Backbone N-Amination Promotes the Folding of β-Hairpin Peptides via a Network of Hydrogen Bonds

Molecular dynamics (MD) simulations have been used to characterize the effects of backbone N-amination of residues in a model β-hairpin peptide. This modification is of considerable interest as N-aminated peptides have been shown to inhibit amyloid-type aggregation. Six derivatives of the β-hairpin peptide, which contain one, two, or four N-aminated residues, have been studied. For each peptide 100 ns MD simulations starting from the folded β-hairpin structure were performed. The effects of the N-amination prove to be very sequence dependent. N-Amination of a residue involved in interstrand hydrogen bonding (Val3) leads to unfolding of the β-hairpin, whereas N-amination of a residue toward the C-terminus (Leu11) gives fraying at the termini of the peptide. In the other derivatives the peptide remains folded, with increasing levels of N-amination reducing the right-handed twist of the β-hairpin and favoring population of a type II' rather than a type I' β-turn. MD simulations (100 ns) have also been run for each peptide starting from an unfolded extended chain. Here, the peptide with four N-aminated residues shows the most folding into the β-hairpin (34%). Analysis of the simulations shows that N-amination favors the population of β (φ, ψ) conformations by the preceding residue due to, at least in part, a network of weak NH₂(i)-CO(i) and NH₂(i)-CO(i-2) hydrogen bonds. It also leads to a reduction of misfolding because of changes in the hydrogen-bonding potential. Both of these features help funnel the peptide to the folded β-hairpin structure. The conformational insights provided through this work give a firm foundation for the design of N-aminated peptide inhibitors for modulating protein-protein interactions and aggregation.

998 IMPROVING COMMUNICATION ON MEDICAL WARD ROUNDS IN PATIENTS WITH LIMITED ENGLISH BY IMPLEMENTING MEDICAL COMMUNICATION CHARTS

Aim

To improve communication on the medical ward round with patients with limited English through implementation of a medical communication chart.

Introduction

King’s College Hospital (KCH), London, is situated in Southwark in which 11% of households have no members that speak English as a first language, 4.1% of London’s population report they do not speak English well. Language barriers impair healthcare delivery including during daily ward rounds. This has been exacerbated by the need for PPE during the SARS-CoV2 pandemic. Effective communication between healthcare teams and patients is essential for high quality, patient-centred care. Communication tools commonly used include online, telephone and face-to-face translation services but these have limitations.

Method

Face-to-face patient questionnaires were conducted in the pre-QIP (baseline) group to assess communication on medical ward rounds. Medical communication charts were designed by adapting pre-existing aids commonly used by speech and language therapy. Charts were translated into commonly spoken languages among KCH inpatients. Patients with limited English were selected from both COVID-19 and non-Covid wards. Pre-intervention and post-intervention questionnaires were completed in three Plan–Do–Study–Act (PDSA) cycles.

Results

At baseline, patients agreed or strongly agreed that the ward round addressed physical symptoms (8/8), concerns or anxieties (7/8), ongoing needs (7/8). Only 2/8 doctors felt they could communicate effectively with patients. In PDSA 1, 4/5 patients reported high satisfaction in communicating physical symptoms, anxieties or concerns pre-intervention with 5/5 post-chart implementation. 5/5 patients reported high satisfaction in communicating ongoing needs pre-intervention but only 3/5 post-intervention. In PDSA 2, 2/5 patients reported increased satisfaction in communicating physical symptoms, concerns or anxieties with 4/4 doctors reporting improved satisfaction in communication in PDSA 2 and 2/3 doctors reporting higher satisfaction in communication in PDSA 3.

Conclusion

Medical communication charts can help in delivering high-quality, patient-centred care in multicultural and multilingual healthcare settings within the NHS.

A Method to Derive Structural Information on Molecules from Residual Dipolar Coupling NMR Data

A method for structure refinement of molecules based on residual dipolar coupling (RDC) data is proposed. It calculates RDC values using rotational and molecule-internal configurational sampling instead of the common refinement procedure that is based on the approximation of the nonuniform rotational distribution of the molecule by a single alignment tensor representing the average nonuniformity of this distribution. Using rotational sampling, as is occurring in the experiment leading to observable RDCs, the method stays close to the experiment. It avoids the use of an alignment tensor and thus the assumption that the overall rotation of the molecule is decoupled from its internal motions and that the molecule be rigid. Two simple molecules, two-united-atomic ethane and a cyclooctane molecule with eight side chains, containing 24 united atoms, serve as the so-called "toy model" test systems. The method demonstrates the influence of molecular flexibility and force-field deficiencies on the outcome of structure refinement based on RDCs. For a molecule of a given size (number of atoms N_at), there must be a sufficiently large number N_RDC of measured RDC values available to allow the restraining forces to bias the overall orientation distribution of the molecule. If the ratio N_RDC/N_at gets too small, the RDC-restraining forces will either not be strong enough to change the overall rotational direction of the molecule such that the target RDC values are approximated well or will be so strong that they induce a local deformation of the molecule. In the latter case, the size or inertia of the molecule hinders a restraining-induced overall rotation and the internal structure of the molecule is not strong enough to avoid local deformation due to the restraining forces.

The 'Shape-Shifter' Peptide from the Disulphide Isomerase PmScsC Shows Context-Dependent Conformational Preferences

Multiple crystal structures of the homo-trimeric protein disulphide isomerase PmScsC reveal that the peptide which links the trimerization stalk and catalytic domain can adopt helical, β-strand and loop conformations. This region has been called a 'shape-shifter' peptide. Characterisation of this peptide using NMR experiments and MD simulations has shown that it is essentially disordered in solution. Analysis of the PmScsC crystal structures identifies the role of intermolecular contacts, within an assembly of protein molecules, in stabilising the different linker peptide conformations. These context-dependent conformational properties may be important functionally, allowing for the binding and disulphide shuffling of a variety of protein substrates to PmScsC. They also have a relevance for our understanding of protein aggregation and misfolding showing how intermolecular quaternary interactions can lead to β-sheet formation by a sequence that in other contexts adopts a helical structure. This 'shape-shifting' peptide region within PmScsC is reminiscent of one-to-many molecular recognition features (MoRFs) found in intrinsically disordered proteins which are able to adopt different conformations when they fold upon binding to their protein partners.

