Biomedical subjects

Jane Clarke

Publications and source records attributed to Jane Clarke.

At least 19 recordsLinked to original sources

PubMed2007

Single molecule studies of protein folding using atomic force microscopy.

Atomic force microscopy (AFM) offers new insights into the ability of proteins to resist mechanical force. The technique has been opened up by the availability of easy-to-use instruments that are commercially available, so that the technique no longer relies on the need to build instruments in the lab. Indeed it may become common for AFM instruments to sit beside stopped-flow apparatus in protein folding laboratories. In this chapter, we describe the instrument set-up, the preparation of suitable protein substrate, and the collection of data. Data selection and analysis are more complex than for conventional stopped-flow ensemble studies, but offer new insights into the function of proteins in vivo.

Microscopy, Atomic Force↗

PubMed2006

Mouse lymphoma thymidine kinase gene mutation assay: meeting of the International Workshop on Genotoxicity Testing, San Francisco, 2005, recommendations for 24-h treatment.

The Mouse Lymphoma Assay (MLA) Workgroup of the International Workshop on Genotoxicity Testing (IWGT), comprised of experts from Japan, Europe and the United States, met on September 9, 2005, in San Francisco, CA, USA. This meeting of the MLA Workgroup was devoted to reaching a consensus on issues involved with 24-h treatment. Recommendations were made concerning the acceptable values for the negative/solvent control (mutant frequency, cloning efficiency and suspension growth) and the criteria to define an acceptable positive control response. Consensus was also reached concerning the use of the global evaluation factor (GEF) and appropriate statistical trend analysis to define positive and negative responses for the 24-h treatment. The Workgroup agreed to continue their support of the International Committee on Harmonization (ICH) recommendation that the MLA assay should include a 24-h treatment (without S-9) in those situations where the short treatment (3-4 h) gives negative results.

Animals↗

PubMed2006

BPPred: a Web-based computational tool for predicting biophysical parameters of proteins.

We exploit the availability of recent experimental data on a variety of proteins to develop a Web-based prediction algorithm (BPPred) to calculate several biophysical parameters commonly used to describe the folding process. These parameters include the equilibrium m-values, the length of proteins, and the changes upon unfolding in the solvent-accessible surface area, in the heat capacity, and in the radius of gyration. We also show that the knowledge of any one of these quantities allows an estimate of the others to be obtained, and describe the confidence limits with which these estimations can be made. Furthermore, we discuss how the kinetic m-values, or the Beta Tanford values, may provide an estimate of the solvent-accessible surface area and the radius of gyration of the transition state for protein folding. Taken together, these results suggest that BPPred should represent a valuable tool for interpreting experimental measurements, as well as the results of molecular dynamics simulations.

Algorithms↗

PubMed2006

Apparent cooperativity in the folding of multidomain proteins depends on the relative rates of folding of the constituent domains.

Approximately 75% of eukaryotic proteins contain more than one so-called independently folding domain. However, there have been relatively few systematic studies to investigate the effect of interdomain interactions on protein stability and fewer still on folding kinetics. We present the folding of pairs of three-helix bundle spectrin domains as a paradigm to indicate how complex such an analysis can be. Equilibrium studies show an increase in denaturant concentration required to unfold the domains with only a single unfolding transition; however, in some cases, this is not accompanied by the increase in m value, which would be expected if the protein is a truly cooperative, all-or-none system. We analyze the complex kinetics of spectrin domain pairs, both wild-type and carefully selected mutants. By comparing these pairs, we are able to demonstrate that equilibrium data alone are insufficient to describe the folding of multidomain proteins and to quantify the effects that one domain can have on its neighbor.

Kinetics↗

PubMed2006

Spectrin domains lose cooperativity in forced unfolding.

Spectrin is a multidomain cytoskeletal protein, the component three-helix bundle domains are expected to experience mechanical force in vivo. In thermodynamic and kinetic studies, neighboring domains of chicken brain alpha-spectrin R16 and R17 have been shown to behave cooperatively. Is this cooperativity maintained under force? The effect of force on these spectrin domains was investigated using atomic force microscopy. The response of the individual domains to force was compared to that of the tandem repeat R1617. Importantly, nonhelical linkers (all-beta immunoglobulin domains) were used to avoid formation of nonnative helical linkers. We show that, in contrast to previous studies on spectrin repeats, only 3% of R1617 unfolding events gave an increase in contour length consistent with cooperative two-domain unfolding events. Furthermore, the unfolding forces for R1617 were the same as those for the unfolding of R16 or R17 alone. This is a strong indication that the cooperative unfolding behavior observed in the stopped-flow studies is absent between these spectrin domains when force is acting as a denaturant. Our evidence suggests that the rare double unfolding events result from misfolding between adjacent repeats. We suggest that this switch from cooperative to independent behavior allows multidomain proteins to maintain integrity under applied force.

