Loop-driven conformational transition between the alternative and collapsed form of prethrombin-2: targeted molecular dynamics study

Two distinct crystal structures of prethrombin-2, the alternative and collapsed forms, are elucidated by X-ray crystallogrphy. We analyzed the conformational transition from the alternative to the collapsed form employing targeted molecular dynamics (TMD) simulation. Despite small RMSD difference in the two X-ray crystal structures, some hydrophobic residues (W60d, W148, W215, and F227) show a significant difference between the two conformations. TMD simulation shows that the four hydrophobic residues undergo concerted movement from dimer to trimer transition via tetramer state in the conformational change from the alternative to the collapsed form. We reveal that the concerted movement of the four hydrophobic residues is controlled by movement of specific loop regions behind. In this paper, we propose a sequential scenario for the conformational transition from the alternative form to the collapsed form, which is partially supported by the mutant W148A simulation.     

Native aggregation as a cause of origin of temporary cellular structures needed for all forms of cellular activity,signaling and transformations

According to the hypothesis explored in this paper, native aggregation is genetically controlled (programmed) reversible aggregation that occurs when interacting proteins form new temporary structures through highly specific interactions. It is assumed that Anfinsen's dogma may be extended to protein aggregation: composition and amino acid sequence determine not only the secondary and tertiary structure of single protein, but also the structure of protein aggregates (associates). Cell function is considered as a transition between two states (two states model), the resting state and state of activity (this applies to the cell as a whole and to its individual structures). In the resting state, the key proteins are found in the following inactive forms: natively unfolded and globular. When the cell is activated, secondary structures appear in natively unfolded proteins (including unfolded regions in other proteins), and globular proteins begin to melt and their secondary structures become available for interaction with the secondary structures of other proteins. These temporary secondary structures provide a means for highly specific interactions between proteins. As a result, native aggregation creates temporary structures necessary for cell activity.     

Structure of bovine beta-lactoglobulin at 6A resolution.

Bovine β-lactoglobulin is a dimer with a molecular weight of 2 × 18,400. In solution it undergoes a pH-dependent transition at pH 7.0 between two alternative structures, named N and R. The structures of four different crystal forms have been determined by multiple isomorphous replacement with heavy-atoms. Two of them, lattices K and X, were crystallised at pH 6.5, corresponding to the N state in solution; and the other two, lattices Y and Z, were crystallised at pH 7.5, corresponding to the R state in solution. The figures of merit of the phase angles determined for these lattices were 0.76, 0.77, 0.80 and 0.80, respectively. The four structures that emerged are similar and show certain features suggestive of α-helices and pleated sheets, but the resolution is insufficient to trace the entire course of the polypeptide chain. No clear distinction can yet be made between the structures above or below pH 7.0, nor between the native molecule and the molecule from which the C-terminal leucine and histidine residues have been cleaved. Analyses at higher resolution are in progress.     

A reduced set of coordinates for modeling DNA structures: (I). A B-to-A transition pathway driven by pseudorotational angle.

The A-DNA and the B-DNA are two well characterized polymorphous forms of DNA duplex. By using Metropolis Monte Carlo Simulations in a reduced coordinate space, we have shown that the B in equilibrium with A transitions can be induced by forcing pseudorotational angle (W) to change between C3'-endo and C2'-endo puckerings. The energy barrier for the transition pathway is less than 10 Kcal.mol-1. Base-pair parameters x-displacement (Dx) and roll (rho), which have the largest differences between the two forms of structures, cannot drive the transition. Our results support the view that the bistable states of the DNA duplex are due to the bistable structures of the sugar ring.     

A unique four-stranded model of a homologous recombination intermediate

This paper proposes a model of four-stranded DNA synapsis during recombination between homologous segments of two DNA duplexes. The proposed intermediate is one of only two known models having relative chain orientations about the synaptic junction that are consistent with recent topological results on the integrative recombination of bacteriophage lambda. This model has the advantage of providing a mechanism for recognition of sequence homology between duplexes through specific hydrogen-bond formation; other models are discussed in comparison. The new model is based on an alternative family of DNA structures having chain directions opposite to those of the Watson-Crick family of structures. Idealized coordinates for generating both right- and left-handed forms of these alternative structures are presented for further study.     

