Is protein folding hierarchic? II. Folding intermediates and transition states

The folding reactions of some small proteins show clear evidence of a hierarchic process, whereas others, lacking detectable intermediates, do not. Evidence from folding intermediates and transition states suggests that folding begins locally, and that the formation of native secondary structure precedes the formation of tertiary interactions, not the reverse. Some notable examples in the literature have been interpreted to the contrary. For these examples, we have simulated the local structures that form when folding begins by using the LINUS program with nonlocal interactions turned off. Our results support a hierarchic model of protein folding.     

Mouse ApoM displays an unprecedented seven-stranded lipocalin fold: folding decoy or alternative native fold?

Mouse apolipoprotein M (m-apoM) displays a 79% sequence identity to human apolipoprotein M (h-apoM). Both proteins are apolipoproteins associated with high-density lipoproteins, with similar anticipated biological functions. The structure of h-apoM has recently been determined by X-ray crystallography, which revealed that h-apoM displays, as expected, a lipocalin-like fold characterized by an eight-stranded β?barrel that encloses an internal fatty-acid-binding site. Surprisingly, this is not true for m-apoM. After refolding from inclusion bodies, the crystal structure of m-apoM (reported here at 2.5 Å resolution) displays a novel yet unprecedented seven-stranded β-barrel structure. The fold difference is not caused by a mere deletion of a single β-strand; instead, β-strands E and F are removed and replaced by a single β-strand A′ formed from residues from the N-terminus. Molecular dynamics simulations suggest that m-apoM is able to adopt both a seven-stranded barrel structure and an eight-stranded barrel structure in solution, and that both folds are comparably stable. Thermal unfolding simulations identify the position where β-strand exchange occurs as the weak point of the β-barrel. We wonder whether the switch in topology could have a biological function and could facilitate ligand release, since it goes hand in hand with a narrowing of the barrel diameter. Possibly also, the observed conformation represents an on-pathway or off-pathway folding intermediate of apoM. The difference in fold topology is quite remarkable, and the fold promiscuity observed for m-apoM might possibly provide a glimpse at potential cross-points during the evolution of β-barrels.     

Catecholamine sulfates: end products or metabolic intermediates?

Dopamine-beta-hydroxylase catalyzes the beta-oxidation of dopamine to noradrenaline while phenylethanolamine-N-methyltransferase converts noradrenaline to adrenaline. Since catecholamine sulfates represent the predominant form of catecholamines in human tissues, we have studied the role of dopamine sulfate and noradrenaline sulfate as alternate substrates for dopamine-beta-hydroxylase and phenylethanolamine-N-methyltransferase, respectively. Dopamine 3-sulfate, dopamine 4-sulfate and noradrenaline 3-sulfate were chemically synthesized and exhaustively purified by ion-exchange chromatography. Dopamine-beta-hydroxylase and phenylethanolamine-N-methyltransferase were partially purified from human adrenals. Using tyramine as substrate, dopamine-beta-hydroxylase is slightly inhibited by dopamine 3-sulfate according to some irreversible or mixed mechanisms. When dopamine-beta-hydroxylase was incubated with dopamine 3-sulfate or dopamine 4-sulfate, we were not able to find any synthesis of either noradrenaline sulfate or free noradrenaline. Using phenylethanolamine as substrate, the enzymatic activity of phenylethanolamine-N-methyltransferase remains unchanged with addition of dopamine 3-sulfate, dopamine 4-sulfate or noradrenaline 3-sulfate. It was concluded that dopamine sulfate is not an alternate substrate for either dopamine-beta-hydroxylase or phenylethanolamine-N-methyltransferase nor is noradrenaline 3-sulfate an alternate substrate for phenylethanolamine-N-methyltransferase.     

Community assembly: alternative stable states or alternative transient states?

