Towards a data transfer agreement for the South African research community: The empowerment approach

The idea of a data transfer agreement (DTA) template for the South African (SA) research community is receiving increasing attention. While developing such a DTA template is certainly a worthwhile project, questions regarding the project's practical execution should be addressed, including how to best operationalise the envisioned DTA template, and the content of the envisioned DTA template. It is proposed that an empowerment approach be followed in operationalising the envisioned DTA template, which is contrasted with the regulatory approach followed with the material transfer agreement that the Minister of Health promulgated in 2018. While the regulatory approach would entail government making the use of the envisioned DTA template compulsory regardless of the quality of such a template, the empowerment approach, by contrast, entails a focus on developing a high-quality, professionally drafted DTA template for the SA research community and making the use thereof a matter of own choice. Regarding the content of the envisioned DTA template, four hot-button content provisions are analysed, and it is argued that SA research institutions and researchers should be empowered to: (i) have clarity and legal certainty regarding their ownership of data, where relevant; (ii) be able to commercialise their research findings without unnecessary contractual constraints; (iii) avoid falling into the trap of unlawful benefit sharing with research participants; and (iv) be aware that their legal role as responsible parties, where relevant, cannot be contracted out via a DTA.

Diversity Drives Innovation: The Impact of Female-Driven Publications

BACKGROUND

Gender disparities are pervasive in academic plastic surgery. Previous research demonstrates articles authored by women receive fewer citations than those written by men, suggesting the presence of implicit gender bias.

OBJECTIVES

The aim of this study was to describe current citation trends in plastic surgery literature and assess gender bias. The expectation was that women would be cited less frequently than their male peers.

METHODS

Articles published between 2017 and 2019 were collected from 8 representative plastic surgery journals stratified by impact factor. Names of primary and senior authors of the 50 most cited articles per year per journal were collected and author gender was determined via online database and internet search. The median numbers of citations by primary and senior author gender were compared by Kruskal-Wallis test.

RESULTS

Among 1167 articles, women wrote 27.3% as primary author and 18% as senior author. Women-authored articles were cited as often as those authored by men (P > 0.05) across all journal tiers. Articles with a female primary and male senior author had significantly more citations than articles with a male primary author (P = 0.038).

CONCLUSIONS

No implicit gender bias was identified in citation trends, a finding unique to plastic surgery. Women primary authors are cited more often than male primary authors despite women comprising a small fraction of authorship overall. Additionally, variegated authorship pairings outperformed homogeneous ones. Therefore, increasing gender diversity within plastic surgery academia remains critical.

Artificial intelligence in healthcare: Proposals for policy development in South Africa

Despite the tremendous promise offered by artificial intelligence (AI) for healthcare in South Africa, existing policy frameworks are inadequate for encouraging innovation in this field. Practical, concrete and solution-driven policy recommendations are needed to encourage the creation and use of AI systems. This article considers five distinct problematic issues which call for policy development: (i) outdated legislation; (ii) data and algorithmic bias; (iii) the impact on the healthcare workforce; (iv) the imposition of liability dilemma; and (v) a lack of innovation and development of AI systems for healthcare in South Africa. The adoption of a national policy framework that addresses these issues directly is imperative to ensure the uptake of AI development and deployment for healthcare in a safe, responsible and regulated manner.

Large-scale discovery of novel genetic causes of developmental disorders

Despite three decades of successful, predominantly phenotype-driven discovery of the genetic causes of monogenic disorders, up to half of children with severe developmental disorders of probable genetic origin remain without a genetic diagnosis. Particularly challenging are those disorders rare enough to have eluded recognition as a discrete clinical entity, those with highly variable clinical manifestations, and those that are difficult to distinguish from other, very similar, disorders. Here we demonstrate the power of using an unbiased genotype-driven approach to identify subsets of patients with similar disorders. By studying 1,133 children with severe, undiagnosed developmental disorders, and their parents, using a combination of exome sequencing and array-based detection of chromosomal rearrangements, we discovered 12 novel genes associated with developmental disorders. These newly implicated genes increase by 10% (from 28% to 31%) the proportion of children that could be diagnosed. Clustering of missense mutations in six of these newly implicated genes suggests that normal development is being perturbed by an activating or dominant-negative mechanism. Our findings demonstrate the value of adopting a comprehensive strategy, both genome-wide and nationwide, to elucidate the underlying causes of rare genetic disorders.

