Autocatalytic maturation, physical/chemical properties, and crystal structure of group N HIV-1 protease: Relevance to drug resistance

The mature protease from Group N human immunodeficiency virus Type 1 (HIV‐1) (PR1_N) differs in 20 amino acids from the extensively studied Group M protease (PR1_M) at positions corresponding to minor drug‐resistance mutations (DRMs). The first crystal structure (1.09 Å resolution) of PR1_N with the clinical inhibitor darunavir (DRV) reveals the same overall structure as PR1_M, but with a slightly larger inhibitor‐binding cavity. Changes in the 10s loop and the flap hinge propagate to shift one flap away from the inhibitor, whereas L89F and substitutions in the 60s loop perturb inhibitor‐binding residues 29–32. However, kinetic parameters of PR1_N closely resemble those of PR1_M, and calorimetric results are consistent with similar binding affinities for DRV and two other clinical PIs, suggesting that minor DRMs coevolve to compensate for the detrimental effects of drug‐specific major DRMs. A miniprecursor (TFR 1 - 54 ‐PR1_N) comprising the transframe region (TFR) fused to the N‐terminus of PR1_N undergoes autocatalytic cleavage at the TFR/PR1_N site concomitant with the appearance of catalytic activity characteristic of the dimeric, mature enzyme. This cleavage is inhibited at an equimolar ratio of precursor to DRV (～6 μM), which partially stabilizes the precursor dimer from a monomer. However, cleavage at L34/W35 within the TFR, which precedes the TFR 1 - 54 /PR1_N cleavage at pH ≤ 5, is only partially inhibited. Favorable properties of PR1_N relative to PR1_M include its suitability for column fractionation by size under native conditions and >10‐fold higher dimer dissociation constant (150 nM). Exploiting these properties may facilitate testing of potential dimerization inhibitors that perturb early precursor processing steps.     

Loss of protease dimerization inhibition activity of darunavir is associated with the acquisition of resistance to darunavir by HIV-1

Dimerization of HIV protease is essential for the acquisition of protease's proteolytic activity. We previously identified a group of HIV protease dimerization inhibitors, including darunavir (DRV). In the present work, we examine whether loss of DRV's protease dimerization inhibition activity is associated with HIV development of DRV resistance. Single amino acid substitutions, including I3A, L5A, R8A/Q, L24A, T26A, D29N, R87K, T96A, L97A, and F99A, disrupted protease dimerization, as examined using an intermolecular fluorescence resonance energy transfer (FRET)-based HIV expression assay. All recombinant HIV(NL4-3)-based clones with such a protease dimerization-disrupting substitution failed to replicate. A highly DRV-resistant in vitro-selected HIV variant and clinical HIV strains isolated from AIDS patients failing to respond to DRV-containing antiviral regimens typically had the V32I, L33F, I54M, and I84V substitutions in common in protease. None of up to 3 of the 4 substitutions affected DRV's protease dimerization inhibition, which was significantly compromised by the four combined substitutions. Recombinant infectious clones containing up to 3 of the 4 substitutions remained sensitive to DRV, while a clonal HIV variant with all 4 substitutions proved highly resistant to DRV with a 205-fold 50% effective concentration (EC(50)) difference compared to HIV(NL4-3). The present data suggest that the loss of DRV activity to inhibit protease dimerization represents a novel mechanism contributing to HIV resistance to DRV. The finding that 4 substitutions in PR are required for significant loss of DRV's protease dimerization inhibition should at least partially explain the reason DRV has a high genetic barrier against HIV's acquisition of DRV resistance.     

