The folding mechanics of a knotted protein

An increasing number of proteins are being discovered with a remarkable and somewhat surprising feature, a knot in their native structures. How the polypeptide chain is able to "knot" itself during the folding process to form these highly intricate protein topologies is not known. Here we perform a computational study on the 160-amino-acid homodimeric protein YibK, which, like other proteins in the SpoU family of MTases, contains a deep trefoil knot in its C-terminal region. In this study, we use a coarse-grained C(alpha)-chain representation and Langevin dynamics to study folding kinetics. We find that specific, attractive nonnative interactions are critical for knot formation. In the absence of these interactions, i.e., in an energetics driven entirely by native interactions, knot formation is exceedingly unlikely. Further, we find, in concert with recent experimental data on YibK, two parallel folding pathways that we attribute to an early and a late formation of the trefoil knot, respectively. For both pathways, knot formation occurs before dimerization. A bioinformatics analysis of the SpoU family of proteins reveals further that the critical nonnative interactions may originate from evolutionary conserved hydrophobic segments around the knotted region.

A critical assessment of the topomer search model of protein folding using a continuum explicit-chain model with extensive conformational sampling

Recently, a series of closely related theoretical constructs termed the "topomer search model" (TSM) has been proposed for the folding mechanism of small, single-domain proteins. A basic assumption of the proposed scenarios is that the rate-limiting step in folding is an essentially unbiased, diffusive search for a conformational state called the native topomer defined by an overall native-like topological pattern. Successes in correlating TSM-predicted folding rates with that of real proteins have been interpreted as experimental support for the model. To better delineate the physics entailed, key TSM concepts are examined here using extensive Langevin dynamics simulations of continuum C(alpha) chain models. The theoretical native topomers of four experimentally well-studied two-state proteins are characterized. Consistent with the TSM perspective, we found that the sizes of the native topomers increase with experimental folding rate. However, a careful determination of the corresponding probabilities that the native topomers are populated during a random search fails to reproduce the previously predicted folding rates. Instead, our results indicate that an unbiased TSM search for the native topomer amounts to a Levinthal-like process that would take an impossibly long average time to complete. Furthermore, intraprotein contacts in all four native topomers considered exhibit no apparent correlation with the experimental phi-values determined from the folding kinetics of these proteins. Thus, the present findings suggest that certain basic, generic yet essential energetic features in protein folding are not accounted for by TSM scenarios to date.

Sequence-based study of two related proteins with different folding behaviors

Z(SPA-1) is an engineered protein that binds to its parent, the three-helix-bundle Z domain of staphylococcal protein A. Uncomplexed Z(SPA-1) shows a reduced helix content and a melting behavior that is less cooperative, compared with the wild-type Z domain. Here we show that the difference in folding behavior between these two sequences can be partly understood in terms of an off-lattice model with 5-6 atoms per amino acid and a minimalistic potential, in which folding is driven by backbone hydrogen bonding and effective hydrophobic attraction.

Thermodynamics of alpha- and beta-structure formation in proteins

An atomic protein model with a minimalistic potential is developed and then tested on an alpha-helix and a beta-hairpin, using exactly the same parameters for both peptides. We find that melting curves for these sequences to a good approximation can be described by a simple two-state model, with parameters that are in reasonable quantitative agreement with experimental data. Despite the apparent two-state character of the melting curves, the energy distributions are found to lack a clear bimodal shape, which is discussed in some detail. We also perform a Monte Carlo-based kinetic study and find, in accord with experimental data, that the alpha-helix forms faster than the beta-hairpin.

Two-state folding over a weak free-energy barrier

We present a Monte Carlo study of a model protein with 54 amino acids that folds directly to its native three-helix-bundle state without forming any well-defined intermediate state. The free-energy barrier separating the native and unfolded states of this protein is found to be weak, even at the folding temperature. Nevertheless, we find that melting curves to a good approximation can be described in terms of a simple two-state system, and that the relaxation behavior is close to single exponential. The motion along individual reaction coordinates is roughly diffusive on timescales beyond the reconfiguration time for a single helix. A simple estimate based on diffusion in a square-well potential predicts the relaxation time within a factor of two.