Pharmacophore model of the quercetin binding site of the SIRT6 protein

SIRT6 is a histone deacetylase that has been proposed as a potential therapeutic target for metabolic disorders and the prevention of age-associated diseases. We have previously reported on the identification of quercetin and vitexin as SIRT6 inhibitors, and studied structurally related flavonoids including luteolin, kaempferol, apigenin and naringenin. It was determined that the SIRT6 protein remained active after immobilization and that a single frontal displacement could correctly predict the functional activity of the immobilized enzyme. The previous study generated a preliminary pharmacophore for the quercetin binding site on SIRT6, containing 3 hydrogen bond donors and one hydrogen bond acceptor. In this study, we have generated a refined pharmacophore with an additional twelve quercetin analogs. The resulting model had a positive linear behavior between the experimental elution time verses the fit values obtained from the model with a correlation coefficient of 0.8456.

The major determinant of exendin-4/glucagon-like peptide 1 differential affinity at the rat glucagon-like peptide 1 receptor N-terminal domain is a hydrogen bond from SER-32 of exendin-4

BACKGROUND AND PURPOSE

Exendin-4 (exenatide, Ex4) is a high-affinity peptide agonist at the glucagon-like peptide-1 receptor (GLP-1R), which has been approved as a treatment for type 2 diabetes. Part of the drug/hormone binding site was described in the crystal structures of both GLP-1 and Ex4 bound to the isolated N-terminal domain (NTD) of GLP-1R. However, these structures do not account for the large difference in affinity between GLP-1 and Ex4 at this isolated domain, or for the published role of the C-terminal extension of Ex4. Our aim was to clarify the pharmacology of GLP-1R in the context of these new structural data.

EXPERIMENTAL APPROACH

The affinities of GLP-1, Ex4 and various analogues were measured at human and rat GLP-1R (hGLP-1R and rGLP-1R, respectively) and various receptor variants. Molecular dynamics coupled with in silico mutagenesis were used to model and interpret the data.

KEY RESULTS

The membrane-tethered NTD of hGLP-1R displayed similar affinity for GLP-1 and Ex4 in sharp contrast to previous studies using the soluble isolated domain. The selectivity at rGLP-1R for Ex4(9-39) over Ex4(9-30) was due to Ser-32 in the ligand. While this selectivity was not observed at hGLP-1R, it was regained when Glu-68 of hGLP-1R was mutated to Asp.

CONCLUSIONS AND IMPLICATIONS

GLP-1 and Ex4 bind to the NTD of hGLP-1R with similar affinity. A hydrogen bond between Ser32 of Ex4 and Asp-68 of rGLP-1R, which is not formed with Glu-68 of hGLP-1R, is responsible for the improved affinity of Ex4 at the rat receptor.

Second primary cancers in patients with skin cancer: a population-based study in Northern Ireland

Among all 14,500 incident cases of basal cell carcinoma (BCC), 6405 squamous cell carcinomas (SCC) and 1839 melanomas reported to the Northern Ireland Cancer Registry between 1993 and 2002, compared with the general population, risk of new primaries after BCC or SCC was increased by 9 and 57%, respectively. The subsequent risk of cancer, overall, was more than double after melanoma.

Peptide binding at the GLP-1 receptor

The receptor for GLP-1 [glucagon-like peptide-1-(7-36)-amide] is a member of the 'Family B' of GPCRs (G-protein-coupled receptors) comprising an extracellular N-terminal domain containing six conserved cysteine residues (the N-domain) and a core domain (or J-domain) comprising the seven transmembrane helices and interconnecting loop regions. According to the two-domain model for peptide binding, the N-domain is primarily responsible for providing most of the peptide binding energy, whereas the core domain is responsible for binding the N-terminal region of the peptide agonists and transmitting the signal to the intracellular G-protein. Two interesting differences between the binding properties of two GLP-1 receptor agonists, GLP-1 and EX-4 (exendin-4), can be observed. First, while GLP-1 requires its full length to maintain high affinity, the eight N-terminal residues of EX-4 can be removed with little reduction in affinity. Secondly, EX-4 (but not GLP-1) can bind to the fully isolated N-domain of the receptor with an affinity matching that of the full-length receptor. In order to better understand these differences, we have studied the interaction between combinations of full-length or truncated ligands with full-length or truncated receptors.

