Photo-CIDNP NMR spectroscopy of a heme-containing protein

There are relatively few examples of the application of photo-CIDNP NMR spectroscopy to chromophore-containing proteins. The most likely reason for this is that simultaneous absorption of light by the photosensitiser molecule and the protein chromophore reduces the effectiveness of the photochemical reaction that produces the observed nuclear polarisation. We present details of experiments performed on the air-oxidised form of a small cytochrome, from the thermophilic bacterium Hydrogenobacter thermophilus, using both the wild-type protein and apo and holo forms of a double alanine b-type mutant. We show that, along with the apo state, it is possible to generate CIDNP in the air-oxidised form of the b-type mutant, but not in the corresponding c-type cytochrome. This finding is supported by control experiments using horse-heart cytochrome c.

Validation of the GROMOS force-field parameter set 45Alpha3 against nuclear magnetic resonance data of hen egg lysozyme

The quality of molecular dynamics (MD) simulations of proteins depends critically on the biomolecular force field that is used. Such force fields are defined by force-field parameter sets, which are generally determined and improved through calibration of properties of small molecules against experimental or theoretical data. By application to large molecules such as proteins, a new force-field parameter set can be validated. We report two 3.5 ns molecular dynamics simulations of hen egg white lysozyme in water applying the widely used GROMOS force-field parameter set 43Alpha1 and a new set 45Alpha3. The two MD ensembles are evaluated against NMR spectroscopic data NOE atom-atom distance bounds, (3)J(NHalpha) and (3)J(alphabeta) coupling constants, and (15)N relaxation data. It is shown that the two sets reproduce structural properties about equally well. The 45Alpha3 ensemble fulfills the atom-atom distance bounds derived from NMR spectroscopy slightly less well than the 43Alpha1 ensemble, with most of the NOE distance violations in both ensembles involving residues located in loops or flexible regions of the protein. Convergence patterns are very similar in both simulations atom-positional root-mean-square differences (RMSD) with respect to the X-ray and NMR model structures and NOE inter-proton distances converge within 1.0-1.5 ns while backbone (3)J(HNalpha)-coupling constants and (1)H-(15)N order parameters take slightly longer, 1.0-2.0 ns. As expected, side-chain (3)J(alphabeta)-coupling constants and (1)H-(15)N order parameters do not reach full convergence for all residues in the time period simulated. This is particularly noticeable for side chains which display rare structural transitions. When comparing each simulation trajectory with an older and a newer set of experimental NOE data on lysozyme, it is found that the newer, larger, set of experimental data agrees as well with each of the simulations. In other words, the experimental data converged towards the theoretical result.

Asparagine and glutamine side-chain conformation in solution and crystal: a comparison for hen egg-white lysozyme using residual dipolar couplings

Experimental (15)N-(1)H and (1)H-(1)H residual dipolar couplings (RDCs) for the asparagine (Asn) and glutamine (Gln) side chains of hen egg-white lysozyme are measured and analysed in conjunction with (1)N relaxation data, information about chi(1) torsion angles in solution and molecular dynamics simulations. The RDCs are compared to values predicted from 16 high-resolution crystal structures. Two distinct groups of Asn and Gln side chains are identified. The first contains residues whose side chains show a fixed, relatively rigid, conformation in solution. For these residues there is good agreement between the experimental and predicted RDCs. This agreement improves when the experimental order parameter, S, is included in the calculation of the RDCs from the crystal structures. The comparison of the experimental RDCs with values calculated from the X-ray structures shows that the similarity between the oxygen and nitrogen electron densities is a limitation to the correct assignment of the Asn and Gln side-chain orientation in X-ray structures. In the majority of X-ray structures a 180 degrees rotation about chi(2) or chi(3), leading to the swapping of N(delta/epsilon 2) and O(delta/epsilon 1), is necessary for at least one Asn or Gln residue in order to achieve good agreement between experimental and predicted RDCs. The second group contains residues whose side chains do not adopt a single, well-defined, conformation in solution. These residues do not show a correlation between the experimental and predicted RDCs. In many cases the family of crystal structures shows a range of orientations for these side chains, but in others the crystal structures show a well-defined side-chain position. In the latter case, this is found to arise from crystallographic contacts and does not represent the behaviour of the side chain in solution.