Backbone assignment of E. coli NfsB and the effects of addition of the cofactor analogue nicotinic acid

E. coli nitroreductase NfsB (also called NfnB) has been studied extensively, largely due to its potential for cancer gene therapy. A homodimeric flavoprotein of 216 residues, it catalyses the reduction of nitroaromatics to cytotoxic hydroxylamines by NADH and NADPH and also the reduction of quinones to hydroxyquinones. Its role in vivo is not known but it is postulated to be involved in reducing oxidative stress. The crystal structures of the wild type protein and several homologues have been determined in the absence and presence of ligands, including nicotinate as a mimic of the headpiece of the nicotinamide cofactors. There is little effect on the overall structure of the protein on binding ligands, but, from the B factors, there appears to be a decrease in mobility of 2 helices near the active site. As a first step towards examining the dynamics of the protein in solution with and without ligand, we have assigned the backbone ¹³C, ¹⁵N, and ¹H_N resonances of NfsB and examined the effect of the binding of nicotinate on the amide ¹⁵N, and ¹H_N shifts.

On the use of 3J-coupling NMR data to derive structural information on proteins

Values of ³J-couplings as obtained from NMR experiments on proteins cannot easily be used to determine protein structure due to the difficulty of accounting for the high sensitivity of intermediate ³J-coupling values (4-8 Hz) to the averaging period that must cover the conformational variability of the torsional angle related to the ³J-coupling, and due to the difficulty of handling the multiple-valued character of the inverse Karplus relation between torsional angle and ³J-coupling. Both problems can be solved by using ³J-coupling time-averaging local-elevation restraining MD simulation. Application to the protein hen egg white lysozyme using 213 backbone and side-chain ³J-coupling restraints shows that a conformational ensemble compatible with the experimental data can be obtained using this technique, and that accounting for averaging and the ability of the algorithm to escape from local minima for the torsional angle induced by the Karplus relation, are essential for a comprehensive use of ³J-coupling data in protein structure determination.

On the Use of Side-Chain NMR Relaxation Data to Derive Structural and Dynamical Information on Proteins: A Case Study Using Hen Lysozyme

Values of S2CH and S2NH order parameters derived from NMR relaxation measurements on proteins cannot be used straightforwardly to determine protein structure because they cannot be related to a single protein structure, but are defined in terms of an average over a conformational ensemble. Molecular dynamics simulation can generate a conformational ensemble and thus can be used to restrain S2CH and S2NH order parameters towards experimentally derived target values S2CH (exp) and S2NH (exp). Application of S2CH and S2NH order‐parameter restraining MD simulation to bond vectors in 63 side chains of the protein hen egg white lysozyme using 51 S2CH (exp) target values and 28 S2NH (exp) target values shows that a conformational ensemble compatible with the experimentally derived data can be obtained by using this technique. It is observed that S2CH order‐parameter restraining of C−H bonds in methyl groups is less reliable than S2NH order‐parameter restraining because of the possibly less valid assumptions and approximations used to derive experimental S2CH (exp) values from NMR relaxation measurements and the necessity to adopt the assumption of uniform rotational motion of methyl C−H bonds around their symmetry axis and of the independence of these motions from each other. The restrained simulations demonstrate that side chains on the protein surface are highly dynamic. Any hydrogen bonds they form and that appear in any of four different crystal structures, are fluctuating with short lifetimes in solution.

An NMR and MD study of complexes of bacteriophage lambda lysozyme with tetra- and hexa-N-acetylchitohexaose

The X-ray structure of lysozyme from bacteriophage lambda (λ lysozyme) in complex with the inhibitor hexa-N-acetylchitohexaose (NAG6) (PDB: 3D3D) has been reported previously showing sugar units from two molecules of NAG6 bound in the active site. One NAG6 is bound with four sugar units in the ABCD sites and the other with two sugar units in the E'F' sites potentially representing the cleavage reaction products; each NAG6 cross links two neighboring λ lysozyme molecules. Here we use NMR and MD simulations to study the interaction of λ lysozyme with the inhibitors NAG4 and NAG6 in solution. This allows us to study the interactions within the complex prior to cleavage of the polysaccharide. 1 HN and 15 N chemical shifts of λ lysozyme resonances were followed during NAG4/NAG6 titrations. The chemical shift changes were similar in the two titrations, consistent with sugars binding to the cleft between the upper and lower domains; the NMR data show no evidence for simultaneous binding of a NAG6 to two λ lysozyme molecules. Six 150 ns MD simulations of λ lysozyme in complex with NAG4 or NAG6 were performed starting from different conformations. The simulations with both NAG4 and NAG6 show stable binding of sugars across the D/E active site providing low energy models for the enzyme-inhibitor complexes. The MD simulations identify different binding subsites for the 5th and 6th sugars consistent with the NMR data. The structural information gained from the NMR experiments and MD simulations have been used to model the enzyme-peptidoglycan complex.

Structural Aspects of the O-glycosylation Linkage in Glycopeptides via MD Simulations and Comparison with NMR Experiments

A powerful conformational searching and enhanced sampling simulation method, and unbiased molecular dynamics simulations have been used along with NMR spectroscopic observables to provide a detailed structural view of O‐glycosylation. For four model systems, the force‐field parameters can accurately predict experimental NMR observables (J couplings and NOE's). This enables us to derive conclusions based on the generated ensembles, in which O‐glycosylation affects the peptide backbone conformation by forcing it towards to an extended conformation. An exception is described for β‐GalNAc‐Thr where the α content is increased and stabilized via hydrogen bonding between the sugar and the peptide backbone, which was not observed in the rest of the studied systems. These observations might offer an explanation for the evolutionary preference of α‐linked GalNAc glycosylation instead of a β link.