On the roles of substrate binding and hinge unfolding in conformational changes of adenylate kinase

We characterized the conformational change of adenylate kinase (AK) between open and closed forms by conducting five all-atom molecular-dynamics simulations, each of 100 ns duration. Different initial structures and substrate binding configurations were used to probe the pathways of AK conformational change in explicit solvent, and no bias potential was applied. A complete closed-to-open and a partial open-to-closed transition were observed, demonstrating the direct impact of substrate-mediated interactions on shifting protein conformation. The sampled configurations suggest two possible pathways for connecting the open and closed structures of AK, affirming the prediction made based on available x-ray structures and earlier works of coarse-grained modeling. The trajectories of the all-atom molecular-dynamics simulations revealed the complexity of protein dynamics and the coupling between different domains during conformational change. Calculations of solvent density and density fluctuations surrounding AK did not show prominent variation during the transition between closed and open forms. Finally, we characterized the effects of local unfolding of an important hinge near Pro¹⁷⁷ on the closed-to-open transition of AK and identified a novel mechanism by which hinge unfolding modulates protein conformational change. The local unfolding of Pro¹⁷⁷ hinge induces alternative tertiary contacts that stabilize the closed structure and prevent the opening transition.     

A quantitative genetic model of two-policy games between relatives

Equations are derived for the change per generation of the population mean of the probability that an individual adopts a policy 1 as opposed to a policy 2 in a behavioral interaction between two diploid individuals of the same generation in which two policies are possible. The probability is assumed to be a quantitative genetic trait determined by many additively acting genes of small effects and an independent environmental component. Equations are derived for the case that interactions occur at random between all members of the population and also for the case that interactions occur between relatives of the same average degree of relatedness. It is assumed that each group of relatives and the number of such groups is sufficiently large. For a quantitative genetic trait with the additional assumption of unlinked loci the latter equation can be heuristically derived from the first by substituting the corresponding inclusive fitness effects. When per locus selection coefficients are small and linkage equilibrium holds, the average degree of relatedness can be equated approximately with Wright's coefficient of relationship. Thus, the quantitative genetic model provides a genetic basis for the inclusive fitness approach toward games between relatives. By contrast, in a monogenic system with major gene effects we obtain substantially different results which contradict those obtained by the inclusive fitness approach in game theory. Applications are made to the hawk-dove game, and the simple and iterated forms of the prisoner's dilemma.     

Perspectives on endothelial-to-mesenchymal transition: potential contribution to vascular remodeling in chronic pulmonary hypertension

All forms of pulmonary hypertension are characterized by structural changes in pulmonary arteries. Increased numbers of cells expressing alpha-smooth muscle (alpha-SM) actin is a nearly universal finding in the remodeled artery. Traditionally, it was assumed that resident smooth muscle cells were the exclusive source of these newly appearing alpha-SM actin-expressing cells. However, rapidly emerging experimental evidence suggests other, alternative cellular sources of these cells. One possibility is that endothelial cells can transition into mesenchymal cells expressing alpha-SM actin and that this process contributes to the accumulation of SM-like cells in vascular pathologies. We review the evidence that endothelial-mesenchymal transition is an important contributor to cardiac and vascular development as well as to pathophysiological vascular remodeling. Recent work has provided evidence for the role of transforming growth factor-beta, Wnt, and Notch signaling in this process. The potential roles of matrix metalloproteinases and serine proteases are also discussed. Importantly, endothelial-mesenchymal transition may be reversible. Thus insights into the mechanisms controlling endothelial-mesenchymal transition are relevant to vascular remodeling and are important as we consider new therapies aimed at reversing pulmonary vascular remodeling.     

Unfolding pathways of goat alpha-lactalbumin as revealed in multiple alignment of molecular dynamics trajectories

Molecular dynamics simulations of protein unfolding were performed at an elevated temperature for the authentic and recombinant forms of goat alpha-lactalbumin. Despite very similar three-dimensional structures, the two forms have significantly different unfolding rates due to an extra N-terminal methionine in the recombinant protein. To identify subtle differences between the two forms in the highly stochastic kinetics of unfolding, we classified the unfolding trajectories using the multiple alignment method based on the analogy between the biological sequences and the molecular dynamics trajectories. A dendrogram derived from the multiple trajectory alignment revealed a clear difference in the unfolding pathways of the authentic and recombinant proteins, i.e. the former reached the transition state in an all-or-none manner while the latter unfolded less cooperatively. It was also found in the classification that the two forms of the protein shared a common transition state structure, which was in excellent agreement with the transition state structure observed experimentally in the Phi-value analysis.     

