Direct observation of translocation in individual DNA polymerase complexes

Complexes of phi29 DNA polymerase and DNA fluctuate on the millisecond time scale between two ionic current amplitude states when captured atop the α-hemolysin nanopore in an applied field. The lower amplitude state is stabilized by complementary dNTP and thus corresponds to complexes in the post-translocation state. We have demonstrated that in the upper amplitude state, the DNA is displaced by a distance of one nucleotide from the post-translocation state. We propose that the upper amplitude state corresponds to complexes in the pre-translocation state. Force exerted on the template strand biases the complexes toward the pre-translocation state. Based on the results of voltage and dNTP titrations, we concluded through mathematical modeling that complementary dNTP binds only to the post-translocation state, and we estimated the binding affinity. The equilibrium between the two states is influenced by active site-proximal DNA sequences. Consistent with the assignment of the upper amplitude state as the pre-translocation state, a DNA substrate that favors the pre-translocation state in complexes on the nanopore is a superior substrate in bulk phase for pyrophosphorolysis. There is also a correlation between DNA sequences that bias complexes toward the pre-translocation state and the rate of exonucleolysis in bulk phase, suggesting that during DNA synthesis the pathway for transfer of the primer strand from the polymerase to exonuclease active site initiates in the pre-translocation state.     

Relation between the conformational heterogeneity and reaction cycle of Ras: molecular simulation of Ras

Ras functions as a molecular switch by cycling between the active GTP-bound state and the inactive GDP-bound state. It is known experimentally that there is another GTP-bound state called state 1. We investigate the conformational changes and fluctuations arising from the difference in the coordinations between the switch regions and ligands in the GTP- and GDP-bound states using a total of 830 ns of molecular-dynamics simulations. Our results suggest that the large fluctuations among multiple conformations of switch I in state 1 owing to the absence of coordination between Thr-35 and Mg²⁺ inhibit the binding of Ras to effectors. Furthermore, we elucidate the conformational heterogeneity in Ras by using principal component analysis, and propose a two-step reaction path from the GDP-bound state to the active GTP-bound state via state 1. This study suggests that state 1 plays an important role in signal transduction as an intermediate state of the nucleotide exchange process, although state 1 itself is an inactive state for signal transduction.     

The mitochondrial channel VDAC has a cation-selective open state

The mitochondrial channel VDAC is known to have two major classes of functional states, a large conductance "open" state that is anion selective, and lower conductance substates that are cation selective. The channel can reversibly switch between open and half-open states, with the latter predominant at increasing membrane voltages of either polarity. We report the presence of a new functional state of VDAC, a cation-selective state with conductance approximately equal to that of the canonical open state. This newly described state of VDAC can be reached from either the half-open cation-selective state or from the open anion-selective state. The latter transition implies that a mechanism exists for selectivity gating in VDAC that is separate from partial closure, which may be relevant to the physiological regulation of this channel and mitochondrial outer membrane permeability.     

A new mechanism for adaptation to changes in light intensity and quality in the red alga,Porphyra perforata. II. Characteristics of state II—state III transitions

Characteristics of state II—state III transitions in the red alga, Porphyra perforata, were studied by measuring the fluorescence time course at room temperature and fluorescence spectra at 77 K. The state II to III transition was induced by system II light and was sensitive to uncouplers of photophosphorylation. This state II to III transition has a dark step(s) that could be easily separated from the light process. A state III to II transition occurred in the dark, but system I light accelerated the transition. The accelerating effect of system I light was not sensitive to uncouplers of photophosphorylation, but was inhibited by the addition of valinomycin + KCl or antimycin A. Compared to state I—state II transitions, the state II—state III transitions occurred more rapidly. The state II to state III transitions are different from the state I to state II transitions in that in state III the activity of photosystem II is changed without having any effect on photosystem I activity (Satoh and Fork, Biochim. Biophys, Acta, in press, 1982). It is suggested that the state II—state III transition represents a mechanism by which the alga can avoid photodamage resulting from absorption of excess light energy by photosystem II.     