1H, 13C and 15N NMR assignments of self-incompatibility protein homologue 15 from Arabidopsis thaliana

The SPH proteins are a large family of small, disulphide-bonded, secreted proteins, originally found to be involved in the self-incompatibility response in the field poppy (Papaver rhoeas). They are now known to be widely distributed in plants, many containing multiple members of this protein family. Apart from the PrsS proteins in Papaver the function of these proteins is unknown but they are thought to be involved in plant development and cell signalling. There has been no structural study of SPH proteins to date. Using the Origami strain of E. coli, we cloned and expressed one member of this family, SPH15 from Arabidopsis thaliana, as a folded thioredoxin-fusion protein, purified it from the cytosol, and cleaved it to obtain the secreted protein. We here report the assignment of the NMR spectra of SPH15, which contains 112 residues plus three N-terminal amino acids from the vector. The secondary structure propensity from TALOS⁺ shows that it contains eight beta strands and connecting loops. This is largely in agreement with predictions from the amino acid sequence, which show an additional C-terminal strand.

Activation of RyR2 by class I kinase inhibitors

BACKGROUND AND PURPOSE

Kinase inhibitors are a common treatment for cancer. Class I kinase inhibitors that target the ATP-binding pocket are particularly prevalent. Many of these compounds are cardiotoxic and can cause arrhythmias. Spontaneous release of Ca²⁺ via cardiac ryanodine receptors (RyR2), through a process termed store overload-induced Ca²⁺ release (SOICR), is a common mechanism underlying arrhythmia. We explored whether class I kinase inhibitors could modify the activity of RyR2 and trigger SOICR to determine if this contributes to the cardiotoxic nature of these compounds.

EXPERIMENTAL APPROACH

The impact of class I and II kinase inhibitors on SOICR was studied in HEK293 cells and ventricular myocytes using single-cell Ca²⁺ imaging. A specific effect on RyR2 was confirmed using single channel recordings. Ventricular myocytes were also used to determine if drug-induced changes in SOICR could be reversed using anti-SOICR agents.

KEY RESULTS

Class I kinase inhibitors increased the propensity of SOICR. Single channel recording showed that this was due to a specific effect on RyR2. Class II kinase inhibitors decreased the activity of RyR2 at the single channel level but had little effect on SOICR. The promotion of SOICR mediated by class I kinase inhibitors could be reversed using the anti-SOICR agent VK-II-86.

CONCLUSIONS AND IMPLICATIONS

Part of the cardiotoxicity of class I kinase inhibitors can be assigned to their effect on RyR2 and increase in SOICR. Compounds with anti-SOICR activity may represent an improved treatment option for patients.

Validation of Molecular Simulation: An Overview of Issues

Computer simulation of molecular systems enables structure-energy-function relationships of molecular processes to be described at the sub-atomic, atomic, supra-atomic, or supra-molecular level. To interpret results of such simulations appropriately, the quality of the calculated properties must be evaluated. This depends on the way the simulations are performed and on the way they are validated by comparison to values Q^exp of experimentally observable quantities Q. One must consider 1) the accuracy of Q^exp , 2) the accuracy of the function Q(r^N ) used to calculate a Q-value based on a molecular configuration r^N of N particles, 3) the sensitivity of the function Q(r^N ) to the configuration r^N , 4) the relative time scales of the simulation and experiment, 5) the degree to which the calculated and experimental properties are equivalent, and 6) the degree to which the system simulated matches the experimental conditions. Experimental data is limited in scope and generally corresponds to averages over both time and space. A critical analysis of the various factors influencing the apparent degree of (dis)agreement between simulations and experiment is presented and illustrated using examples from the literature. What can be done to enhance the validation of molecular simulation is also discussed.

Opportunity for interprofessional collaborative care-findings from a sample of federally qualified health center patients in the Midwest

OBJECTIVES

Federally qualified health centers (FQHCs) frequently serve more socio-economically disadvantaged populations; existing literature suggests that underserved groups are more likely to experience various chronic physical and mental health conditions. FQHC patients may have significant needs for various specialty services that are beyond common FQHC providers. This study examines chronic condition prevalence, healthcare satisfaction, and use of multiprovider services in a Midwest FQHC patient population. We also evaluated the potential of interprofessional collaborative practices in FQHC settings.

STUDY DESIGN

Cross-sectional study.

METHODS

A total of 232 participants were recruited prior to or immediately after their scheduled clinic visit within an FQHC located on the fringes of an urban area. Respondents were invited to complete a brief questionnaire and grant access to their electronic medical records.

RESULTS

Nearly half of participants were covered by Medicaid, private insurance carriers (19.4%), or Medicare (17.7%). The most prevalent chronic conditions included diabetes, depression, anxiety, and chronic pain. Almost half (46.6%) of participants were seen by two or three providers; 20% had 7+ office visits in the last year. While 35.3% reported health dissatisfaction, 30.6% reported health satisfaction. When asked if they were satisfied with their health care, nearly 70% reported satisfaction with health care, while only 4.7% reported healthcare dissatisfaction.

CONCLUSIONS

The authors of this study recommend an interprofessional collaborate healthcare model be explored to address the complex and multifaceted healthcare needs of this population. Future research in this area should prospectively examine the utility of monitoring patient satisfaction in a collaborative practice setting.

Using Complementary NMR Data Sets To Detect Inconsistencies and Model Flaws in the Structure Determination of Human Interleukin-4

The derivation of protein structure from values of observable quantities measured in NMR experiments is a rather nontrivial task due to (i) the limited number of data compared to degrees of freedom of a protein, (ii) the uncertainty inherent to the function connecting an observable quantity to molecular structure, (iii) the finite quality of biomolecular models and force fields used in structure refinement, and (iv) the conformational freedom of a protein in aqueous solution, which requires extensive conformational sampling and appropriate conformational averaging when calculating or restraining to sets of NMR data. The protein interleukin-4 (IL-4) has been taken as a test case using NOE distances, S² order parameters, and ³J-couplings as test data and the former two types of data as restraints. It is shown that, by combining sets of different, complementary NMR data as restraints in MD simulations, inconsistencies in the data or flaws in the model and procedures used to derive protein structure from NMR data can be detected. This leads to an improved structural interpretation of such data particularly in more mobile loop regions.

