Probing the dark state tertiary structure in the cytoplasmic domain of rhodopsin: proximities between amino acids deduced from spontaneous disulfide bond formation between cysteine pairs engineered in cytoplasmic loops 1, 3, and 4

To probe proximities between amino acids in the cytoplasmic domain by using mutants containing engineered cysteine pairs, three sets of rhodopsin mutants have been prepared. In the first two sets, a cysteine was placed, one at a time, at positions 311-314 in helix VIII, while the second cysteine was fixed at position 246 (set I) and at position 250 (set II) at the cytoplasmic end of helix VI. In the third set, one cysteine was fixed at position 65 while the second cysteine was varied between amino acid positions 306 and 321 located at the cytoplasmic end of helix VII and throughout in helix VIII. Rapid disulfide bond formation in the dark was found between the cysteine pairs in mutants A246C/Q312C,A246C/K311C and in mutants H65C/C316, H65C/315C and H65C/312C. Disulfide bond formation at much lower rates was found in mutants A246C/F313C, V250C/Q312C, H65C/N310C, H65C/K311C, H65C/F313C, and H65C/R314C; the remaining mutants showed no significant disulfide bond formation. Comparisons of the results from disulfide bond formation in solution with the distances observed in the rhodopsin crystal structure showed that the rates of disulfide bond formation in most cases were consistent with the amino acid proximities as revealed in crystal structure. However, deviations were also found, in particular, in the set containing fixed cysteine at position Cys246 and cysteines at positions 311-314. The results implicate significant effects of structural dynamics on disulfide bond formation in solution.     

Effects of lipid environment on the light-induced conformational changes of rhodopsin. 2. Roles of lipid chain length, unsaturation, and phase state

When rhodopsin is incorporated into the saturated short-chain phospholipid dimyristoylphosphatidylcholine, photolysis of the protein results in an abnormal sequence of spectral transitions, and the dominant product of metarhodopsin I decay is free retinal plus opsin [Baldwin, P. A., & Hubbell, W. L. (1985) Biochemistry (preceding paper in this issue)]. By incorporation of rhodopsin into a series of phosphatidylcholines of defined composition, we have determined the properties of the lipid environment that are responsible for the altered spectral behavior. Metarhodopsin II is not found in appreciable amounts in bilayers containing acyl chains that are too short (14 or fewer carbon atoms in length), in the presence of only n-alkyl chains, or below the characteristic phase-transition temperature of recombinant membranes. Double bonds are not required for the formation of the metarhodopsin II intermediate, as it is observed in diphytanoylphosphatidylcholine recombinants.     

Testing for changes in biomass dynamics in large‐scale forest datasets

Tropical forest responses to climate and atmospheric change are critical to the future of the global carbon budget. Recent studies have reported increases in estimated above‐ground biomass (EAGB) stocks, productivity, and mortality in old‐growth tropical forests. These increases could reflect a shift in forest functioning due to global change and/or long‐lasting recovery from past disturbance. We introduce a novel approach to disentangle the relative contributions of these mechanisms by decomposing changes in whole‐plot biomass fluxes into contributions from changes in the distribution of gap‐successional stages and changes in fluxes for a given stage. Using 30 years of forest dynamic data at Barro Colorado Island, Panama, we investigated temporal variation in EAGB fluxes as a function of initial EAGB (EAGB_i) in 10 × 10 m quadrats. Productivity and mortality fluxes both increased strongly with initial quadrat EAGB. The distribution of EAGB (and thus EAGB_i) across quadrats hardly varied over 30 years (and seven censuses). EAGB fluxes as a function of EAGB_i varied largely and significantly among census intervals, with notably higher productivity in 1985–1990 associated with recovery from the 1982–1983 El Niño event. Variation in whole‐plot fluxes among census intervals was explained overwhelmingly by variation in fluxes as a function of EAGB_i, with essentially no contribution from changes in EAGB_i distributions. The high observed temporal variation in productivity and mortality suggests that this forest is very sensitive to climate variability. There was no consistent long‐term trend in productivity, mortality, or biomass in this forest over 30 years, although the temporal variability in productivity and mortality was so strong that it could well mask a substantial trend. Accurate prediction of future tropical forest carbon budgets will require accounting for disturbance‐recovery dynamics and understanding temporal variability in productivity and mortality.     