Helical and expanded conformation of equine beta-lactoglobulin in the cold-denatured state

The thermal unfolding transition of equine beta-lactoglobulin (ELG) was investigated by circular dichroism (CD) over a temperature range of -15 degrees C to 85 degrees C. In the presence of 2 M urea, a cooperative unfolding transition was observed both with increasing and decreasing temperature. The CD spectrum indicated that the heat and cold-denatured states of ELG have substantial secondary structures but lack persistent tertiary packing of the side-chains. In order to clarify the relation between the heat or cold-denatured state and the acid-denatured (A) state characterized previously, we have attempted to observe the temperature dependence of the CD spectrum at pH 1.5. The CD spectrum in the heat-denatured state is similar to that in the A state. The CD spectrum in the A state does not change cooperatively with increasing temperature. These results indicate that the heat-denatured state and the A state are the same structural state. On the other hand, the CD intensity at acid pH cooperatively increased with decreasing temperature. The CD spectrum at low temperature and acid pH is consistent with that in the cold-denatured state. Therefore, the cold-denatured state is distinguished from the heat-denatured state or the A state, and ELG assumes a larger amount of non-native alpha-helices in the cold-denatured state. Small angle X-ray scattering and analytical ultracentrifugation have indicated that ELG assumes an expanded chain-like conformation in the cold-denatured state in contrast to the compact globular conformation in the A state. The relation between the molecular size and the helical content in the partially folded states is discussed.     

The Association between State Attachment Security and State Mindfulness

Recent research suggests that attachment and mindfulness are related, though the nature of this association is unclear. Here we present two studies examining whether there is a causal relationship between state attachment and state mindfulness. Study 1 investigated the effects of experimentally increasing state mindfulness on state attachment security. State mindfulness was successfully enhanced, but this led to no change in state attachment security. Study 2 investigated the effects of experimentally enhancing state attachment security on state mindfulness. State attachment security was successfully enhanced, but this did not lead to any change in state mindfulness. These findings suggest that there is not a direct, immediate causal relationship between state attachment and state mindfulness as a result of brief experimental manipulations. Future research should examine these associations in longer term interventions.     

Chinese ethnicities in neoliberal Singapore? State designs and dialect(ical) struggles of community associations

Since the late 1990s, Singaporean state authorities have been increasingly marketing the city state as a knowledge-based hub between mainland China and western societies. Their focus on Mandarin-speaking mainlanders contrasts with Singapore's historical Chinese roots. By investigating the daily activities of Hokkien and Teochew community associations, I argue that these associations are finding ways to adapt to state initiatives that market a China-centric identity and target mainlanders. These dialect-based associations try to profit from state designs, while at the same time reclaiming their own historical distinctiveness. Drawing on qualitative work, I document the temporal practices of local dialect-based associations in reaction to neoliberal state initiatives that reduce Chineseness to a de-historicized skill set and stress how state–community interactions shape evolving Chinese ethnicities of the city state.     

Ancestral state estimation and taxon sampling density

A set of experiments based on simulation and analysis found that using the parsimony algorithm for ancestral state estimation can benefit from increased sampling of terminal taxa. Estimation at the base of small clades showed strong sensitivity to tree topology and number of descendent tips. These effects were largely driven by the creation and negation of ambiguity across a topology. Root state and internal state estimation showed similar behavior. We conclude that increased taxon sampling density is generally advisable, and attention to topological effects may be advisable in evaluating the confidence placed in state estimation. We also explore the factors affecting ancestral state estimation and conjecture that as taxa are added to a tree, the total amount of information for root state estimation depends on the tree topology and distance to root state of added taxa. For a pure-birth model tree, we conjecture that the addition of N taxa increases root state information in proportion to log(N).     

Shape of the free energy barriers for protein folding probed by multiple perturbation analysis

The characterization of the free energy barriers has been a major goal in studies on the mechanism of protein folding. Testing the effect of mutations or denaturants on protein folding reactions revealed that transition state movement is rare, suggesting that folding barriers are robust and narrow maxima on the free energy landscape. Here we demonstrate that the application of multiple perturbations allows the observation of small transition state movements that escape detection in single perturbation experiments. We used tendamistat as a model protein to test the broadness of the free energy barriers. Tendamistat folds over two consecutive transition states and through a high-energy intermediate. Measuring the combined effect of temperature and denaturant on the position of the transition state in the wild-type protein and in several mutants revealed that the early transition state shows significant transition state movement. Its accessible surface area state becomes more native-like with destabilization of the native state by temperature. To the same extent, the entropy of the early transition state becomes more native-like with increasing denaturant concentration, in accordance with Hammond behavior. The position of the late transition state, in contrast, is much less sensitive to the applied perturbations. These results suggest that the barriers in protein folding become increasingly narrow as the folding polypeptide chain approaches the native state.     

