PubMed Health⌕ Search

Biomedical subjects

Ryan Day

Publications and source records attributed to Ryan Day.

12 recordsLinked to original sources
PubMed2006

Direct observation of microscopic reversibility in single-molecule protein folding.

Both folded and unfolded conformations should be observed for a protein at its melting temperature (T(m)), where DeltaG between these states is zero. In an all-atom molecular dynamics simulation of chymotrypsin inhibitor 2 (CI2) at its experimental T(m), the protein rapidly loses its low-temperature native structure; it then unfolds before refolding to a stable, native-like conformation. The initial unfolding follows the unfolding pathway described previously for higher-temperature simulations: the hydrophobic core is disrupted, the beta-sheet pulls apart and the alpha-helix unravels. The unfolded state reached under these conditions maintains a kernel of structure in the form of a non-native hydrophobic cluster. Refolding simply reverses this path, the side-chain interactions shift, the helix refolds, and the native packing and hydrogen bonds are recovered. The end result of this refolding is not the initial crystal structure; it contains the proper topology and the majority of the native contacts, but the structure is expanded and the contacts are long. We believe this to be the native state at elevated temperature, and the change in volume and contact lengths is consistent with experimental studies of other native proteins at elevated temperature and the chemical denaturant equivalent of T(m).

Computer Simulation↗
PubMed2005

Characterization of a possible amyloidogenic precursor in glutamine-repeat neurodegenerative diseases.

Several neurodegenerative diseases are linked to expanded repeats of glutamine residues, which lead to the formation of amyloid fibrils and neuronal death. The length of the repeats correlates with the onset of Huntington's disease, such that healthy individuals have <38 residues and individuals with >38 repeats exhibit symptoms. Because it is difficult to obtain atomic-resolution structural information for poly(l-glutamine) (polyQ) in aqueous solution experimentally, we performed molecular dynamics simulations to investigate the conformational behavior of this homopolymer. In simulations of 20-, 40-, and 80-mer polyQ, we observed the formation of the "alpha-extended chain" conformation, which is characterized by alternating residues in the alpha(L) and alpha(R) conformations to yield a sheet. The structural transition from disordered random-coil conformations to the alpha-extended chain conformation exhibits modest length and temperature dependence, in agreement with the experimental observation that aggregation depends on length and temperature. We propose that fibril formation in polyQ may occur through an alpha-sheet structure, which was proposed by Pauling and Corey. Also, we propose an atomic-resolution model of how the inhibitory peptide QBP1 (polyQ-binding peptide 1) may bind to polyQ in an alpha-extended chain conformation to inhibit fibril formation.

Amyloid↗
PubMed2005

Ensemble versus single-molecule protein unfolding.

Molecular dynamics (MD) simulations are the classic single-molecule "experiments," providing atomic-resolution structural and dynamic information. However, the single-molecule nature of the technique has also been its shortcoming, with frequent criticisms of sampling inadequacies and questions regarding the ensemble behavior of large numbers of molecules. Given the increase in computer power, we now address this issue by performing a large number of simulations and comparing individual and ensemble properties. One hundred independent MD simulations of the protein chymotrypsin inhibitor 2 were carried out for 20 ns each at 498 K in water to more fully describe the potentially diverse routes of protein unfolding and investigate how representative a single trajectory can be. Rapid unfolding was observed in all cases with the trajectories distributed about an average "ensemble" path in which secondary and tertiary structure was lost concomitantly, with tertiary structure loss occurring slightly faster. Individual trajectories did, however, sample conformations far from the average path with very heterogeneous time-dependent properties. Nevertheless, all of the simulations but one followed the average ensemble pathway, such that a small number of simulations (5-10) are sufficient to capture the average properties of these states and the unfolding pathway.

Hydrogen Bonding↗
PubMed2005

The structure of the major transition state for folding of an FF domain from experiment and simulation.

We have analysed the transition state of folding of the four-helix FF domain from HYPA/FBP11 by high-resolution experiment and simulation as part of a continuing effort to understand the principles of folding and the refinement of predictive methods. The major transition state for folding was subjected to a Phi-value analysis utilising 50 mutants. The transition state contained a nucleus for folding centred around the end of helix 1 (H1) and the beginning of helix 2 (H2). Secondary structure in this region was fully formed (PhiF=0.9-1) and tertiary interactions were well developed. Interactions in the distal part of the native structure were weak (PhiF=0-0.2). The hydrophobic core and other parts of the protein displayed intermediate Phi-values, suggesting that interactions coalesce as the end of H1 and beginning of H2 are in the process of being formed. The distribution of Phi-values resembled that of barnase, which folds via an intermediate, rather than that of CI2 which folds by a concerted nucleation-condensation mechanism. The overall picture of the transition state structure identified in molecular dynamics simulations is in qualitative agreement, with the turn connecting H1 and H2 being formed, a loosened core, and H4 partially unfolded and detached from the core. There are some differences in the details and interpretation of specific Phi-values.

