The effect of mutation on an aggregation-prone protein: An in vivo, in vitro, and in silico analysis.

Aggregation of initially stably structured proteins is involved in more than 20 human amyloid diseases. Despite intense research, however, how this class of proteins assembles into amyloid fibrils remains poorly understood, principally because of the complex effects of amino acid substitutions on protein stability, solubility, and aggregation propensity. We address this question using ß2-microglobulin (ß2m) as a model system, focusing on D76N-ß2m that is involved in hereditary amyloidosis. This amino acid substitution causes the aggregation-resilient wild-type protein to become highly aggregation prone in vitro, although the mechanism by which this occurs remained elusive. Here, we identify the residues key to protecting ß2m from aggregation by coupling aggregation with antibiotic resistance in E. coli using a tripartite ß-lactamase assay (TPBLA). By performing saturation mutagenesis at three different sites (D53X-, D76X-, and D98X-ß2m) we show that residue 76 has a unique ability to drive ß2m aggregation in vivo and in vitro. Using a randomly mutated D76N-ß2m variant library, we show that all of the mutations found to improve protein behavior involve residues in a single aggregation-prone region (APR) (residues 60 to 66). Surprisingly, no correlation was found between protein stability and protein aggregation rate or yield, with several mutations in the APR decreasing aggregation without affecting stability. Together, the results demonstrate the power of the TPBLA to develop proteins that are resilient to aggregation and suggest a model for D76N-ß2m aggregation involving the formation of long-range couplings between the APR and Asn76 in a nonnative state.

The epidemiology of in-hospital cardiac arrests in Australia and New Zealand.

BACKGROUND: The epidemiology of in-hospital cardiac arrests (IHCA) in Australia and New Zealand (ANZ) has not been systematically assessed. AIM: To conduct a systematic review of the frequency, characteristics and outcomes of adult IHCA in ANZ. METHODS: Medline search for studies published in 1964-2014 using MeSH terms 'arrest AND hospital AND Australia', 'arrest AND hospital AND New Zealand', 'inpatient AND arrest AND Australia' and 'inpatient AND arrest AND New Zealand'. RESULTS: We screened 934 studies, analysed 50 and included 30. Frequency of IHCA ranged from 1.31 to 6.11 per 1000 admissions in 4 population studies and 0.58 to 4.59 per 1000 in 16 cohort studies. The frequency was 4.11 versus 1.32 per 1000 admissions in hospitals with rapid response system (RRS) compared with those without (odds ratio: 0.32; 95% confidence interval 0.28-0.37; P < 0.001). On aggregate, the initial cardiac rhythm was ventricular tachycardia/fibrillation in 31.4% (range 19.0-48.8%) in 10 studies reporting such data. On aggregate, IHCA were witnessed in 80.2% cases (three studies) and monitored patients in 53.4% cases (four studies). Details of life support were poorly documented. On aggregate, return of spontaneous circulation occurred in 46.0% of patients. Overall, 74.6% (range 59.4-77.5%) died in-hospital but survival was higher among monitored or younger patients, in those with a shockable rhythm, or during working hours. CONCLUSION: IHCA are uncommon in ANZ and three quarters die in-hospital. However, their frequency varies markedly across institutions and may be affected by the presence of RRS. Where reported, the long-term outcomes survivors appear to have acceptable neurological outcomes.

Advances in ion mobility spectrometry-mass spectrometry reveal key insights into amyloid assembly.

Interfacing ion mobility spectrometry to mass spectrometry (IMS-MS) has enabled mass spectrometric analyses to extend into an extra dimension, providing unrivalled separation and structural characterization of lowly populated species in heterogeneous mixtures. One biological system that has benefitted significantly from such advances is that of amyloid formation. Using IMS-MS, progress has been made into identifying transiently populated monomeric and oligomeric species for a number of different amyloid systems and has led to an enhanced understanding of the mechanism by which small molecules modulate amyloid formation. This review highlights recent advances in this field, which have been accelerated by the commercial availability of IMS-MS instruments. This article is part of a Special Issue entitled: Mass spectrometry in structural biology.

The making of a nutrition professional: the Association for Nutrition register.