Tenascin C Promiscuously Binds Growth Factors via Its Fifth Fibronectin Type III-Like Domain

Tenascin C (TNC) is an extracellular matrix protein that is upregulated during development as well as tissue remodeling. TNC is comprised of multiple independent folding domains, including 15 fibronectin type III-like (TNCIII) domains. The fifth TNCIII domain (TNCIII5) has previously been shown to bind heparin. Our group has shown that the heparin-binding fibronectin type III domains of fibronectin (FNIII), specifically FNIII12–14, possess affinity towards a large number of growth factors. Here, we show that TNCIII5 binds growth factors promiscuously and with high affinity. We produced recombinant fragments of TNC representing the first five TNCIII repeats (TNCIII1–5), as well as subdomains, including TNCIII5, to study interactions with various growth factors. Multiple growth factors of the platelet-derived growth factor (PDGF) family, the fibroblast growth factor (FGF) family, the transforming growth factor beta (TGF-β) superfamily, the insulin-like growth factor binding proteins (IGF-BPs), and neurotrophins were found to bind with high affinity to this region of TNC, specifically to TNCIII5. Surface plasmon resonance was performed to analyze the kinetics of binding of TNCIII1–5 with TGF-β1, PDGF-BB, NT-3, and FGF-2. The promiscuous yet high affinity of TNC for a wide array of growth factors, mediated mainly by TNCIII5, may play a role in multiple physiological and pathological processes involving TNC.     

A systematic comparison of summary characteristics for quantifying point patterns in ecology

Many functional summary characteristics such as Ripley's K function have been used in ecology to describe the spatial structure of point patterns to aid understanding of the underlying processes. However, their use is poorly guided in ecology because little is understood how well single summary characteristics, or a combination of them, capture the spatial structure of real world patterns. Here, we systematically tested the performance of combinations of eight summary characteristics [i.e. pair correlation function g(r), K‐function K(r), the proportion E(r) of points with no neighbor at distance r, the nearest neighbor distribution function D(r), the spherical contact distribution H_s(r), the kth nearest‐neighbor distribution functions D_k(r), the mean distance nn(k) to the kth neighbor, and the intensity function λ( x )]. To this end we used point pattern data covering a wide range of spatial structures including simulated (stationary) as well as real, possibly non‐stationary, patterns on tree species in a tropical forest in Panamá. To measure the information contained in a given combination of summary characteristics we used simulated annealing to reconstruct the observed patterns based only on the limited information provided by this combination and assessed how well other characteristics of the observed pattern were recovered. We found that the number of summary characteristics required to capture the spatial structure of stationary patterns varied between one (for patterns with near random structures) and three (for patterns with complex cluster and superposition structures), but with a robust ranking g(r), D_k(r), and H_s(r) that was largely independent on pattern idiosyncrasies. Stationary summary characteristics [with ranking g(r), D_k(r), H_s(r), E(r)] captured small‐ to intermediate scale properties of non‐stationary patterns, but for describing large‐scale spatial structures the intensity function was required. Our finding revealed that the current practice in ecology of using only one or two summary characteristics bears danger that essential characteristics of more complex patterns would not be detected. The technique of pattern reconstruction presented here has wide applications in ecology.     

Few residues within an extensive binding interface drive receptor interaction and determine the specificity of arrestin proteins

Arrestins bind active phosphorylated forms of G protein-coupled receptors, terminating G protein activation, orchestrating receptor trafficking, and redirecting signaling to alternative pathways. Visual arrestin-1 preferentially binds rhodopsin, whereas the two non-visual arrestins interact with hundreds of G protein-coupled receptor subtypes. Here we show that an extensive surface on the concave side of both arrestin-2 domains is involved in receptor binding. We also identified a small number of residues on the receptor binding surface of the N- and C-domains that largely determine the receptor specificity of arrestins. We show that alanine substitution of these residues blocks the binding of arrestin-1 to rhodopsin in vitro and of arrestin-2 and -3 to β2-adrenergic, M2 muscarinic cholinergic, and D2 dopamine receptors in intact cells, suggesting that these elements critically contribute to the energy of the interaction. Thus, in contrast to arrestin-1, where direct phosphate binding is crucial, the interaction of non-visual arrestins with their cognate receptors depends to a lesser extent on phosphate binding and more on the binding to non-phosphorylated receptor elements.     

Species diversity in local neutral communities

We extend the neutral theory of macroecology by deriving biodiversity models (relative species abundance and species-area relationships) in a local community-metacommunity system in which the local community is embedded within the metacommunity. We first demonstrate that the local species diversity patterns converge to that of the metacommunity as the size (scale) of the embedded local community increases. This result shows that in continuous landscapes no sharp boundaries dividing the communities at the two scales exist; they are an artificial distinction made by the current spatially implicit neutral theory. Second, we remove the artificial restriction that speciation cannot occur in a local community, even if the effects of local speciation are small. Third, we introduce stochasticity into the immigration rate, previously treated as constant, and demonstrate that local species diversity is a function not only of the mean but also of the variance in immigration rate. High variance in immigration rates reduces species diversity in local communities. Finally, we show that a simple relationship exists between the fundamental diversity parameter of neutral theory and Simpson's index for local communities. Derivation of this relationship extends recent work on diversity indices and provides a means of evaluating the effect of immigration on estimates of the fundamental diversity parameter derived from relative species abundance data on local communities.