PAI-1 gain-of-function genotype, factors increasing PAI-1 levels, and airway obstruction: The GALA II Cohort

BACKGROUND

PAI-1 gain-of-function variants promote airway fibrosis and are associated with asthma and with worse lung function in subjects with asthma.

OBJECTIVE

We sought to determine whether the association of a gain-of-function polymorphism in plasminogen activator inhibitor-1 (PAI-1) with airway obstruction is modified by asthma status, and whether any genotype effect persists after accounting for common exposures that increase PAI-1 level.

METHODS

We studied 2070 Latino children (8-21y) with genotypic and pulmonary function data from the GALA II cohort. We estimated the relationship of the PAI-1 risk allele with FEV1/FVC by multivariate linear regression, stratified by asthma status. We examined the association of the polymorphism with asthma and airway obstruction within asthmatics via multivariate logistic regression. We replicated associations in the SAPPHIRE cohort of African Americans (n=1056). Secondary analysis included the effect of the at-risk polymorphism on postbronchodilator lung function.

RESULTS

There was an interaction between asthma status and the PAI-1 polymorphism on FEV₁ /FVC (P=.03). The gain-of-function variants, genotypes (AA/AG), were associated with lower FEV₁ /FVC in subjects with asthma (β=-1.25, CI: -2.14,-0.35, P=.006), but not in controls. Subjects with asthma and the AA/AG genotypes had a 5% decrease in FEV₁ /FVC (P<.001). In asthmatics, the risk genotype (AA/AG) was associated with a 39% increase in risk of clinically relevant airway obstruction (OR=1.39, CI: 1.01, 1.92, P=.04). These associations persisted after exclusion of factors that increase PAI-1 including tobacco exposure and obesity.

CONCLUSIONS AND CLINICAL RELEVANCE

The decrease in the FEV₁ /FVC ratio associated with the risk genotype was modified by asthma status. The genotype increased the odds of airway obstruction by 75% within asthmatics only. As exposures known to increase PAI-1 levels did not mitigate this association, PAI-1 may contribute to airway obstruction in the context of chronic asthmatic airway inflammation.

Interpretation of Seemingly Contradictory Data: Low NMR S2 Order Parameters Observed in Helices and High NMR S2 Order Parameters in Disordered Loops of the Protein hGH at Low pH

At low pH, human growth hormone (hGH) adopts a partially folded state, in which the native helices are maintained, but the long loop regions and side-chain packing become disordered. Some of the S² order parameters for backbone N-H vectors derived from NMR relaxation measurements on hGH at low pH initially seem contradictory. Three isolated residues (15, 20, and 171) in helices A and D exhibit low order parameter values (<0.5) indicating flexibility, whereas residue 143 in the centre of a long flexible loop region has a high order parameter (0.82). Using S² order parameter restraining MD simulations, this paradox has been resolved. Low S² values in helices are due to the presence of a mixture of 3₁₀ -helical and α-helical hydrogen bonds. High S² values in relatively disordered parts of a protein may be due to fluctuating networks of hydrogen bonds between the backbone and the side chains, which restrict the motion of N-H bond vectors.

Deriving Structural Information from Experimentally Measured Data on Biomolecules

During the past half century, the number and accuracy of experimental techniques that can deliver values of observables for biomolecular systems have been steadily increasing. The conversion of a measured value Q^exp of an observable quantity Q into structural information is, however, a task beset with theoretical and practical problems: 1) insufficient or inaccurate values of Q^exp , 2) inaccuracies in the function Q(r→) used to relate the quantity Q to structure r→ , 3) how to account for the averaging inherent in the measurement of Q^exp , 4) how to handle the possible multiple-valuedness of the inverse r→(Q) of the function Q(r→) , to mention a few. These apply to a variety of observable quantities Q and measurement techniques such as X-ray and neutron diffraction, small-angle and wide-angle X-ray scattering, free-electron laser imaging, cryo-electron microscopy, nuclear magnetic resonance, electron paramagnetic resonance, infrared and Raman spectroscopy, circular dichroism, Förster resonance energy transfer, atomic force microscopy and ion-mobility mass spectrometry. The process of deriving structural information from measured data is reviewed with an eye to non-experts and newcomers in the field using examples from the literature of the effect of the various choices and approximations involved in the process. A list of choices to be avoided is provided.

On the use of time-averaging restraints when deriving biomolecular structure from ³J -coupling values obtained from NMR experiments

Deriving molecular structure from [Formula: see text]-couplings obtained from NMR experiments is a challenge due to (1) the uncertainty in the Karplus relation [Formula: see text] connecting a [Formula: see text]-coupling value to a torsional angle [Formula: see text], (2) the need to account for the averaging inherent to the measurement of [Formula: see text]-couplings, and (3) the sampling road blocks that may emerge due to the multiple-valuedness of the inverse function [Formula: see text] of the function [Formula: see text]. Ways to properly handle these issues in structure refinement of biomolecules are discussed and illustrated using the protein hen egg white lysozyme as example.

Defect-Rich Ultrathin ZnAl-Layered Double Hydroxide Nanosheets for Efficient Photoreduction of CO2 to CO with Water

Defect-rich ultrathin ZnAl-layered double hydroxide nanosheets are successfully prepared. Under UV-vis irradiation, these nanosheets are superior efficient catalysts for the photoreduction of CO2 to CO with water. The formed oxygen vacancies lead to the formation of coordinatively unsaturated Zn(+) centers within the nanosheets, responsible for the very high photocatalytic activities.

Radiographic, computed tomographic and surgical anatomy of the equine sphenopalatine sinus in normal and diseased horses

REASONS FOR PERFORMING STUDY

Knowledge of imaging anatomy, surgical anatomy and disorders affecting the sphenopalatine sinus are currently lacking.