Unmasking the Conformational Stability and Inhibitor Binding to SARS-CoV-2 Main Protease Active Site Mutants and Miniprecursor

We recently demonstrated that inhibitor binding reorganizes the oxyanion loop of a monomeric catalytic domain of SARS CoV-2 main protease (MPro) from an unwound (E) to a wound (active, E*) conformation, independent of dimerization. Here we assess the effect of the flanking N-terminal residues, to imitate the MPro precursor prior to its autoprocessing, on conformational equilibria rendering stability and inhibitor binding. Thermal denaturation (T_m) of C145A mutant, unlike H41A, increases by 6.8 °C, relative to wild-type mature dimer. An inactivating H41A mutation to maintain a miniprecursor containing TSAVL[Q or E] of the flanking nsp4 sequence in an intact form [^(-6)MPro^H41A and ^(-6*)MPro^H41A, respectively], and its corresponding mature MPro^H41A were systematically examined. While the H41A mutation exerts negligible effect on T_m and dimer dissociation constant (K_dimer) of MPro^H41A, relative to the wild type MPro, both miniprecursors show a 4–5 °C decrease in T_m and > 85-fold increase in K_dimer as compared to MPro^H41A. The K_d for the binding of the covalent inhibitor GC373 to ^(-6*)MPro^H41A increases ～12-fold, relative to MPro^H41A, concomitant with its dimerization. While the inhibitor-free dimer exhibits a state in transit from E to E* with a conformational asymmetry of the protomers’ oxyanion loops and helical domains, inhibitor binding restores the asymmetry to mature-like oxyanion loop conformations (E*) but not of the helical domains. Disorder of the terminal residues 1–2 and 302–306 observed in both structures suggest that N-terminal autoprocessing is tightly coupled to the E-E* equilibrium and stable dimer formation.     

Photosynthetic performance at low temperature of Bouteloua gracilis Lag., a high-altitude C4 grass from the Rocky Mountains, USA

The mechanisms controlling the photosynthetic performance of C₄ plants at low temperature were investigated using ecotypes of Bouteloua gracilis Lag. from high (3000 m) and low (1500 m) elevation sites in the Rocky Mountains of Colorado. Plants were grown in controlled‐environment cabinets at a photon flux density of 700 μ mol m^?2 s^?1 and day/night temperatures of 26/16 °C or 14/7 °C. The thermal response of the net CO₂ assimilation rate (A) was evaluated using leaf gas‐exchange analysis and activity assays of ribulose‐1,5‐bisphosphate carboxylase/oxygenase (Rubisco), phosphoenolpyruvate carboxylase (PEPCase) and pyruvate,orthophosphate dikinase (PPDK). In both ecotypes, a reduction in measurement temperature caused the CO₂‐saturated rate of photosynthesis to decline to a greater degree than the initial slope of A versus the intercellular CO₂ response, thereby reducing the photosynthetic CO₂ saturation point. As a consequence, A in normal air was CO₂‐saturated at sub‐optimal temperatures. Ecotypic variation was low when grown at 26/16 °C, with the major difference between the ecotypes being that the low‐elevation plants had higher A; however, the ecotypes responded differently when grown at cool temperature. At temperatures below the thermal optimum, A in high‐elevation plants grown at 14/7 °C was enhanced relative to plants grown at 26/16 °C, while A in low‐elevation plants grown at 14/7 °C was reduced compared to 26/16 °C‐grown plants. Photoinhibition at low growth temperature was minor in both ecotypes as indicated by small reductions in dark‐adapted F_v/F_m. In both ecotypes, the activity of Rubisco was equivalent to A below 17 °C but well in excess of A above 25 °C. Activities of PEPCase and PPDK responded to temperature in a similar proportion relative to Rubisco, and showed no evidence for dissociation that would cause them to become principal limitations at low temperature. Because of the similar temperature response of Rubisco and A, we propose that Rubisco is a major limitation on C₄ photosynthesis in B. gracilis below 17 °C. Based on these results and for theoretical reasons associated with how C₄ plants use Rubisco, we further suggest that Rubisco capacity may be a widespread limitation upon C₄ photosynthesis at low temperature.     

