Geometrical Frustration in Interleukin-33 Decouples the Dynamics of the Functional Element from the Folding Transition State Ensemble

Interleukin-33 (IL-33) is currently the focus of multiple investigations into targeting pernicious inflammatory disorders. This mediator of inflammation plays a prevalent role in chronic disorders such as asthma, rheumatoid arthritis, and progressive heart disease. In order to better understand the possible link between the folding free energy landscape and functional regions in IL-33, a combined experimental and theoretical approach was applied. IL-33 is a pseudo- symmetrical protein composed of three distinct structural elements that complicate the folding mechanism due to competition for nucleation on the dominant folding route. Trefoil 1 constitutes the majority of the binding interface with the receptor whereas Trefoils 2 and 3 provide the stable scaffold to anchor Trefoil 1. We identified that IL-33 folds with a three-state mechanism, leading to a rollover in the refolding arm of its chevron plots in strongly native conditions. In addition, there is a second slower refolding phase that exhibits the same rollover suggesting similar limitations in folding along parallel routes. Characterization of the intermediate state and the rate limiting steps required for folding suggests that the rollover is attributable to a moving transition state, shifting from a post- to pre-intermediate transition state as you move from strongly native conditions to the midpoint of the transition. On a structural level, we found that initially, all independent Trefoil units fold equally well until a Q_CA of 0.35 when Trefoil 1 will backtrack in order to allow Trefoils 2 and 3 to fold in the intermediate state, creating a stable scaffold for Trefoil 1 to fold onto during the final folding transition. The formation of this intermediate state and subsequent moving transition state is a result of balancing the difficulty in folding the functionally important Trefoil 1 onto the remainder of the protein. Taken together our results indicate that the functional element of the protein is geometrically frustrated, requiring the more stable elements to fold first, acting as a scaffold for docking of the functional element to allow productive folding to the native state.     

A model for the conquest of a tree by bark beetles

A model for the interaction between attacking bark beetles and a tree is developed and discussed. It is shown that in addition to the more intuitive outcomes where the tree wins or the beetles win, it is also deduced that under certain conditions there may exist a stable coexistence (at least for some period of time) between the beetles and a living tree. Finally, it is demonstrated that the outcome of the tree-beetle interaction often depends on initial conditions such as the number of colonizing beetles.
These results are discussed with reference to empirical findings, as well as to the development of proper population dynamics models for bark beetles in a forest stand, and models developed for assisting forest managers in avoiding bark beetle outbreaks and for minimizing the damage caused by a bark beetle outbreak.     

Phytosulfokine Regulates Growth in Arabidopsis through a Response Module at the Plasma Membrane That Includes CYCLIC NUCLEOTIDE-GATED CHANNEL17, H+-ATPase,and BAK1

Phytosulfokine (PSK) is perceived by the leucine-rich repeat receptor kinase PSKR1 and promotes growth in Arabidopsis thaliana. PSKR1 is coexpressed with the CYCLIC NUCLEOTIDE-GATED CHANNEL gene CNGC17. PSK promotes protoplast expansion in the wild type but not in cngc17. Protoplast expansion is likewise promoted by cGMP in a CNGC17-dependent manner. Furthermore, PSKR1-deficient protoplasts do not expand in response to PSK but are still responsive to cGMP, suggesting that cGMP acts downstream of PSKR1. Mutating the guanylate cyclase center of PSKR1 impairs seedling growth, supporting a role for PSKR1 signaling via cGMP in planta. While PSKR1 does not interact directly with CNGC17, it interacts with the plasma membrane-localized H⁺-ATPases AHA1 and AHA2 and with the BRI-associated receptor kinase 1 (BAK1). CNGC17 likewise interacts with AHA1, AHA2, and BAK1, suggesting that PSKR1, BAK1, CNGC17, and AHA assemble in a functional complex. Roots of deetiolated bak1-3 and bak1-4 seedlings were unresponsive to PSK, and bak1-3 and bak1-4 protoplasts expanded less in response to PSK but were fully responsive to cGMP, indicating that BAK1 acts in the PSK signal pathway upstream of cGMP. We hypothesize that CNGC17 and AHAs form a functional cation-translocating unit that is activated by PSKR1/BAK1 and possibly other BAK1/RLK complexes.     

