Symptoms and impacts of ambulatory nonsense mutation Duchenne muscular dystrophy: a qualitative study and the development of a patient-centred conceptual model

Background

Duchenne muscular dystrophy is a rare genetic neuromuscular disorder, which can result in early death due to disease progression. Ataluren is indicated for the treatment of nonsense mutation Duchenne muscular dystrophy, in ambulatory individuals aged two years and older. This study explored the symptoms and impacts of nonsense mutation Duchenne muscular dystrophy and experience with ataluren.

Methods

Qualitative interviews were conducted with caregivers in the UK. Interviews were conducted by telephone, were recorded and transcribed. Data were analysed using thematic analysis and saturation was recorded.

Results

Ten interviews were conducted with parents of individuals aged 4–19 years. Key symptoms included muscle weakness and muscle breakdown, which were associated with limitations in physical function and pain. These impacted individuals’ daily activities, social activities and emotional wellbeing. These concepts and relationships were illustrated in a conceptual model, along with positive and negative moderating factors. Experience with ataluren and changes since initiation with treatment were discussed.

Conclusion

Individuals with nonsense mutation Duchenne muscular dystrophy experience a range of interrelated symptoms and functional issues which impact their broader health-related quality of life. Treatments which address this high unmet need have the potential to improve the health-related quality of life of these individuals.

Supplementary Information

The online version contains supplementary material available at 10.1186/s41687-021-00341-x.

A qualitative study on the impact of caring for an ambulatory individual with nonsense mutation Duchenne muscular dystrophy

Background

Duchenne muscular dystrophy is a rare genetic neuromuscular disorder, which can result in early death due to disease progression. Ataluren is indicated for the treatment of nonsense mutation Duchenne muscular dystrophy, in ambulatory individuals aged two years and older. This study explored the impact of caring for an ambulatory individual with nonsense mutation Duchenne muscular dystrophy, as well as the impact of treatment with ataluren on the caregiver experience, using retrospective recall.

Methods

Qualitative interviews were conducted with caregivers in the UK. Interviews were conducted by telephone, were recorded and transcribed. Data were analysed using thematic analysis and saturation was recorded.

Results

Ten interviews were conducted with parents of individuals aged 4–19 years. Caregivers reported proximal impacts (physical, emotional, time-related), and distal impacts (work, relationships, social life) of caring for their sons. The relationships between these impacts were illustrated in a conceptual model. Changes to the caregiver experience since initiation with their son’s treatment were discussed.

Conclusion

Caring for an ambulatory individual with nonsense mutation Duchenne muscular dystrophy has a substantial multifaceted impact on caregivers. Treatments which have the potential to improve symptoms or delay progression, may also have a positive impact on the quality of life of caregivers.

Supplementary Information

The online version contains supplementary material available at 10.1186/s41687-021-00344-8.

Algebraic expressions for Carr-Purcell-Meiboom-Gill relaxation dispersion for N-site chemical exchange

The Carr-Purcell-Meiboom-Gill (CPMG) NMR relaxation dispersion experiment measures the effective relaxation rate constant during a train of spin-echo pulse sequence elements as a function of the echo time. The CPMG experiment is a powerful method for characterizing chemical and conformational dynamic processes, termed chemical and conformational exchange, on μs-ms time scales, comparable to the experimentally accessible echo times. Approximate theoretical expressions for the effective relaxation rate constant for N-site chemical exchange have been reported (H. Koss, M. Rance, and A. G. Palmer, Biochemistry 57, 4753-4763 (2018)). Expressions for the effective relaxation rate constant have been improved by using the Cayley-Hamilton theorem to obtain simple and accurate approximations of the average Liouvillian for the CPMG experiment. The improved accuracy of the results allows efficient analyses of experimental data. In addition, the relationship is clarified between the approach of Koss and coworkers and that of Jen (1978).

Compact expressions for R1ρ relaxation for N-site chemical exchange using Schur decomposition

The rotating-frame spin relaxation rate constant, R_1ρ, is a powerful probe of macromolecular chemical and conformational dynamics in relaxation dispersion, CEST, and DEST NMR experiments. The R_1ρ relaxation rate constant is given by the absolute value of the largest (least negative) eigenvalue of the Bloch-McConnell evolution matrix; however, estimation of this eigenvalue require inversion of 3 N × 3 N dimensional matrices, in which N is the number of interconverting sites or states for a given nuclear spin in a molecule. The Schur complement is used to reduce the problem of calculating the characteristic polynomial of a 3 N × 3 N matrix to that of calculating the characteristic polynomial of a 3 × 3 matrix. The resulting expressions for N-site chemical exchange are more numerically tractable, because the largest matrix inversion also is of dimension 3 × 3. In addition, the simplifications offered by the Schurr complement conveniently illustrate the effects of fast or slow kinetic steps within an N-site kinetic topology.

Effect of monovalent ion binding on molecular dynamics of the S100-family calcium-binding protein calbindin D9k

Calbindin D_9k is a member of the S100 subfamily of EF-hand calcium binding proteins, and has served as an important model system for biophysical studies. The fast timescale dynamics of the calcium-free (apo) state is characterized using molecular dynamics simulations. Order parameters for the backbone NH bond vectors are determined from the simulations and compared with experimentally derived values, with a focus on the dynamics of calcium-binding site I. There is a significant discrepancy between simulated and experimental order parameters for site I residues in the case of no ion bound in site I. However, it was found in the simulations that a Na⁺ ion can bind in site I, and the resulting order parameters determined from the simulations are in excellent agreement with experiment. Comparisons are made to X-ray structures of other S100 family members in which Na⁺ ions were observed or suggested to be bound in site I. © 2019 Wiley Periodicals, Inc.