Testing similarity measures with continuous and discrete protein models

There are many ways to define the distance between two protein structures, thus assessing their similarity. Here, we investigate and compare the properties of five different distance measures, including the standard root-mean-square deviation (cRMSD). The performance of these measures is studied from different perspectives with two different protein models, one continuous and the other discrete. Using the continuous model, we examine the correlation between energy and native distance, and the ability of the different measures to discriminate between the two possible topologies of a three-helix bundle. Using the discrete model, we perform fits to real protein structures by minimizing different distance measures. The properties of the fitted structures are found to depend strongly on the distance measure used and the scale considered. We find that the cRMSD measure very effectively describes long-range features but is less effective with short-range features, and it correlates weakly with energy. A stronger correlation with energy and a better description of short-range properties is obtained when we use measures based on intramolecular distances.

Folding of a small helical protein using hydrogen bonds and hydrophobicity forces

A reduced protein model with five to six atoms per amino acid and five amino acid types is developed and tested on a three-helix-bundle protein, a 46-amino acid fragment from staphylococcal protein A. The model does not rely on the widely used Go approximation, which ignores non-native interactions. We find that the collapse transition is considerably more abrupt for the protein A sequence than for random sequences with the same composition. The chain collapse is found to be at least as fast as helix formation. Energy minimization restricted to the thermodynamically favored topology gives a structure that has a root-mean-square deviation of 1.8 A from the native structure. The sequence-dependent part of our potential is pairwise additive. Our calculations suggest that fine-tuning this potential by parameter optimization is of limited use.

Three-helix-bundle protein in a Ramachandran model

We study the thermodynamic behavior of a model protein with 54 amino acids that forms a three-helix bundle in its native state. The model contains three types of amino acids and five to six atoms per amino acid and has the Ramachandran torsional angles phi(i), psi(i) as its degrees of freedom. The force field is based on hydrogen bonds and effective hydrophobicity forces. For a suitable choice of the relative strength of these interactions, we find that the three-helix-bundle protein undergoes an abrupt folding transition from an expanded state to the native state. Also shown is that the corresponding one- and two-helix segments are less stable than the three-helix sequence.

A conflict of strategies: Medicaid managed care and Medicaid maximization

OBJECTIVE

To examine the influence of state strategies aimed at increasing federal Medicaid matching dollars on the design of states' Medicaid managed care programs.

STUDY DESIGN

Data obtained from the 1996-1997 case studies of 13 states to examine how states have adapted the design of their Medicaid managed care programs in part because of maximization strategies, to accommodate the many roles and responsibilities that Medicaid has assumed over the years.

PRINCIPAL FINDINGS

Our study showed that as states made the shift to managed care, some found that the responsibilities undertaken in part through maximization strategies proved to be in conflict with their Medicaid managed care initiatives. Among other things, the study revealed that most states included provisions that preserved the health care safety net, such as adapting the managed care benefit package and promoting the participation of safety net providers in managed care programs. In addition, most of the study states continued to pay special subsidies to safety net providers, including hospitals and clinics.

CONCLUSIONS

States have made real progress in moving a large number of Medicaid beneficiaries into managed care. At the same time, many states have specially crafted their managed care programs to accommodate safety net providers and existing funding mechanisms. By making these adaptations states, in the long run, may compromise the central goals of managed care: controlling costs and improving Medicaid beneficiaries' access to and quality of care.

High-Resolution Spectroscopy of TaS in the Visible and Near-Infrared Regions

The spectrum of TaS between 4000 and 20 000 cm-1 has been recorded in emission from a microwave discharge with a resolution between 0.011 and 0.025 cm-1. Seventeen electronic transitions have been rotationally analyzed. Fifteen of these have the ground state, 2Delta, as the lower state and two of them are transitions between excited states. The ground state has been fitted to a Hund's case (a) Hamiltonian. Effective molecular constants have been determined for the excited states, which are mainly described as Hund's case (c). Perturbations that have been found in the excited states are discussed. Transitions between states that are connected neither to the ground state nor to any of the other 14 electronic states of this work have been found. No analysis is presented for these transitions, but some of their characteristic features are described. Copyright 1998 Academic Press.

On the Singlet Spectrum of ZrS

Three electronic transitions in the singlet manifold of the zirconium sulphide (ZrS) molecule have been rotationally analyzed. They are the B1Pi-X1Sigma+, C1Sigma+-X1Sigma+, and E1Sigma+-X1Sigma+ systems with (0,0) band heads at 924.60, 731.51, and 494.47 nm, respectively. The ground state X1Sigma+ has an equilibrium bond distance of 2.15661(4) Å. Perturbations in the B1Pi and C1Sigma+ states are discussed. Copyright 1998 Academic Press.