OBJECTIVE: Nutritionists in the UK are at the start of an exciting time of professional development. The establishment of the Association for Nutrition in 2010 has presented an opportunity to review, revitalize and expand the UK Voluntary Register of Nutritionists. In the UK and elsewhere, there is a need for a specialist register of nutritionists with title protection as a public safeguard. DESIGN: The new structure will base professional registration on demonstration of knowledge and application in five core competencies. Initially, there will be five specialist areas: animal; public health; nutritional scientist; food; sports and exercise. The wording and requirements linking the specialist areas to the competencies have been carefully defined by leading individuals currently on the existing register in these specialist areas. These have been evaluated by a random sample of existing registrants to check for accuracy of definitions and examples. Other work aims to establish a clear quality assurance framework in nutrition for workers in the health and social care sectors (UK Public Health Skills and Career Framework Levels 1-4) who contribute to nutrition activity, such as community food workers, nutrition assistants and pharmacists. Students, co-professional affiliates and senior fellows will also find a place in the new Association. The title 'nutritionist' is not currently legally protected in the UK and it is used freely to cover a range of unregulated practice. CONCLUSIONS: The establishment of a professional register to protect the public and to provide a clear identity for nutritionists is a vital step forward.

The cytological effect of ecdysterone on the midgut cells of the flesh-fly Sarcophaga bullata.

Larvae of the flesh-fly, Sarcophaga bullata, were injected with the synthetic moulting hormone ecdysterone or saline at the beginning of the third and final larval instar. One group was left untreated. The ecdysterone-injected larvae showed an increase in number of secondary lysosomes in the midgut epithelial cells similar to that observed at the onset of metamorphosis, an event which would normally occur about 48 hr later in these larvae.

Detection of transient protein folding populations by mass spectrometry.

Hydrogen-deuterium exchange measurements are becoming increasingly important in studies of the dynamics of protein molecules and, particularly, of their folding behavior. Electrospray ionization mass spectrometry (ESI-MS) has been used to obtain the distribution of masses within a population of protein molecules that had undergone hydrogen exchange in solution. This information is complementary to that from nuclear magnetic resonance spectroscopy (NMR) experiments, which measure the average occupancy of individual sites over the distribution of protein molecules. In experiments with hen lysozyme, a combination of ESI-MS and NMR was used to distinguish between alternative mechanisms of hydrogen exchange, providing insight into the nature and populations of transient folding intermediates. These results have helped to detail the pathways available to a protein during refolding.

Protein folding: progress made and promises ahead.

Over the past 25 years, enormous breakthroughs have been made in understanding protein folding mechanisms. We have now reached an exciting stage, with consensuses beginning to emerge that combine both theoretical and experimental approaches. In addition, new fields have emerged and burgeoned, including in vivo folding and the study of protein misfolding diseases. In today's post-genomic world, understanding protein folding has never been more important and the topic has wide-ranging impact in fields from structural biology to materials science.

Understanding how proteins fold: the lysozyme story so far.

Hen lysozyme is one of the best characterized and most studied of all proteins. Recently, we have used a range of different methods to examine the events involved in the in vitro folding pathway of this protein. In this review we show that, by combining complementary techniques, it has been possible to piece together a detailed model for the folding of this enzyme. Important questions prompted by this work are highlighted and we then propose some ideas consistent with our data, as well as those of others, which we believe begin to provide insight into one of the most intriguing of structural problems in biology--how proteins can achieve their complex native forms from disordered denatured states.

The role of ß-barrels 1 and 2 in the enzymatic activity of factor XIII A-subunit.

Essentials The roles of ß-barrels 1 and 2 in factor XIII (FXIII) are currently unknown. FXIII truncations lacking ß-barrel 2, both ß-barrels, or full length FXIII, were made. Removing ß-barrel 2 caused total loss of activity, removing both ß-barrels returned 30% activity. ß-barrel 2 is necessary for exposure of the active site cysteine during activation. SUMMARY: Background Factor XIII is composed of an activation peptide segment, a ß-sandwich domain, a catalytic core, and, finally, ß-barrels 1 and 2. FXIII is activated following cleavage of its A-subunits by thrombin. The resultant transglutaminase activity leads to increased resistance of fibrin clots to fibrinolysis. Objectives To assess the functional roles of ß-barrels 1 and 2 in FXIII, we expressed and characterized the full-length FXIII A-subunit (FXIII-A) and variants truncated to residue 628 (truncated to ß-barrel 1 [TB1]), residue 515 (truncated to catalytic core [TCC]), and residue 184 (truncated to ß-sandwich). Methods Proteins were analyzed by gel electrophoresis, circular dichroism, fluorometric assays, and colorimetric activity assays, clot structure was analyzed by turbidity measurements and confocal microscopy, and clot formation was analyzed with a Chandler loop system. Results and Conclusions Circular dichroism spectroscopy and tryptophan fluorometry indicated that full-length FXIII-A and the truncation variants TCC and TB1 retain their secondary and tertiary structure. Removal of ß-barrel 2 (TB1) resulted in total loss of transglutaminase activity, whereas the additional removal of ß-barrel 1 (TCC) restored enzymatic activity to ~ 30% of that of full-length FXIII-A. These activity trends were observed with physiological substrates and smaller model substrates. Our data suggest that the ß-barrel 1 domain protects the active site cysteine in the FXIII protransglutaminase, whereas the ß-barrel 2 domain is necessary for exposure of the active site cysteine during activation. This study demonstrates the importance of individual ß-barrel domains in modulating access to the FXIII active site region.