Defining a Canonical Ligand-Binding Pocket in the Orphan Nuclear Receptor Nurr1

Nuclear receptor-related 1 protein (Nurr1/NR4A2) is an orphan nuclear receptor (NR) that is considered to function without a canonical ligand-binding pocket (LBP). A crystal structure of the Nurr1 ligand-binding domain (LBD) revealed no physical space in the conserved region where other NRs with solvent accessible apo-protein LBPs bind synthetic and natural ligands. Using solution nuclear magnetic resonance spectroscopy, hydrogen/deuterium exchange mass spectrometry, and molecular dynamics simulations, we show that the putative canonical Nurr1 LBP is dynamic with high solvent accessibility, exchanges between two or more conformations on the microsecond-to-millisecond timescale, and can expand from the collapsed crystallized conformation to allow binding of unsaturated fatty acids. These findings should stimulate future studies to probe the ligandability and druggability of Nurr1 for both endogenous and synthetic ligands, which could lead to new therapeutics for Nurr1-related diseases, including Parkinson's disease and schizophrenia.

General Expressions for Carr-Purcell-Meiboom-Gill Relaxation Dispersion for N-Site Chemical Exchange

The Carr-Purcell-Meiboom-Gill (CPMG) nuclear magnetic resonance experiment is widely used to characterize chemical exchange phenomena in biological macromolecules. Theoretical expressions for the nuclear spin relaxation rate constant for two-site chemical exchange during CPMG pulse trains valid for all time scales are well-known as are descriptions of N-site exchange in the fast limit. We have obtained theoretical expressions for N-site exchange outside of the fast limit by using approximations to an average Liouvillian describing the decay of magnetization during a CPMG pulse train. We obtain general expressions for CPMG experiments for any N-site scheme and all experimentally accessible time scales. For sufficiently slow chemical exchange, we obtain closed-form expressions for the relaxation rate constant and a general characteristic polynomial for arbitrary kinetic schemes. Furthermore, we highlight features that qualitatively characterize CPMG curves obtained for various N-site kinetic topologies, quantitatively characterize CPMG curves obtained from systems in various N-site exchange situations, and test distinguishability of kinetic models.

Lysine Side-Chain Dynamics in the Binding Site of Homeodomain/DNA Complexes As Observed by NMR Relaxation Experiments and Molecular Dynamics Simulations

An important but poorly characterized contribution to the thermodynamics of protein-DNA interactions is the loss of entropy that occurs from restricting the conformational freedom of amino acid side chains. The effect of restricting the flexibility of several side chains at a protein-DNA interface may be comparable in many cases to the other factors that determine the binding thermodynamics and may, therefore, play a key role in dictating the binding affinity and/or specificity. Because the entropic contributions, including the presence and influence of side-chain dynamics, are especially difficult to estimate based on structural information, it is important to pursue experimental and theoretical studies that can provide direct information regarding these issues. We report on studies of a model system, the homeodomain/DNA complex, focusing on the Lys50 class of homeodomains where a key lysine residue in position 50 was shown previously to be critical for binding site specificity. NMR methodology was employed for determining the dynamics of lysine side-chain amino groups via 15N relaxation measurements in the Lys50-class homeodomains from the Drosophila protein Bicoid and the human protein Pitx2. In the case of Pitx2, complexes with both a consensus and a nonconsensus DNA binding site were examined. NMR-derived order parameters indicated moderate to substantial conformational freedom for the lysine NH3+ group in the complexes studied. To complement the experimental NMR measurements, molecular dynamics simulations were performed for the consensus complexes to gain further, detailed insights regarding the dynamics of the Lys50 side chain and other important residues in the protein-DNA interface.

General expressions for R1ρ relaxation for N-site chemical exchange and the special case of linear chains

Exploration of dynamic processes in proteins and nucleic acids by spin-locking NMR experiments has been facilitated by the development of theoretical expressions for the R_1ρ relaxation rate constant covering a variety of kinetic situations. Herein, we present a generalized approximation to the chemical exchange, R_ex, component of R_1ρ for arbitrary kinetic schemes, assuming the presence of a dominant major site population, derived from the negative reciprocal trace of the inverse Bloch-McConnell evolution matrix. This approximation is equivalent to first-order truncation of the characteristic polynomial derived from the Bloch-McConnell evolution matrix. For three- and four-site chemical exchange, the first-order approximations are sufficient to distinguish different kinetic schemes. We also introduce an approach to calculate R_1ρ for linear N-site schemes, using the matrix determinant lemma to reduce the corresponding 3N×3N Bloch-McConnell evolution matrix to a 3×3 matrix. The first- and second order-expansions of the determinant of this 3×3 matrix are closely related to previously derived equations for two-site exchange. The second-order approximations for linear N-site schemes can be used to obtain more accurate approximations for non-linear N-site schemes, such as triangular three-site or star four-site topologies. The expressions presented herein provide powerful means for the estimation of R_ex contributions for both low (CEST-limit) and high (R_1ρ-limit) radiofrequency field strengths, provided that the population of one state is dominant. The general nature of the new expressions allows for consideration of complex kinetic situations in the analysis of NMR spin relaxation data.

