARD-NAIVE SUBJECTS WITH ACTIVE PSORIATIC ARTHRITIS

Background:

Apremilast (APR) is associated with comparable ACR response rates in DMARD-naive vs DMARD-experienced patients (pts) with psoriatic arthritis (PsA).1,2A question that remains is if DMARD-naive pts treated with APR have greater chances of achieving treatment targets than DMARD-experienced pts. cDAPSA is a commonly used treatment target.

Objectives:

To assess the predictive value of baseline (BL) clinical disease status on achieving long-term cDAPSA treatment targets at Wk 52 among DMARD-naive subjects in PALACE 4; to compare these findings vs those recently reported from the PALACE 1-3 studies in subjects with prior exposure to DMARDs; and to provide further evidence that at a group level, achievement of cDAPSA disease targets with APR is associated with no or mild articular and extra-articular disease activity by Wk 52.

Methods:

This post hoc analysis included subjects assigned to APR 30 mg twice daily at BL who had available cDAPSA data at BL. We calculated the probabilities of shifting across different cDAPSA categories (remission [REM]: ≤4; low disease activity [LDA]: >4 to ≤13; moderate disease activity [Mod]: >13 to ≤27; high disease activity [HDA]: >273) from BL to Wk 52. Mean values of articular and non-articular variables (e.g., PASI, SJC/TJC, MASES, dactylitis) from BL to Wk 52 were assessed by cDAPSA category achieved at Wk 52 to determine the association between achievement of targets and control of articular and non-articular manifestations. Results from the current analyses were compared with the previously reported results from PALACE 1-3.

Results:

A total of 175 subjects receiving APR were included; at BL, 66.3% were in HDA, 31.4% in Mod, and 2.3% were in LDA. Overall, subjects who achieved treatment targets (LDA or REM) by Wk 52 had lower levels of disease activity at BL, as shown by a lower number of swollen and tender joints and lower presence of enthesitis and dactylitis. Higher prevalence of psoriasis-involved body surface area ≥3% at BL was observed. Subjects in Mod at BL were estimated to be more than twice as likely to achieve REM or LDA at Wk 52 vs subjects in HDA at BL; for subjects in LDA at BL, the estimated probability of achieving cDAPSA treatment targets was 100% (Figure). PALACE 4 subjects with LDA and Mod at BL exhibited higher estimated probabilities of achieving treatment targets (100.0% and 61.7%, respectively) than those observed in the DMARD-experienced population of PALACE 1-3 (71.1% and 46.9%). Subjects in PALACE 4 who achieved REM or LDA by Wk 52 showed no or mild articular and extra-articular disease activity by Wk 52, similar to what was observed in the PALACE 1-3 population.4

Conclusion:

DMARD-naive subjects in PALACE 4 who had LDA or Mod at BL had the highest likelihood of achieving treatment targets (cDAPSA REM or LDA) by Wk 52 with continued APR treatment. Results from the current probability analyses revealed higher probability rates than those observed in the DMARD-experienced PALACE 1-3 population; control of articular and extra-articular manifestations was observed in the DMARD-naive and DMARD-experienced populations.

References:

[1]Wells AF, et al. Rheumatology. 2018;57:1253-63. 2. Kavanaugh A, et al. Arthritis Res Ther. 2019;21:118. 3. Machado PM. Ann Rheum Dis. 2016;75:787-90. 4. Mease PJ, et al. Arthritis Care Res. 2020 Jan 7.

Disclosure of Interests:

Philip J Mease Grant/research support from: Abbott, Amgen, Biogen Idec, BMS, Celgene Corporation, Eli Lilly, Novartis, Pfizer, Sun Pharmaceutical, UCB – grant/research support, Consultant of: Abbott, Amgen, Biogen Idec, BMS, Celgene Corporation, Eli Lilly, Novartis, Pfizer, Sun Pharmaceutical, UCB – consultant, Speakers bureau: Abbott, Amgen, Biogen Idec, BMS, Eli Lilly, Genentech, Janssen, Pfizer, UCB – speakers bureau, Arthur Kavanaugh Grant/research support from: Abbott, Amgen, AstraZeneca, BMS, Celgene Corporation, Centocor-Janssen, Pfizer, Roche, UCB – grant/research support, Alexis Ogdie Grant/research support from: Novartis, Pfizer – grant/research support, Consultant of: AbbVie, BMS, Eli Lilly, Novartis, Pfizer, Takeda – consultant, Alvin F. Wells Grant/research support from: AbbVie, Celgene Corporation, Lilly – grant/research support, Consultant of: AbbVie, Alexion, Amgen, BMS, Celgene Corporation, Horizon, Lilly, Novartis, UCB – consultant, Speakers bureau: AbbVie, Alexion, Amgen, BMS, Celgene Corporation, Horizon, Lilly, Novartis, UCB – speakers bureau, Martin Bergman Shareholder of: Johnson & Johnson – stockholder, Consultant of: AbbVie, BMS, Celgene Corporation, Genentech, Janssen, Merck, Novartis, Pfizer, Sanofi – consultant, Speakers bureau: AbbVie, Celgene Corporation, Novartis, Pfizer, Sanofi – speakers bureau, Dafna D Gladman Grant/research support from: AbbVie, Amgen Inc., BMS, Celgene Corporation, Janssen, Novartis, Pfizer, UCB – grant/research support, Consultant of: AbbVie, Amgen Inc., BMS, Celgene Corporation, Janssen, Novartis, Pfizer, UCB – consultant, Frank Behrens Grant/research support from: AbbVie, Chugai, Janssen, Roche, Pfizer – grant/research support, Consultant of: AbbVie Biotest, Boehringer Ingelheim, Celgene Corporation, Chugai, Eli Lilly, Genzyme, Janssen, Novartis, Pfizer, Roche, UCB – consultant, Speakers bureau: AbbVie, Biotest, BMS, Celgene Corporation, Chugai, Eli Lilly, Genzyme, Janssen, Merck Sharp & Dohme, Novartis, Pfizer, Roche, Sandoz, UCB - speaker, Sven Richter Employee of: Amgen Inc. – employment; Celgene Corporation – employment at the time of study conduct, Michele Brunori Employee of: Amgen Inc. – employment; Celgene Corporation – employment at the time of study conduct, Lichen Teng Employee of: Amgen Inc. – employment; Celgene Corporation – employment at the time of study conduct, Benoit Guerette Employee of: Amgen Inc. – employment; Celgene Corporation – employment at the time of study conduct, Josef S. Smolen Grant/research support from: AbbVie, Eli Lilly, Janssen, Merck Sharp & Dohme, Pfizer, Roche – grant/research support, Consultant of: AbbVie, Amgen Inc., AstraZeneca, Astro, Celgene Corporation, Celtrion, Eli Lilly, Glaxo, ILTOO, Janssen, Medimmune, Merck Sharp & Dohme, Novartis, Pfizer, Roche, Samsung, Sanofi, UCB – consultant, Speakers bureau: AbbVie, Amgen Inc., AstraZeneca, Astro, Celgene Corporation, Celtrion, Eli Lilly, Glaxo, ILTOO, Janssen, Medimmune, Merck Sharp & Dohme, Novartis, Pfizer, Roche, Samsung, Sanofi, UCB – speaker

Templated folding of intrinsically disordered proteins

Much of our current knowledge of biological chemistry is founded in the structure-function relationship, whereby sequence determines structure that determines function. Thus, the discovery that a large fraction of the proteome is intrinsically disordered, while being functional, has revolutionized our understanding of proteins and raised new and interesting questions. Many intrinsically disordered proteins (IDPs) have been determined to undergo a disorder-to-order transition when recognizing their physiological partners, suggesting that their mechanisms of folding are intrinsically different from those observed in globular proteins. However, IDPs also follow some of the classic paradigms established for globular proteins, pointing to important similarities in their behavior. In this review, we compare and contrast the folding mechanisms of globular proteins with the emerging features of binding-induced folding of intrinsically disordered proteins. Specifically, whereas disorder-to-order transitions of intrinsically disordered proteins appear to follow rules of globular protein folding, such as the cooperative nature of the reaction, their folding pathways are remarkably more malleable, due to the heterogeneous nature of their folding nuclei, as probed by analysis of linear free-energy relationship plots. These insights have led to a new model for the disorder-to-order transition in IDPs termed "templated folding," whereby the binding partner dictates distinct structural transitions en route to product, while ensuring a cooperative folding.