Computer Simulation↗

PubMed2006

Paediatric thoracic tumours presenting as empyema.

Ultrasonography (US) is considered to be adequate for the preoperative evaluation of childhood empyema. This study was aimed to improve awareness that paediatric intra-thoracic tumours can mimic childhood post-pneumonic empyema and highlights the value of computed tomogram (CT) scan with intravenous (IV) contrast in preoperative evaluation of childhood empyema. The data were analysed on eight children (four boys and four girls) presented at the median age of 6.2 years (1.8-15 years) for the management of empyema and later confirmed to have intra-thoracic tumours. Intra-thoracic tumours in 8 (5.3%) children out of 150 cases of post-pneumonic empyema were managed during the study period. All eight had clinical features, increased white cell count, raised inflammatory markers and biochemical parameters suggestive of childhood empyema. Chest X-ray showed localised opacity in 3/8 while in other five suggested significant pleural collection with mediastinal shift. Additional investigations in referring hospital were suggestive of empyema in four children; US in three, CT scan without IV contrast in one. Referring hospital carried out non-diagnostic thoracocentesis in four children with blood stained pleural tap in two. In four children corroborative evidence suggestive of infection within pleural cavity and acute respiratory distress led to an emergency mini-thoracotomy resulting in significant intra-operative bleeding in two children. Histology on biopsy of the infected material showed primitive neuroectodermal tumour (PNET) in one, pleuropulmonary blastoma in one, metastatic malignant melanoma in one and cytology of pleural fluid diagnosed lymphoma in one. Pre-operative CT scan with IV contrast in four children correctly identified underlying intra-thoracic tumour (two benign teratoma, two PNET). In two cases CT with IV contrast was performed because chest X-ray suggested mediastinal loculated empyema while in other two high clinical index of suspicion prompted preoperative evaluation with CT scan with IV contrast. We advocate caution and increased awareness before considering therapeutic options in childhood empyema and recommend preoperative CT scan with IV contrast in some selected and unusual cases.

Adolescent↗

PubMed2006

Using model proteins to quantify the effects of pathogenic mutations in Ig-like proteins.

It has proved impossible to purify some proteins implicated in disease in sufficient quantities to allow a biophysical characterization of the effect of pathogenic mutations. To overcome this problem we have analyzed 37 different disease-causing mutations located in the L1 and IL2Rgamma proteins in well characterized related model proteins in which mutations that are identical or equivalent to pathogenic mutations were introduced. We show that data from these models are consistent and that changes in stability observed can be correlated to severity of disease, to correct trafficking within the cell and to in vitro ligand binding studies. Interestingly, we find that any mutations that cause a loss of stability of more than 2 kcal/mol are severely debilitating, even though some model proteins with these mutations can be easily expressed and analyzed. Furthermore we show that the severity of mutation can be predicted by a DeltaDeltaG(evolution) scale, a measure of conservation. Our results demonstrate that model proteins can be used to analyze disease-causing mutations when wild-type proteins are not stable enough to carry mutations for biophysical analysis.

Genetic Predisposition to Disease↗

PubMed2006

Structural comparison of the two alternative transition states for folding of TI I27.

TI I27, a beta-sandwich domain from the human muscle protein titin, has been shown to fold via two alternative pathways, which correspond to a change in the folding mechanism. Under physiological conditions, TI I27 folds by a classical nucleation-condensation mechanism (diffuse transition state), whereas at extreme conditions of temperature and denaturant it switches to having a polarized transition state. We have used experimental Phi-values as restraints in ensemble-averaged molecular dynamics simulations to determine the ensembles of structures representing the two transition states. The comparison of these ensembles indicates that when native interactions are substantially weakened, a protein may still be able to fold if it can access an alternative transition state characterized by a much larger entropic contribution. Analysis of the probability distribution of Phi-values derived from ensemble averaged simulations, enables us to identify residues that form contacts in some members of the ensemble but not in others illustrating that many interactions present in transition states are not strictly required for the successful completion of the folding process.

