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PubMed1994

Structure of the transition state for the folding/unfolding of the barley chymotrypsin inhibitor 2 and its implications for mechanisms of protein folding.

The equilibrium and kinetics of folding of the single-domain protein chymotrypsin inhibitor 2 conform to the simple two-state model. The structure of the rate-determining transition state has been mapped out at the resolution of individual side chains by using the protein engineering method on 74 mutants that have been constructed at 37 of the 64 residues. The structure contains no elements of secondary structure that are fully formed. The majority of interactions are weakened by > 50% in the transition state, although most regions do have some very weak structure. The structure of the transition state appears to be an expanded form of the native state in which secondary and tertiary elements have been partly formed concurrently. This is consistent with a "global collapse" model of folding rather than a framework model in which folding is initiated from fully preformed local secondary structural elements. This may be a general feature for the folding of proteins lacking a folding intermediate and is perhaps representative of the early stages of folding for multidomain or multimodule proteins. The major transition state for the folding of barnase, for example, has some fully formed secondary and tertiary structural elements in the major transition state, and barnase appears to form by a framework process. However, the fully formed framework may be preceded by a global collapse, and a unified folding scheme is presented.

Chymotrypsin↗

PubMed2001

Circularization changes the folding transition state of the src SH3 domain.

Native state topology has been implicated as a major determinant of protein-folding mechanisms. Here, we test experimentally the robustness of the src SH3-domain folding transition state to changes in topology by covalently constraining regions of the protein with disulfide crosslinks and then performing kinetic analysis on point mutations in the context of these modified proteins. Circularization (crosslinking the N and C termini) of the src SH3 domain makes the protein topologically symmetric and causes delocalization of structure in the transition state ensemble suggesting a change in the folding mechanism. In contrast, crosslinking a single structural element (the distal beta-hairpin) which is an essential part of the transition state, results in a protein that folds 30 times faster, but does not change the distribution of structure in the transition state. As the transition states of distantly related SH3 domains were previously found to be very similar, we conclude that the free energy landscape of this protein family contains deep features which are relatively insensitive to sequence variations but can be altered by changes in topology.

Amino Acid Substitution↗

PubMed1998

The DNA binding activity of metal response element-binding transcription factor-1 is activated in vivo and in vitro by zinc, but not by other transition metals.

We examined the DNA binding activity of mouse and human MTF-1 in whole cell extracts from cells cultured in medium containing zinc or cadmium and from untreated cells after the in vitro addition of zinc or cadmium, as well as using recombinant MTF-1 transcribed and translated in vitro and treated with various transition metals. Incubation of human (HeLa) or mouse (Hepa) cells in medium containing cadmium (5-15 microM) did not lead to a significant increase (<2-fold) in the amount of MTF-1 DNA binding activity, whereas zinc (100 microM) led to a 6-15-fold increase within 1 h. MTF-1 binding activity was low, but detectable, in control whole cell extracts and was increased (>10-fold) after the in vitro addition of zinc (30 microM) and incubation at 37 degrees C for 15 min. In contrast, addition of cadmium (6 or 60 microM) did not activate MTF-1 binding activity. Recombinant mouse and human MTF-1 were also dependent on exogenous zinc for DNA binding activity. Cadmium did not facilitate activation of recombinant MTF-1, but instead inhibited the activation of the recombinant protein by zinc. Interestingly, glutathione (1 mM) protected recombinant MTF-1 from inactivation by cadmium, and allowed for activation by zinc. It was also noted that zinc-activated recombinant MTF-1 was protected from cadmium only when bound to DNA. These results suggest that cadmium interacts with the zinc fingers of MTF-1 and forms an inactive complex. Of the several transition metals (zinc, cadmium, nickel, silver, copper, and cobalt) examined, only zinc facilitated activation of the DNA binding activity of recombinant MTF-1. These data suggest that transition metals, other than zinc, that activate MT gene expression may do so by mechanisms independent of an increase in the DNA binding activity of MTF-1.

Animals↗

PubMed1979

Ultrastructural transitions associated with the development of the bladder cells of the trichomes of Atriplex.

Early in development, bladder cells are characterized by the absence of a vacuole or vacuoles, the presence of autophagic vesicles, and numerous, unaggregated ribosomes. With the formation and expansion of the central vacuole, the ribosomes become aggregated and elements of rough endoplasmic reticulum become apparent. This developmental transition is probably related to the production of proteins involved in ion accumulation in the vacuole. Throughout expansion, invaginations of the tonoplast and membraneous structures are associated with the vacuole. These may be indicative of a continued lytic function for this compartment. Also, dictyosomes are continuously present and dictyosome vesicles are associated with both the plasmalemma and tonoplast, which suggest that they contribute to both membrane systems during expansion of the cell and vacuole.