Skin cancer trends in Northern Ireland and consequences for provision of dermatology services

BACKGROUND

The incidence of skin cancer, both melanoma and nonmelanoma skin cancer (NMSC), is rising throughout the world. The evaluation of trends in skin cancer will allow better planning of the future development of skin cancer services.

OBJECTIVES

Using data collected from the Northern Ireland Cancer Registry (NICR), the incidence of the three major cutaneous cancers, basal cell carcinoma (BCC), squamous cell carcinoma (SCC) and malignant melanoma (MM), was determined and the workload associated with their management assessed.

METHODS

The records of patients with a first diagnosis of BCC, SCC or MM occurring between 1993 and 2002 were retrieved from the NICR database. The annual age- and sex-adjusted incidence rates of all three skin cancers were computed per 100 000 person-years by direct standardization according to the European Standard Population. Trends in incidence were estimated by calculating the estimated annual percentage change using Microsoft Excel. For patients registered with the NICR as having BCC, SCC or MM, the number of pathological reports where malignant samples had been examined was counted and then summed to provide the number of specimens examined each year between 1993 and 2004.

RESULTS

For all three cancers the age-specific rates for both males and females increased with age, except for MM in men aged 75 years and over, where the rates were seen to decrease. Over the 12-year period there was a 62% increase in the overall number of skin cancer samples processed by local pathology laboratories and a 20% increase in the number of patients. These data highlight the fact that many patients will have more than one skin cancer, which reinforces the benefit in collecting data for both patient and sample numbers in order to obtain a true reflection of the workload. The data have also shown that more affluent men and women have higher rates of BCC and MM than their less affluent counterparts.

CONCLUSIONS

In view of the data presented it is clear that management of NMSC and MM will impose significant demands on services in the years ahead. This will impact on the entire multidisciplinary team. Future planning, in terms of manpower and resources, will prove essential if we are to remain in a position to manage our patients with these malignant tumours appropriately.

Neuroprotective potential of ceftriaxone in in vitro models of stroke

Astrocytic glutamate transporters are considered an important target for neuroprotective therapies as the function of these transporters is abnormal in stroke and other neurological disorders associated with excitotoxicity. Recently, Rothstein et al., [Rothstein JD, Patel S, Regan MR, Haenggeli C, Huang YH, Bergles DE, Jin L, Dykes Hoberg M, Vidensky S, Chung DS, Toan SV, Bruijn LI, Su ZZ, Gupta P, Fisher PB (2005) Beta-lactam antibiotics offer neuroprotection by increasing glutamate transporter expression. Nature 433:73-77] reported that beta-lactam antibiotics (including ceftriaxone, which easily crosses the blood-brain barrier) increase glutamate transporter 1 (GLT-1) expression and reduce cell death resulting from oxygen-glucose deprivation (OGD) in dissociated embryonic cortical cultures. To determine whether a similar neuroprotective mechanism operates in more mature neurons, which show a different pattern of response to ischemia than primary cultures, we exposed acute hippocampal slices obtained from rats treated with ceftriaxone for 5 days (200 mg/kg; i.p.) to OGD. Whole-cell patch clamp recording of glutamate-induced N-methyl-d-aspartate (NMDA) currents from CA1 pyramidal neurons showed a larger potentiation of these currents after application of 15 microM dl-threo-beta-benzyloxyaspartic acid (TBOA; a potent blocker of glutamate transporters) in ceftriaxone-injected animals than in untreated animals, indicating increased glutamate transporter activity. Western blot analysis did not reveal GLT-1 upregulation in the hippocampus. Delay to OGD-induced hypoxic spreading depression (HSD) recorded in slices obtained from ceftriaxone-treated rats was longer (6.3+/-0.2 vs. 5.2+/-0.2 min; P<0.001) than that in the control group, demonstrating a neuroprotective action of the antibiotic in this model. The effect of ceftriaxone was also tested in organotypic hippocampal slices obtained from P7-9 rats (>14 days in vitro). OGD or glutamate (3.5-5.0 mM) damaged CA1 pyramidal neurons as assessed by propidium iodide (PI) fluorescence. Similar damage was observed after pre-treatment with ceftriaxone (10-200 microM; 5 days) and ceftriaxone exposure did not result in GLT-1 upregulation as assayed by Western blot. Treatment of slice cultures with dibutyryl cAMP (100-250 microM; 5 days) increased GLT-1 expression but did not reduce cell damage induced by OGD or glutamate. Thus we confirm the neuroprotective effect of antibiotic exposure on OGD-induced injury, but suggest that this action is related to independent modulation of transporter activity rather than to the level of GLT-1 protein expression. In addition, our results indicate that the protective effects of beta-lactam antibiotics are highly dependent on the experimental model.