Computer Simulation↗

PubMed2006

The folding pathway of spectrin R17 from experiment and simulation: using experimentally validated MD simulations to characterize States hinted at by experiment.

We present an experimental and computational analysis of the folding pathway of the 17th domain of chicken brain alpha-spectrin, R17. Wild-type R17 folds in a two-state manner and the chevron plot (plot of the logarithm of the observed rate constant against concentration of urea) shows essentially linear folding and unfolding arms. A number of mutant proteins, however, show a change in slope of the unfolding arm at high concentration of denaturant, hinting at complexity in the folding landscape. Through a combination of mutational studies and high temperature molecular dynamics simulations we show that the folding of R17 can be described by a model with two sequential transition states separated by an intermediate species. The rate limiting transition state for folding in water has been characterized both through experimental Phi-value analysis and by simulation. In contrast, a detailed analysis of the transition state predicted to dominate under highly denaturing conditions is only possible by simulation.

Amino Acid Sequence↗

PubMed2006

Mouse lymphoma thymidine kinase gene mutation assay: follow-up meeting of the International Workshop on Genotoxicity Testing--Aberdeen, Scotland, 2003--Assay acceptance criteria, positive controls, and data evaluation.

The Mouse Lymphoma Assay (MLA) Workgroup of the International Workshop on Genotoxicity Testing (IWGT), comprised of experts from Japan, Europe, and the United States, met on August 29, 2003, in Aberdeen, Scotland, United Kingdom. This meeting of the MLA Workgroup was devoted to reaching a consensus on the appropriate approach to data evaluation and on acceptance criteria for both the positive and negative/vehicle controls. The Workgroup reached consensus on the acceptance criteria for both the agar and microwell versions of the MLA. Recommendations include acceptable ranges for mutant frequency, cloning efficiency, and suspension growth of the negative/vehicle controls and on criteria to define an acceptable positive control response. The recommendation for the determination of a positive/negative test chemical response includes both the requirement that the response exceeds a defined value [the global evaluation factor (GEF)] and that there also be a positive dose-response (evaluated by an appropriate statistical method).

Animals↗

PubMed2005

Complex folding kinetics of a multidomain protein.

Spectrin domains are three-helix bundles, commonly found in large tandem arrays. Equilibrium studies have shown that spectrin domains are significantly stabilized by their neighbors. In this work we show that domain:domain interactions can also have profound effects on their kinetic behavior. We have studied the folding of a tandem pair of spectrin domains (R1617) using a combination of single- and double-jump stopped flow experiments (monitoring folding by both circular dichroism and fluorescence). Mutant proteins were also used to investigate the complex folding kinetics. We find that, although the domains fold and unfold individually, there is a single rate-determining step for both folding and unfolding of the protein. This is consistent with the equilibrium observation of cooperative folding of the entire two-domain protein. The results may have important biological implications. Not only will the protein fold more efficiently during cotranslational folding, but the ability of the multidomain protein to withstand thermal unfolding in the cell will be dramatically increased. This study suggests that caution has to be exercised when extrapolating from single domains to larger proteins with a number of independently folding modules arranged in tandem. The multidomain protein spectrin is certainly more than "the sum of its parts".

Binding Sites↗

PubMed2005

The importance of sequence diversity in the aggregation and evolution of proteins.

Incorrect folding of proteins, leading to aggregation and amyloid formation, is associated with a group of highly debilitating medical conditions including Alzheimer's disease and late-onset diabetes. The issue of how unwanted protein association is normally avoided in a living system is particularly significant in the context of the evolution of multidomain proteins, which account for over 70% of all eukaryotic proteins, where the effective local protein concentration in the vicinity of each domain is very high. Here we describe the aggregation kinetics of multidomain protein constructs of immunoglobulin domains and the ability of different homologous domains to aggregate together. We show that aggregation of these proteins is a specific process and that the efficiency of coaggregation between different domains decreases markedly with decreasing sequence identity. Thus, whereas immunoglobulin domains with more than about 70% identity are highly prone to coaggregation, those with less than 30-40% sequence identity do not detectably interact. A bioinformatics analysis of consecutive homologous domains in large multidomain proteins shows that such domains almost exclusively have sequence identities of less than 40%, in other words below the level at which coaggregation is likely to be efficient. We propose that such low sequence identities could have a crucial and general role in safeguarding proteins against misfolding and aggregation.

Amyloid↗

PubMed2005

Mechanical unfolding of TNfn3: the unfolding pathway of a fnIII domain probed by protein engineering, AFM and MD simulation.