Carrier Proteins↗
PubMed2005

Simulation and experiment at high temperatures: ultrafast folding of a thermophilic protein by nucleation-condensation.

We used Phi-value analysis to characterise the transition state for folding of a thermophilic protein at the relatively high temperature of 325 K. PhiF values for the folding of the three-helix bundle, peripheral subunit binding domain from Bacillus stearothermophilus (E3BD) were determined by temperature-jump experiments in the absence of chemical denaturants. E3BD folded in microseconds through a highly diffuse transition state. Excellent agreement was observed between experiment and the results from eight (independent) molecular dynamics simulations of unfolding at 373 K. We used a combination of heteronuclear NMR experiments and molecular dynamics simulations to characterise the denatured ensemble, and found that it contained very little persistent, residual structure. However, those regions that adopt helical structure in the native state were found by simulation to be poised for helix formation in the denatured state. These regions also had significant structure in the transition state for folding. The overall folding pathway appears to be nucleation-condensation.

Bacterial Proteins↗
PubMed2005

Sensitivity of the folding/unfolding transition state ensemble of chymotrypsin inhibitor 2 to changes in temperature and solvent.

To better characterize the transition state for folding/unfolding and its sensitivity to environmental changes, we have run multiple molecular dynamics simulations of chymotrypsin inhibitor 2 (CI2) under varying solvent conditions and temperature. The transition state structures agree well with experiment, and are similar under all of the conditions investigated here. Increasing the temperature leads to some movement in the position of the transition state along several reaction coordinates, as measured by changes in properties of the transition state structures. These structural changes are in the direction of a more native-like transition state as denaturation conditions become more severe, as expected for a Hammond effect. These structural changes are not, however, reflected in the global structure as measured by the total number of contacts or the average S-values. These results suggest that the small changes in average Phi-values with temperature seen by experiment may be due to an increase in the sensitivity of the transition state to mutation rather than a change in the average structure of the transition state. A simple analysis of the rates of unfolding indicates that the free energy barrier to unfolding decreases with increasing temperature, but even in our very high temperature simulations there is a small free energy barrier.

Peptides↗
PubMed2004

Demonstration of a low-energy on-pathway intermediate in a fast-folding protein by kinetics, protein engineering, and simulation.

It is controversial whether fast-folding proteins can form productive on-pathway intermediates that are more stable than the denatured state because noncovalent intermediates are usually evanescent. Here, we apply the classical criteria for the existence of intermediates: namely, the intermediates form and react rapidly enough to be on pathway and they can be isolated and characterized. The folding of the 71-residue, mainly alpha-helical FF domain from human HYPA/FBP11 fulfills these classical criteria, as was found for Im7. The FF domain folds in two phases, one on the micros and the other on the ms time scale. An engineered mutant folds only to a partly folded state, with some 20-40% of the native helical content. The kinetic properties of the mutant are identical to those found for the fast phase of the wild-type protein, and it is likely that the mutant folds just to the intermediate state. A full kinetic analysis of the folding of wild-type protein, using the amplitudes of its native and denatured states and the observed values for the mutant, rules out an off-pathway scheme but fits an on-pathway scheme, with a low energy intermediate that is modeled by the mutant. The experimental proof benchmarks a molecular dynamics method that identifies an obligatory intermediate observed in multiple simulations. The conformational space defining this intermediate is visited several times in the simulations, leading to high populations consistent with the presence of a low energy intermediate.

Kinetics↗
PubMed2003

Sleep during titration predicts continuous positive airway pressure compliance.