Energy distribution in the photochemical apparatus of Porphyridium cruentum in state I and state II

Fluorescence of Porphyridium cruentum in state I (cells equilibrated in light absorbed predominantly by Photosystem I) and in state II (cells equilibrated in light absorbed appreciably by Photosystem II) was examined to determine how the distribution of excitation energy was altered in the transitions between state I and state II. Low temperature emission spectra of cells frozen in state I and state II confirmed that a larger fraction of the excitation energy is delivered to Photosystem II in state I. Low temperature measurements showed that the yield of energy transfer from Photosystem II to Photosystem I was greater in state II and calculations indicated that the photochemical rate constant for such energy transfer was approximately twice as large in state II. Measurements at low temperature also showed that the cross sections and the spectral properties of the photosystems did not change in the transitions between state I and state II. In agreement with predictions made from the parameters measured at low temperature, the action spectra for oxygen evolution measured at room temperature were found to be the same in state I and state II.     

Compact molten globule-like state of hUBF HMG Box1 at extremely low pH

Using far and near-UV CD, ANS fluorescence and 2D NMR spectroscopy, an acid-induced partly folded state (A state) at extremely low pH for hUBF HMG Box1 was identified and characterized. As compared to the native state (N), the A state has similar secondary structure, less compact pack with larger amounts of exposed hydrophobic surface, and narrower chemical shift dispersion in (1)H-(15)N HSQC spectrum, which implies that it is a molten globule (MG)-like species. On the other hand, substantial tertiary contacts and cooperative thermal denaturing transition indicate that the A state is closer-relative to the classic MG-to the native folded state. In addition, when the solution pH is adjusted to neutrality, the protein in the A state refolds to the native state easily. All these data suggest that the A state of hUBF HMG Box1 could represent a potential folding intermediate on protein folding pathway.     

Characterization of the denatured structure of pyrrolidone carboxyl peptidase from a hyperthermophile under nondenaturing conditions: role of the C-terminal alpha-helix of the protein in folding and stability

The cysteine-free pyrrolidone carboxyl peptidase (PCP-0SH) from a hyperthermophile, Pyrococcus furiosus, can be trapped in the denatured state under nondenaturing conditions, corresponding to the denatured structure that exists in equilibrium with the native state under physiological conditions. The denatured state is the initial state (D1 state) in the refolding process but differs from the completely denatured state (D2 state) in the concentrated denaturant. Also, it has been found that the D1 state corresponds to the heat-denatured state. To elucidate the structural basis of the D1 state, H/D exchange experiments with PCP-0SH were performed at pD 3.4 and 4 degrees C. The results indicated that amide protons in the C-terminal alpha6-helix region hardly exchanged in the D1 state with deuterium even after 7 days, suggesting that the alpha6-helix (from Ser188 to Glu205) of PCP-0SH was stably formed in the D1 state. In order to examine the role of the alpha6-helix in folding and stability, H/D exchange experiments with a mutant, A199P, at position 199 in the alpha6-helix region were performed. The alpha6-helix region of A199P in the D1 state was partially unprotected, while some hydrophobic residues were protected against the H/D exchange, although these hydrophobic residues were unprotected in the wild-type protein. These results suggest that the structure of A199P in the D1 state formed a temporary stable denatured structure with a non-native hydrophobic cluster and the unstructured alpha6-helix. Both the stability and the refolding rate decreased by the substitution of Pro for Ala199. We can conclude that the native-like helix (alpha6-helix) of PCP-0SH is already constructed in the D1 state and is necessary for efficient refolding into the native structure and stabilization of PCP-0SH.     

Structural studies of translating ribosomes. II. Comparative sedimentation analysis of pre- and post-translocation states

Using the solid-phase translation system technique where template poly(U) is covalently coupled to Sepharose through cleavable disulfide bridges translating monoribosomes carrying a polypeptide (polyPhe) of 10 to 20 amino acids long have been isolated. Both pre-translocation state and post-translocation state ribosomes have been obtained. It has been shown that the sedimentation coefficient of the pre-translocation state ribosomes exceeds that of the post-translocation state ribosomes by a magnitude of about 1S. This difference is independent on the sedimentation rate (hydrostatic pressure) in the range of 20 000 to 40 000 rev/min and, most likely, is not a direct contribution of the increase of the particle mass at the expense of an additional tRNA in the pre-translocation state ribosomes. Together with other data, this result suggests that translating ribosomes in the pre-translocation state are more compact than post-translocation state ribosomes.     