Highly conserved glycine 86 and arginine 87 residues contribute differently to the structure and activity of the mature HIV‐1 protease

The structural and functional role of conserved residue G86 in HIV‐1 protease (PR) was investigated by NMR and crystallographic analyses of substitution mutations of glycine to alanine and serine (PR_G86A and PR_G86S). While PR_G86S had undetectable catalytic activity, PR_G86A exhibited ～6000‐fold lower catalytic activity than PR. ¹H‐¹⁵N NMR correlation spectra revealed that PR_G86A and PR_G86S are dimeric, exhibiting dimer dissociation constants (K_d) of ～0.5 and ～3.2 μM, respectively, which are significantly lower than that seen for PR with R87K mutation (K_d > 1 mM). Thus, the G86 mutants, despite being partially dimeric under the assay conditions, are defective in catalyzing substrate hydrolysis. NMR spectra revealed no changes in the chemical shifts even in the presence of excess substrate, indicating very poor binding of the substrate. Both NMR chemical shift data and crystal structures of PR_G86A and PR_G86S in the presence of active‐site inhibitors indicated high structural similarity to previously described PR/inhibitor complexes, except for specific perturbations within the active site loop and around the mutation site. The crystal structures in the presence of the inhibitor showed that the region around residue 86 was connected to the active site by a conserved network of hydrogen bonds, and the two regions moved further apart in the mutants. Overall, in contrast to the role of R87 in contributing significantly to the dimer stability of PR, G86 is likely to play an important role in maintaining the correct geometry of the active site loop in the PR dimer for substrate binding and hydrolysis. Proteins 2010. © 2009 Wiley‐Liss, Inc.     

Downstream processing,characterization, and structure–function relationship of solvent‐, detergent‐, psychro‐, thermo‐, alkalistable metalloprotease from metal‐, solvent‐tolerant psychrotrophic Pseudomonas putida SKG‐1 isolate

The purification and characterization of psychro‐thermoalkalistable protease from psychrotrophic Pseudomonas putida isolate is being reported for the first time. A ～53 kDa protease was purified 21.4‐folds with 57.2% recovery by ultrafiltration and hydrophobic interaction chromatography. Kinetic analyses revealed the K_m and V_max to be 1.169 mg mL^?1 and 0.833 mg mL^?1 min^?1, respectively. The k_cat value of 3.05 × 10² s^?1 indicated high affinity and catalytic efficiency toward casein. The protease was most active at pH 9.5 and 40°C, with 100% stability in pH and temperature range of 6.0–11.0 and 10–40°C, respectively. Presence of Zn²⁺ increased the thermostability of protease (at 70°C) by 433%. Ethylene diamine tetra acetic acid (EDTA) and 1,10‐phenanthroline were inhibitory, whereas phenyl methyl sulfonyl fluoride (PMSF), p‐chloro mercuric benzoate (PCMB), and β‐mercaptoethanol were ineffective, revealing the enzyme to be a metalloprotease. Zinc, calcium, iron, nickel, and copper at 1 mM increased the enzyme activity (102–134%). Complete reversion of enzyme inhibition (caused by Ethylene diamine tetra acetic acid [EDTA]) by Zn²⁺ affirmed this enzyme as zinc‐dependent metalloprotease. At 0.1% concentration, Triton X‐100 and Tween 80 slightly increased, while SDS and H₂O₂ reduced the protease activity. In the presence of 0.1% commercial detergents, the enzyme was fairly stable (54–81%). In the presence of organic solvent, the protease was remarkably stable exhibiting 72–191% activities. In contrast, savinase exhibited good stability in the presence of hydrophilic solvents, while chymotrypsin showed elevated activities with benzene, toluene, and xylene only. Circular dichroism analysis revealed the protease as a β‐rich protein, having large fraction (～40%) of β‐sheets. Presence of different environmental conditions altered the β‐content, which accordingly affected the protease activity. © 2012 American Institute of Chemical Engineers Biotechnol. Prog., 2013     

The biotechnological potential of subtilisin‐like fibrinolytic enzyme from a newly isolated Lactobacillus plantarum KSK‐II in blood destaining and antimicrobials