Cell Membrane↗

PubMed2004

Basics of cardiac development for the understanding of congenital heart malformations.

Cardiovascular development has become a crucial element of transgene technology in that many transgenic and knockout mice unexpectedly present with a cardiac phenotype, which often turns out to be embryolethal. This demonstrates that formation of the heart and the connecting vessels is essential for the functioning vertebrate organism. The embryonic mesoderm is the source of both the cardiogenic plate, giving rise to the future myocardium as well as the endocardium that will line the system on the inner side. Genetic cascades are unravelled that direct dextral looping and subsequent secondary looping and wedging of the outflow tract of the primitive heart tube. This tube consists of a number of transitional zones and intervening primitive cardiac chambers. After septation and valve formation, the mature two atria and two ventricles still contain elements of the primitive chambers as well as transitional zones. An essential additional element is the contribution of extracardiac cell populations like neural crest cells and epicardium-derived cells. Whereas the neural crest cell is of specific importance for outflow tract septation and formation of the pharyngeal arch arteries, the epicardium-derived cells are essential for proper maturation of the myocardium and coronary vascular formation. Inductive signals, sometimes linked to apoptosis, of the extracardiac cells are thought to be instructive for differentiation of the conduction system. In summary, cardiovascular development is a complex interplay of many cell-cell and cell-matrix interactions. Study of both (transgenic) animal models and human pathology is unravelling the mechanisms underlying congenital cardiac anomalies.

Animals↗

PubMed2003

Distance dependence of electron transfer across peptides with different secondary structures: the role of Peptide energetics and electronic coupling.

The charge-transfer transition energies and the electronic-coupling matrix element, |H(DA)|, for electron transfer from aminopyridine (ap) to the 4-carbonyl-2,2'-bipyridine (cbpy) in cbpy-(gly)(n)-ap (gly = glycine, n = 0-6) molecules were calculated using the Zerner's INDO/S, together with the Cave and Newton methods. The oligopeptide linkages used were those of the idealized protein secondary structures, the alpha-helix, 3(10)-helix, beta-strand, and polyproline I- and II-helices. The charge-transfer transition energies are influenced by the magnitude and direction of the dipole generated by the peptide secondary structure. The electronic coupling |H(DA)| between (cbpy) and (ap) is also dependent on the nature of the secondary structure of the peptide. A plot of 2.ln|H(DA)| versus the charge-transfer distance (assumed to be the dipole moment change between the ground state and the charge-transfer states) showed that the polyproline II structure is a more efficient bridge for long-distance electron-transfer reactions (beta = 0.7 A(-1)) than the other secondary structures (beta approximately 1.3 A(-1)). Similar calculations on charged dipeptide derivatives, [CH(3)CONHCH(2)CONHCH(3)](+/)(-), showed that peptide-peptide interaction is more dependent on conformation in the cationic than in the anionic dipeptides. The alpha-helix and polyproline II-helix both have large peptide-peptide interactions (|H(DA)| > 800 cm(-1)) which arise from the angular dependence of their pi-orbitals. Such an interaction is much weaker than in the beta-strand peptides. These combined results were found to be consistent with electron-transfer rates experimentally observed across short peptide bridges in polyproline II (n = 1-3). These results can also account for directional electron transfer observed in an alpha-helical structure (different ET rates versus the direction of the molecular dipole).

2,2'-Dipyridyl↗

PubMed1999

A Theoretical Investigation of the Renner Interactions and Magnetic Dipole Transitions in the Ã-&Xtilde; Electronic Band System of HO(2).

The Ã(2)A' --> &Xtilde;(2)A" electronic band system of HO(2) has been simulated in emission using an extended version of the program RENNER (P. Jensen, M. Brumm, W. P. Kraemer, and P. R. Bunker, J. Mol. Spectrosc. 171, 31-57 (1995)). The two electronic states involved in this transition have strongly bent equilibrium geometries but they correlate together to form a (2)Pi state at linearity. As a result the energy level pattern in the states is affected by electronic angular momentum effects (i.e., the Renner effect and spin-orbit coupling). To simulate the spectrum, we have calculated ab initio the potential energy surfaces, electric dipole moment surfaces, magnetic dipole moment surfaces, spin-orbit coupling parameter, and the electronic angular momentum matrix elements. Some of the forbidden DeltaK(a) = 0 transitions occurring in the spectrum are induced by the magnetic dipole transition moment, and the others are electric dipole transitions that gain intensity because of the Renner interaction, spin-orbit coupling, or because of rotation-vibration interaction. All of these effects are allowed for in our calculation. The electric dipole transition moment is very small (0.017 D at the ground state equilibrium geometry) and because of this the magnetic dipole transitions are quite visible; the strongest magnetic dipole transitions are calculated to be about 10 times weaker than the strongest electric dipole transitions. In this way previous experimental assignments (E. H. Fink and D. A. Ramsay, J. Mol. Spectrosc. 185, 304-324 (1997)) are confirmed theoretically. Copyright 1999 Academic Press.