Intermodular Linker Flexibility Revealed from Crystal Structures of Adjacent Cellulosomal Cohesins of Acetivibrio cellulolyticus

Cellulosome complexes comprise an intercalated set of multimodular dockerin-containing enzymatic subunits connected to cohesin-containing nonenzymatic subunits called scaffoldins. The adjoining modules in each cellulosomal subunit are interconnected by a variety of linker segments of different lengths and composition. The exact role of the cellulosomal linkers has yet to be described, although it is assumed that they contribute to the architecture and action of the cellulosome by providing the protein subunits with flexibility and by providing spacers between the enzymatic modules that could enhance interactions with the cellulose substrate. Here we present four crystal structures of Acetivibrio cellulolyticus cellulosomal type II cohesins with linker extensions. Two of the structures represent two different crystal forms (trigonal and orthorhombic) of the same N-terminal cohesin module (CohB1) together with its full (6-residue) native C-terminal linker, derived from scaffoldin B. The other two structures belong to the adjacent (second) cohesin module (CohB2), each of which was crystallized with the same 6-residue linker segment, but now positioned at the N-terminus and with either a truncated (5-residue) or a full-length (45-residue) C-terminal linker, respectively. Comparison between the two CohB1 structures revealed significant differences in the conformation of their equivalent C-terminal linker segment. In one crystal form a helical conformation was observed, as opposed to an extended conformation in the other. The CohB2 structures also displayed diverse conformations in their linker segments. In these structures, different linker conformations were observed in the individual molecules within the asymmetric unit of each structure. This conformational diversity implies that the linkers may adopt alternative conformations in their natural environment, consistent with varying environmental conditions. The findings suggest that linkers can play an important role in the assembly, dynamics and function of the cellulosomal components.     

Structural comparison of the two alternative transition states for folding of TI I27

TI I27, a beta-sandwich domain from the human muscle protein titin, has been shown to fold via two alternative pathways, which correspond to a change in the folding mechanism. Under physiological conditions, TI I27 folds by a classical nucleation-condensation mechanism (diffuse transition state), whereas at extreme conditions of temperature and denaturant it switches to having a polarized transition state. We have used experimental Phi-values as restraints in ensemble-averaged molecular dynamics simulations to determine the ensembles of structures representing the two transition states. The comparison of these ensembles indicates that when native interactions are substantially weakened, a protein may still be able to fold if it can access an alternative transition state characterized by a much larger entropic contribution. Analysis of the probability distribution of Phi-values derived from ensemble averaged simulations, enables us to identify residues that form contacts in some members of the ensemble but not in others illustrating that many interactions present in transition states are not strictly required for the successful completion of the folding process.     

Emergence of Super Cooperation of Prisoner’s Dilemma Games on Scale-Free Networks

Recently, the authors proposed a quantum prisoner’s dilemma game based on the spatial game of Nowak and May, and showed that the game can be played classically. By using this idea, we proposed three generalized prisoner’s dilemma (GPD, for short) games based on the weak Prisoner’s dilemma game, the full prisoner’s dilemma game and the normalized Prisoner’s dilemma game, written by GPD_W, GPD_F and GPD_N respectively. Our games consist of two players, each of which has three strategies: cooperator (C), defector (D) and super cooperator (denoted by Q), and have a parameter γ to measure the entangled relationship between the two players. We found that our generalised prisoner’s dilemma games have new Nash equilibrium principles, that entanglement is the principle of emergence and convergence (i.e., guaranteed emergence) of super cooperation in evolutions of our generalised prisoner’s dilemma games on scale-free networks, that entanglement provides a threshold for a phase transition of super cooperation in evolutions of our generalised prisoner’s dilemma games on scale-free networks, that the role of heterogeneity of the scale-free networks in cooperations and super cooperations is very limited, and that well-defined structures of scale-free networks allow coexistence of cooperators and super cooperators in the evolutions of the weak version of our generalised prisoner’s dilemma games.     

A patch-dynamics approach to savanna dynamics and woody plant encroachment – Insights from an arid savanna

The coexistence of woody and grassy plants in savannas has often been attributed to a rooting-niche separation (two-layer hypothesis). Water was assumed to be the limiting resource for both growth forms and grasses were assumed to extract water from the upper soil layer and trees and bushes from the lower layers. Woody plant encroachment (i.e. an increase in density of woody plants often unpalatable to domestic livestock) is a serious problem in many savannas and is believed to be the result of overgrazing in ‘two-layer systems’. Recent research has questioned the universality of both the two-layer hypothesis and the hypothesis that overgrazing is the cause of woody plant encroachment.

We present an alternative hypothesis explaining both tree–grass coexistence and woody plant encroachment in arid savannas. We propose that woody plant encroachment is part of a cyclical succession between open savanna and woody dominance and is driven by two factors: rainfall that is highly variable in space and time, and inter-tree competition. In this case, savanna landscapes are composed of many patches (a few hectares in size) in different states of transition between grassy and woody dominance, i.e. we hypothesize that arid savannas are patch-dynamic systems. We summarize patterns of tree distribution observed in an arid savanna in Namibia and show that these patterns are in agreement with the patch-dynamic savanna hypothesis. We discuss the applicability of this hypothesis to fire-dominated savannas, in which rainfall variability is low and fire drives spatial heterogeneity.