Nod factor enhances calcium uptake by soybean

Inoculation with rhizobia or application of Nod factors (lipo-chitooligosaccharides, LCOs) causes transient increases in cytosolic calcium concentration in root hairs of legume plants. We conducted experiments to evaluate whether application of LCO and inoculation with rhizobia improved (45)CaCl(2) uptake into soybean (Glycine max [L.] Merr.) leaves. Roots of soybean seedlings with one developing trifoliolate were immersed in Murashige and Skoog (MS) basal liquid medium containing treatment solutions and (45)CaCl(2), and the plants were incubated under continuous light. After 24 h, leaf samples were taken, and their radioactivity levels were determined. Addition of NodBj-V (C18:1 MeFuc) at a concentration of 10(-7) M increased (45)Ca(2+) uptake. Inoculation with genistein-induced Bradyrhizobium japonicum strain 532C and USDA3 also increased (45)Ca(2+) uptake; whereas, inoculation with strain Bj-168, a nodC-mutant incapable of producing LCO, did not. Rhizobia that do not normally nodulate soybean, i.e. Rhizobium leguminosarum, and Sinorhizobium meliloti did not affect calcium uptake, nor did the tetramer or pentamer of chitosan, or lumichrome. Surprisingly, Rhizobium sp. NGR234, which can nodulate some types of soybean, although without effective N(2)-fixation, also did not affect calcium uptake. This work suggests that the rhizobial symbiosis, in addition to its known role in provision of nitrogen fixation, also improves early calcium uptake into soybean plants.

Indoor air modification interventions for prolonged non-specific cough in children

BACKGROUND

Non-specific cough has been defined as non-productive cough in the absence of identifiable respiratory disease or known aetiology and is common in childhood. These children are treated with a variety of therapies, including non-pharmacological treatments. There is a wide variety and a growing market for these non-pharmacological treatments that include air-modification modalities.

OBJECTIVES

To determine the efficacy of air-modification modalities, (ionisers, vaporisers, humidifiers, air filters, regular vacuuming), in treating children with non-specific cough.

SEARCH STRATEGY

The Cochrane Central Register of Controlled Trials (CENTRAL), MEDLINE, OLDMEDLINE and EMBASE databases were searched by the Cochrane Airways Group. The latest searches were performed in November 2005.

SELECTION CRITERIA

All randomised controlled trials comparing air-modification modalities with a placebo treatment, for any duration.

DATA COLLECTION AND ANALYSIS

Results of searches were reviewed against pre-determined criteria for inclusion. Five papers were considered for inclusion but no eligible trials were identified and thus no data was available for analysis.

MAIN RESULTS

No randomised controlled trials that examined the efficacy of air-modification modalities in the management of prolonged, non-specific cough in children were found.

AUTHORS' CONCLUSIONS

Based on the evidence currently available, a recommendation can not be given for air-modification interventions in the treatment of prolonged, non-specific cough in children.

