Disorder and order in unfolded and disordered peptides and proteins: A view derived from tripeptide conformational analysis. II. Tripeptides with short side chains populating asx and β‐type like turn conformations

In the preceding paper, we found that ensembles of tripeptides with long or bulky chains can include up to 20% of various turns. Here, we determine the structural and thermodynamic characteristics of GxG peptides with short polar and/or ionizable central residues (D, N, C), whose conformational distributions exhibit higher than average percentage (>20%) of turn conformations. To probe the side‐chain conformations of these peptides, we determined the ³J(H^α,H^β) coupling constants and derived the population of three rotamers with χ₁‐angles of ?60°, 180° and 60°, which were correlated with residue propensities by DFT‐calculations. For protonated GDG, the rotamer distribution provides additional evidence for asx‐turns. A comparison of vibrational spectra and NMR coupling constants of protonated GDG, ionized GDG, and the protonated aspartic acid dipeptide revealed that side chain protonation increases the pPII content at the expense of turn populations. The charged terminal groups, however, have negligible influence on the conformational properties of the central residue. Like protonated GDG, cationic GCG samples asx‐turns to a significant extent. The temperature dependence of the UVCD spectra and ³J(H^NH^α) constants suggest that the turn populations of GDG and GNG are practically temperature‐independent, indicating enthalpic and entropic stabilization. The temperature‐independent J‐coupling and UVCD spectra of GNG require a three‐state model. Our results indicate that short side chains with hydrogen bonding capability in GxG segments of proteins may serve as hinge regions for establishing compact structures of unfolded proteins and peptides. Proteins 2013. © 2012 Wiley Periodicals, Inc.     

Solution structures of Mycobacterium tuberculosis thioredoxin C and models of intact thioredoxin system suggest new approaches to inhibitor and drug design

Here, we report the NMR solution structures of Mycobacterium tuberculosis (M. tuberculosis) thioredoxin C in both oxidized and reduced states, with discussion of structural changes that occur in going between redox states. The NMR solution structure of the oxidized TrxC corresponds closely to that of the crystal structure, except in the C‐terminal region. It appears that crystal packing effects have caused an artifactual shift in the α4 helix in the previously reported crystal structure, compared with the solution structure. On the basis of these TrxC structures, chemical shift mapping, a previously reported crystal structure of the M. tuberculosis thioredoxin reductase (not bound to a Trx) and structures for intermediates in the E. coli thioredoxin catalytic cycle, we have modeled the complete M. tuberculosis thioredoxin system for the various steps in the catalytic cycle. These structures and models reveal pockets at the TrxR/TrxC interface in various steps in the catalytic cycle, which can be targeted in the design of uncompetitive inhibitors as potential anti‐mycobacterial agents, or as chemical genetic probes of function. © Proteins 2013. © 2012 Wiley Periodicals, Inc.     

Rates of readmission and death associated with leaving hospital against medical advice: a population-based study

Background:

Leaving hospital against medical advice may have adverse consequences. Previous studies have been limited by evaluating specific types of patients, small sample sizes and incomplete determination of outcomes. We hypothesized that leaving hospital against medical advice would be associated with increases in subsequent readmission and death.

Methods:

In a population-based analysis involving all adults admitted to hospital and discharged alive in Manitoba from Apr. 1, 1990, to Feb. 28, 2009, we evaluated all-cause 90-day mortality and 30-day hospital readmission. We used multivariable regression, adjusted for age, sex, socioeconomic status, year of hospital admission, patient comorbidities, hospital diagnosis, past frequency of admission to hospital, having previously left hospital against medical advice and data clustering (patients with multiple admissions). For readmission, we assessed both between-person and within-person effects of leaving hospital against medical advice.

Results:

Leaving against medical advice occurred in 21 417 of 1 916 104 index hospital admissions (1.1%), and was associated with higher adjusted rates of 90-day mortality (odds ratio [OR] 2.51, 95% confidence interval [CI] 2.18–2.89), and 30-day hospital readmission (within-person OR 2.10, CI 1.99–2.21; between-person OR 3.04, CI 2.79–3.30). In our additional analyses, elevated rates of readmission and death associated with leaving against medical advice were manifest within 1 week and persisted for at least 180 days after discharge.