Cost-effectiveness of linaclotide compared to antidepressants in the treatment of irritable bowel syndrome with constipation in Scotland

Presently, linaclotide is the only EMA-approved therapy indicated for the treatment of irritable bowel syndrome with constipation (IBS-C). This study sought to determine the cost-effectiveness of linaclotide compared to antidepressants for the treatment of adults with moderate to severe IBS-C who have previously received antispasmodics and/or laxatives. A Markov model was created to estimate costs and QALYs over a 5-year time horizon from the perspective of NHS Scotland. Health states were based on treatment satisfaction (satisfied, moderately satisfied, not satisfied) and mortality. Transition probabilities were based on satisfaction data from the linaclotide pivotal studies and Scottish general all-cause mortality statistics. Treatment costs were calculated from the British National Formulary. NHS resource use and disease-related costs for each health state were estimated from Scottish clinician interviews in combination with NHS Reference costs. Quality of life was based on EQ-5D data collected from the pivotal studies. Costs and QALYs were discounted at 3.5 % per annum. Uncertainty was explored through extensive deterministic and probabilistic sensitivity analyses. Over a 5-year time horizon, the additional costs and QALYs generated with linaclotide were £659 and 0.089, resulting in an incremental cost-effectiveness ratio of £7370 per QALY versus antidepressants. Based on the probabilistic sensitivity analysis, the likelihood that linaclotide was cost-effective at a willingness to pay of £20,000 per QALY was 73 %. Linaclotide can be a cost-effective treatment for adults with moderate-to-severe IBS-C who have previously received antispasmodics and/or laxatives in Scotland.

Burden of irritable bowel syndrome in an increasingly cost-aware National Health Service

BACKGROUND

The National Health Service (NHS) is faced with increasing cost pressures that make the efficient use of resources paramount. Irritable bowel syndrome (IBS) places a large burden on the NHS as it has been estimated that at least 12% of the UK population is affected. However, poor clinical coding makes accurate assessment of this burden challenging.

OBJECTIVE

To calculate primary-care prescribing and both hospital outpatient and admission costs associated with the management of IBS in England.

DESIGN AND MAIN OUTCOME MEASURES

Hospital Episode Statistics data for 2012-2013 for all clinical commissioning groups in England were analysed to calculate the tariff cost of IBS. Prescribing analysis and cost tabulation (PACT) data for this period were also analysed.

RESULTS

In 2012-2013, there were 1 219 961 outpatient attendances in gastroenterology and colorectal surgery specialties. Despite this, only 1982 patients were recorded with IBS-specific codes, with a total estimated tariff cost of £812 336. In addition, 28 849 patients were recorded with IBS-related symptom codes at a cost of £11 002 874. In 2011-2012, there were 658 698 diagnostic lower gastrointestinal endoscopies at a tariff cost of £16 967 670 4. Of these, 323 752 (49%) had no further follow-up in secondary care over the subsequent 12 months. PACT data indicated that £44 977 959 and £25 582 752, respectively, were spent on selected laxatives and antispasmodics commonly used to treat IBS in primary care.

CONCLUSIONS

Better diagnosing, through improved clinical coding and standardisation of diagnostic criteria, is required to more accurately assess the true burden and allow optimal management of IBS.

Targeting substrate-site in Jak2 kinase prevents emergence of genetic resistance

Emergence of genetic resistance against kinase inhibitors poses a great challenge for durable therapeutic response. Here, we report a novel mechanism of JAK2 kinase inhibition by fedratinib (TG101348) that prevents emergence of genetic resistance. Using in vitro drug screening, we identified 211 amino-acid substitutions conferring resistance to ruxolitinib (INCB018424) and cross-resistance to the JAK2 inhibitors AZD1480, CYT-387 and lestaurtinib. In contrast, these resistant variants were fully sensitive to fedratinib. Structural modeling, coupled with mutagenesis and biochemical studies, revealed dual binding sites for fedratinib. In vitro binding assays using purified proteins showed strong affinity for the substrate-binding site (K_d = 20 nM) while affinity for the ATP site was poor (K_d = ~8 μM). Our studies demonstrate that mutations affecting the substrate-binding pocket encode a catalytically incompetent kinase, thereby preventing emergence of resistant variants. Most importantly, our data suggest that in order to develop resistance-free kinase inhibitors, the next-generation drug design should target the substrate-binding site.

Structural mechanism for signal transduction in RXR nuclear receptor heterodimers

A subset of nuclear receptors (NRs) function as obligate heterodimers with retinoid X receptor (RXR), allowing integration of ligand-dependent signals across the dimer interface via an unknown structural mechanism. Using nuclear magnetic resonance (NMR) spectroscopy, x-ray crystallography and hydrogen/deuterium exchange (HDX) mass spectrometry, here we show an allosteric mechanism through which RXR co-operates with a permissive dimer partner, peroxisome proliferator-activated receptor (PPAR)-γ, while rendered generally unresponsive by a non-permissive dimer partner, thyroid hormone (TR) receptor. Amino acid residues that mediate this allosteric mechanism comprise an evolutionarily conserved network discovered by statistical coupling analysis (SCA). This SCA network acts as a signalling rheostat to integrate signals between dimer partners, ligands and coregulator-binding sites, thereby affecting signal transmission in RXR heterodimers. These findings define rules guiding how NRs integrate two ligand-dependent signalling pathways into RXR heterodimer-specific responses.