Computational methods for generating models of denatured and partially folded proteins

Partially folded and denatured proteins can give important insights into protein folding, misfolding, and aggregation. Such non-native states of proteins are however very difficult to characterise in detail as they are dynamic, heterogeneous systems comprising of ensembles of interconverting conformers. This article describes methods that produce models for non-native proteins in atomic detail. A variety of molecular dynamics based protocols are discussed together with some recent procedures that include restraints from experimental data. These models provide an important framework for interpreting experimental data from studies of non-native states using nuclear magnetic resonance spectroscopy, fluorescence, circular dichroism, and small angle scattering techniques.

NMR Analysis Shows That a b-Type Variant of Hydrogenobacter thermophilus Cytochrome c552 Retains Its Native Structure

Conversion of Hydrogenobacter thermophilus cytochrome c(552) into a b-type cytochrome by mutagenesis of both heme-binding cysteines to alanines significantly reduces the stability of the protein (Tomlinson, E. J., and Ferguson, S. J. (2000) Proc. Natl. Acad. Sci. U. S. A. 97, 5156-5160). To understand the effects of this change on the structure and dynamics of the protein, hetero-nuclear (15)N-edited NMR techniques have been used to characterize this b-type variant. The backbone (15)N, (1)H(N), and (1)H(alpha), and (1)H(beta) resonances of the protein have been assigned. Analysis of (3)J(HN)alpha coupling constants, nuclear Overhauser enhancement intensities, and chemical shift index data demonstrates that the four alpha-helices present in the wild-type protein are retained in the b-type variant. Comparison of the chemical shifts for the b-type and wild-type proteins indicates that the tertiary structures of the two proteins are closely similar. Some subtle differences are, however, observed for residues in the N-terminal region and in the vicinity of the heme-binding pocket. Hydrogen exchange studies show that there are 25 backbone amide protons that exchange very slowly in the b-type variant and confirm that the fluctuations within the b-type protein are of a similar extent to those in the wild-type protein. These data demonstrate the notable retention of the native secondary structure and tertiary fold despite the absence of covalent linkages between the heme group and the protein.

A review of general hepatitis C virus lookbacks in Canada

BACKGROUND AND OBJECTIVES

This article reviews the Canadian experience with general hepatitis C virus (HCV) lookback programmes.

MATERIALS AND METHODS

Comprehensive literature searches were conducted in PubMed, Medline, HealthSTAR and EMBASE. In addition, bibliographic searches were performed on all retrieved articles, and provinces were contacted to determine whether they had performed general HCV lookbacks.

RESULTS

Of the seven Canadian general HCV lookbacks identified, two focused specifically on the paediatric population. The proportion of transfused patients presumed to be alive varied from 48.9 to 97.5%. Between 55.3 and 99.1% of letters were successfully delivered. The proportion of patients tested for HCV and subsequently found to be HCV positive varied considerably (66.2-80.4% and 0.9-5.0%, respectively). Newly diagnosed patients represented 42-58% of cases identified.

CONCLUSIONS

The Canadian general HCV lookback experience successfully identified previously undiagnosed HCV-positive patients, but the resources required to notify patients are high and the yield is relatively low. The effectiveness may be greatest in the paediatric population.

Effect of high-dose vitamins, coenzyme Q and high-fat diet in paediatric patients with mitochondrial diseases

We reviewed the medical records of all patients with confirmed mitochondrial diseases treated with any or all of thiamin, riboflavin, coenzyme Q, vitamin C (approximately 10 mg/kg per day) and a high-fat diet (50-60% of caloric intake) between 1997 and 2003. There were 15 patients (9 male): 10 had enzymatic deficiency and 10 had a molecular diagnosis. Age at diagnosis was 11 months to 17 years 10 months. Treatment was commenced at time of clinical diagnosis in 12 patients. Follow-up period was 3 days to 7 years (median 22 months). Improvement was reported in 9 patients, of whom 4 attained further developmental skills, but this was only temporary in 6 patients. Five patients died during the follow-up period (3 days to 7 years). Patients with the 3243A > G mutation showed no significant change in the course of their disease, except for fewer migraine attacks. Of the six patients who had seizures, one has had a significant reduction in the severity of the seizures and one has had no further seizures. Plasma lactate levels were noncontributory. We conclude that high-dose vitamin and cofactor treatment and, where applicable, high-fat diet, are well tolerated and possibly effective in the short term, but ineffective in the longer term.