Ligand pathways in neuroglobin revealed by low-temperature photodissociation and docking experiments

A combined biophysical approach was applied to map gas-docking sites within murine neuroglobin (Ngb), revealing snapshots of events that might govern activity and dynamics in this unique hexacoordinate globin, which is most likely to be involved in gas-sensing in the central nervous system and for which a precise mechanism of action remains to be elucidated. The application of UV-visible microspectroscopy in crystallo, solution X-ray absorption near-edge spectroscopy and X-ray diffraction experiments at 15-40 K provided the structural characterization of an Ngb photolytic intermediate by cryo-trapping and allowed direct observation of the relocation of carbon monoxide within the distal heme pocket after photodissociation. Moreover, X-ray diffraction at 100 K under a high pressure of dioxygen, a physiological ligand of Ngb, unravelled the existence of a storage site for O2 in Ngb which coincides with Xe-III, a previously described docking site for xenon or krypton. Notably, no other secondary sites were observed under our experimental conditions.

Identification of a novel nucleophosmin-interaction motif in the tumor suppressor p14arf

The tumor suppressor p14arf interacts, in response to oncogenic signals, with the p53 E3-ubiquitin ligase HDM2, thereby resulting in p53 stabilization and activation. In addition, it also exerts tumor-suppressive functions in p53-independent contexts. The activities of p14arf are regulated by the nucleolar chaperone nucleophosmin (NPM1), which controls its levels and cellular localization. In acute myeloid leukemia with mutations in the NPM1 gene, mutated NPM1 aberrantly translocates in the cytosol carrying with itself p14arf that is subsequently degraded, thus impairing the p14arf-HDM2-p53 axis. In this work we investigated the complex between these two proteins by means of NMR and other techniques. We identified a novel NPM1-interacting motif in the C-terminal region of p14arf, which corresponds to its predicted nucleolar localization signal. This motif recognizes a specific region of the NPM1 N-terminal domain and, upon binding, the two proteins form soluble high molecular weight complexes. By NMR, we identified critical residues on both proteins involved in the interaction. Collectively, our data provide a structural framework to rationalize the overall assembly of the p14arf-NPM1 supramolecular complexes. A number of p14arf cancer-associated mutations cluster in this motif and their effect on the interaction with NPM1 was also analyzed.

The Folding Pathway of the KIX Domain

The KIX domain is an 89-residues globular domain with an important role in mediating protein-protein interactions. The presence of two distinct binding sites in such a small domain makes KIX a suitable candidate to investigate the effect of the potentially divergent demands between folding and function. Here, we report an extensive mutational analysis of the folding pathway of the KIX domain, based on 30 site-directed mutants, which allow us to assess the structures of both the transition and denatured states. Data reveal that, while the transition state presents mostly native-like interactions, the denatured state is somewhat misfolded. We mapped some of the non-native contacts in the denatured state using a second round of mutagenesis, based on double mutant cycles on 15 double mutants. Interestingly, such a misfolding arises from non-native interactions involving the residues critical for the function of the protein. The results described in this work appear to highlight the diverging demands between folding and function that may lead to misfolding, which may be observed in the early stages of folding.

Towards a structural biology of the hydrophobic effect in protein folding

The hydrophobic effect is a major driving force in protein folding. A complete understanding of this effect requires the description of the conformational states of water and protein molecules at different temperatures. Towards this goal, we characterise the cold and hot denatured states of a protein by modelling NMR chemical shifts using restrained molecular dynamics simulations. A detailed analysis of the resulting structures reveals that water molecules in the bulk and at the protein interface form on average the same number of hydrogen bonds. Thus, even if proteins are 'large' particles (in terms of the hydrophobic effect, i.e. larger than 1 nm), because of the presence of complex surface patterns of polar and non-polar residues their behaviour can be compared to that of 'small' particles (i.e. smaller than 1 nm). We thus find that the hot denatured state is more compact and richer in secondary structure than the cold denatured state, since water at lower temperatures can form more hydrogen bonds than at high temperatures. Then, using Φ-value analysis we show that the structural differences between the hot and cold denatured states result in two alternative folding mechanisms. These findings thus illustrate how the analysis of water-protein hydrogen bonds can reveal the molecular origins of protein behaviours associated with the hydrophobic effect.

A molecule for all seasons: The heme

If life without heme-Fe were at all possible, it would definitely be different. Indeed this complex and versatile iron-porphyrin macrocycle upon binding to different “globins” yields hemeproteins crucial to sustain a variety of vital functions, generally classified, for convenience, in a limited number of functional families. Over-and-above the array of functions briefly outlined below, the spectacular progress in molecular genetics seen over the last 30 years led to the discovery of many hitherto unknown novel hemeproteins in prokaryotes and eukaryotes. Here, we highlight a few basic aspects of the chemistry of the hemeprotein universe, in particular those that are relevant to the control of heme-Fe reactivity and specialization, as sculpted by a variety of interactions with the protein moiety.