Some nuclear receptors dimerize with retinoid X receptor to allow ligand-dependent signalling. Here, Kojetin et al. use structural and biophysical techniques to identify structural changes that guide these complex signalling networks.

Effects of interleukin-10 on cutaneous wounds and scars in humans of African continental ancestral origin

Scars in humans of African continental ancestry heal with an exaggerated inflammatory response and a generally wider scar. Interleukin-10 is an anti-inflammatory and antifibrotic cytokine. A randomized controlled trial in Caucasians found that exogenous interleukin-10 resulted in improved macroscopic scar appearance and reduced scar redness. We investigated the effects of interleukin-10 on cutaneous scarring in volunteers of African ancestral origin in an exploratory, single-center, within-subject, double-blind randomized controlled trial. Fifty-six subjects received two of four potential prerandomized concentrations of interleukin-10 (5, 25, 100, and 250 ng/100 µL) in two full-thickness incisions on the upper inner arms. Anatomically matching incisions on the contralateral arm were treated with placebo. Scars were excised at 1 month for histological analysis and were redosed with the same regimen. Resultant excision scars were followed up for 12 months for scar width measurement and scoring. Scoring was performed by trial doctors, subjects, and a panel. Incisions treated with 100 ng/100 µL interleukin-10 had significantly reduced microscopic scar widths. Incisions treated with 5 and 25 ng/100 µL interleukin-10 were also narrower, but not significantly. There were no differences observed in pro-inflammatory or pro-fibrotic markers between interleukin-10 and placebo treatment. There was no long-term evidence that 100 ng/100 µL interleukin-10 had a therapeutic effect on macroscopic scar width or appearance, as excisions treated with this concentration were significantly wider than placebo between 8 and 12 months of maturation. Doctors showed a trend toward favoring the macroscopic appearance of placebo-treated excisions compared with those treated with 250 ng/100 µL interleukin-10. Panelists scored placebo-treated excisions as significantly better-appearing than those treated with 250 ng/100 µL interleukin-10. Doctors' scores showed a trend toward favoring treatment with 5 ng/100 µL interleukin-10 at 10 and 11 months post-excision. Subjects showed a trend toward favoring treatment with 5 ng/100 µL interleukin-10 between 5 and 9 months postexcision. Analysis of images of markedly improved scars revealed a potential subset of responders among those treated with 5 ng/100 µL interleukin-10. No concentration of interleukin-10 produced a statistically significant improvement in scarring compared with placebo.

Rotation operator propagators for time-varying radiofrequency pulses in NMR spectroscopy: applications to shaped pulses and pulse trains

The propagator for trains of radiofrequency pulses can be directly integrated numerically or approximated by average Hamiltonian approaches. The former provides high accuracy and the latter, in favorable cases, convenient analytical formula. The Euler-angle rotation operator factorization of the propagator provides insights into performance that are not as easily discerned from either of these conventional techniques. This approach is useful in determining whether a shaped pulse can be represented over some bandwidth by a sequence τ1-Rϕ(β)-τ2, in which Rϕ(β) is a rotation by an angle β around an axis with phase ϕ in the transverse plane and τ1 and τ2 are time delays, allowing phase evolution during the pulse to be compensated by adjusting time periods prior or subsequent to the pulse. Perturbation theory establishes explicit formulas for τ1 and τ2 as proportional to the average transverse magnetization generated during the shaped pulse. The Euler-angle representation of the propagator also is useful in iterative reduction of pulse-interrupted-free precession schemes. Application to Carr-Purcell-Meiboom-Gill sequences identifies an eight-pulse phase alternating scheme that generates a propagator nearly equal to the identity operator.

Ligand and receptor dynamics contribute to the mechanism of graded PPARγ agonism

Ligand binding to proteins is not a static process, but rather involves a number of complex dynamic transitions. A flexible ligand can change conformation upon binding its target. The conformation and dynamics of a protein can change to facilitate ligand binding. The conformation of the ligand, however, is generally presumed to have one primary binding mode, shifting the protein conformational ensemble from one state to another. We report solution nuclear magnetic resonance (NMR) studies that reveal peroxisome proliferator-activated receptor γ (PPARγ) modulators can sample multiple binding modes manifesting in multiple receptor conformations in slow conformational exchange. Our NMR, hydrogen/deuterium exchange and docking studies reveal that ligand-induced receptor stabilization and binding mode occupancy correlate with the graded agonist response of the ligand. Our results suggest that ligand and receptor dynamics affect the graded transcriptional output of PPARγ modulators.

¹H, ¹³C and ¹⁵N chemical shift assignments for the human Pitx2 homeodomain in complex with a 22-base hairpin DNA

As one of the most important eukaryotic DNA-binding motifs, the homeodomain has been identified in over one thousand proteins. Transcription factors containing homeodomains play critical roles in diverse biological processes and are often implicated in human genetic disorders. The human Pitx2 protein is a central downstream transcription factor in both the TGF-β and Wnt/β-catenin signaling pathways, and involved in the regulation of cell differentiation, cell pattern formation and tissue maintenance. To better understand how Pitx2 regulates its target genes, we are investigating the mechanisms that confer DNA-binding specificity on its homeodomain. Here, we report complete (1)H, (13)C and (15)N protein chemical shift assignments of the human Pitx2 homeodomain in complex with a non-consensus DNA sequence.