A pilot study of oral L-arginine in cystic fibrosis

Exhaled nitric oxide has previously been found to be low in cystic fibrosis. The aim of this study was to determine whether exhaled nitric oxide levels would increase in response to oral L-arginine supplementation administered daily for 4 weeks. Exhaled and nasal nitric oxide was measured weekly. Plasma L-arginine levels increased in response to supplementation but this was not reflected in an increase in eNO levels.

Ratio spectra derivative spectrophotometry for the determination of furosemide and spironolactone in a capsule formulation

The determination of furosemide and spironolactone in a capsule formulation has been investigated using techniques such as Vierordt's method and derivative spectroscopy dA/d lambda and d2A/d lambda2 applying the zero-crossing technique following reported methods. In our hands, using standard mixtures, these methods gave unreliable results. We have therefore investigated the use of ratio spectra derivative spectrophotometry for this determination. The technique of ratio spectra derivative spectrophotometry was developed in 1990, and has recently been used for a number of analyses of co-formulated products. The method was applied to the analysis of standard mixtures of the two drugs and the combined contents of 20 capsules resulting in values (mean +/- standard deviation) of 102.1 +/- 1.9% and 101.4 +/- 4.0% of the stated content for furosemide and spironolactone, respectively. Similarly, the analysis of individual capsules resulted in values of 101.5 +/- 1.6% and 102.2 +/- 1.4% of the stated content for furosemide and spironolactone, respectively.

Transcription profile of brewery yeast under fermentation conditions

AIMS

Yeast strains, used in the brewing industry, experience distinctive physiological conditions. During a brewing fermentation, yeast are exposed to anaerobic conditions, high pressure, high specific gravity and low temperatures. The purpose of this study was to examine the global gene expression profile of yeast subjected to brewing stress.

METHODS AND RESULTS

We have carried out a microarray analysis of a typical brewer's yeast during the course of an 8-day fermentation in 15 degrees P wort. We used the probes derived from Saccharomyces cerevisiae genomic DNA on the chip and RNA isolated from three stages of brewing. This analysis shows a high level of expression of genes involved in fatty acid and ergosterol biosynthesis early in fermentation. Furthermore, genes involved in respiration and mitochondrial protein synthesis also show higher levels of expression.

CONCLUSIONS

Surprisingly, we observed a complete repression of many stress response genes and genes involved in protein synthesis throughout the 8-day period compared with that at the start of fermentation.

SIGNIFICANCE AND IMPACT OF THE STUDY

This microarray data set provides an analysis of gene expression under brewing fermentation conditions. The data provide an insight into the various metabolic processes altered or activated by brewing conditions of growth. This study leads to future experiments whereby selective alterations in brewing conditions could be introduced to take advantage of the changing transcript profile to improve the quality of the brew.

Determination of yeast glycogen content by individual cell spectroscopy using image analysis

A rapid technique has been developed to determine the glycogen content of yeast on an individual cell basis using a combination of image analysis technology and staining of yeast cells with an I(2):KI solution. Changes in mean cellular glycogen content during alcoholic fermentation have been reported using this technique. The glycogen content of stored brewer's yeast is heterogeneous compared to freshly propagated yeast which have a more uniform distribution of glycogen. Analysis of the distribution of yeast glycogen during fermentation indicates that a fraction of yeast cells do not dissimilate glycogen. Therefore, conventional analysis of the mean glycogen content of yeast used to inoculate fermentations is of limited use, unless information regarding the proportion of cells which utilize glycogen is known. Analysis of the distribution of glycogen within a yeast population can serve as a useful indicator of yeast quality.

The stress response is repressed during fermentation in brewery strains of yeast

Yeast cells encounter a variety of environmental stresses during brewing and must respond to ensure cell survival. Cells can respond to stress by inducing a Heat Shock Response in which heat shock proteins (Hsps) are synthesized. In laboratory strains of Saccharomyces cerevisiae, the heat shock protein, Hsp104, plays a major role in the acquisition of tolerance to a variety of stresses such as heat, ethanol and sodium arsenite, and as such acts as an excellent stress indicator. The induction of Hsp104 in bottom-and top-fermenting brewery strains was examined when grown under laboratory and industrial fermentation conditions, and it was found that each brewing strain exhibits its own unique pattern of Hsp104 expression. During industrial fermentations, brewery strains are capable of mounting a stress response at the early stages of fermentation. However, as the fermentation proceeds, the response is repressed. The results suggest that conditions experienced in industrial brewing prevent the activation of the stress response. This study increases our understanding of alterations in gene expression patterns during the brewing process, and yields information that will aid in the definition of best practice in yeast management.