Glassy State and Seed Storage Stability: A Viability Equation Analysis

Dry seeds exist generally in a glassy (or vitrified) state.The high viscosity of the glassy state would be expected tohave a retarding effect on deteriorative reactions in the cytoplasm.Thus the glassy state may be considered to be a biophysicalbarrier for seed deterioration. The present study aims to testthe hypothesis that seed storage stability is associated withthe glassy state. With the equations derived from the seed viabilityequation, we have calculated the maximum temperature (Tmax)for long-term storage of corn, pea and soybeans. The Tmax forlong-term seed storage is found to be in a good agreement withthe glass transition temperature (Tg) in each instance, suggestingthat seed deterioration would be accelerated when seeds arenot in the glassy state. Experiments with soybeans given acceleratedageing show that the loss of glassy state is followed by a rapiddecrease in seed viability. These observations provide indirectevidence that the glassy state may play a significant role inseed storage stability.Copyright 1994, 1999 Academic Press Glassy state, seed longevity, storage stability, viability analysis     

Mechanism of the light state transition in photosynthesis. III. Kinetics of the state transition in Porphyridium cruentum

The kinetics of the light state transition in the red alga Porphyridium cruentum were studied in low intensities of initiating light and in saturating flashes brief enough to elicit single turnovers of the photochemical apparatus. We confirm that the state transition is dose-dependent, but also found that the transition to state 2 was biphasic. The slow phase was correlated with the induction of photosynthesis and was eliminated if the preceding time spent in state 1 was very short. The full transition to state 1 developed following a minimum of 15 turnovers of Photosystem I, and the optimal frequency for the flash sequence was determined to be 2.5 Hz. In contrast, the turnover time required for the transition to state 2 was found to be smaller than 30 ms. The data are consistent with a mechanism we have recently proposed for the state transition in organisms that contain phycobilisomes. The mechanism proposed involves a small conformational change within the thylakoid that is brought about by localized differences in electrochemical potential. A Photosystem-I-generated potential difference of H⁺ is prerequisite for the initiation of state 1 and, under certain conditions, a localized electric-field generated by Photosystem II may play a significant role in the transition to state 2.     

The methanol-induced transition and the expanded helical conformation in hen lysozyme.

Methanol-induced conformational transitions of hen egg white lysozyme were investigated with a combined use of far- and near-UV CD and NMR spectroscopies, ANS binding and small-angle X-ray scattering. Addition of methanol induced no global change in the native conformation itself, but induced a transition from the native state to the denatured state which was highly cooperative, as shown by the coincidence of transition curves monitored by the far- and near-UV CD spectroscopy, by isodichroic points in the far- and near-UV CD spectra and by the concomitant disappearance of individual 1H NMR signals of the native state. The ANS binding experiments could detect no intermediate conformer similar to the molten globule state in the process of the methanol denaturation. However, at high concentration of methanol, e.g., 60% (v/v) methanol/water, a highly helical state (H) was realized. The H state had a helical content much higher than the native state, monitored by far-UV CD spectroscopy, and had no specific tertiary structure, monitored both by near-UV CD and NMR spectroscopy. The radius of gyration in the H state, 24.9 angstroms, was significantly larger than that in the native state (15.7 angstroms). The Kratky plot for the H state did not show a clear peak and was quite similar to that for the urea-denatured state, indicating a complete lack of globularity. Thus we conclude that the H state has a considerably expanded, flexible broken rod-like conformation which is clearly distinguishable from the "molten globule" state. The stability of both N and H states depends on pH and methanol concentration. Thus a phase diagram involving N and H was constructed.     

Conformational states of beta-lactamase: molten-globule states at acidic and alkaline pH with high salt

We present evidence that beta-lactamase is close to fully unfolded (i.e., random coil conformation) at low ionic strength at the extremes of pH and that the presence of salt causes a cooperative transition to a conformation with the properties of a molten globule, namely, a compact state with native-like secondary structure but disordered side chains (tertiary structure). The conformation of beta-lactamase I from Bacillus cereus was examined over the pH 1.5-12.5 region by circular dichroism (CD), tryptophan fluorescence, dynamic light scattering, and 1-anilino-8-naphthalenesulfonate (ANS) binding. Under conditions of low ionic strength (I = 0.05) beta-lactamase was unfolded below pH 2.5 and above pH 11.5, on the basis of the far-UV and near-UV CD and tryptophan fluorescence. However, at high ionic strength and low pH an intermediate conformation (state A) was observed, with a secondary structure content similar to that of the native protein but a largely disordered tertiary structure. The transition from the unfolded state (U) to state A induced by KCl was cooperative and had a midpoint at 0.12 M KCl (I = 0.17 M) at pH 1.6. A similar conformation (state B) was observed at high pH and high ionic strength. The transition from the alkaline U state to state B induced by KCl at pH 12.2 was cooperative and had a midpoint at 0.6 M KCl (I = 0.65 M). Light scattering measurements showed that state B was compact although somewhat expanded compared to the N state. The compactness of state A could not be determined due to its strong propensity to aggregate.(ABSTRACT TRUNCATED AT 250 WORDS)     