An antimicrobial oxidative‐ and SDS‐stable fibrinolytic alkaline protease designated as KSK‐II was produced by Lactobacillus plantarum KSK‐II isolated from kishk, a traditional Egyptian food. Maximum enzyme productivity was obtained in medium containing 1% lactose and 0.5% soybean flour as carbon and nitrogen sources, respectively. Purification of enzyme increased its specific activity to 1,140‐fold with a recovery of 33% and molecular weight of 43.6 kDa. Enzyme activity was totally lost in the presence of ethylenediaminetetraacetic acid and was restored after addition of Fe²⁺ suggesting that KSK‐II is a metalloprotease and Fe²⁺ acts as cofactor. Enzyme hydrolyzed not only the natural proteins but also synthetic substrates, particularly Suc‐Ala‐Ala‐Pro‐Phe‐pNA. KSK‐II can hydrolyze the Lys‐X easier than Arg‐X; thus, it was considered as a subtilisin‐family protease. Its apparent K_m, V_max, and K_cat were 0.41 mM, 6.4 µmol mg^?1 min^?1, and 28.0 s^?1, respectively. KSK‐II is industrially important from the perspectives of its maximal activity at 50°C (stable up to 70°C), ability to function at alkaline pH (10.0), stability at broad pH ranges (7.5–12.0) in addition to its stability toward SDS, H₂O₂, organic solvents, and detergents. We emphasize for the first time the potential of fibrinolytic activity for alkaline proteases used in detergents especially in blood destaining. © 2014 American Institute of Chemical Engineers Biotechnol. Prog., 31:316–324, 2015     

Photosynthetic responses of two eucalypts to industrial‐age changes in atmospheric [CO2] and temperature

The unabated rise in atmospheric [CO₂] is associated with increased air temperature. Yet, few CO₂‐enrichment studies have considered pre‐industrial [CO₂] or warming. Consequently, we quantified the interactive effects of growth [CO₂] and temperature on photosynthesis of faster‐growing Eucalyptus saligna and slower‐growing E. sideroxylon. Well‐watered and ‐fertilized tree seedlings were grown in a glasshouse at three atmospheric [CO₂] (290, 400, and 650 µL L^?1), and ambient (26/18 °C, day/night) and high (ambient + 4 °C) air temperature. Despite differences in growth rate, both eucalypts responded similarly to [CO₂] and temperature treatments with few interactive effects. Light‐saturated photosynthesis (A_sat) and light‐ and [CO₂]‐saturated photosynthesis (A_max) increased by ～50% and ～10%, respectively, with each step‐increase in growth [CO₂], underpinned by a corresponding 6–11% up‐regulation of maximal electron transport rate (J_max). Maximal carboxylation rate (V_cmax) was not affected by growth [CO₂]. Thermal photosynthetic acclimation occurred such that A_sat and A_max were similar in ambient‐ and high‐temperature‐grown plants. At high temperature, the thermal optimum of A_sat increased by 2–7 °C across [CO₂] treatments. These results are the first to suggest that photosynthesis of well‐watered and ‐fertilized eucalypt seedlings will remain strongly responsive to increasing atmospheric [CO₂] in a future, warmer climate.     

Standard metabolic rate models for Carmine Shiner (Notropis percobromus) and Common Shiner (Luxilus cornutus) across different temperature regimes

Standard metabolic rates (SMR) were measured empirically for carmine shiner Notropis percobromus and common shiner Luxilus cornutus to develop SMR models that predict metabolic responses of each species under thermal conditions observed in the wild. SMR increased significantly with body mass and rising water temperature, ranging from 0.05 mg O₂ h⁻¹ at 10°C to 0.89 mg O₂ h⁻¹ at 20°C for N. percobromus weighing 0.6–2.5 g and from 0.11 mg O₂ h⁻¹ at 10°C to 0.98 mg O₂ h⁻¹ at 20°C for L. cornutus weighing 0.8–6.6 g. SMR models significantly differed between sympatric species on account of differences in model intercepts (RA) and temperature coefficients (RQ), however, the allometric relationships between mass and SMR did not significantly differ between species. Known distribution of N. percobromus and L. cornutus includes the Birch River located in Manitoba, Canada, where N. percobromus is listed as Endangered. Little is known about the physiology of N. percobromus or the species' ability to acclimate or adapt to different environmental conditions. While size differences between species contributed, in part, to differences in SMR predictions for Birch River populations, SMR trends (< 2 mg O₂ h⁻¹) for individuals weighing 1 g were similar for both species across daily temperatures. Respirometry experiments contributed to developing species-specific SMR models and inform on the effect of natural and anthropogenic stressors, namely water temperature, on the conservation of N. percobromus in this ecosystem.     