Conserved polar residues in the transmembrane domain of the human tachykinin NK2 receptor: functional roles and structural implications

We have studied the effects of agonist and antagonist binding, agonist-induced activation and agonist-induced desensitization of the human tachykinin NK2 receptor mutated at polar residues Asn-51 [in transmembrane helix 1 (TM1)], Asp-79 (TM2) and Asn-303 (TM7), which are highly conserved in the transmembrane domain in the rhodopsin family of G-protein-coupled receptors. Wild-type and mutant receptors were expressed in both COS-1 cells and Xenopus oocytes. The results show that the N51D mutation results in a receptor which, in contrast with the wild-type receptor, is desensitized by the application of a concentration of 1 microM of the partial agonist GR64349, indicating that the mutant is more sensitive to agonist activation than is the wild-type receptor. In addition, we show that, whereas the D79E mutant displayed activation properties similar to those of the wild-type receptor, the D79N and D79A mutants displayed a severely impaired ability to activate the calcium-dependent chloride current. This suggests that it is the negative charge at Asn-79, rather than the ability of this residue to hydrogen-bond, that is critical for the activity of the receptor. Interestingly, the placement of a negative charge at position 303 could compensate for the removal of the negative charge at position 79, since the double mutant D79N/N303D displayed activation properties similar to those of the wild-type receptor. This suggests that these two residues are functionally coupled, and may even be in close proximity in the three-dimensional structure of the human tachykinin NK2 receptor. A three-dimensional model of the receptor displaying this putative interaction is presented.

The relationship between the agonist-induced activation and desensitization of the human tachykinin NK2 receptor expressed in Xenopus oocytes

1. Repeated applications of neurokinin A (NKA) to oocytes injected with 25 ng wild-type hNK2 receptor cRNA caused complete attenuation of second and subsequent NKA-induced responses while analogous experiments using repeated applications of GR64349 and [Nle10]NKA(4-10) resulted in no such desensitization. This behaviour has been previously attributed to the ability of the different ligands to stabilize different active conformations of the receptor that have differing susceptibilities to receptor kinases (Nemeth & Chollet. 1995). 2. However, for Xenopus oocytes injected (into the nucleus) with 10 ng wild-type hNK2 receptor cDNA, a single 100 nM concentration of any of the three ligands resulted in complete desensitization to further concentrations. 3. On the other hand, none of the ligands caused any desensitization in oocytes injected with 0.25 ng wild-type hNK2 receptor cRNA. even at concentrations up to 10 microM. 4. The two N-terminally truncated analogues of neurokinin A have a lower efficacy than NKA and it is likely that it is this property which causes the observed differences in desensitization, rather than the formation of alternative active states of the receptor. 5. The peak calcium-dependent chloride current is not a reliable measure of maximal receptor stimulation and efficacy is better measured in this system by studying agonist-induced desensitization. 6. The specific adenylyl cyclase inhibitor SQ22536 can enhance NKA and GR64349-mediated desensitization which suggests that agonist-induced desensitization involves the inhibition of adenylyl cyclase and the subsequent down-regulation of the cyclic AMP-dependent protein kinase, possibly by cross-talk to a second signalling pathway.

The arrangement of the transmembrane helices in the secretin receptor family of G-protein-coupled receptors

The members of the secretin receptor family of G-protein-coupled receptors share no significant sequence similarity to the more familiar rhodopsin-like family. However, multiple sequence alignment analysis reveals seven hydrophobic regions with significant alpha-helical periodicity. Residues that are likely to be buried on the interior of the helical bundle and others that are likely to contact the lipid bilayer are identified. A predicted arrangement of the helical bundle is described in which, by comparison with the arrangement in the rhodopsin family, helices 2 and 7 are more buried within the bundle while helix 3 is more exposed to the lipid bilayer.