Interpretation:

Adults who left the hospital against medical advice had higher rates of hospital readmission and death. The persistence of these effects suggests that they are not solely a result of incomplete treatment of acute illness. Interventions aimed at reducing these effects may need to include longitudinal interventions extending beyond admission to hospital.Patients leaving hospital against medical advice have been discussed in the medical literature for more than 50 years.¹ Reported to occur in 1%–2% of patients in general hospitals,^2,3 the numbers are large; in the United States, 368 000 patients left against medical advice in 2007,³ and rates higher than 10% have been documented in certain subgroups, including Canadian patients with HIV and predominantly poor residents of inner city areas.^4,5 The main concern over leaving hospital against medical advice is that it may increase morbidity or mortality. Previous studies attempting to assess this effect^2,4–13 have all been restricted to specific types of patients, and most studies were limited by small sample sizes and incomplete determination of outcomes. In this study, we used data that avoided these limitations to test the hypothesis that patients who leave hospital against medical advice have higher rates of hospital readmission and death.     

Cranial morphology of an Early Cretaceous Monjurosuchid (Reptilia: Diapsida) from Liaoning Province of China and evolution of the choristoderan palate

A new specimen of Philydrosaurus proseilus from the Early Cretaceous Chiufotang (Jiufotang) Formation preserves the first complete palate of a monjurosuchid choristodere. As in other choristoderes, the palate of Philydrosaurus is akinetic, extended by a broad contact between the vomer and maxilla, and equipped with multiple batteries of palatal teeth. This specimen provides phylogenetically significant information and clarifies the distribution of many apomorphies within Choristodera. Philydrosaurus is primitive relative to the Neochoristodera in that it exhibits only a moderate degree of posterior displacement of the choanae and retains a relatively large interpterygoid vacuity. However, Philydrosaurus also exhibits several derived features previously considered diagnostic of the Neochoristodera, including establishment of a long midline contact of the pterygoids and development of a distinct nasopalatal trough extending from the choana. The choristodere palate exhibits significant modification of the primitive diapsid condition, including elongation of the vomers, establishment of a vomer–maxilla contact, posterior displacement of the choanae, development of the nasopalatal trough, and reduction of the interpterygoid vacuity.     

Kairomonal Responses of Natural Enemies and Associates of the Southern Ips (Coleoptera: Curculionidae: Scolytinae) to Ipsdienol, Ipsenol and Cis-Verbenol

Bark beetle infested pines are an ephemeral habitat utilized by a diverse assemblage of insects. Although many bark beetle insect associates have little or no measurable impact on bark beetle brood production, some reduce brood production by either competing with brood for the limited phloem tissue or by feeding on brood. Several studies have observed synchrony between the colonization of hosts by bark beetles and the arrival of insect associates. Some insect associates mediate synchrony with bark beetle mass attacks with kairomonal responses to bark beetle aggregation pheromones. The objectives of this study were to document the community of Coleoptera associated with the southern Ips (Ips avulsus, Ips calligraphus and Ips grandicollis) and to test the hypothesis that synchrony of insect associates with the southern Ips is mediated by kairomonal responses to aggregation pheromones. A large community of Coleoptera (109 species) was recorded from traps baited with southern Ips pheromones. A significant treatment effect was observed for the guilds of meristem feeders, natural enemies and woodborers. The southern Ips pheromone ipsenol was broadly attractive to meristem feeders, natural enemies and woodborers and in general blends were more attractive than individual compounds. These results demonstrate that a diverse community of Coleoptera is associated with the southern Ips and that several members of this community facilitate synchrony with kairomonal responses to southern Ips aggregation pheromones.     

Two-Dimensional 1H NMR Study of a Tetradecapeptide with the Consensus Sequence Arg5-Asp-Val-Arg-Gly9: Structural Effects of the Outside Substitution Ser12 by Ala12

Abstract

Conformation of a tetradecapeptide with a RXVRG consensus sequence, Arg^s-Asp-Val-Arg-Gly⁹, found in several precursors of antibacterian peptides, was investigated in dimethylsulfoxide solution by proton NMR spectroscopy. Complete resonance assignments and conformational parameters were obtained through correlated (COSY) and nuclear Overhauser (NOESY) techniques. The ³J(αH, βH) coupling constants and the intramolecular NOE, NH…βH, were used to analyse the conformers around the Cα-Cβ bond and, in four cases, to obtain stereospecific assignments.

Use of restraints derived from NOE connectivities and ³J(NH, αH) coupling constants allows the determination of a range of φ and ψ dihedral angles for all the residues in the sequence. The present NMR results provide favourable evidence for the formation of two bends in the consensus sequence of the tetradecapeptide. The first one has most of the features of a Glu⁴- Val⁷ β–turn (low temperature coefficient of the Val⁷NH chemical shift, Arg⁵αH…Val⁷NH and Asp⁶NH.-.Val⁷NH NOE correlations). The second one exhibits only the Asp⁶αH…Arg⁷NH and Val⁷NH…Arg⁸NH NOE interactions. These consensus sequence organizations proposed were confirmed by molecular modeling based on low potential energy structure on the [4–9] fragment with high agreement of NOE data.