Stimulation and inhibition of fibril formation by a peptide in the presence of different concentrations of SDS

Sodium dodecyl sulphate (SDS), a detergent that mimics some characteristics of biological membranes, has been found to affect significantly fibril formation by a peptide from human complement receptor 1. In aqueous solution the peptide is unfolded but slowly aggregates to form fibrils. In sub-micellar concentrations of SDS the peptide is initially alpha-helical but converts rapidly to a beta-sheet structure and large quantities of fibrils form. In SDS above the critical micellar concentration the peptide adopts a stable alpha-helical structure and no fibrils are observed. These findings demonstrate the sensitivity of fibril formation to solution conditions and suggest a possible role for membrane components in amyloid fibril formation in living systems.

A non-aphid-transmissible isolate of bean yellow mosaic potyvirus has an altered NAG motif in its coat protein

An isolate of Bean yellow mosaic virus (BYMV) not transmitted by aphids (NAT) was compared with the aphid-transmissible isolate (MI) from which it was derived. For each isolate, the sequence of the coat protein and parts of the helper component was determined. A single nucleotide substitution caused a NAG to NAS alteration in the coat protein of the non aphid-transmissible isolate. Loss of aphid transmissibility in isolate BYMV(MI)-NAT was most likely caused by this mutation within the NAG motif. Systemic movement and accumulation of the virus in infected plants were not affected by the mutation.

Assessing equilibration and convergence in biomolecular simulations

If molecular dynamics simulations are used to characterize the folding of peptides or proteins, a wide range of conformational states needs to be sampled. This study reports an analysis of peptide simulations to identify the best methods for assessing equilibration and sampling in these systems where there is significant conformational disorder. Four trajectories of a beta peptide in methanol and four trajectories of an alpha peptide in water, each of 5 ns in length, have been studied. Comparisons have also been made with two 50-ns trajectories of the beta peptide in methanol. The convergence rates of quantities that probe both the extent of conformational sampling and the local dynamical properties have been characterized. These include the numbers of hydrogen bonds populated, clusters identified, and main chain torsion angle transitions in the trajectories. The relative equilibrium rates of different quantities are found to vary significantly between the two systems studied reflecting both the differences in peptide primary structure and the different solvents used. A cluster analysis of the simulation trajectories is identified as a very effective method for judging the convergence of the simulations. This is particularly the case if the analysis includes a comparison of multiple trajectories calculated for the same system from different starting structures.

Long-range interactions within a nonnative protein

Protein folding and unfolding are coupled to a range of biological phenomena, from the regulation of cellular activity to the onset of neurodegenerative diseases. Defining the nature of the conformations sampled in nonnative proteins is crucial for understanding the origins of such phenomena. We have used a combination of nuclear magnetic resonance (NMR) spectroscopy and site-directed mutagenesis to study unfolded states of the protein lysozyme. Extensive clusters of hydrophobic structure exist within the wild-type protein even under strongly denaturing conditions. These clusters involve distinct regions of the sequence but are all disrupted by a single point mutation that replaced residue Trp62 with Gly located at the interface of the two major structural domains in the native state. Thus, nativelike structure in the denatured protein is stabilized by the involvement of Trp62 in nonnative and long-range interactions.

Entropy calculations on the molten globule state of a protein: side-chain entropies of alpha-lactalbumin

We present entropy estimates based on molecular dynamics simulations of models of the molten globule state of the protein alpha-lactalbumin at low pH. The entropy calculations use the covariance matrix of atom-positional fluctuations and yield the complete configurational entropy. The configurational entropy of the entire protein and of each of its side chains is calculated. Exposed side chains show a larger entropy compared to buried side chains. A comparison to data from rotamer counting is made and significant differences are found.