The conformational change responsible for AT1 receptor activation is dependent upon two juxtaposed asparagine residues on transmembrane helices III and VII

A model of the angiotensin AT1 receptor and site-directed mutagenesis were used to identify key residues involved in ligand binding. Receptors were stably expressed in human embryonic kidney 293 cells, and their binding properties compared. Wild type receptors exhibited low and high affinity binding sites for peptides. Substitution of Asn111, situated in the third transmembrane helix, resulted in a significant alteration in ligand binding with only high affinity binding of the peptides, angiotensin II, angiotensin III, and [p-amino-Phe6]angiotensin II and a marked loss in the binding affinity of the AT1 receptor selective non-peptide antagonist losartan. From our model it was apparent that Asn111 was in close spatial proximity to Asn295 in the seventh transmembrane helix. Substitution of Asn295, produced identical changes in the receptor's pharmacological profile. Furthermore, the Ser111AT1A and Ser295AT1A mutants did not require the association of a G-protein for high affinity agonist binding. Finally, the Ser295AT1A mutant maintained higher basal generation of inositol trisphosphate than the wild type, indicating constitutive activation. We propose that substitution of these residues causes the loss of an interaction between transmembrane helices III and VII, which allows the AT1 receptor to "relax" into its active conformation.

The ligand binding site of the neurokinin 2 receptor. Site-directed mutagenesis and identification of neurokinin A binding residues in the human neurokinin 2 receptor

Thirteen residues in the human neurokinin 2 (NK2) receptor were identified as potential ligand-binding residues by molecular modeling and amino acid sequence analysis. Site-directed mutagenesis was used to alter these residues in order to ascertain their importance in binding neurokinin A (NKA), the physiological peptide ligand for the NK2 receptor, and the non-peptide NK2 receptor selective antagonist SR48968. Four sites appear to be critical for NKA binding (Gln109, His198, Ile202, and Gly273). The mutant receptors Gln109-->His, Ile202-->Val, Gly273-->Pro, and Gly273-->Thr maintain their affinity for SR48968, despite being unable to bind the peptide ligand. His198-->Ala and His198-->Leu no longer bind NKA or SR48968. We have also identified a residue (Leu292) which appears to play a minor role in the binding of substance P (SP) and neurokinin B (NKB) to the NK2 receptor. The mutant receptor Leu292-->Ser binds NKB and SP with approximately a 5-fold greater affinity in comparison with the wild type receptor while the affinity of NKA remains unaffected. The results suggest that intramembranous residues, as well as residues which lie close to the extracellular side of transmembrane helices 3, 5, and 6, form part of the NK2 receptor binding site. Binding of SP and NKB to the NK2 receptor may also be influenced by residues near the extracellular side of helix 7. These results suggest that some regions of the binding site for NKA in the NK2 receptor are not used for binding SP in the NK1 receptor. However, it also seems that the NKA binding site includes regions that are also used by other G-protein-coupled receptors such as rhodopsin and the beta 2-adrenergic receptors.

The prediction and orientation of alpha-helices from sequence alignments: the combined use of environment-dependent substitution tables, Fourier transform methods and helix capping rules

Amino acid substitution tables are used to estimate the extent to which amino acids in families of homologous proteins are exposed to the solvent. The approach depends on the comparison of difference environment-dependent tables for solvent accessible/inaccessible residues with amino acid substitutions at each position in an aligned set of sequences. The periodicity in the predicted accessible/inaccessible residues is calculated using a Fourier transform procedure modified from that used to calculate hydrophobic moments. alpha-Helices are identified from the characteristic periodicities and the solvent accessible face of the helix is defined. The initial helix predictions are refined using rules for identifying the N- and C-termini of helices from sequence alignments. These rules have been defined from a study of protein structures. The combined method correctly predicts 79% of the residues in helices and incorrectly predicts only 12% of the nonhelical residues as helical. In addition, since the method is reliable at predicting the correct number of helices in the correct position in the sequence and since it also predicts the internal face of each helix, the results can be used to postulate 3-D arrangements of the secondary structure elements.