Selection of Drug-Resistant Feline Immunodeficiency Virus (FIV) Encoding FIV/HIV Chimeric Protease in the Presence of HIV-Specific Protease Inhibitors

An infectious chimeric feline immunodeficiency virus (FIV)/HIV strain carrying six HIV-like protease (PR) mutations (I37V/N55M/V59I/I98S/Q99V/P100N) was subjected to selection in culture against the PR inhibitor lopinavir (LPV), darunavir (DRV), or TL-3. LPV selection resulted in the sequential emergence of V99A (strain S-1X), I59V (strain S-2X), and I108V (strain S-3X) mutations, followed by V37I (strain S-4X). Mutant PRs were analyzed in vitro, and an isogenic virus producing each mutant PR was analyzed in culture for LPV sensitivity, yielding results consistent with the original selection. The 50% inhibitory concentrations (IC₅₀s) for S-1X, S-2X, S-3X, and S-4X were 95, 643, 627, and 1,543 nM, respectively. The primary resistance mutations, V99⁸²A, I59⁵⁰V, and V37³²I, are consistent with the resistance pattern developed by HIV-1 under similar selection conditions. While resistance to LPV emerged readily, similar PR mutations causing resistance to either DRV or TL-3 failed to emerge after passage for more than a year. However, a G37D mutation in the nucleocapsid (NC) was observed in both selections and an isogenic G37D mutant replicated in the presence of 100 nM DRV or TL-3, whereas parental chimeric FIV could not. An additional mutation, L92V, near the PR active site in the folded structure recently emerged during TL-3 selection. The L92V mutant PR exhibited an IC₅₀ of 50 nM, compared to 35 nM for 6s-98S PR, and processed the NC-p2 junction more efficiently, consistent with increased viral fitness. These findings emphasize the role of mutations outside the active site of PR in increasing viral resistance to active-site inhibitors and suggest additional targets for inhibitor development.     

Effect of the active site D25N mutation on the structure, stability, and ligand binding of the mature HIV-1 protease

All aspartic proteases, including retroviral proteases, share the triplet DTG critical for the active site geometry and catalytic function. These residues interact closely in the active, dimeric structure of HIV-1 protease (PR). We have systematically assessed the effect of the D25N mutation on the structure and stability of the mature PR monomer and dimer. The D25N mutation (PR(D25N)) increases the equilibrium dimer dissociation constant by a factor >100-fold (1.3 +/- 0.09 microm) relative to PR. In the absence of inhibitor, NMR studies reveal clear structural differences between PR and PR(D25N) in the relatively mobile P1 loop (residues 79-83) and flap regions, and differential scanning calorimetric analyses show that the mutation lowers the stabilities of both the monomer and dimer folds by 5 and 7.3 degrees C, respectively. Only minimal differences are observed in high resolution crystal structures of PR(D25N) complexed to darunavir (DRV), a potent clinical inhibitor, or a non-hydrolyzable substrate analogue, Ac-Thr-Ile-Nle-r-Nle-Gln-Arg-NH(2) (RPB), as compared with PR.DRV and PR.RPB complexes. Although complexation with RPB stabilizes both dimers, the effect on their T(m) is smaller for PR(D25N) (6.2 degrees C) than for PR (8.7 degrees C). The T(m) of PR(D25N).DRV increases by only 3 degrees C relative to free PR(D25N), as compared with a 22 degrees C increase for PR.DRV, and the mutation increases the ligand dissociation constant of PR(D25N).DRV by a factor of approximately 10(6) relative to PR.DRV. These results suggest that interactions mediated by the catalytic Asp residues make a major contribution to the tight binding of DRV to PR.     