Structural and biophysical insights into the ligand-free Pitx2 homeodomain and a ring dermoid of the cornea inducing homeodomain mutant

The homeodomain-containing transcription factor Pitx2 (pituitary homeobox protein 2) is present in many developing embryonic tissues, including the heart. Its homeodomain is responsible for the recognition and binding to target DNA sequences and thus constitutes a major functional unit in the Pitx2 protein. Nuclear magnetic resonance techniques were employed to determine the solution structure of the native Pitx2 homeodomain and a R24H mutant that causes autosomal dominantly inherited ring dermoid of the cornea syndrome. The structures reveal that both isoforms possess the canonical homeodomain fold. However, the R24H mutation results in a 2-fold increase in DNA binding affinity and a 5 °C decrease in thermal stability, while changing the dynamic environment of the homeodomain only locally. When introduced into full-length Pitx2c, the mutation results in an only 25% loss of transactivation activity. Our data correlate well with clinical observations suggesting a milder deficiency for the R24H mutation compared to those of other Pitx2 homeodomain mutations.

1H, 13C and 15N chemical shift assignments for the human Pitx2 homeodomain and a R24H homeodomain mutant

The homeodomain is one of the most important eukaryotic DNA-binding motifs and has been identified in over one thousand proteins. Homeodomain proteins play critical roles in diverse biological processes, including cell differentiation and cell pattern formation. The human Pitx2 homeodomain binds several different DNA sequences and is a pivotal component of both the TGF-β and Wnt/β-catenin signaling pathways. As the recognition of specific DNA sequences represents an essential biochemical function of all DNA-binding proteins, we have chosen the Pitx2 homeodomain model to investigate the mechanisms that convey biological specificity in these protein-DNA interactions. Here, we report complete chemical shift assignments of the human Pitx2 homeodomain and the R24H mutation that induces ring dermoid of the cornea syndrome.

Observing selected domains in multi-domain proteins via sortase-mediated ligation and NMR spectroscopy

NMR spectroscopy has distinct advantages for providing insight into protein structures, but faces significant resolution challenges as protein size increases. To alleviate such resonance overlap issues, the ability to produce segmentally labeled proteins is beneficial. Here we show that the S. aureus transpeptidase sortase A can be used to catalyze the ligation of two separately expressed domains of the same protein, MecA (B. subtilis). The yield of purified, segmentally labeled MecA protein conjugate is approximately 40%. The resultant HSQC spectrum obtained from this domain-labeled conjugate demonstrates successful application of sortase A for segmental labeling of multi-domain proteins for solution NMR study.

Protein side-chain dynamics and residual conformational entropy

Changes in residual conformational entropy of proteins can be significant components of the thermodynamics of folding and binding. Nuclear magnetic resonance (NMR) spin relaxation is the only experimental technique capable of probing local protein entropy, by inference from local internal conformational dynamics. To assess the validity of this approach, the picosecond-to-nanosecond dynamics of the arginine side-chain N(epsilon)-H(epsilon) bond vectors of Escherichia coli ribonuclease H (RNase H) were determined by NMR spin relaxation and compared to the mechanistic detail provided by molecular dynamics (MD) simulations. The results indicate that arginine N(epsilon) spin relaxation primarily reflects persistence of guanidinium salt bridges and correlates well with simulated side-chain conformational entropy. In particular cases, the simulations show that the aliphatic part of the arginine side chain can retain substantial disorder while the guanidinium group maintains its salt bridges; thus, the N(epsilon)-H(epsilon) bond-vector orientation is conserved and side-chain flexibility is concealed from N(epsilon) spin relaxation. The MD simulations and an analysis of a rotamer library suggest that dynamic decoupling of the terminal moiety from the remainder of the side chain occurs for all five amino acids with more than two side-chain dihedral angles (R, K, E, Q, and M). Dynamic decoupling thus may represent a general biophysical strategy for minimizing the entropic penalties of folding and binding.

Structural and motional contributions of the Bacillus subtilis ClpC N-domain to adaptor protein interactions

The AAA(+) (ATPases associated with a variety of cellular activities) superfamily protein ClpC is a key regulator of cell development in Bacillus subtilis. As part of a large oligomeric complex, ClpC controls an array of cellular processes by recognizing, unfolding, and providing misfolded and aggregated proteins as substrates for the ClpP peptidase. ClpC is unique compared to other HSP100/Clp proteins, as it requires an adaptor protein for all fundamental activities. The NMR solution structure of the N-terminal repeat domain of ClpC (N-ClpCR) comprises two structural repeats of a four-helix motif. NMR experiments used to map the MecA adaptor protein interaction surface of N-ClpCR reveal that regions involved in the interaction possess conformational flexibility and conformational exchange on the microsecond-to-millisecond timescale. The electrostatic surface of N-ClpCR differs substantially from the N-domain of Escherichia coli ClpA and ClpB, suggesting that the electrostatic surface characteristics of HSP100/Clp N-domains may play a role in adaptor protein and substrate interaction specificity, and perhaps contribute to the unique adaptor protein requirement of ClpC.