STUDY OBJECTIVES: Poor compliance with continuous positive airway pressure (CPAP) has been identified as a significant obstacle in the treatment of obstructive sleep apnea. While previous studies have focused on diagnostic screening variables, side effects, health beliefs, and measures of disease severity, investigators have generally ignored sleep parameters assessed during CPAP titration as predictors of compliance. As the titration night represents patients' initial exposure to nocturnal CPAP treatment, we hypothesized that nocturnal polysomnographic (PSG) variables, representing improved sleep at this time, would predict higher subsequent compliance. DESIGN: Prospective analyses of a sequential case series were undertaken using nocturnal PSG variables during titration as early predictors of CPAP compliance. SETTING: Accredited sleep center. PATIENTS: Seventy-one patients with sleep apnea, aged 31-78 years, with a mean respiratory disturbance index of 62.0 +/- 32.2. INTERVENTIONS: N/A. MEASUREMENTS AND RESULTS: Compliance was calculated as mean hours per night of CPAP use over the initial follow-up period (mean 46.9 days). Standard PSG variables and subjective reports of sleep were used as predictive variables in multivariate analyses. Mean objective compliance was 5.04 hours per night +/- 2.59. Consistent with our hypothesis, the best predictor of compliance was change in sleep efficiency (SE) from diagnostic to titration night [F (1,66) = 17.31, p < .000 (r = .48)], indicating that patients whose sleep improved most on the titration night had the highest levels of compliance. This relationship was also significant after controlling for measures of disease severity obtained during the diagnostic testing night. Importantly, individuals whose sleep improved on the CPAP titration night had nightly compliance rates of approximately 2 hours greater than patients whose sleep did not improve during titration. CONCLUSIONS: The findings suggest that patients' initial experience with CPAP treatment and, in particular, the degree of improvement in sleep during CPAP titration may be crucial factors in determining their subsequent use of this treatment modality.

Adult↗
PubMed2003

A consensus view of fold space: combining SCOP, CATH, and the Dali Domain Dictionary.

We have determined consensus protein-fold classifications on the basis of three classification methods, SCOP, CATH, and Dali. These classifications make use of different methods of defining and categorizing protein folds that lead to different views of protein-fold space. Pairwise comparisons of domains on the basis of their fold classifications show that much of the disagreement between the classification systems is due to differing domain definitions rather than assigning the same domain to different folds. However, there are significant differences in the fold assignments between the three systems. These remaining differences can be explained primarily in terms of the breadth of the fold classifications. Many structures may be defined as having one fold in one system, whereas far fewer are defined as having the analogous fold in another system. By comparing these folds for a nonredundant set of proteins, the consensus method breaks up broad fold classifications and combines restrictive fold classifications into metafolds, creating, in effect, an averaged view of fold space. This averaged view requires that the structural similarities between proteins having the same metafold be recognized by multiple classification systems. Thus, the consensus map is useful for researchers looking for fold similarities that are relatively independent of the method used to compare proteins. The 30 most populated metafolds, representing the folds of about half of a nonredundant subset of the PDB, are presented here. The full list of metafolds is presented on the Web.

Amino Acid Motifs↗
PubMed2003

The alerting effects of dexamethasone.

The purpose of this study was to characterize the level of sleepiness/alertness following the nocturnal administration of dexamethasone. Thirteen healthy men participated in this study. Following the initial screening, dexamethasone (4 mg) or placebo was administered at 22:30 hr in a randomized double-blind procedure. Subjects were given nap opportunities at 23:00, 1:00, 3:00, 4:30, 5:30, 7:30, 9:30, 11:30, 13:30, 15:30, 17:30, and 19:30 hr. The administration of dexamethasone resulted in an overall lengthening of sleep latency. Although the two groups displayed comparable latencies to stage 1 for the 23:00-7:30 hr nap opportunities, the administration of dexamethasone resulted in significantly longer latencies on the 9:30-19:30 hr nap opportunities. Consistent with these results, participants reported significantly greater levels of alertness on the Stanford Sleepiness Scale. The results of this study revealed greater levels of daytime alertness following the nocturnal administration of dexamethasone.

Adolescent↗
PubMed2002

Increasing temperature accelerates protein unfolding without changing the pathway of unfolding.

We have traditionally relied on extremely elevated temperatures (498K, 225 degrees C) to investigate the unfolding process of proteins within the timescale available to molecular dynamics simulations with explicit solvent. However, recent advances in computer hardware have allowed us to extend our thermal denaturation studies to much lower temperatures. Here we describe the results of simulations of chymotrypsin inhibitor 2 at seven temperatures, ranging from 298K to 498K. The simulation lengths vary from 94ns to 20ns, for a total simulation time of 344ns, or 0.34 micros. At 298K, the protein is very stable over the full 50ns simulation. At 348K, corresponding to the experimentally observed melting temperature of CI2, the protein unfolds over the first 25ns, explores partially unfolded conformations for 20ns, and then refolds over the last 35ns. Above its melting temperature, complete thermal denaturation occurs in an activated process. Early unfolding is characterized by sliding or breathing motions in the protein core, leading to an unfolding transition state with a weakened core and some loss of secondary structure. After the unfolding transition, the core contacts are rapidly lost as the protein passes on to the fully denatured ensemble. While the overall character and order of events in the unfolding process are well conserved across temperatures, there are substantial differences in the timescales over which these events take place. We conclude that 498K simulations are suitable for elucidating the details of protein unfolding at a minimum of computational expense.

Binding Sites↗