OBJECTIVES

To describe the computed tomographic (CT) and surgical anatomy of the sphenopalatine sinus and diagnosis, treatment and outcome in clinical cases with sphenopalatine sinus disease.

STUDY DESIGN

Cadaver observational study and retrospective case series.

METHODS

The sphenopalatine sinuses of 10 normal cadaver heads were examined with digital radiography, CT and sinoscopic examination prior to anatomical sectioning. Sphenopalatine sinus anatomy was described and compared between cadaver specimens across the imaging modalities. Medical records (January 2004-2014) of cases diagnosed with sphenopalatine sinus disease were reviewed.

RESULTS

The anatomy of the sphenopalatine sinus was variable. The borders of the sphenopalatine sinus were not identifiable on plain radiographs, whereas CT provided useful anatomical information. The palatine portion of the sphenopalatine sinus was consistently accessible sinoscopically and the sphenoidal portion was accessible in 6/10 cadaver heads. Fourteen cases of sphenopalatine sinus disease were identified, presenting with one or more clinical signs of exophthalmos, blindness, unilateral epistaxis or unilateral nasal discharge. Diagnoses included neoplasia (7), progressive ethmoidal haematoma (4), sinus cyst (2) and empyema (1). Computed tomography provided diagnostic information but could not differentiate the nature of soft tissue masses. Standing sinoscopic access to the palatine portion of the sphenopalatine sinus was possible for evaluation, biopsy and resection of abnormal soft tissues. Surgical access to the sphenoidal portion was limited. Eight horses were alive at 1 year after diagnosis, with a worse outcome associated with CT evidence of bone loss and a diagnosis of neoplasia.

CONCLUSIONS

Sphenopalatine sinus disease should be considered a rare cause of the clinical signs described. Knowledge of the anatomical variation of the sphenopalatine sinus is vital for interpreting CT images. A combination of CT and sinoscopy provides the most comprehensive approach for diagnosis and treatment of sphenopalatine sinus disease.

Comparison of the backbone dynamics of wild-type Hydrogenobacter thermophilus cytochrome c(552) and its b-type variant

Cytochrome c552 from the thermophilic bacterium Hydrogenobacter thermophilus is a typical c-type cytochrome which binds heme covalently via two thioether bonds between the two heme vinyl groups and two cysteine thiol groups in a CXXCH sequence motif. This protein was converted to a b-type cytochrome by substitution of the two cysteine residues by alanines (Tomlinson and Ferguson in Proc Natl Acad Sci USA 97:5156-5160, 2000a). To probe the significance of the covalent attachment of the heme in the c-type protein, (15)N relaxation and hydrogen exchange studies have been performed for the wild-type and b-type proteins. The two variants share very similar backbone dynamic properties, both proteins showing high (15)N order parameters in the four main helices, with reduced values in an exposed loop region (residues 18-21), and at the C-terminal residue Lys80. Some subtle changes in chemical shift and hydrogen exchange protection are seen between the wild-type and b-type variant proteins, not only for residues at and neighbouring the mutation sites, but also for some residues in the heme binding pocket. Overall, the results suggest that the main role of the covalent linkages between the heme group and the protein chain must be to increase the stability of the protein.

APC promoter 1B deletion in seven American families with familial adenomatous polyposis

Familial adenomatous polyposis (FAP) is a colorectal cancer predisposition syndrome caused by mutations in the adenomatous polyposis coli (APC) gene. Clinical genetic testing fails to identify disease causing mutations in up to 20% of clinically apparent FAP cases. Following the inclusion of multiplex ligation-dependent probe amplification (MLPA) probes specific for APC promoter 1B, seven probands were identified with a deletion of promoter 1B. Using haplotype analysis spanning the APC locus, the seven families appear to be identical by descent from a common founder. The clinical phenotype of 19 mutation carriers is classical FAP with colectomy at an average age of 24. The majority of cases had a large number of duodenal and gastric polyps. Measurements of allele-specific expression of APC mRNA using TaqMan assay confirmed that relative expression in the allele containing the promoter 1B deletion was reduced 42-98%, depending on tissue type. This study confirms the importance of APC promoter deletions as a cause of FAP and identifies a founder mutation in FAP patients from the United States.

Multiple binding modes for palmitate to barley lipid transfer protein facilitated by the presence of proline 12

Molecular dynamics simulations have been used to characterise the binding of the fatty acid ligand palmitate in the barley lipid transfer protein 1 (LTP) internal cavity. Two different palmitate binding modes (1 and 2), with similar protein-ligand interaction energies, have been identified using a variety of simulation strategies. These strategies include applying experimental protein-ligand atom-atom distance restraints during the simulation, or protonating the palmitate ligand, or using the vacuum GROMOS 54B7 force-field parameter set for the ligand during the initial stages of the simulations. In both the binding modes identified the palmitate carboxylate head group hydrogen bonds with main chain amide groups in helix A, residues 4 to 19, of the protein. In binding mode 1 the hydrogen bonds are to Lys 11, Cys 13, and Leu 14 and in binding mode 2 to Thr 15, Tyr 16, Val 17, Ser 24 and also to the OH of Thr 15. In both cases palmitate binding exploits irregularity of the intrahelical hydrogen-bonding pattern in helix A of barley LTP due to the presence of Pro 12. Simulations of two variants of barley LTP, namely the single mutant Pro12Val and the double mutant Pro12Val Pro70Val, show that Pro 12 is required for persistent palmitate binding in the LTP cavity. Overall, the work identifies key MD simulation approaches for characterizing the details of protein-ligand interactions in complexes where NMR data provide insufficient restraints.