We conclude that field studies are more likely to contribute to a general understanding of tree–grass coexistence and woody plant encroachment if they consider both primary (rain and nutrients) and secondary (fire and grazing) determinants of patch properties across different savannas.     

Additivity in both thermodynamic stability and thermal transition temperature for rubredoxin chimeras via hybrid native partitioning

Given any operational definition of pairwise interaction, the set of residues that differ between two structurally homologous proteins can be uniquely partitioned into subsets of clusters for which no such interactions occur between clusters. Although hybrid protein sequences that preserve such clustering are consistent with tertiary structures composed of only parental native-like interactions, the stability of such predicted structures will depend upon the physical robustness of the assumed interaction potential. A simple distance cutoff criterion was applied to the most thermostable protein known to predict such a seven-residue cluster in the metal binding site region of Pyrococcus furiosus rubredoxin and a mesophile homolog. Both conformational stability and thermal transition temperature measurements demonstrate that 39% of the differential stability arises from these seven residues.     

The evolution of altruism: game theory in multilevel selection and inclusive fitness

Although the prisoner's dilemma (PD) has been used extensively to study reciprocal altruism, here we show that the n-player prisoner's dilemma (NPD) is also central to two other prominent theories of the evolution of altruism: inclusive fitness and multilevel selection. An NPD model captures the essential factors for the evolution of altruism directly in its parameters and integrates important aspects of these two theories such as Hamilton's rule, Simpson's paradox, and the Price covariance equation. The model also suggests a simple interpretation of the Price selection decomposition and an alternative decomposition that is symmetrical and complementary to it. In some situations this alternative shows the temporal changes in within- and between-group selection more clearly than the Price equation. In addition, we provide a new perspective on strong vs. weak altruism by identifying their different underlying game structures (based on absolute fitness) and showing how their evolutionary dynamics are nevertheless similar under selection (based on relative fitness). In contrast to conventional wisdom, the model shows that both strong and weak altruism can evolve in periodically formed random groups of non-conditional strategies if groups are multigenerational. An integrative approach based on the NPD helps unify different perspectives on the evolution of altruism.     

Catastrophic shifts in vertical distributions of phytoplankton The existence of a bifurcation set

A model of phytoplankton dynamics within a water column was analyzed with special consideration on the existence of a bifurcation set in the parameter space. We considered two resources, light and a limiting nutrient, for phytoplankton growth and assumed that the water column is separated into two layers by thermal and/or density stratification. It was shown that there exists a bifurcation set in the parameter space when the growth function meets several conditions that are general for growth functions of two essential resources. Specifically, these conditions include that a less abundant of the two resources limits the growth while the effect of the other is sufficiently small. Folded structure with two stable states separated by one unstable state appears in the catastrophe manifold when parameters move to a certain direction with a certain curvature from a point in the bifurcation set. These results suggest that occurrence of discontinuous transition between two alternative vertical patterns is possible nature of phytoplankton dynamics within a stratified water column.     

Constructing biological pathways by a two-step counting approach

Networks are widely used in biology to represent the relationships between genes and gene functions. In Boolean biological models, it is mainly assumed that there are two states to represent a gene: on-state and off-state. It is typically assumed that the relationship between two genes can be characterized by two kinds of pairwise relationships: similarity and prerequisite. Many approaches have been proposed in the literature to reconstruct biological relationships. In this article, we propose a two-step method to reconstruct the biological pathway when the binary array data have measurement error. For a pair of genes in a sample, the first step of this approach is to assign counting numbers for every relationship and select the relationship with counting number greater than a threshold. The second step is to calculate the asymptotic p-values for hypotheses of possible relationships and select relationships with a large p-value. This new method has the advantages of easy calculation for the counting numbers and simple closed forms for the p-value. The simulation study and real data example show that the two-step counting method can accurately reconstruct the biological pathway and outperform the existing methods. Compared with the other existing methods, this two-step method can provide a more accurate and efficient alternative approach for reconstructing the biological network.     

Physical characterization of serpin conformations

The native serpin fold is characterized by being metastable. This thermodynamic characteristic is manifested in the conversion of the native state to other more stable conformations. Whilst this structural transition is required for proteinase inhibition and regulation of a range of biological phenomena, inappropriate structural changes can result in a number of disease states. Identification of these alternative conformations has been essential in our understanding of serpin structure and function. However, identifying these alternative forms is also important if we are not to misinterpret data due to the formation of these states during in vitro studies. The different physical properties of these alternative serpin conformational states make it possible to use a range of standard laboratory techniques to identify these structures. In this chapter, we will outline these general approaches that can be used routinely to identify the alternative serpin conformational states.