Effects of temperature on the development and survival of an endangered butterfly,Lycaeides argyrognomon (Lepidoptera: Lycaenidae) with estimation of optimal and threshold temperatures using linear and nonlinear models

The effects of temperature on the development and survival of Lycaeides argyrognomon were examined in the laboratory. The eggs, larvae and pupae were reared at temperatures of 15, 17.5, 20, 25, 30 and 33°C under a long‐day photoperiod of 16‐h light and 8‐h darkness. The survival rates of the first–third instars ranged from 40.0 to 82.4%. The mortalities of the fourth instar were lower than those of the first–third instars. The development time of the overall immature stage decreased from 78.33 days at 15°C to 21.07 days at 30°C, and then increased to 24.33 days at 33°C. The common linear model and the Ikemoto–Takai model were used to estimate the thermal constant (K) and the developmental zero (T₀). The values of T₀ and K for the overall immature stages were 10.50°C and 418.83 degree‐days, and 9.71°C and 451.68 degree‐days by the common model and the Ikemoto–Takai model, respectively. The upper temperature thresholds (T_max) and the optimal temperatures (T_opt) of the egg, the first–third instars and the overall immature stages were estimated by the three nonlinear models. The ranges of T_opt estimated were from 30.33°C to 32.46°C in the overall immature stages and the estimates of T_max of the overall immature stages by the Briere‐1 and the Briere‐2 models were 37.18°C and 33.00°C, respectively. The method to predict the developmental period of L. argyrognomon using the nonlinear models was discussed based on the data of the average temperature per hour.     

Temperature effects on the hydrodynamic radius of the intrinsically disordered N‐terminal region of the p53 protein

Intrinsically disordered proteins (IDPs) are often characterized in terms of the hydrodynamic radius, R_h. The R_h of IDPs are known to depend on fractional proline content and net charge, where increased numbers of proline residues and increased net charge cause larger R_h. Though sequence and charge effects on the R_h of IDPs have been studied, the temperature sensitivity has been noted only briefly. Reported here are R_h measurements in the temperature range of 5–75°C for the intrinsically disordered N‐terminal region of the p53 protein, p53(1–93). Of note, the R_h of this protein fragment was highly sensitive to temperature, decreasing from 35 Å at 5°C to 26 Å at 75°C. Computer generated simulations of conformationally dynamic and disordered polypeptide chains were performed to provide a hypothesis for the heat‐induced compaction of p53(1–93) structure, which was opposite to the heat‐induced increase in R_h observed for a model folded protein. The simulations demonstrated that heat caused R_h to trend toward statistical coil values for both proteins, indicating that the effects of heat on p53(1–93) structure could be interpreted as thermal denaturation. The simulation data also predicted that proline content contributed minimally to the native R_h of p53(1–93), which was confirmed by measuring R_h for a substitution variant that had all 22 proline residues changed for glycine. Proteins 2014; 82:668–678. © 2013 Wiley Periodicals, Inc.     

Physical interaction between the strawberry allergen Fra a 1 and an associated partner FaAP: Interaction of Fra a 1 proteins and FaAP

The strawberry fruit allergens Fra a 1.01E, Fra a 1.02 and Fra a 1.03 belong to the group of pathogenesis‐related 10 (PR‐10) proteins and are homologs of the major birch pollen Bet v 1 and apple allergen Mal d 1. Bet v 1 related proteins are the most extensively studied allergens but their physiological function in planta remains elusive. Since Mal d 1‐Associated Protein has been previously identified as interaction partner of Mal d 1 we studied the binding of the orthologous Fra a 1‐Associated Protein (FaAP) to Fra a 1.01E/1.02/1.03. As the C‐terminal sequence of FaAP showed strong auto‐activation activity in yeast 2‐hybrid analysis a novel time resolved DNA‐switching system was successfully applied. Fra a 1.01E, Fra a 1.02, and Fra a 1.03 bind to FaAP with K_D of 4.5 ± 1.1, 15 ± 3, and 11 ± 2 nM, respectively. Fra a 1.01E forms a dimer, whereas Fra a 1.02 and Fra a 1.03 bind as monomer. The results imply that PR‐10 proteins might be integrated into a protein‐interaction network and FaAP binding appears to be essential for the physiological function of the Fra a 1 proteins.     