Insights into the nature of DNA binding of AbrB-like transcription factors

Understanding the DNA recognition and binding by the AbrB-like family of transcriptional regulators is of significant interest since these proteins enable bacteria to elicit the appropriate response to diverse environmental stimuli. Although these "transition-state regulator" proteins have been well characterized at the genetic level, the general and specific mechanisms of DNA binding remain elusive. We present RDC-refined NMR solution structures and dynamic properties of the DNA-binding domains of three Bacillus subtilis transition-state regulators: AbrB, Abh, and SpoVT. We combined previously investigated DNase I footprinting, DNA methylation, gel-shift assays, and mutagenic and NMR studies to generate a structural model of the complex between AbrBN(55) and its cognate promoter, abrB8. These investigations have enabled us to generate a model for the specific nature of the transition-state regulator-DNA interaction, a structure that has remained elusive thus far.

NMR assignment of the N-terminal repeat domain of Bacillus subtilis ClpC

The HSP100/AAA+ superfamily protein ClpC is a key regulator of cell development in Bacillus subtilis. We present here the backbone and side-chain assignments of the N-terminal repeat domain (residues 1-145) of ClpC from Bacillus subtilis.

Temperature dependence of the NMR generalized order parameter

The study of protein conformational dynamics is motivated in large part by a desire to understand the forces present at different sites throughout the molecular structure. The generalized order parameter determined by NMR spectroscopy has played a central role in the study of protein dynamics on the picosecond-nanosecond time scale. A modeling procedure is presented for analysis of the temperature dependence of the generalized order parameter that extends a previous analysis (Massi and Palmer, J Am Chem Soc 2003;125:11158-11159). As part of this procedure, the potential of mean force is characterized for the N-H bond vectors of the protein backbone. This procedure accounts for the observed temperature dependence of the generalized order parameter in a representative data set from the B1 domain of Streptococcal protein G (Seewald, Pichumani, Stowell, Tibbals, Regan, and Stone, Protein Sci 2000;9:1177-1193). The results indicate a general trend, in which the force constants associated with the potential of mean force decrease with increasing temperature. The analysis also provides evidence for variations in the potential of mean force for different secondary structural elements.

Protein requirements in male adolescent soccer players

Few investigations have studied protein metabolism in children and adolescent athletes which makes difficult the assessment of daily recommended dietary protein allowances in this population. The problematic in paediatric competitors is the determination of additional protein needs resulting from intensive physical training. The aim of this investigation was to determine protein requirement in 14-year-old male adolescent soccer players. Healthy male adolescent soccer players (N = 11, 13.8 +/- 0.1 year) participated in a short term repeated nitrogen balance study. Diets were designed to provide proteins at three levels: 1.4, 1.2 and 1.0 g protein per kg body weight (BW). Nutrient and energy intakes were assessed from 4 day food records corresponding to 4 day training periods during 3 weeks. Urine was collected during four consecutive days and analysed for nitrogen. The nitrogen balances were calculated from mean daily protein intake, mean urinary nitrogen excretion and estimated faecal and integumental nitrogen losses. Nitrogen balance increased with both protein intake and energy balance. At energy equilibrium, the daily protein intake needed to balance nitrogen losses was 1.04 g kg(-1) day(-1). This corresponds to an estimated average requirement (EAR) for protein of 1.20 g kg(-1) day(-1) and a recommended daily allowance (RDA) of 1.40 g kg(-1) day(-1) assuming a daily nitrogen deposition of 11 mg kg(-1). The results of the present study suggest that the protein requirements of 14-year-old male athletes are above the RDA for non-active male adolescents.

Effects of Calcium Binding on the Side-chain Methyl Dynamics of Calbindin D9k: A 2H NMR Relaxation Study

The effects of Ca(2+) binding on the side-chain methyl dynamics of calbindin D(9k) have been characterized by (2)H NMR relaxation rate measurements. Longitudinal, transverse in-phase, quadrupolar order, transverse anti-phase and double quantum relaxation rates are reported for both the apo and Ca(2+)-loaded states of the protein at two magnetic field strengths. The relatively large size of the data set allows for a detailed analysis of the underlying conformational dynamics by spectral density mapping and model-free fitting procedures. The results reveal a correlation between a methyl group's distance from the Ca(2+) binding sites and its conformational dynamics. Several methyl groups segregate into two limiting classes, one proximal and the other distal to the binding sites. Methyl groups in these two classes respond differently to Ca(2+) binding, both in terms of the timescale and amplitude of their fluctuations. Ca(2+) binding elicits a partial immobilization among methyl groups in the proximal class, which is consistent with previous studies of calbindin's backbone dynamics. The distal class, however, exhibits a trend that could not be inferred from the backbone data in that its mobility actually increases with Ca(2+) binding. We have introduced the term polar dynamics to describe this type of organization across the molecule. The trend may represent an important mechanism by which calbindin D(9k) achieves high affinity binding while minimizing the corresponding loss of conformational entropy.

Alendronate-induced chemical laryngitis

Alendronate is a bisphosphonate used in treating osteoporosis. Its recognized side-effects include oesophageal irritation and ulceration. The authors describe a case of laryngitis induced by transient contact of this medication with the laryngeal mucosa. Successful management of this case is also detailed.