Molecular medicine - To be or not to be

Molecular medicine is founded on the synergy between Chemistry, Physics, Biology and Medicine, with the ambitious goal of tackling diseases from a molecular perspective. This Review aims at retracing a personal outlook of the birth and development of molecular medicine, as well as at highlighting some of the most urgent challenges linked to aging and represented by incurable neurodegenerative diseases caused by protein misfolding. Furthermore, we emphasize the emerging role of the retromer dysfunctions and improper protein sorting in Alzheimer's disease and other important neurological disordered.

Identification and Structural Characterization of an Intermediate in the Folding of the Measles Virus X Domain

Although most proteins fold by populating intermediates, the transient nature of such states makes it difficult to characterize their structures. In this work we identified and characterized the structure of an intermediate of the X domain of phosphoprotein (P) of measles virus. We obtained this result by a combination of equilibrium and kinetic measurements and NMR chemical shifts used as structural restraints in replica-averaged metadynamics simulations. The structure of the intermediate was then validated by rationally designing four mutational variants predicted to affect the stability of this state. These results provide a detailed view of an intermediate state and illustrate the opportunities offered by a synergistic use of experimental and computational methods to describe non-native states at atomic resolution.

One-year safety and efficacy of ustekinumab and results of dose adjustment after switching from inadequate methotrexate treatment: the TRANSIT randomized trial in moderate-to-severe plaque psoriasis

BACKGROUND

There are limited long-term, 'real-world' data on ustekinumab, or the effect of dose adjustment in suboptimal responders.

OBJECTIVES

We describe 52-week data from TRANSIT, which initiated ustekinumab by licensed regimen and investigated exploratory dose adjustment.

METHODS

Patients with moderate-to-severe psoriasis and inadequate methotrexate response received ustekinumab, with immediate or gradual methotrexate withdrawal. Outcomes were similar between treatment arms at week 12 (primary endpoint), so week 52 data were pooled. Patients weighing ≤ 100 kg or > 100 kg were administered ustekinumab 45 or 90 mg, respectively. Patients weighing ≤ 100 kg without 75% improvement in Psoriasis Area and Severity Index (PASI 75) response at weeks 28 or 40 received a dose adjustment to 90 mg. The primary analysis used observed data.

RESULTS

Overall, 391 and 98 patients received ustekinumab 45 and 90 mg, respectively. Forty-four patients (9%) discontinued before week 52 (0·4% due to adverse events). At week 52 (in the overall population), 369 patients (83%) achieved a PASI score ≤ 5, and 341 patients (77%) achieved PASI 75; the median PASI score decreased from 15 at baseline to 1·8. At weeks 28 and 40, 84 and 31 patients, respectively, did not achieve PASI 75 and received a dose adjustment; by week 52, 35/82 (43%) and 15/31 (48%) of these patients, respectively, achieved PASI 75 (two discontinued between weeks 28 and 40).

CONCLUSIONS

Ustekinumab showed sustained 1-year efficacy and was well tolerated when initially administered according to label. Adjusting the ustekinumab dose to 90 mg may result in clinically meaningful improvement in response in patients weighing ≤ 100 kg with suboptimal initial response.

Understanding the frustration arising from the competition between function, misfolding, and aggregation in a globular protein

Folding and function may impose different requirements on the amino acid sequences of proteins, thus potentially giving rise to conflict. Such a conflict, or frustration, can result in the formation of partially misfolded intermediates that can compromise folding and promote aggregation. We investigate this phenomenon by studying frataxin, a protein whose normal function is to facilitate the formation of iron-sulfur clusters but whose mutations are associated with Friedreich's ataxia. To characterize the folding pathway of this protein we carry out a Φ-value analysis and use the resulting structural information to determine the structure of the folding transition state, which we then validate by a second round of rationally designed mutagenesis. The analysis of the transition-state structure reveals that the regions involved in the folding process are highly aggregation-prone. By contrast, the regions that are functionally important are partially misfolded in the transition state but highly resistant to aggregation. Taken together, these results indicate that in frataxin the competition between folding and function creates the possibility of misfolding, and that to prevent aggregation the amino acid sequence of this protein is optimized to be highly resistant to aggregation in the regions involved in misfolding.