Journal Article↗

PubMed2001

Importance of the amino-acid composition of the shutter region of plasminogen activator inhibitor-1 for its transitions to latent and substrate forms.

The serpins are of general protein chemical interest due to their ability to undergo a large conformational change consisting of the insertion of the reactive centre loop (RCL), which becomes strand 4, into the central beta sheet A. To make space for the incoming RCL, the 'shutter region' opens by the beta strands 3A and 5A sliding apart over the underlying alpha helix B. Loop insertion occurs during the formation of complexes of serpins with their target serine proteinases and during latency transition. This type of loop insertion is unique to plasminogen activator inhibitor-1 (PAI-1). We report here that amino-acid substitutions in a buried cluster of three residues forming a hydrogen bonding network in the shutter region drastically accelerate PAI-1 latency transition; that the rate was in all cases normalized by the PAI-1 binding protein vitronectin; and that substitution of an adjacent beta strand 5A Lys residue, believed to anchor beta strand 5A to other secondary structural elements, had differential effects on the rates of latency transition in the absence and the presence of vitronectin, respectively. An overlapping, but not identical set of substitutions resulted in an increased tendency to substrate behaviour of PAI-1 at reaction with its target proteinases. These findings show that vitronectin regulates the movements of the RCL through conformational changes of the shutter region and beta strand 5A, are in agreement with RCL insertion proceeding by different routes during latency transition and complex formation, and contribute to the biochemical basis for the potential use of PAI-1 as a therapeutic target in cancer and cardiovascular diseases.

Amino Acid Substitution↗

PubMed1992

The transcriptionally-active MMTV promoter is depleted of histone H1.

We have used an ultraviolet light cross-linking and immunoadsorption assay to demonstrate that histones H1 and H2B are bound to the repressed MMTV promoter. Hormone activation results in reduced H1 content with little or no change in H2B. High resolution analysis of the glucocorticoid-inducible DNaseI hypersensitive region demonstrates an NF-1 footprint as well as specific sites of enhanced cleavage on nucleosome B and in the nucleosome B/nucleosome A linker. These results are consistent with a model in which binding of the glucocorticoid receptor to glucocorticoid regulatory elements on the surface of nucleosome B induces a chromatin transition that is necessary for transcription factor (NF-1 and TFIID) recruitment to the MMTV promoter. We hypothesize that association of histone H1 with important cis-elements on the promoter masks these sites, and glucocorticoid-induced displacement of H1 is necessary to expose factor binding sites at the 3' edge of nucleosome B, in the nucleosome B/nucleosome A linker and at the 5' edge of nucleosome A.

Base Sequence↗

PubMed1995

A distal Sp1-element is necessary for maximal activity of the human gastrin gene promoter.

Studies of transgenic mice have shown that transcriptional control of the gastrin gene exhibits significant species differences. Transfection of the human gastrin promoter in murine cells have depicted proximal Sp1, E-box and CACC elements as the major determinants of transcription. We have examined cis-regulatory elements of the human promoter on a human gastrin expressing cell line and find that a distal -135 to -142 Sp1 element is necessary for maximal activity. Alignment of the mouse and human promoters shows that the proximal human Sp1 and CACC elements are not conserved, whereas the E-box element is retained. The distal Sp1 element is present in mouse but exhibits a C to T transition in the core that is likely to reduce binding affinity of Sp1. We conclude that gastrin gene transcription is regulated by distinct elements in man and rodents.

Adenocarcinoma↗

PubMed2003

Influence of substrate salinity on structure characteristics of petiole vessel elements of Bruguiera gymnorrhiza.

The anatomy of the mature leaf's petioles of one-year-old Bruguiera gymnorrhiza seedlings cultured in greenhouse was studied in this paper. The results are as follows: (1) Most of the vessel elements of the petioles of B. gymnorrhiza are of scalariform. Helical vessels and their transition type only account for a small portion of the total vessels. However, there is a notable increase in the number of helical vessels and their transition type with increasing salinity. (2) The length of petioles, diameter and length of scalariform vessel elements, and bar number of a scalariform perforation plate all exhibit of parabolic relationship with substrate salinity. They maximized at salinity between 20 g/L and 30 g/L. (3) It is new phenomenon that there are two scalariform perforation plates, facing differently, at the polar of the vessel element of the petioles in the seedlings under 10 g/L treatment. (4) Under low salinity, the changes in the structure of vessel elements had the tendency to promote the transportation of water with increasing salinity. While under high salinity, it tended to raise the reliability of the water transportation. The adaptive significance of the morphological characteristics of vessel elements in the petiole was discussed.