The solution structure of the native K50 Bicoid homeodomain bound to the consensus TAATCC DNA-binding site

The solution structure of the homeodomain of the Drosophila morphogenic protein Bicoid (Bcd) complexed with a TAATCC DNA site is described. Bicoid is the only known protein that uses a homeodomain to regulate translation, as well as transcription, by binding to both RNA and DNA during early Drosophila development; in addition, the Bcd homeodomain can recognize an array of different DNA sites. The dual functionality and broad recognition capabilities signify that the Bcd homeodomain may possess unique structural/dynamic properties. Bicoid is the founding member of the K50 class of homeodomain proteins, containing a lysine residue at the critical 50th position (K50) of the homeodomain sequence, a residue required for DNA and RNA recognition; Bcd also has an arginine residue at the 54th position (R54), which is essential for RNA recognition. Bcd is the only known homeodomain with the K50/R54 combination of residues. The Bcd structure indicates that this homeodomain conforms to the conserved topology of the homeodomain motif, but exhibits a significant variation from other homeodomain structures at the end of helix 1. A key result is the observation that the side-chains of the DNA-contacting residues K50, N51 and R54 all show strong signs of flexibility in the protein-DNA interface. This finding is supportive of the adaptive-recognition theory of protein-DNA interactions.

Peak leg muscle power, peak VO2 and its correlates with physical activity in 57 to 70-year-old women

The two aims of this study were first to measure short-term muscle power (STMP) by means of a cycling force-velocity test (cycling peak power: CPP) and a vertical jump test (jumping peak performance: JPP) and second, to examine the relationships between physical activity (PA) level, peak oxygen uptake (peak VO2) and STMP in healthy elderly women. Twenty-three independent community-dwelling elderly women (mean age: 64+/-4.4) performed on separate days, a peak oxygen uptake test on cycle ergometer, a cycling force-velocity test and a vertical jump test. A questionnaire (QUANTAP) was used to assess lifespan exercise habits. Four indices expressed in kJ day(-1) kg(-1) were calculated. Two indices represented average past PA level: 1/quantity of habitual physical activity (QHPA), 2/quantity of sports activities (QSA). Two indices represented the actual PA level: 3/actual quantity of habitual physical activity (AQHPA), 4/actual quantity of sports activities (AQSA). CPP (6.3+/-1.2 W kg(-1)) was closely correlated to JPP (14.8+/-3.4 cm) (r=0.80, P<0.001). AQHPA and AQSA were only positively associated with peak VO2 (ml min(-1) kg(-1)) (r=0.49; r=0.50, P<0.05, respectively). Past PA level was not related to fitness measurements. Results show that in this population: (1) jumping peak performance was closely related to CPP measured in the laboratory; (2) the cardio-respiratory fitness was related to the actual habitual physical activity level; (3) only age and anthropometric variables explained the actual performances in multivariate analysis.

Validity of a V·O2maxPrediction Equation of the 2-km Walk Test in Female Seniors

Walking is a useful exercise mode for most adults due to its general ease, acceptability, and safety. Therefore, many field tests based on performance in walking have been developed to predict V.O (2 max). Even if these tests are much easier to perform than laboratory tests, field tests have to be valid. The objective of the paper was to explore the accuracy and bias of a V.O (2 max) prediction equation of the 2-km Walk Test, in an active female senior group (n=18, mean age: 66.1+/-4.4). V.O (2 max) (l . min (-1)) was measured during cycle ergometry by direct gas analysis from a maximal test (step: 30 W, time: 2 min 30). V.O (2 max) related to body mass was then calculated (ml . min (-1) . kg (-1)). Subjects completed also the 2-km Walk Test (UKK Institute). V.O (2 max) (ml . min (-1) . kg (-1)) was then predicted from age, sex, body mass index, heart rate, and walking time measured during the 2-km Walk Test. Predicted V.O (2 max) and measured V.O (2 max) were highly correlated (r=0.63, p<0.01). Predicted V.O (2 max) (20.5+/-6.1 ml . min (-1) . kg (-1)) was not significantly different from measured V.O (2 max) (18.7+/-3.4 ml . min (-1) . kg (-1)). Prediction equation bias with its 95 % limits of agreement was - 1.8+/-4.8 ml . min (-1) . kg (-1) with a coefficient of variation of 24.2 %. In an active female senior population, the 2-km Walk Test offers a fairly accurate V.O (2 max) prediction. The training and learning effects can be neglected because when the test was repeated no significant bias was observed between the two trials.

Solution structure of the K50 class homeodomain PITX2 bound to DNA and implications for mutations that cause Rieger syndrome

We have determined the solution structure of a complex containing the K50 class homeodomain Pituitary homeobox protein 2 (PITX2) bound to its consensus DNA site (TAATCC). Previous studies have suggested that residue 50 is an important determinant of differential DNA-binding specificity among homeodomains. Although structures of several homeodomain-DNA complexes have been determined, this is the first structure of a native K50 class homeodomain. The only K50 homeodomain structure determined previously is an X-ray crystal structure of an altered specificity mutant, Engrailed Q50K (EnQ50K). Analysis of the NMR structure of the PITX2 homeodomain indicates that the lysine at position 50 makes contacts with two guanines on the antisense strand of the DNA, adjacent to the TAAT core DNA sequence, consistent with the structure of EnQ50K. Our evidence suggests that this side chain may make fluctuating interactions with the DNA, which is complementary to the crystal data for EnQ50K. There are differences in the tertiary structure between the native K50 structure and that of EnQ50K, which may explain differences in affinity and specificity between these proteins. Mutations in the human PITX2 gene are responsible for Rieger syndrome, an autosomal dominant disorder. Analysis of the residues mutated in Rieger syndrome indicates that many of these residues are involved in DNA binding, while others are involved in formation of the hydrophobic core of the protein. Overall, the role of K50 in homeodomain recognition is further clarified, and the results indicate that native K50 homeodomains may exhibit differences from altered specificity mutants.