Molecular dynamics simulations of barley and maize lipid transfer proteins show different ligand binding preferences in agreement with experimental data

Experimental studies of barley and maize lipid transfer proteins (LTPs) show that the two proteins bind the ligand palmitate in opposite orientations in their internal cavities. Moreover, maize LTP is reported to bind the ligand caprate in the internal cavity in a mixture of two orientations with approximately equal occupancy. Six 30 ns molecular dynamics (MD) simulations of maize and barley LTP with ligands bound in two orientations (modes M and B) have been used to understand the different ligand binding preferences. The simulations show that both maize and barley LTP could bind palmitate in the orientation observed experimentally for maize LTP (mode M), with the predominant interaction being a salt bridge between the ligand carboxylate headgroup and a conserved arginine side chain. However, the simulation of barley LTP with palmitate in the mode B orientation shows the most favorable protein-ligand interaction energy. In contrast, the simulations of maize LTP with palmitate and with caprate in the mode B orientation show no persistent ligand binding, the ligands leaving the cavity during the simulations. Sequence differences between maize and barley LTP in the AB loop region, in residues at the base of the hydrophobic cavity, and in the helix A region are identified as contributing to the different behavior. The simulations reproduce well the experimentally observed binding preferences for palmitate and suggest that the experimental data for maize LTP with caprate reflect ligand mobility in binding mode M rather than the population of binding modes M and B.

Structure of hen egg-white lysozyme solvated in TFE/water: a molecular dynamics simulation study based on NMR data

Various experimental studies of hen egg white lysozyme (HEWL) in water and TFE/water clearly indicate structural differences between the native state and TFE state of HEWL, e.g. the helical content of the protein in the TFE state is much higher than in the native state. However, the available detailed NMR studies were not sufficient to determine fully a structure of HEWL in the TFE state. Different molecular dynamics (MD) simulations, i.e. at room temperature, at increased temperature and using proton-proton distance restraints derived from NMR NOE data, have been used to generate configurational ensembles corresponding to the TFE state of HEWL. The configurational ensemble obtained at room temperature using atom-atom distance restraints measured for HEWL in TFE/water solution satisfies the experimental data and has the lowest protein energy. In this ensemble residues 50-58, which are part of the β-sheet in native HEWL, adopt fluctuating α-helical secondary structure.

How long should a routine EEG be?

Cost-benefit analysis in neurology practice deserves continual reassessment. One example is the duration of a routine electroencephalography (EEG) required to optimise accuracy of diagnosis. Recommended guidelines of recording a routine EEG for 20 or more minutes are not based on scientific evidence. In many countries, EEG is not economically viable with costs outweighing financial remuneration. We prospectively studied 420 consecutive routine EEGs to see if a shorter record decreased diagnostic accuracy. A carefully structured 15 min routine EEG protocol produced comparable results with the 25 min recording. Shorter routine EEGs would make EEG more cost effective without compromising diagnostic accuracy.

Lung spirometry parameters and diffusion capacity are decreased in patients with Type 2 diabetes

AIMS

In cohort studies, Type 2 diabetes mellitus has been associated with decreased forced 1 s expiratory volume and forced vital capacity. We examined if forced vital capacity, forced 1 s expiratory volume and diffusion lung capacity correlate with diabetes mellitus across different races in a clinical setting.

METHODS

We examined the medical records of 19,882 adults 18-97 years of age in our centre from 1 January 2000 to 1 May 2009. After excluding patients with diseases causing abnormal lung function, 4164 subjects were available for analysis. We used multiple linear regressions to examine cross-sectional differences in forced vital capacity, forced 1 s expiratory volume and carbon monoxide diffusing capacity between patients with and without diabetes mellitus, after adjustment for age, sex, race, height, smoking, BMI and heart failure.

RESULTS

Patients with diabetes (n = 560) were older (62 ± 12 vs. 55 ± 16 years), more likely to be men (56 vs. 43%), overweight (BMI 31.7 ± 8.5 vs. 27.3 ± 6.7 kg/m2 ), have heart failure (33 vs. 14%) and less likely to be Caucasians (65 vs. 76%) and never smokers (66 vs. 72%) compared with patients without diabetes (n = 3604). The mean unadjusted values in patients with diabetes vs. those without were: forced vital capacity 2.78 ± 0.91 vs. 3.19 ± 1.03 l; forced 1 s expiratory volume 2.17 ± 0.74 vs. 2.49 ± 0.0.83; and carbon monoxide diffusing capacity 16.67 ± 5.53 vs. 19.18 ± 6.72 ml(-1) min(-1) mmHg, all P < 0.0001. These differences remained significant after adjustment for covariates. After race stratification, only Caucasians with diabetes had a significant decrease in all lung function measures.

CONCLUSIONS

Patients with diabetes have decreased lung function compared with those without diabetes. Caucasians with diabetes have more global lung function impairment compared with African-Americans and Hispanics.

Characterization of an alternative low energy fold for bovine α-lactalbumin formed by disulfide bond shuffling

Bovine α-lactalbumin (αLA) forms a misfolded disulfide bond shuffled isomer, X-αLA. This X-αLA isomer contains two native disulfide bridges (Cys 6-Cys 120 and Cys 28-Cys 111) and two non-native disulfide bridges (Cys 61-Cys 73 and Cys 77-Cys 91). MD simulations have been used to characterize the X-αLA isomer and its formation via disulfide bond shuffling and to compare it with the native fold of αLA. In the simulations of the X-αLA isomer the structure of the α-domain of native αLA is largely retained in agreement with experimental data. However, there are significant rearrangements in the β-domain, including the loss of the native β-sheet and calcium binding site. Interestingly, the energies of X-αLA and native αLA in simulations in the absence of calcium are closely similar. Thus, the X-αLA isomer represents a different low energy fold for the protein. Calcium binding to native αLA is shown to help preserve the structure of the β-domain of the protein limiting possibilities for disulfide bond shuffling. Hence, binding calcium plays an important role in both maintaining the native structure of αLA and providing a mechanism for distinguishing between folded and misfolded species.