The concept of alternative stable states has long been a dominant framework for studying the influence of historical contingency in community assembly. This concept focuses on stable states, yet many real communities are kept in a transient state by disturbance, and the utility of predictions for stable states in explaining transient states remains unclear. Using a simple model of plant community assembly, we show that the conditions under which historical contingency affects community assembly can differ greatly for stable versus transient states. Differences arise because the contribution of such factors as mortality rate, environmental heterogeneity and plant-soil feedback to historical contingency changes as community assembly proceeds. We also show that transient states can last for a long time relative to immigration rate and generation time. These results argue for a conceptual shift of focus from alternative stable states to alternative transient states for understanding historical contingency in community assembly.     

Kinetic competence of enzymic intermediates: fact or fiction?

A number of enzymatic reactions involve intermediates that are not normally released during the reaction. Whether such an intermediate when added to the enzyme reacts as fast or faster than the normal substrates, and thus is "kinetically competent", depends on the degree to which the equilibrium constant for forming the intermediate from the substrates is different on the enzyme surface and in solution, as well as on the relative affinities of the enzyme for substrate and intermediate. Similar values for these equilibrium constants require that the intermediate react slowly, while a far more favorable value for intermediate formation on the enzyme allows the intermediate to react at up to the diffusion-limiting rate. When one intermediate is formed from two substrates, it may react much more rapidly than when two intermediates are formed from two substrates, or one from one. Comparison of the kinetics of the putative intermediate(s) and the substrate(s) can reveal a great deal about the mechanism of the catalytic reaction and the kinetic barrier that normally keeps the intermediate(s) on the enzyme.     

Does native state topology determine the RNA folding mechanism?

Recent studies in protein folding suggest that native state topology plays a dominant role in determining the folding mechanism, yet an analogous statement has not been made for RNA, most likely due to the strong coupling between the ionic environment and conformational energetics that make RNA folding more complex than protein folding. Applying a distributed computing architecture to sample nearly 5000 complete tRNA folding events using a minimalist, atomistic model, we have characterized the role of native topology in tRNA folding dynamics: the simulated bulk folding behavior predicts well the experimentally observed folding mechanism. In contrast, single-molecule folding events display multiple discrete folding transitions and compose a largely diverse, heterogeneous dynamic ensemble. This both supports an emerging view of heterogeneous folding dynamics at the microscopic level and highlights the need for single-molecule experiments and both single-molecule and bulk simulations in interpreting bulk experimental measurements.     

Making the leap from structure to mechanism: are the open states of mammalian complex I identified by cryoEM resting states or catalytic intermediates?

Respiratory complex I (NADH:ubiquinone oxidoreductase) is a multi-subunit, energy-transducing mitochondrial enzyme that is essential for oxidative phosphorylation and regulating NAD⁺/NADH pools. Despite recent advances in structural knowledge and a long history of biochemical analyses, the mechanism of redox-coupled proton translocation by complex I remains unknown. Due to its ability to separate molecules in a mixed population into distinct classes, single-particle electron cryomicroscopy has enabled identification and characterisation of different complex I conformations. However, deciding on their catalytic and/or regulatory properties to underpin mechanistic hypotheses, especially without detailed biochemical characterisation of the structural samples, has proven challenging. In this review we explore different mechanistic interpretations of the closed and open states identified in cryoEM analyses of mammalian complex I.     

Sexual competition among females: What causes courtship-role reversal?

In most animals, males are the competitive sex whereas females are typically non-competitive and choosy of mates. In a variety of taxa, certain species (or populations within species) show a reversal in these typical courtship roles. Recent research with these organisms supports a central tenet of sexual selection theory: that it is the relative investment of the sexes in offspring that controls the number of males and females available for mating, and thus is the main determinant of the degree of sexual competition in each sex.     

What causes the depolarization of trypsin and trypsinogen fluorescence: Intramolecular mobility or non-radiative energy transfer?