Protein folding: pulling back the frontiers.

In the past few years, it has become possible to measure the forces required to mechanically unfold single protein molecules. Recently, the mechanical properties of heteropolyproteins have been studied, shedding new light on the mechanical design of modular proteins such as titin.

Kinetic studies of beta-sheet protein folding.

New studies have shown that folding of beta-sheet proteins can occur with and without intermediates, with fast to slow refolding rates and late to very late transition states. These experiments demonstrate that, despite early speculation to the contrary, beta-sheet protein folding does not appear to be fundamentally different from that of helical and mixed alpha, beta proteins.

Protein folding mechanisms: new methods and emerging ideas.

During the past year, advances in our understanding of folding mechanisms have been made through detailed experimental and theoretical studies of a number of proteins. The development of new methods has allowed the earliest events in folding to be probed and the measurement of folding at the level of individual molecules is now possible, opening the door to exciting new experiments.

Progressive glycosylation of albumin and its effect on the binding of homocysteine may be a key step in the pathogenesis of vascular damage in diabetes mellitus.

The majority of diabetes research to date has rightly focussed on the direct effects of hyperglycaemia on tissues and a number of theories relating to the pathogenesis of vascular disease have been proposed. This research is important as until methods are found to achieve glycaemic control in all diabetic patients, prophylactic interventions to prevent vasculopathy will be required. One of the major blood proteins, human albumin is known to be covalently modified by extended incubation with glucose, leading to an impairment of ligand binding. One of the important ligands bound by albumin is homocysteine. There is increasing and compelling clinical, experimental and epidemiological evidence that homocysteine, and in particular the free unbound fraction, is vasculotoxic. If homocysteine binding to albumin is impaired by increasing glycosylation of albumin then either drugs which reduce homocysteine levels (pyridoxine, folic acid and cobalamin) or inhibit glycosylation (aminoguanidines) may be of benefit in the prevention of vascular damage in diabetic patients.

Potential donor families' experiences of organ and tissue donation-related communication, processes and outcome.

We aimed to describe the experiences of families of potential organ and tissue donors eligible for donation after circulatory death or brain death. Forty-nine family members of potential donors from four Melbourne hospitals were interviewed to assess their experiences of communication, processes and the outcomes of donation. Interviews were recorded, transcribed verbatim and analysed thematically. Families expressed a range of perspectives on themes of communication, hospital processes and care, the processes of consent and donation and reflected on decisions and outcomes. They expressed satisfaction overall with communication when receiving bad news, discussing death and donation. Honest and frank communication and being kept up-to-date and prepared for potential outcomes were important aspects for families, especially those of post circulatory death donors. Participants reported high levels of trust in healthcare professionals and satisfaction with the level of care received. Many donor families indicated the process was lengthy and stressful, but not significantly enough to adversely affect their satisfaction with the outcome. Both the decision itself and knowing others' lives had been saved provided them with consolation. No consenting families, and only some non-consenting families, regretted their decisions. Many expressed they would benefit from a follow-up opportunity to ask questions and clarify possible misunderstandings. Overall, while experiences varied, Australian families valued frank communication, trusted health professionals, were satisfied with the care their family member received and with donation processes, despite some apparent difficulties. Family satisfaction, infrequently assessed, is an important outcome and these findings may assist education for Australian organ donation professionals.

A mutant pyruvate dehydrogenase complex of Escherichia coli deleted in the (alanine + proline)-rich region of the acetyltransferase component.