Engineering the internal cavity of neuroglobin demonstrates the role of the haem-sliding mechanism

Neuroglobin is a member of the globin family involved in neuroprotection; it is primarily expressed in the brain and retina of vertebrates. Neuroglobin belongs to the heterogeneous group of hexacoordinate globins that have evolved in animals, plants and bacteria, endowed with the capability of reversible intramolecular coordination, allowing the binding of small gaseous ligands (O2, NO and CO). In a unique fashion among haemoproteins, ligand-binding events in neuroglobin are dependent on the sliding of the haem itself within a preformed internal cavity, as revealed by the crystal structure of its CO-bound derivative. Point mutants of the neuroglobin internal cavity have been engineered and their functional and structural characterization shows that hindering the haem displacement leads to a decrease in CO affinity, whereas reducing the cavity volume without interfering with haem sliding has negligible functional effects.

The mechanism of binding of the KIX domain to the mixed lineage leukemia protein and its allosteric role in the recognition of c-Myb

The KIX domain is a mediator of the interaction between different transcription factors. This complex function is carried out via two distinct binding sites located on opposite sides of the protein; namely, the 'c-Myb site' and the 'MLL site', named after their characteristic ligands-the transactivation domain of c-Myb and the mixed lineage leukemia protein (MLL). Both these ligands are unstructured in isolation and fold only upon binding, posing the KIX domain as an ideal candidate to explore the binding induced folding reaction of intrinsically unstructured proteins. Here, we complement the recent kinetic description on the interaction between KIX and c-Myb, by characterizing the binding kinetics between KIX and MLL, at different pH and ionic strength conditions. Furthermore, we analyze quantitatively the mechanism of allosteric communication between the topologically distinct c-Myb and MLL sites. The implications of our results are discussed in the light of previous work on other intrinsically unstructured systems.

The kinetics of folding of frataxin

The role of the denatured state in protein folding represents a key issue for the proper evaluation of folding kinetics and mechanisms. The yeast ortholog of the human frataxin, a mitochondrial protein essential for iron homeostasis and responsible for Friedreich's ataxia, has been shown to undergo cold denaturation above 0 °C, in the absence of chemical denaturants. This interesting property provides the unique opportunity to explore experimentally the molecular mechanism of both the hot and cold denaturation. In this work, we present the characterization of the temperature and urea dependence of the folding kinetics of yeast frataxin, and show that while at neutral pH and in the absence of a denaturant a simple two-state model may satisfactorily describe the temperature dependence of the folding and unfolding rate constants, the results obtained in urea over a wide range of pH reveal an intriguing complexity, suggesting that folding of frataxin involves a broad smooth free energy barrier.

Efficacy and tolerability of bendamustine, bortezomib and dexamethasone in patients with relapsed-refractory multiple myeloma: a phase II study

Bendamustine demonstrated synergistic efficacy with bortezomib against multiple myeloma (MM) cells in vitro and seems an effective treatment for relapsed-refractory MM (rrMM). This phase II study evaluated bendamustine plus bortezomib and dexamethasone (BVD) administered over six 28-day cycles and then every 56 days for six further cycles in patients with rrMM treated with ⩽4 prior therapies and not refractory to bortezomib. The primary study end point was the overall response rate after four cycles. In total, 75 patients were enrolled, of median age 68 years. All patients had received targeted agents, 83% had 1–2 prior therapies and 33% were refractory to the last treatment. The response rate⩾partial response (PR) was 71.5% (16% complete response, 18.5% very good PR, 37% partial remission). At 12 months of follow-up, median time-to-progression (TTP) was 16.5 months and 1-year overall survival was 78%. According to Cox regression analysis, only prior therapy with bortezomib plus lenalidomide significantly reduced TTP (9 vs 17 months; hazard ratio=4.5; P=0.005). The main severe side effects were thrombocytopenia (30.5%), neutropenia (18.5%), infections (12%), neuropathy (8%) and gastrointestinal and cardiovascular events (both 6.5%). The BVD regimen is feasible, effective and well-tolerated in difficult-to-treat patients with rrMM.