Overall, the substitution of Ser¹² by Ala¹² shifts the conformation of the hydrophobic moiety [10–14] towards a quite random coil structure in this fragment and strongly destabilizes the folded structures of the consensus domain where only one NH (Val⁷) is solvent-shielded opposed to three (Asp⁶ to Arg⁸) in the [Ser¹²] tetradecapeptide. These conformational changes could be related to the processing enzyme activities on these model oligopeptides.     

Novel insights into the dynamics behavior of glucagon-like peptide-1 receptor with its small molecule agonists

Abstract

The glucagon-like peptide-1 receptor (GLP-1R) is a well-known target of therapeutics industries for the treatment of various metabolic diseases like type 2 diabetes and obesity. The structural–functional relationships of small molecule agonists and GLP-1R are yet to be understood. Therefore, an attempt was made on structurally known GLP-1R agonists (Compound 1, Compound 2, Compound A, Compound B, and (S)-8) to study their interaction with the extracellular domain of GLP-1R. In this study, we explored the dynamics, intrinsic stability, and binding mechanisms of these molecules through computational modeling, docking, molecular dynamics (MD) simulations and molecular mechanics Poisson–Boltzmann surface area (MM/PBSA) binding free energy estimation. Molecular docking study depicted that hydrophobic interaction (pi–pi stacking) plays a crucial role in maintaining the stability of the complex, which was also supported by intermolecular analysis from MD simulation study. Principal component analysis suggested that the terminal ends along with the turns/loops connecting adjacent helix and strands exhibit a comparatively higher movement of main chain atoms in most of the complexes. MM/PBSA binding free energy study revealed that non-polar solvation (van der Waals and electrostatic) energy subsidizes significantly to the total binding energy, and the polar solvation energy opposes the binding agonists to GLP-1R. Overall, we provide structural features information about GLP-1R complexes that would be conducive for the discovery of new GLP-1R agonists in the future for the treatment of various metabolic diseases.

Communicated by Ramaswamy H. Sarma     

Synthesis and FTIR Conformational Studies of Peptides From the Basic Region of c-Jun: a Critical Analysis on the Basis of CD and NMR Data

Abstract

The peptide (35 residues) corresponding to the basic subdomain (bSD) of c-Jun (residues 252–281) and its fragments NP (N-terminal peptide, 1–19) and CP (C-terminal peptide, 1635) were synthesized in stepwise solid-phase using the tert-butyloxycarbonyl/benzyl strategy. In a previous paper, we have shown that during its binding to the DNA site CRE (cAMP- responsive element) the bSD structure was converted into α-helix from an initial random coil conformation [Krebs, D., Dahmani, B., El Antri, S., Monnot, M., Convert, O., Mauffret, O., Troalen, F. & Fermandjian, S. Eur. J. Biochem. 231, 370–380 (1995)]. Our results suggested both a high flexibility and a helical potential in bSD, these two properties seeming crucial for the accommodation of the basic subdomain of c-Jun to its specific DNA targets. In this work, we assessed the conformational variability of bSD through the study of the secondary structures of its NP and CP fragments in trifluoroethanol (TFE)/²H₂O mixtures, using Fourier transform infrared (FTIR) spectroscopy. The IR results were critically analyzed in light of our previously reported circular dichroism (CD) and NMR data [Krebs, D., Dahmani, B., Monnot, M., Mauffret, O., Troalen, F. & Fermandjian, S. Eur. J. Biochem. 235, 699–712 (1996)]. Upon addition of TFE, the relative areas of the seven components of the amide I band (1700–1620 cm^?1) reflected the conversion of a large amount of random coil conformation into α-helix for the two fragments and bSD. This effect was accompanied by more subtle variations of the less populated structures, in agreement with the results of CD and NMR experiments. The IR results stipulated the conservation of the parent bSD secondary structures in both fragments; however, NP and CP peptides did not display similar random-to-α-helix stabilization pattern upon additions of TFE to aqueous solutions. The profile from CD signal at 222 nm was found sigmoidal for NP and almost linear for CP, while that corresponding to the parent peptide bSD was just in between those of its fragments. Thus, the present study confirms the high flexibility and helix propensity of the c-Jun basic subdomain and suggests that the N- and C-terminal parts of the peptide do not follow the same random-to-helix conversion profile during their complexation with DNA.