Inhibition of p53 expression by peptide-conjugated phosphorodiamidate morpholino oligomers sensitizes human cancer cells to chemotherapeutic drugs

The p53 tumor suppressor gene encodes a transcription factor that is commonly mutated in cancer. Tumors arise when premalignant cells are unable to undergo p53-dependent apoptosis, cell cycle arrest or DNA repair. The p53-signaling pathway affects not only tumor development, but also the response of tumors to chemotherapeutic drugs. In this study, we use cell penetrating peptide conjugates of phosphorodiamidate morpholino oligomers (PPMOs) to inhibit p53 expression. We examine the functional properties of endogenous p53 isoforms that are produced upon PPMO-mediated inhibition of p53 translation and splicing, and report that loss of N-terminal or C-terminal sequences interferes with the transcriptional activity of p53. Importantly, we report that PPMO-mediated inhibition of p53 expression sensitizes human cancer cells with wild-type p53 to chemotherapeutic drugs.

Residual dipolar couplings: are multiple independent alignments always possible?

RDCs for the 14 kDa protein hen egg-white lysozyme (HEWL) have been measured in eight different alignment media. The elongated shape and strongly positively charged surface of HEWL appear to limit the protein to four main alignment orientations. Furthermore, low levels of alignment and the protein's interaction with some alignment media increases the experimental error. Together with heterogeneity across the alignment media arising from constraints on temperature, pH and ionic strength for some alignment media, these data are suitable for structure refinement, but not the extraction of dynamic parameters. For an analysis of protein dynamics the data must be obtained with very low errors in at least three or five independent alignment media (depending on the method used) and so far, such data have only been reported for three small 6-8 kDa proteins with identical folds: ubiquitin, GB1 and GB3. Our results suggest that HEWL is likely to be representative of many other medium to large sized proteins commonly studied by solution NMR. Comparisons with over 60 high-resolution crystal structures of HEWL reveal that the highest resolution structures are not necessarily always the best models for the protein structure in solution.

Heme proteins--diversity in structural characteristics, function, and folding

The characteristics of heme prosthetic groups and their binding sites have been analyzed in detail in a data set of nonhomologous heme proteins. Variations in the shape, volume, and chemical composition of the binding site, in the mode of heme binding and in the number and nature of heme-protein interactions are found to result in significantly different heme environments in proteins with different functions in biology. Differences are also seen in the properties of the apo states of the proteins. The apo states of proteins that bind heme permanently in their functional form show some disorder, ranging from local unfolding in the heme binding pocket to complete unfolding to give a random coil. In contrast, proteins that bind heme transiently are fully folded in their apo and holo states, presumably allowing both apo and holo forms to remain biologically active resisting aggregation or proteolysis. The principles identified here provide a framework for the design of de novo proteins that will exhibit tight heme ligand binding and for the identification of the function of structural genomic target proteins with heme ligands.

Systematic review of the association between lung function and Type 2 diabetes mellitus

AIMS

To describe the association between lung function and Type 2 diabetes mellitus.

METHODS

We identified English language studies evaluating the association between lung function and diabetes mellitus in the MEDLINE database from 1 January 1975 to 31 December 2009. We evaluated study quality based on established criteria (54 studies were reviewed, 34 met the inclusion criteria).

RESULTS

Cross-sectional studies showed that adults with diabetes mellitus have lower forced vital capacity (FVC) and forced expiratory volume in one second (FEV1), with reductions in FVC more consistent than FEV1 and lower diffusion capacity (DLCO) compared with their non-diabetic counterparts. The reduced lung function in patients with diabetes is inversely related to blood glucose levels, duration of diabetes and its severity and is independent of smoking or obesity. Findings in cohort studies have been less consistent, with only a few studies identifying an increased rate of lung function decline in adults with diabetes. In addition, other cohort studies have reported an association between decreased lung function and incident insulin resistance and diabetes. Studies evaluating biological mechanisms to explain the association between lung impairment and diabetes identified microangiopathy of the alveolar capillaries and pulmonary arterioles, chronic inflammation, autonomic neuropathy involving the respiratory muscles, loss of elastic recoil secondary to collagen glycosylation of lung parenchyma, hypoxia-induced insulin resistance and low birthweight, as being associated with both insulin resistance and impaired lung function.

CONCLUSIONS

There is an association between diabetes mellitus and decreased lung function, but the definitive direction as well as the exact pathophysiological mechanism to explain this association requires further investigation.

Lean mass predicts asthma better than fat mass among females

The obesity phenotype associated with asthma is not known. Our objective was to define the relative contribution of various distributions of fat and lean mass to asthma prevalence. Data were obtained from 2,525 participants (including 1,422 females) who underwent dual-energy X-ray absorptiometry (DEXA) at the year 20 examination in the Coronary Artery Risk Development in Young Adults (CARDIA) cohort. Total, truncal, arm and leg distributions of fat and lean mass were adjusted to the person's height. Self-reported asthma was the outcome. Asthma among females was associated with greater total fat mass, arm fat mass, total lean mass, truncal lean mass and arm lean mass. Among males, none of these mass measures were significantly associated with asthma. Among females, the association with asthma was stronger for total lean mass than for total fat mass. Further, among various regional distributions of lean and fat mass in females, truncal lean mass was the strongest predictor. Total lean mass is more strongly associated with asthma than total fat mass among females. These findings are contrary to the popular perception that excess physiological fat drives the obesity-asthma association. Rather, we hypothesise that ectopic fat within the "lean" tissues drives this association among females.