Mapping chemical exchange in proteins with MW > 50 kD

Chemical exchange reveals motions in proteins that are critical for ligand binding, catalysis, and allosteric regulation at the microsecond to millisecond time scale. The detection of chemical exchange is inherently difficult in large proteins because of the fast transverse relaxation rate (R2) and spectral overlap. Here we report novel pulse sequences for the rapid identification of chemical exchange applicable to large deuterated proteins with MW greater than 30 kD. The success of our method is demonstrated in triosephosphate isomerase (TIM, MW = 54 kD).

Dynamics of ATP-binding cassette contribute to allosteric control, nucleotide binding and energy transduction in ABC transporters

ATP-binding cassette (ABC) transporters move solutes across membranes and are associated with important diseases, including cystic fibrosis and multi-drug resistance. These molecular machines are energized by their charateristic ABC modules, molecular engines fuelled by ATP hydrolysis. A solution NMR study of a model ABC, Methanococcus jannaschii protein MJ1267, reveals that ADP-Mg binding alters the flexibilities of key ABC motifs and induces allosteric changes in conformational dynamics in the LivG insert, over 30A away from the ATPase active site. (15)N spin relaxation data support a "selected-fit" model for nucleotide binding. Transitions between rigidity and flexibility in key motifs during the ATP hydrolysis cycle may be crucial to mechanochemical energy transduction in ABC transporters. The restriction of correlated protein motions is likely a central mechanism for allosteric communications. Comparison between dynamics data from NMR and X-ray crystallography reveals their overall consistency and complementarity.

Multiple time scale backbone dynamics of homologous thermophilic and mesophilic ribonuclease HI enzymes

Backbone conformational fluctuations on multiple time scales in a cysteine-free Thermus thermophilus ribonuclease HI mutant (ttRNH(*)) are quantified using (15)N nuclear magnetic spin relaxation. Laboratory-frame relaxation data acquired at 310 K and at static magnetic field strengths of 11.7, 14.1 and 18.8 T are analysed using reduced spectral density mapping and model-free approaches. Chemical exchange line broadening is characterized using Hahn-echo transverse and multiple quantum relaxation data acquired over a temperature range of 290-320 K and at a static magnetic field strength of 14.1 T. Results for ttRNH(*) are compared to previously published data for a mesophilic homologue, Escherichia coli ribonuclease HI (ecRNH). Intramolecular conformational fluctuations on the picosecond-to-nanosecond time scale generally are similar for ttRNH(*) and ecRNH. beta-Strands 3 and 5 and the glycine-rich region are more rigid while the substrate-binding handle region and C-terminal tail are more flexible in ttRNH(*) than in ecRNH. Rigidity in the two beta-strands and the glycine-rich region, located along the periphery of the central beta-sheet, may be associated with the increased thermodynamic stability of the thermophilic enzyme. Chemical exchange line broadening, reflecting microsecond-to-millisecond time scale conformational changes, is more pronounced in ttRNH(*) than in ecRNH, particularly for residues in the handle and surrounding the catalytic site. The temperature dependence of chemical exchange show an increase of approximately 15 kJ/mol in the apparent activation energies for ttRNH(*) residues in the handle compared to ecRNH. Increased activation barriers, coupled with motion between alpha-helices B and C not present in ecRNH, may be associated with the reduced catalytic activity of the thermophilic enzyme at 310 K.

NMR R1 rho rotating-frame relaxation with weak radio frequency fields

NMR spin relaxation in the rotating frame (R(1 rho)) is one of few methods available to characterize chemical exchange kinetic processes occurring on micros-ms time scales. R(1 rho) measurements for heteronuclei in biological macromolecules generally require decoupling of (1)H scalar coupling interactions and suppression of cross-relaxation processes. Korzhnev and co-workers demonstrated that applying conventional (1)H decoupling schemes while the heteronuclei are spin-locked by a radio frequency (rf) field results in imperfect decoupling [Korzhnev, Skrynnikov, Millet, Torchia, Kay. J. Am. Chem. Soc. 2002, 124, 10743-10753]. Experimental NMR pulse sequences were presented that provide accurate measurements of R(1 rho) rate constants for radio frequency field strengths > 1000 Hz. This paper presents new two-dimensional NMR experiments that allow the use of weak rf fields, between 150 and 1000 Hz, in R(1 rho) experiments. Fourier decomposition and average Hamiltonian theory are employed to analyze the spin-lock sequence and provide a guide for the development of improved experiments. The new pulse sequences are validated using ubiquitin and basic pancreatic trypsin inhibitor (BPTI). The use of weak spin-lock fields in R(1 rho) experiments allows the study of the chemical exchange process on a wider range of time scales, bridging the gap that currently exists between Carr-Purcell-Meiboom-Gill and conventional R(1 rho) experiments. The new experiments also extend the capability of the R(1 rho) technique to study exchange processes outside the fast exchange limit.