Protein unfolding transitions in an intrinsically unstable annexin domain: molecular dynamics simulation and comparison with nuclear magnetic resonance data

Unfolding transitions of an intrinsically unstable annexin domain and the unfolded state structure have been examined using multiple approximately 10-ns molecular dynamics simulations. Three main basins are observed in the configurational space: native-like state, compact partially unfolded or intermediate compact state, and the unfolded state. In the native-like state fluctuations are observed that are nonproductive for unfolding. During these fluctuations, after an initial loss of approximately 20% of the core residue native contacts, the core of the protein transiently completely refolds to the native state. The transition from the native-like basin to the partially unfolded compact state involves approximately 75% loss of native contacts but little change in the radius of gyration or core hydration properties. The intermediate state adopts for part of the time in one of the trajectories a novel highly compact salt-bridge stabilized structure that can be identified as a conformational trap. The intermediate-to-unfolded state transition is characterized by a large increase in the radius of gyration. After an initial relaxation the unfolded state recovers a native-like topology of the domain. The simulated unfolded state ensemble reproduces in detail experimental nuclear magnetic resonance data and leads to a convincing complete picture of the unfolded domain.     

Analysis of membrane fusion as a two-state sequential process: evaluation of the stalk model

We propose a model that accounts for the time courses of PEG-induced fusion of membrane vesicles of varying lipid compositions and sizes. The model assumes that fusion proceeds from an initial, aggregated vesicle state ((A) membrane contact) through two sequential intermediate states (I(1) and I(2)) and then on to a fusion pore state (FP). Using this model, we interpreted data on the fusion of seven different vesicle systems. We found that the initial aggregated state involved no lipid or content mixing but did produce leakage. The final state (FP) was not leaky. Lipid mixing normally dominated the first intermediate state (I(1)), but content mixing signal was also observed in this state for most systems. The second intermediate state (I(2)) exhibited both lipid and content mixing signals and leakage, and was sometimes the only leaky state. In some systems, the first and second intermediates were indistinguishable and converted directly to the FP state. Having also tested a parallel, two-intermediate model subject to different assumptions about the nature of the intermediates, we conclude that a sequential, two-intermediate model is the simplest model sufficient to describe PEG-mediated fusion in all vesicle systems studied. We conclude as well that a fusion intermediate "state" should not be thought of as a fixed structure (e.g., "stalk" or "transmembrane contact") of uniform properties. Rather, a fusion "state" describes an ensemble of similar structures that can have different mechanical properties. Thus, a "state" can have varying probabilities of having a given functional property such as content mixing, lipid mixing, or leakage. Our data show that the content mixing signal may occur through two processes, one correlated and one not correlated with leakage. Finally, we consider the implications of our results in terms of the "modified stalk" hypothesis for the mechanism of lipid pore formation. We conclude that our results not only support this hypothesis but also provide a means of analyzing fusion time courses so as to test it and gauge the mechanism of action of fusion proteins in the context of the lipidic hypothesis of fusion.     

Energetic basis of structural stability in the molten globule state: alpha-lactalbumin

The denatured states of alpha-lactalbumin, which have features of a molten globule state, have been studied to elucidate the energetics of the molten globule state and its contribution to the stability of the native conformation. Analysis of calorimetric and CD data shows that the heat capacity increment of alpha-lactalbumin denaturation highly correlates with the degree of disorder of the residual structure of the state. As a result, the denaturational transition of alpha-lactalbumin from the native to a highly ordered compact denatured state, and from the native to the disordered unfolded state are described by different thermodynamic functions. The enthalpy and entropy of the denaturation of alpha-lactalbumin to compact denatured state are always greater than the enthalpy and entropy of its unfolding. This difference represents the unfolding of the molten globule state. Calorimetric measurements of the heat effect associated with the unfolding of the molten globule state reveal that it is negative in sign over the temperature range of molten globule stability. This observation demonstrates the energetic specificity of the molten globule state, which, in contrast to a protein with unique tertiary structure, is stabilized by the dominance of negative entropy and enthalpy of hydration over the positive conformational entropy and enthalpy of internal interactions. It is concluded that at physiological temperatures the entropy of dehydration is the dominant factor providing stability for the compact intermediate state on the folding pathway, while for the stability of the native state, the conformational enthalpy is the dominant factor.