Dose-Response Relationship, Drug↗

PubMedDate not supplied

Modeling blood flow heterogeneity.

It has been known for some time that regional blood flows within an organ are not uniform. Useful measures of heterogeneity of regional blood flows are the standard deviation and coefficient of variation or relative dispersion of the probability density function (PDF) of regional flows obtained from the regional concentrations of tracers that are deposited in proportion to blood flow. When a mathematical model is used to analyze dilution curves after tracer solute administration, for many solutes it is important to account for flow heterogeneity and the wide range of transit times through multiple pathways in parallel. Failure to do so leads to bias in the estimates of volumes of distribution and membrane conductances. Since in practice the number of paths used should be relatively small, the analysis is sensitive to the choice of the individual elements used to approximate the distribution of flows or transit times. Presented here is a method for modeling heterogeneous flow through an organ using a scheme that covers both the high flow and long transit time extremes of the flow distribution. With this method, numerical experiments are performed to determine the errors made in estimating parameters when flow heterogeneity is ignored, in both the absence and presence of noise. The magnitude of the errors in the estimates depends upon the system parameters, the amount of flow heterogeneity present, and whether the shape of the input function is known. In some cases, some parameters may be estimated to within 10% when heterogeneity is ignored (homogeneous model), but errors of 15-20% may result, even when the level of heterogeneity is modest. In repeated trials in the presence of 5% noise, the mean of the estimates was always closer to the true value with the heterogeneous model than when heterogeneity was ignored, but the distributions of the estimates from the homogeneous and heterogeneous models overlapped for some parameters when outflow dilution curves were analyzed. The separation between the distributions was further reduced when tissue content curves were analyzed. It is concluded that multipath models accounting for flow heterogeneity are a vehicle for assessing the effects of flow heterogeneity under the conditions applicable to specific laboratory protocols, that efforts should be made to assess the actual level of flow heterogeneity in the organ being studied, and that the errors in parameter estimates are generally smaller when the input function is known rather than estimated by deconvolution.

Algorithms↗

PubMed2005

Theoretical study of inversion and topomerization processes of substituted cyclohexanes: the relevance of the energy 3D hypersurface.

Although the potential energy surface of highly symmetric cyclohexane has been extensively reviewed, no attention has been paid to the study of the effect of substitution of a methylene group by a heteroatom. The substitution may cause changes in molecular symmetry as well as the dipole moment, and the unshared electron pairs associated with the heteroatom may also introduce changes in molecular reactivity. However, these phenomena are not yet completely understood. To address these issues, a rigorous description of the inversion-topomerization process of methylcyclohexane and a revision of the conformational potential energy of oxane and thiane are presented. Moreover, the usefulness of providing a three-dimensional representation of these processes is discussed. In the case of methylcyclohexane, calculations show that three transition states are associated with inversion and four more with topomerization. In contrast, for oxane and thiane, only two transition states are involved with inversion and two with topomerization. Two fundamental conclusions can be drawn from this study. The first is that the inversion process occurs through elementary, stages that we have denoted "conformational elemental stages", which is an analogous term to that used for reaction mechanism description (minima-transition state-minima) where several elemental steps take place. The second conclusion is that two independent processes, inversion and topomerization, are connected by some common conformers. The inversion process controls the ring interchange, while topomerization allows exchange between skewed boats.

Journal Article↗

PubMed2005

Water content in the transition zone from electrical conductivity of wadsleyite and ringwoodite.

The distribution of water in the Earth's interior reflects the way in which the Earth has evolved, and has an important influence on its material properties. Minerals in the transition zone of the Earth's mantle (from approximately 410 to approximately 660 km depth) have large water solubility, and hence it is thought that the transition zone might act as a water reservoir. When the water content of the transition zone exceeds a critical value, upwelling flow might result in partial melting at approximately 410 km, which would affect the distribution of certain elements in the Earth. However, the amount of water in the transition zone has remained unknown. Here we determined the effects of water and temperature on the electrical conductivity of the minerals wadsleyite and ringwoodite to infer the water content of the transition zone. We find that the electrical conductivity of these minerals depends strongly on water content but only weakly on temperature. By comparing these results with geophysically inferred conductivity, we infer that the water content in the mantle transition zone varies regionally, but that its value in the Pacific is estimated to be approximately 0.1-0.2 wt%. These values significantly exceed the estimated critical water content in the upper mantle, suggesting that partial melting may indeed occur at approximately 410 km depth, at least in this region.