Effects of Carbon Tetrachloride on Perfused Cultures of Hepatic and Neuronal Cells

Cultured hepatocytes and hemisphere neurons from chick embryos and mouse neuroblastoma cells were exposed to carbon tetrachloride (CC14; 0, 1, 2, 3 and 4mM) for 1 hour, using a perfusion system developed for studying the effects of volatile substances. In the perfused cultures, three parameters were compared: lipid peroxidation, membrane integrity and cellular respiration. In addition, cytochrome C oxidase activity was determined after incubation of cell homogenates with CC14. A concentration-dependent increase in lipid peroxidation and membrane permeability was found in the neuroblastoma cells. The hepatocytes responded to a lesser extent with respect to membrane permeability and their lipid peroxidation did not differ from that of controls. The hepatocytes responded with a 35% decrease in respiration when exposed to 3mM CC14, and a 20% decrease in cytochrome C oxidase activity after treatment with 1.5mM CCl4. In the neuronal cells, much smaller decreases in respiration were found and their cytochrome C oxidase activity remained unaffected. These results are very similar to those obtained after incubation in a closed chamber system. However, the perfused cells were found to be less sensitive to CCl4than cells exposed under static conditions.

A hypertext knowledge based for primary care - LIMEDS in LINCKS

In organized health care, primary care is the first level. It is characterized by the wide span of health problems managed as well as remote location from traditional medical information and knowledge sources. The LIMEDS project has formulated the special requirements for integrated knowledge and data base management in primary care. This paper presents Gösta's book , a hypertext knowledge base implemented in LINCKS, an object oriented, networked database system. Firstly, aspects which make integrated hypermedia systems particularly suitable for application in primary health care are explored. We then describe the hypertext knowledge base, consisting of 500 basic text objects and 3000 links, and current implementations using the NODE data model. NODE is implemented on a SUN III fileserver, and the user interface for the hypertext context on Apple Macintosh (TM). Combination of design methods towards a parallel means-ends strategy was found to be necessary to achieve Gösta's book . Design groups need to be composed of computer science, medical, psychological and organizational competences.

Lipid peroxidation and activities of tyrosine aminotransferase and glutamine synthetase in hepatoma and glioma cells grown in bovine colostrum-supplemented medium

The growth stimulating properties of bovine serum and colostrum were compared in rat hepatoma (HTC) and glioma (C6) cell cultures. A colostrum concentration of 2% was optimal for HTC cells, which then reached a terminal density 40% of that in serum-supplemented medium. The corresponding figures for C6 cells were 10 and 81%, respectively. After 4 d in culture, levels of lipid hydroperoxides were measured and compared. Highest levels of lipid hydroperoxides were found in HTC and C6 cells grown in unsupplemented medium. HTC and C6 cells grown in serum supplemented medium contained levels of 52 and 64%, respectively, of that in unsupplemented medium. The corresponding levels for cells grown in presence of colostrum were 40% for HTC and 44% for C6 cells. To obtain information on any functional alterations in the cells due to the presence of colostrum the induction of tyrosine aminotransferase (EC 2.6.1.5) and glutamine synthetase (EC 6.3.1.2) by dexamethasone was studied. Although colostrum seemed to increase the basal activities of the enzymes, no significant effects on the degree of induction could be detected.

Differential optical absorption spectroscopy system used for atmospheric mercury monitoring

A high-resolution differential optical absorption spectroscopy (DOAS) system for long-path atmospheric pollution monitoring is described. The system, consisting of a broadband lamp and a dispersive, fast-scanning optical receiver, separated by a few kilometers, was used in measurements of different pollutants, highlighted by the monitoring of the local concentration of atomic mercury. Mercury levels in the ppt (1:10(12)) range were assessed by comparisons with laboratory measurements.

Simultaneous spatially resolved NO and NO(2) measurements using one- and two-photon laser-induced fluorescence

We demonstrate how spatially resolved distributions of NO and NO(2) can be simultaneously detected by using a single laser pulse at 452 nm. The laser-induced fluorescence from NO was achieved by a two-photon transition in the gamma band at 226 nm followed by UV detection, whereas NO(2) was detected by a one-photon transition followed by Stokes fluorescence.