Analysis of protein data bank information about the coordinates of definite atoms of protein macromolecules provides an opportunity to evaluate the efficiency of non-radiative resonance energy transfer within the model of fixed, strictly oriented oscillators. Such evaluations for trypsin and trypsinogen (and also for trypsin complex with a pancreatic inhibitor) show that the efficiency of energy transfer among each pair of tryptophan residues is negligibly small. It is also shown that a fairly effective energy transfer from tyrosine to tryptophan residues is possible. The conclusions have been made that the Tyr-Trp energy transfer is one of the factors determining the shape of the trypsin polarization spectrum, and that upon fluorescence excitation at the long-wavelength edge of the absorption spectrum, the depolarization of trypsin fluorescence in aqueous solution at ambient temperature - compared to model compounds (tryptophan, N-acetyltryptophan, glycyltryptophan, etc.), under the conditions of infinite viscosity - is due to the Brownian rotational motion of the macromolecules as a whole as well as the intramolecular mobility. The differences in the level and character of intramolecular mobility of trypsin and trypsinogen are discussed.     

Coarse-grained models of protein folding: toy models or predictive tools?

Coarse-grained models are emerging as a practical alternative to all-atom simulations for the characterization of protein folding mechanisms over long time scales. While a decade ago minimalist toy models were mainly designed to test general hypotheses on the principles regulating protein folding, the latest coarse-grained models are increasingly realistic and can be used to characterize quantitatively the detailed folding mechanism of specific proteins. The ability of such models to reproduce the essential features of folding dynamics suggests that each single atomic degree of freedom is not by itself particularly relevant to folding and supports a statistical mechanical approach to characterize folding transitions. When combined with more refined models and with experimental studies, the systematic investigation of protein systems and complexes using coarse-grained models can advance our theoretical understanding of the actual organizing principles that emerge from the complex network of interactions among protein atomic constituents.     

What causes population cycles of forest Lepidoptera?

Hypotheses for the causes of regular cycles in populations of forest Lepidoptera have invoked pathogen-insect or foliage-insect interactions. However, the available data suggest that forest caterpillar cycles are more likely to be the result of interactions with insect parasitoids, an old argument that seems to have been neglected in recent years.     

What causes extended lows in microtine cycles?

Summary Synchronous declines of sympatric shrew and microtine populations in boreal regions of Fennoscandia have been claimed as evidence that predation deepens and extends the low phase of the microtine population cycles. Assuming that shrews and microtines have the same maximum intrinsic rate of increase, and that the predators kill the shrews and microtines that they encounter unselectively, this hypothesis predicts that sympatric shrew and microtine populations will decline and increase simultaneously. In this study conducted at 60°56N in southeast Norway, as well as in 13 of 15 other studies at sites in Fennoscandia, the shrew populations declined simultaneously with the sympatric microtine populations, but recovered sooner. The shrew-microtine ratio among animals trapped peaked about 2 years after the peak in the microtine population. The same pattern was found in the diet of raptors in Fennoscandia. Since the maximum intrinsic rate of increase does not seem to be higher in shrews than in microtines, the pattern suggests that either predation is not causing the extended lows in the microtine populations, or that the proportion of predators that selectively kill microtines fluctuates during the microtine cycle. The most likely candidates for selective killers are weasels.     

Influence of organization of native protein structure on its folding: Modeling of the folding of α-helical proteins

An important question that is addressed here is whether the modeling of protein folding can catch the difference between the folding of proteins with similar structures but with different folding mechanisms. In this work, the modeling of folding of four α-helical proteins from the homeodomain family, which are similar in size, was done using the Monte Carlo and dynamic programming methods. A frequently observed order of folding of α-helices for each protein was determined using the Monte Carlo method. A correlation between the experimental folding rate and the number of Monte Carlo steps was also demonstrated. Amino acid residues that are important for the folding were determined using the dynamic programming method. The defined regions correlate with the order of folding of secondary-structure elements in the proteins both in experiments and in modeling.     

What causes lymphocyte hyporesponsiveness during filarial nematode infection?

Filarial nematodes persist in the parasitized host by modulating immune responsiveness. A feature of this that has been observed in a multitude of studies dating back several decades is an inability of lymphocytes to respond appropriately to filarial nematode antigens and, in some cases, to other stimuli. The consistency of this observation, allied to the ease of measurement of lymphocyte hyporesponsiveness, has resulted in many attempts to understand its cause.