The structural characteristics of nonspecific lipid transfer proteins explain their resistance to gastroduodenal proteolysis

The structure and stability of the allergenic nonspecific lipid transfer protein (LTP) of peach were compared with the homologous LTP1 of barley and its liganded form LTP1b. All three proteins were resistant to gastric pepsinolysis and were only slowly digested at 1 to 2 out of 14 potential tryptic and chymotryptic cleavage sites under duodenal conditions. Peach LTP was initially cleaved at Tyr79-Lys80 and then at Arg39-Thr40 (a site lost in barley LTP1). Molecular dynamics simulations of the proteins under folded conditions showed that the backbone flexibility is limited, explaining the resistance to duodenal proteolysis. Arg39 and Lys80 side chains were more flexible in simulations of peach compared with barley LTP1. This may explain differences in the rates of cleavage observed experimentally for the two proteins and suggests that the flexibility of individual amino acid side chains could be important in determining preferred proteolytic cleavage sites. In order to understand resistance to pepsinolysis, proteins were characterized by NMR spectroscopy at pH 1.8. This showed that the helical regions of both proteins remain folded at this pH. NMR hydrogen exchange studies confirmed the rigidity of the structures at acidic pH, with barley LTP1 showing some regions with greater protection. Collectively, these data suggest that the rigidity of the LTP scaffold is responsible for their resistance to proteolysis. Gastroduodenal digestion conditions do not disrupt the 3D structure of peach LTP, explaining why LTPs retain their ability to bind IgE after digestion and hence their allergenic potential.

Are horses that undergo an exploratory laparotomy for correction of a right dorsal displacement of the large colon predisposed to post operative colic, compared to other forms of large colon displacement?

REASON FOR PERFORMING STUDY

It is a clinical impression that horses diagnosed with a right dorsal displacement (RDD) of the large colon, are more likely to suffer from recurrent episodes of colic post operatively, compared to other forms of nonstrangulating large colon displacement.

OBJECTIVES

To investigate whether the type of nonstrangulating large colon displacement identified at exploratory laparotomy would influence long-term outcome.

HYPOTHESIS

Horses identified with a RDD of the large colon at exploratory laparotomy would be more likely to experience recurrent episodes of post operative colic than other types of displacement.

MATERIALS AND METHODS

Medical records for horses undergoing an exploratory laparotomy, from 2000-2008, for a nonstrangulating large colon displacement were reviewed. Data retrieved included: subject details, previous medical history, details of current episodes of colic, results of preoperative examination, surgical findings and procedures, post operative management and complications. Follow-up information was obtained by reference to computerised clinical records and by telephone questionnaire administered to the horse's owner or carer, and included details of any colic episodes exhibited by the horse after discharge and whether a repeat celiotomy had been required to resolve the colic episodes.

RESULTS

There were 165 surgeries identified, in 154 horses. It was found that those horses with RDD were significantly more likely to experience recurrent episodes of colic requiring veterinary intervention post operatively compared to other types of displacement.

CLINICAL RELEVANCE

Long-term prognosis and likelihood of post operative complications is an important consideration for both owners and veterinarians.

Survival and complication rates in 300 horses undergoing surgical treatment of colic. Part 4: Early (acute) relaparotomy

REASONS FOR PERFORMING STUDY

Early (acute) relaparotomy after surgery for equine colic is widely considered to be an acceptable treatment option for management of certain post operative complications. However, there is relatively little published information about resulting complication rates and short- and long-term outcomes.

OBJECTIVES

To document the proportions, indications, complication rates and survival rates of horses undergoing acute relaparatomy following colic surgery.

METHODS

History, clinical findings, surgical findings and procedures, post operative treatments and outcome of 300 consecutive surgical colic cases (1994-2001) were reviewed. Long-term follow-up information was retrieved from case records and telephone enquiries from owners.

RESULTS

Acute relaparotomy was performed in 27/254 horses (10.6%) that recovered from initial general anaesthesia. The indications for relaparotomy included persistent pain, persistent ileus, peritonitis and wound breakdown. Of these 27 horses, 21 (77.8%) recovered from the second surgery, of which 8 (29.6%) died during the immediate post operative period. Thirteen of the 27 horses (48.2%) were discharged. Of these 13 horses, 5 (38.5%) were re-admitted to the hospital for surgical treatment of a subsequent bout of colic. The long-term survival rate for the 27 horses that underwent relaparotomy was 22.2%. Colic following discharge after relaparotomy was recorded in 69.2% of cases.

CONCLUSIONS

Relaparotomy is necessary in approximately 10% of horses undergoing surgery for acute colic. Persistent pain and post operative ileus were the most common indications. The short-term survival rate for horses requiring relaparotomy was approximately 50% and the long-term survival rate 22%. Nearly 40% of horses surviving relaparotomy developed episodes of acute colic that necessitated further surgery.

POTENTIAL RELEVANCE

Owners of horses requiring early (acute) relaparotomy should be advised of the high complication rates for this procedure.

Survival and complication rates in 300 horses undergoing surgical treatment of colic. Part 1: Short-term survival following a single laparotomy

REASONS FOR PERFORMING STUDY

A minority of equine colic cases prove fatal unless treated surgically; however, few studies have considered long-term survival and complication rates, and few have attempted to identify factors that might affect outcomes. Such information is required for owners and veterinary surgeons to make informed decisions about the most appropriate treatment for individual cases.

OBJECTIVES

To document short-term survival rates of 300 horses undergoing colic surgery and analyse factors that might have predisposed to short-term death.

METHODS

History, clinical and surgical findings, treatments and outcomes of 300 surgical colic cases (1994-2001) were reviewed. Comparisons among groups of discrete data were made using chi-squared or Student's t tests as appropriate. Significance was set at P < 0.05, and 95% confidence intervals were calculated for percentages.

RESULTS

The short-term survival rate (to discharge) was 70.3% for all horses and 83.1% for those recovering from anaesthesia; for horses that had a single laparotomy it was 87.2%. The most common reasons for death/euthanasia in the post operative period after a single laparotomy were persistent pain/colic, post operative ileus and grass sickness. Horses with lesions involving the small intestine and caecum had lower survival rates (75.2 and 66.7%, respectively) than those with large colon or small colon lesions (89.9 and 100%, respectively). The survival rate for ischaemic/strangulating lesions (68.9%) was lower than for simple obstructions (90.5%).

CONCLUSIONS

Short-term survival of horses undergoing exploratory laparotomy for acute colic is dependent on many factors, including the nature of the underlying disease, cardiovascular status and post operative complications.

POTENTIAL RELEVANCE

These retrospective studies may be used as a basis for prospective studies assessing treatments that could ultimately improve survival and decrease complication rates.