Journal Article↗

PubMed2004

Intermediates and the folding of proteins L and G.

We use a minimalist protein model, in combination with a sequence design strategy, to determine differences in primary structure for proteins L and G, which are responsible for the two proteins folding through distinctly different folding mechanisms. We find that the folding of proteins L and G are consistent with a nucleation-condensation mechanism, each of which is described as helix-assisted beta-1 and beta-2 hairpin formation, respectively. We determine that the model for protein G exhibits an early intermediate that precedes the rate-limiting barrier of folding, and which draws together misaligned secondary structure elements that are stabilized by hydrophobic core contacts involving the third beta-strand, and presages the later transition state in which the correct strand alignment of these same secondary structure elements is restored. Finally, the validity of the targeted intermediate ensemble for protein G was analyzed by fitting the kinetic data to a two-step first-order reversible reaction, proving that protein G folding involves an on-pathway early intermediate, and should be populated and therefore observable by experiment.

Bacterial Proteins↗

PubMed2001

Edge co-occurrence in natural images predicts contour grouping performance.

The human brain manages to correctly interpret almost every visual image it receives from the environment. Underlying this ability are contour grouping mechanisms that appropriately link local edge elements into global contours. Although a general view of how the brain achieves effective contour grouping has emerged, there have been a number of different specific proposals and few successes at quantitatively predicting performance. These previous proposals have been developed largely by intuition and computational trial and error. A more principled approach is to begin with an examination of the statistical properties of contours that exist in natural images, because it is these statistics that drove the evolution of the grouping mechanisms. Here we report measurements of both absolute and Bayesian edge co-occurrence statistics in natural images, as well as human performance for detecting natural-shaped contours in complex backgrounds. We find that contour detection performance is quantitatively predicted by a local grouping rule derived directly from the co-occurrence statistics, in combination with a very simple integration rule (a transitivity rule) that links the locally grouped contour elements into longer contours.

Bayes Theorem↗

PubMed1998

A secondary ion mass spectroscopic study of the elemental composition pattern in rat incisor dental enamel during different stages of ameloblast differentiation.

In most earlier studies on the elemental composition pattern of dental enamel, a picture is presented which describes a limited region. In this study, estimates of the incorporation of some critical elements into enamel were correlated with the differentiation stages of the ameloblasts through out the whole tooth. Elemental analyses of rat incisor dental enamel during the secretory, transitional and maturation phases were performed using two different modes of secondary ion mass spectrometry (SIMS). The results were presented as ion images and three-dimensional spatial resolution graphs. In the elemental images of 23Na, 26CN, 35Cl and 39K, counts were detected during the secretory and maturation phases of amelogenesis. Variations were interpreted as resulting from secretion of elements during the secretory phase and resorption during the maturation phase. In line scans the ion yield from enamel during different stages of differentiation of the ameloblasts was analysed. The elements investigated were 12C, 19F, 23Na, 31P, 39K and 77CaCl. As seen in the images, most elements exhibited a higher ion yield during the earlier stages of secretion, and lower yields during the maturation-phase resorption. Cl, together with P, increased during the phases of maturation. In the most apical portions of the teeth, corresponding to a presecretory phase, an inverse pattern was seen for most of the elements. If the surface yield was high at the onset of the secretory phase, the presecretory yields were lower, and vice versa.

Amelogenesis↗

PubMed1999

Gene transcription through Myc family members in eukaryotic cells.

c-Myc family proteins, encoded by c-myc family proto-oncogenes, play critical roles in mechanisms associated with proliferation, differentiation and apoptotic death in eukaryotic cells. These functions are mediated by transcriptional activity of these proteins through binding to the E-box core sequence CACGTG referred to as a Myc core element located at a promoter or enhancer region of the individual target genes in the nucleus. Recent studies have demonstrated the presence of novel nuclear proteins that specifically recognize a Myc core element, in addition to c-Myc, Max, Mad and Mxi1. On the other hand, a Myc core element has alternating purine/pyrimidine repeats which could undergo a conformational transition from right-handed (B-DNA) to left-handed (Z-DNA) forms in the presence of a high concentration of salts such as Mg2+ and polyamines. Similarly, a Myc element has a homopurine-homopyrimidine site that may take a triplex configuration in particular situations. We have searched for nuclear proteins that can specifically recognize a Myc core element in different topological variations in murine brain.

Base Sequence↗