The mitochondrial Italian Human Proteome Project initiative (mt-HPP)

Mitochondria carry maternally inherited genetic material, called the mitochondrial genome (mtDNA), which can be defined as the 25th human chromosome. The chromosome-centric Human Proteome Project (c-HPP) has initially focused its activities addressing the characterization and quantification of the nuclear encoded proteins. Following the last International HUPO Congress in Boston (September 2012) it was clear that however small the mitochondrial chromosome is, it plays an important role in many biological and physiopathological functions. Mutations in the mtDNA have been shown to be associated with dozens of unexplained disorders and the information contained in the mtDNA should be of major relevance to the understanding of many human diseases. Within this paper we describe the Italian initiative of the Human Proteome Project dedicated to mitochondria as part of both programs: chromosome-centric (c-HPP) and Biology/Disease (B/D-HPP). The mt-HPP has finally shifted the attention of the HUPO community outside the nuclear chromosomes with the general purpose to highlight the mitochondrial processes influencing the human health. Following this vision and considering the large interest and evidence collected on the non-Mendelian heredity of Homo sapiens associated with mt-chromosome and with the microbial commensal ecosystem constituting our organism we may speculate that this program will represent an initial step toward other HPP initiatives focusing on human phenotypic heredity.

Reassessing the folding of the KIX domain: evidence for a two-state mechanism

The debate about the presence and role of intermediates in the folding of proteins has been a critical issue, especially for fast folders. One of the classical methodologies to identify such metastable species is the "burst-phase analysis," whereby the observed signal amplitude from stopped-flow traces is determined as a function of denaturant concentration. However, a complication may arise when folding is sufficiently fast to jeopardize the reliability of the stopped-flow technique. In this study, we reassessed the folding of the KIX domain from cAMP Response Element-Binding (CREB)-binding protein, which has been proposed to involve the formation of an intermediate that accumulates in the dead time of the stopped flow. By using an in-house-built capillary continuous flow with a 50-μs dead time, we demonstrate that this intermediate is not present; the problem arose because of the instrumental limitation of the standard stopped flow to assess very fast refolding rate constants (e.g., ≥ 500 s⁻¹).

A folding-after-binding mechanism describes the recognition between the transactivation domain of c-Myb and the KIX domain of the CREB-binding protein

A large body of evidence suggests that a considerable fraction of the human proteome may be at least in part intrinsically unstructured. While disordered, intrinsically unstructured proteins are nevertheless functional and mediate many interactions. Despite their significant role in regulation, however, little is known about the molecular mechanism whereby intrinsically unstructured proteins exert their function. This basic problem is critical to establish the role, if any, of disorder in cellular systems. Here we present kinetic experiments supporting a mechanism of binding-induced-folding when the KIX domain of the CREB-binding protein binds the transactivation domain of c-Myb, an intrinsically unstructured domain. The high-resolution structure of this physiologically important complex was previously determined by NMR spectroscopy. Our data reveal that c-Myb recognizes KIX by first forming a weak encounter complex in a disordered conformation, which is subsequently locked-in by a folding step, i.e. binding precedes folding. On the basis of the pH dependence of the observed combination and dissociation rate constants we propose a plausible mechanism for complex formation. The implications of our results in the light of previous work on intrinsically unstructured systems are discussed.

The Monod-Wyman-Changeux allosteric model accounts for the quaternary transition dynamics in wild type and a recombinant mutant human hemoglobin

The acknowledged success of the Monod-Wyman-Changeux (MWC) allosteric model stems from its efficacy in accounting for the functional behavior of many complex proteins starting with hemoglobin (the paradigmatic case) and extending to channels and receptors. The kinetic aspects of the allosteric model, however, have been often neglected, with the exception of hemoglobin and a few other proteins where conformational relaxations can be triggered by a short and intense laser pulse, and monitored by time-resolved optical spectroscopy. Only recently the application of time-resolved wide-angle X-ray scattering (TR-WAXS), a direct structurally sensitive technique, unveiled the time scale of hemoglobin quaternary structural transition. In order to test the generality of the MWC kinetic model, we carried out a TR-WAXS investigation in parallel on adult human hemoglobin and on a recombinant protein (HbYQ) carrying two mutations at the active site [Leu(B10)Tyr and His(E7)Gln]. HbYQ seemed an ideal test because, although exhibiting allosteric properties, its kinetic and structural properties are different from adult human hemoglobin. The structural dynamics of HbYQ unveiled by TR-WAXS can be quantitatively accounted for by the MWC kinetic model. Interestingly, the main structural change associated with the R-T allosteric transition (i.e., the relative rotation and translation of the dimers) is approximately 10-fold slower in HbYQ, and the drop in the allosteric transition rate with ligand saturation is steeper. Our results extend the general validity of the MWC kinetic model and reveal peculiar thermodynamic properties of HbYQ. A possible structural interpretation of the characteristic kinetic behavior of HbYQ is also discussed.