The cytochrome c fold can be attained from a compact apo state by occupancy of a nascent heme binding site

NMR techniques and 8-anilino-1-napthalenesulphonate (ANS) binding studies have been used to characterize the apo state of a variant of cytochrome c(552) from Hydrogenobacter thermophilus. In this variant the two cysteines that form covalent thioether linkages to the heme group have been replaced by alanine residues (C11A/C14A). CD studies show that the apo state contains approximately 14% helical secondary structure, and measurements of hydrodynamic radii using pulse field gradient NMR methods show that it is compact (R(h), 16.6 A). The apo state binds 1 mol of ANS/mol of protein, and a linear reduction in fluorescence enhancement is observed on adding aliquots of hemin to a solution of apo C11A/C14A cytochrome c(552) with ANS bound. These results suggest that the bound ANS is located in the heme binding pocket, which would therefore be at least partially formed in the apo state. Consistent with these characteristics, the formation of the holo state of the variant cytochrome c(552) from the apo state on the addition of heme has been demonstrated using NMR techniques. The properties of the apo state of C11A/C14A cytochrome c(552) reported here contrast strongly with those of mitochondrial cytochrome c whose apo state resembles a random coil under similar conditions.

Comparative efficacy of inhaled corticosteroids and antileukotriene drugs in asthma

Asthma is an inflammatory disease of the airways that is best treated by minimising exposure to factors that provoke the inflammation (e.g. allergens) and by administering drugs that reduce the inflammatory response. The cornerstone of asthma treatment is inhaled corticosteroids. Their effectiveness is a result of their potent and broad anti-inflammatory properties. Antileukotriene drugs (leukotriene modifiers) provide an alternative and novel approach to the treatment of asthma. The novelty of these new compounds is that their effectiveness is firmly based on the pathophysiology of asthma, specifically the role played by the cysteinyl leukotrienes. At the same time, the availability of the antileukotriene drugs has stirred debate over when they should be used and how they compare to inhaled corticosteroids. Although the answers are not fully known at this time, the currently available published and presented data are adequate for us to draw some conclusions about their relative effectiveness and role in asthma treatment. The antileukotriene drugs are more effective than placebo, but they are not as effective as inhaled corticosteroids in improving lung function [measured as the forced expiratory volume in 1 second (FEV(1)) or peak expiratory flow rate (PEFR)], reducing beta(2)-agonist use, and decreasing symptom-free days. In contrast, they may have similar beneficial effects on reducing asthma exacerbations and decreasing peripheral blood eosinophil counts. In the absence of knowing a priori the response of an individual patient to treatment with either therapy, the data favour initiating treatment with an inhaled corticosteroid. However, for patients with mild to moderate disease there are a number of circumstances that support using an antileukotriene drug first. A few examples are aspirin intolerance, predominantly exercise-induced symptoms and problems with using an inhaler or the adverse effects of inhaled corticosteroids such as dysphonia and thrush. For patients with more severe disease, inhaled corticosteroids remain the treatment of choice. Antileukotriene drugs should be considered as add-on therapy, especially in view of their possible complementary effects on reducing airway inflammation.

Amyloid fibril formation by a helical cytochrome

The substitution of alanines for the two cysteines which form thioether linkages to the haem group in cytochrome c(552) from Hydogenobacter thermophilus destabilises the native protein fold. The holo form of this variant slowly converts into a partially folded apo state that over prolonged periods of time aggregates into fibrillar structures. Characterisation of these structures by electron microscopy and thioflavin-T binding assays shows that they are amyloid fibrils. The data demonstrate that when the native state of this cytochrome is destabilised by loss of haem, even this highly alpha-helical protein can form beta-sheet structures of the type most commonly associated with protein deposition diseases.

Structure of alkaloid 275A, a novel 1-azabicyclo[5.3.0]decane from a dendrobatid frog, Dendrobates lehmanni: synthesis of the tetrahydrodiastereomers

The principal alkaloid 275A in skins of the Colombian poison frog Dendrobates lehmanni has been identified as the pyrrolo[1,2-a]azepane (1), the first occurrence in nature of this "izidine" system. Tetrahydro-1 proved identical to one of the four synthetic diastereomers, 2a--2d, thereby establishing that 1 has the 5Z,10E relative stereochemistry. Alkaloid 1 is often accompanied by other congeners, in particular a 5Z,10Z diastereomer 15, a dihydro analogue 16, and a ketone 17. Such izidines in frogs may arise from dietary ants, as do other classes of izidines.