Biochemistry and Crystal Structure of Ectoine Synthase: A Metal-Containing Member of the Cupin Superfamily

Ectoine is a compatible solute and chemical chaperone widely used by members of the Bacteria and a few Archaea to fend-off the detrimental effects of high external osmolarity on cellular physiology and growth. Ectoine synthase (EctC) catalyzes the last step in ectoine production and mediates the ring closure of the substrate N-gamma-acetyl-L-2,4-diaminobutyric acid through a water elimination reaction. However, the crystal structure of ectoine synthase is not known and a clear understanding of how its fold contributes to enzyme activity is thus lacking. Using the ectoine synthase from the cold-adapted marine bacterium Sphingopyxis alaskensis (Sa), we report here both a detailed biochemical characterization of the EctC enzyme and the high-resolution crystal structure of its apo-form. Structural analysis classified the (Sa)EctC protein as a member of the cupin superfamily. EctC forms a dimer with a head-to-tail arrangement, both in solution and in the crystal structure. The interface of the dimer assembly is shaped through backbone-contacts and weak hydrophobic interactions mediated by two beta-sheets within each monomer. We show for the first time that ectoine synthase harbors a catalytically important metal co-factor; metal depletion and reconstitution experiments suggest that EctC is probably an iron-dependent enzyme. We found that EctC not only effectively converts its natural substrate N-gamma-acetyl-L-2,4-diaminobutyric acid into ectoine through a cyclocondensation reaction, but that it can also use the isomer N-alpha-acetyl-L-2,4-diaminobutyric acid as its substrate, albeit with substantially reduced catalytic efficiency. Structure-guided site-directed mutagenesis experiments targeting amino acid residues that are evolutionarily highly conserved among the extended EctC protein family, including those forming the presumptive iron-binding site, were conducted to functionally analyze the properties of the resulting EctC variants. An assessment of enzyme activity and iron content of these mutants give important clues for understanding the architecture of the active site positioned within the core of the EctC cupin barrel.     

Feedback structures of northern small rodent populations

Regular oscillations of northern small rodents (lemmings, voles and mice) have fascinated ecologists for decades. In particular, cycles exhibited by Fennoscandian voles have inspired population ecologists to propose several hypotheses for their underlying causes. Although there is now some agreement that the interaction with specialist predators is involved, many aspects remain enigmatic, one being the precise ecological mechanism involved in the first-order feedback effect (i.e. direct density dependence). In this paper we evaluate the relative importance of first and second-order negative feedback on small rodent dynamics in 64 data sets, assess the evidence of non-linearity in the feedback structure, and look for similarities and/or differences between species and places. A clear feature of our analysis was the highly consistent pattern of first-order dynamics across species and locations, suggesting the importance of intra-specific interactions independent of local environmental conditions. Second-order feedback generally showed a large degree of variation and appears to be strongly dependent on environmental conditions and locality. There seems to be no consistent latitudinal pattern or non-linearity in the feedback responses. We conclude that northern small rodent populations are basically regulated by both highly consistent first-order feedback (e.g. intra-specific competition, functional responses of generalist predators) and less consistent, site-specific second-order effects (e.g. numerical responses of specialist predators or food plants).     

Nitrogen and phosphorus in mire plants: variation during 50 years in relation to supply rate and vegetation type

Southern Sweden has long been exposed to an increasing atmospheric nitrogen deposition. We investigated the effects of this supply on the Sphagnum mire vegetation in SW Götaland by comparing above‐ground tissue concentrations of N and P and biomass variables in five vascular plant and two Sphagnum species collected during three periods since 1955 at 81 sites representing three vegetation types, viz. ombrotrophic bog, extremely poor fen and moderately poor fen, within two areas differing in annual N deposition. The N:P ratios in the plants were rarely below 17, suggesting P as the growth‐limiting mineral nutrient. In the vascular plants both growth and concentrations of N and P were highest in the moderately poor fen sites because of a higher mineralization rate, the differences between the extremely poor fen and bog sites being smaller in these respects. In the extremely poor fen and bog sites the N concentrations were slightly higher in the area with the highest N deposition. From 1955 to 2002 the concentration of N in the Sphagnum spp. increased proportionally to the supply rate while P remained constant. In the vascular plants the concentrations of P remained constant while N showed slightly decreasing trends in the bog and extremely poor fen sites, but since the size of the plants increased the biomass content of N and P increased, too. The increased N deposition has had its greatest effects on the site types with the highest Sphagnum biomass and peat accumulation rate. The high N concentration in the Sphagnum mosses probably reduced their competitiveness and facilitated the observed expansion of vascular plants. However, the increased N deposition might also have triggered an increased mineralization in the acrotelm increasing the supply of P to the vascular plants and thus also their productivity. This may also explain the slightly higher productivity among the vascular plants in the area with the highest N deposition rate. In conclusion, it seems as the increased N deposition has directly influenced only the growth of the Sphagnum mosses and that the effects on the growth of the vascular plants are indirect.