The acetyltransferase chains of the pyruvate dehydrogenase complex of Escherichia coli contain conformationally mobile (alanine + proline)-rich segments that link the lipoyl domains to each other and to the subunit-binding and catalytic domain, and facilitate the intramolecular coupling of active sites in the complex. A deletion of 12 of the 32 residues of the (Ala + Pro)-rich segment of an acetyltransferase containing only one lipoyl domain was made by deleting the corresponding segment of the aceF gene. A pyruvate dehydrogenase complex was still produced and the catalytic activity of the restructured complex, including active-site coupling, was not detectably impaired.

Fast and slow tracks in lysozyme folding: insight into the role of domains in the folding process.

The folding of lysozyme involves parallel events in which hydrogen exchange kinetics indicate the development of persistent structure at very different rates. We have monitored directly the kinetics of formation of the native molecule by the binding of a fluorescently labelled inhibitor, MeU-diNAG (4-methylumbelliferyl-N,N'-diacetyl-beta-D-chitobioside). The data show that native character monitored in this way also develops with different timescales. Although the rate determining step on the slow pathway (approximately 75% of molecules at pH 5.5, 20 degrees C) can be attributed to the need to reorganise structure formed early in the folding process, the data indicate that the rate determining step on the fast track (involving approximately 25% of molecules) involves the docking of the two constituent domains of the protein. In the fast folding track the data are consistent with a model in which each domain forms persistent structure prior to their docking in a locally cooperative manner on a timescale comparable to the folding of small single domain proteins.

Amide hydrogen exchange in a highly denatured state. Hen egg-white lysozyme in urea.

The amide hydrogen exchange behaviour of hen egg-white lysozyme denatured in 8 M urea has been studied at pH 2.0, 20 degrees C. The observed exchange rates have been compared with those predicted for the same residues in a random coil conformation using recently published parameters for side-chain inductive and temperature effects on exchange catalysis. The protection factors for exchange obtained in this way were found to be close to unity, with 41 of the 61 residues that could be followed having protection factors less than 2. No protection factor was greater than 5. In addition, previous data for hen lysozyme denatured thermally and for a three-disulphide derivative, CM6-127 lysozyme, denatured at pH 2.0 have been reanalysed using the new reference parameters, and the protection factors were found to be similar to those of hen lysozyme denatured in 8 M urea. Thus, although 1H NMR and far UV CD spectroscopy suggest that considerable deviations from random coil behaviour occur in these denatured states, such residual structure is insufficient to protect amide hydrogens significantly against exchange. This behaviour contrasts with that of a partly folded state of hen lysozyme denatured in trifluoroethanol and with that of the molten globule state of a homologous protein, guinea pig alpha-lactalbumin. Here protection factors for many amide hydrogens exceed 30 and belong to residues located in continuous regions of the amino acid sequence, indicating the presence of persistent structure. The study of hydrogen exchange in substantially denatured states of a protein, therefore, provides a basis for the interpretation of protection factors in partially folded states.

Acidic conditions stabilise intermediates populated during the folding of Im7 and Im9.

The helical bacterial immunity proteins Im7 and Im9 have been shown to fold via kinetic mechanisms of differing complexity, despite having 60 % sequence identity. At pH 7.0 and 10 degrees C, Im7 folds in a three-state mechanism involving an on-pathway intermediate, while Im9 folds in an apparent two-state transition. In order to examine the folding mechanisms of these proteins in more detail, the folding kinetics of both Im7 and Im9 (at 10 degrees C in 0.4 M sodium sulphate) have been examined as a function of pH. Kinetic modelling of the folding and unfolding data for Im7 between pH 5.0 and 8.0 shows that the on-pathway intermediate is stabilised by more acidic conditions, whilst the native state is destabilised. The opposing effect of pH on the stability of these states results in a significant population of the intermediate at equilibrium at pH 6.0 and below. At pH 7.0, the folding and unfolding kinetics for Im9 can be fitted adequately by a two-state model, in accord with previous results. However, under acidic conditions there is a clear change of slope in the plot of the logarithm of the folding rate constant versus denaturant concentration, consistent with the population of one or more intermediate(s) early during folding. The kinetic data for Im9 at these pH values can be fitted to a three-state model, where the intermediate ensemble is stabilised and the native state destabilised as the pH is reduced, rationalising previous results that showed that an intermediate is not observed experimentally at pH 7.0. The data suggest that intermediate formation is a general step in immunity protein folding and demonstrate that it is necessary to explore a wide range of refolding conditions in order to show that intermediates do not form in the folding of other small, single-domain proteins.