Protein engineering Phi-value analysis combined with single molecule atomic force microscopy (AFM) was used to probe the molecular basis for the mechanical stability of TNfn3, the third fibronectin type III domain from human tenascin. This approach has been adopted previously to solve the forced unfolding pathway of a titin immunoglobulin domain, TI I27. TNfn3 and TI I27 are members of different protein superfamilies and have no sequence identity but they have the same beta-sandwich structure consisting of two antiparallel beta-sheets. TNfn3, however, unfolds at significantly lower forces than TI I27. We compare the response of these proteins to mechanical force. Mutational analysis shows that, as is the case with TI I27, TNfn3 unfolds via a force-stabilised intermediate. The key event in forced unfolding in TI I27 is largely the breaking of hydrogen bonds and hydrophobic interactions between the A' and G-strands. The mechanical Phi-value analysis and molecular dynamics simulations reported here reveal that significantly more of the TNfn3 molecule contributes to its resistance to force. Both AFM experimental data and molecular dynamics simulations suggest that the rate-limiting step of TNfn3 forced unfolding reflects a transition from the extended early intermediate to an aligned intermediate state. As well as losses of interactions of the A and G-strands and associated loops there are rearrangements throughout the core. As was the case for TI I27, the forced unfolding pathway of TNfn3 is different from that observed in denaturant studies in the absence of force.

Computer Simulation↗

PubMed2005

Cooperative folding in a multi-domain protein.

Most protein domains are found in multi-domain proteins, yet most studies of protein folding have concentrated on small, single-domain proteins or on isolated domains from larger proteins. Spectrin domains are small (106 amino acid residues), independently folding domains consisting of three long alpha-helices. They are found in multi-domain proteins with a number of spectrin domains in tandem array. Structural studies have shown that in these arrays the last helix of one domain forms a continuous helix with the first helix of the following domain. It has been demonstrated that a number of spectrin domains are stabilised by their neighbours. Here we investigate the molecular basis for cooperativity between adjacent spectrin domains 16 and 17 from chicken brain alpha-spectrin (R16 and R17). We show that whereas the proteins unfold as a single cooperative unit at 25 degrees C, cooperativity is lost at higher temperatures and in the presence of stabilising salts. Mutations in the linker region also cause the cooperativity to be lost. However, the cooperativity does not rely on specific interactions in the linker region alone. Most mutations in the R17 domain cause a decrease in cooperativity, whereas proteins with mutations in the R16 domain still fold cooperatively. We propose a mechanism for this behaviour.

Amino Acid Sequence↗

PubMed2005

The remarkable mechanical strength of polycystin-1 supports a direct role in mechanotransduction.

Polycystin-1 is a large membrane-associated protein that interacts with polycystin-2 in the primary cilia of renal epithelial cells to form a mechanosensitive ion channel. Bending of the cilia induces calcium flow into the cells, mediated by the polycystin complex. Antibodies to polycystin-1 and polycystin-2 abolish this activation. Based on this, it has been suggested that the extracellular region of polycystin-1, which has a number of putative binding domains, may act as a mechanosensor. A large proportion of the extracellular region of polycystin-1 consists of beta-sandwich PKD domains in tandem array. We use atomic force microscopy to investigate the mechanical properties of the PKD domains of polycystin-1. We show that these domains, despite having a low thermodynamic stability, exhibit a remarkable mechanical strength, similar to that of immunoglobulin domains in the giant muscle protein titin. In agreement with the experimental results molecular dynamics simulations performed at low constant force show that the first PKD domain of polycystin (PKDd1) has a similar unfolding time as titin I27, under the same conditions. The simulations suggest that the basis for this mechanical stability is the formation of a force-stabilised intermediate. Our results suggest that these domains will remain folded under external force supporting the hypothesis that polycystin-1 could act as a mechanosensor, detecting changes in fluid flow in the kidney tubule.

Biomechanical Phenomena↗

PubMed2005

What contributions to protein side-chain dynamics are probed by NMR experiments? A molecular dynamics simulation analysis.

Molecular dynamics simulations of the structurally homologous proteins TNfn3 and FNfn10 have been used to investigate the contributions to side-chain dynamics measured by NMR relaxation experiments. The results reproduce the variation in core side-chain dynamics observed by NMR and highlight the relevance of anharmonic motion and transitions between local minima for explaining NMR side-chain order parameters. A method is described for calculating converged order parameters by use of replica exchange molecular dynamics in conjunction with an implicit solvent model. These simulations allow the influence of various factors, such as the flexibility of side-chains and their free volume, on the mobility to be tested by perturbing the system. Deletion mutations are found to have the largest effect on the more densely packed FNfn10. Some counterintuitive effects are seen, such as an increase in order parameters close to deletion mutation sites, but these can be rationalized in terms of direct interactions with the modified side-chains. A statistical analysis of published order parameters supports the conclusions drawn from the simulations.

Amino Acids↗

PubMed2005

Insulin-like growth factor binding protein-5 (IGFBP-5) interacts with thrombospondin-1 to induce negative regulatory effects on IGF-I actions.

Insulin-like growth factor binding protein-5 (IGFBP-5) and thrombospondin-1 (TS-1) are both present in extracellular matrix (ECM). Both proteins have been shown to bind to one another with high affinity. The purpose of these studies was to determine how the interaction between IGFBP-5 and TS-1 modulates IGF-I actions in porcine aortic smooth muscle cells (pSMC) in culture. The addition of increasing concentrations of TS-1 to pSMC cultures enhanced the protein synthesis and cell migration responses to IGF-I; whereas the addition of IGFBP-5 alone resulted in minimal changes. In contrast, the addition of IGFBP-5 to cultures that were also exposed to IGF-I and TS-1 resulted in inhibition of protein synthesis. When the cell migration response was assessed, the response to IGF-I plus TS-1 was also significantly inhibited by the addition of IGFBP-5, whereas 1.0 microg/ml of IGFBP-5 alone had no effect on the response to IGF-I. To determine the molecular mechanism by which this inhibition occurred, a mutant form of IGFBP-5 that does not bind to IGF-I was tested. This mutant was equipotent compared to native IGFBP-5 in its ability to inhibit both protein synthesis and cell migration responses to IGF-I plus TS-1 thus excluding the possibility that IGFBP-5 was inhibiting the response to TS-1 and IGF-I by inhibiting IGF-I binding to the IGF-I receptor. To determine if an interaction between TS-1 and IGFBP-5 was the primary determinant of the inhibitory effect of IGFBP-5, an IGFBP-5 mutant that bound poorly to TS-1 was utilized. The addition of 1.0 microg/ml of this mutant did not inhibit the protein synthesis or cell migration responses to IGF-I plus TS-1. To determine the mechanism by which IGFBP-5 binding to TS-1 inhibited cellular responses to TS-1 plus IGF-I, TS-1 binding to integrin associated protein (IAP) was assessed. The addition of IGFBP-5 (1.0 microg/ml) inhibited TS-1-IAP association. In contrast, a mutant form of IGFBP-5 that bound poorly to TS-1 had a minimal effect on TS-1 binding to IAP. Further analysis showed that IGFBP-5 addition altered the ability of TS-1 to modulate the SHPS-1/IAP interaction. When the IGFBP-5 mutant that did not bind to IGF-I was incubated with TS-1 and IGF-I, it inhibited the capacity of TS-1 to enhance the IGF-I receptor phosphorylation and MAP kinase activation in response to IGF-I. In contrast, the IGFBP-5 mutant that did not bind to TS-1 had no effect on IGF-I stimulated IGF-I receptor phosphorylation or MAP kinase activation. These results indicate that IGFBP-5 inhibits the binding of TS-1 to IAP, and this results in an alteration of the ability of TS-1 to modulate the disruption of the IAP/SHPS-1 interaction which leads to attenuation of the ability of TS-1 to enhance cellular responsiveness to IGF-I.

Animals↗

PubMed2005

Spectrin R16: broad energy barrier or sequential transition states?

A number of models have been proposed to account for nonlinearity in the relation between observed rate constants for folding and/or unfolding and denaturant concentration. Where curvature is seen principally in the arm of a chevron plot, three explanations are proposed: a change in the ground state at increasing concentration of urea, movement of the transition state along a broad energy barrier, and a switch between two sequential transition states separated by an on-pathway high-energy intermediate. Here we demonstrate that the latter two models in particular can be used to describe the data for the all-alpha protein spectrin R16. Further, whatever the method of analysis, the pattern of Phi-values seen is robust; thus we would draw the same conclusions from our data set independently of the method used for analysis. While this is not a novel observation, this is the first systematic study where a comparison has been made between Phi-values calculated using the broad and sequential transition state models.

Animals↗