Light and temperature effects on photosynthetic activity of E ucheuma denticulatum and K appaphycus alvarezii (brown and green color morphotypes) from Sulawesi Utara,Indonesia

Knowledge concerning the effects of several abiotic factors on the physiology of carrageenophytes is essential both in ecological and economic standpoints, to ensure their sufficient supply for the sustainability of seaweed‐based industries. This paper presents the photosynthetic characteristics of farmed carrageenophytes, E ucheuma denticulatum and K appaphycus alvarezii [brown (BRN) and green (GRN) color morphotypes] from Sulawesi Utara (Sulawesi Island), Indonesia, as determined by examining their photosynthetic response across different temperatures and irradiances using dissolved oxygen measurements and pulse‐amplitude modulated fluorometer. Net photosynthesis–irradiance ( P – E ) curves at 26°C revealed that net photosynthetic rates of the three seaweeds gradually increased until the estimated saturation irradiances ( E _k ) of 58 μmol photons m^{? 2} s^?1 (49–68 μmol photons m^{? 2} s^?1, 95% Bayesian prediction intervals; BPI) for E . denticulatum, and 158 and 143 μmol photons m^{? 2} s^?1 (134–185 and 99–203 μmol photons m^{? 2} s^?1, 95% BPI) for BRN and GRN K . alvarezii, respectively; and that no photoinhibition was observed at the highest irradiance of 1000 μmol photons m^{? 2} s^?1. All seaweed samples exhibited photosynthetic tolerance to high PAR as shown by their recovery in maximum quantum yields (F_v / F_m ) following chronic exposures; as well as tolerance over a broad range of temperature, which is from 19 to 33°C for E . denticulatum, 20–29°C for BRN K . alvarezii, and 17–32°C for GRN K . alvarezii. Temperature responses of these carrageenophytes indicated that they were well‐adapted to the annual seawater temperatures in the cultivation site; however, they are also likely close to threshold levels for thermal inhibition, given the decline in F_v / F_m above 30°C.     

Folding thermodynamics of the hybrid‐1 type intramolecular human telomeric G‐quadruplex

Guanine‐rich DNA sequences that may form G‐quadruplexes are located in strategic DNA loci with the ability to regulate biological events. G‐quadruplexes have been under intensive scrutiny owing to their potential to serve as novel drug targets in emerging anticancer strategies. Thermodynamic characterization of G‐quadruplexes is an important and necessary step in developing predictive algorithms for evaluating the conformational preferences of G‐rich sequences in the presence or the absence of their complementary C‐rich strands. We use a combination of spectroscopic, calorimetric, and volumetric techniques to characterize the folding/unfolding transitions of the 26‐meric human telomeric sequence d[A₃G₃(T₂AG₃)₃A₂]. In the presence of K⁺ ions, the latter adopts the hybrid‐1 G‐quadruplex conformation, a tightly packed structure with an unusually small number of solvent‐exposed atomic groups. The K⁺‐induced folding of the G‐quadruplex at room temperature is a slow process that involves significant accumulation of an intermediate at the early stages of the transition. The G‐quadruplex state of the oligomeric sequence is characterized by a larger volume and compressibility and a smaller expansibility than the coil state. These results are in qualitative agreement with each other all suggesting significant dehydration to accompany the G‐quadruplex formation. Based on our volume data, 432 ± 19 water molecules become released to the bulk upon the G‐quadruplex formation. This large number is consistent with a picture in which DNA dehydration is not limited to water molecules in direct contact with the regions that become buried but involves a general decrease in solute–solvent interactions all over the surface of the folded structure. © 2013 Wiley Periodicals, Inc. Biopolymers 101: 216–227, 2014.     

Thermodynamics of stabilization of RNA pseudoknots by cobalt(III) hexaammine

Equilibrium unfolding (folding) studies reveal that the autoregulatory RNA pseudoknots derived from the bacteriophage T2 and T4 gene 32 mRNAs exhibit significant stabilization by increasing concentrations of divalent metal ions in solution. In this report, the apparent affinities of exchange inert trivalent Co(NH₃) have been determined, relative to divalent Mg²⁺, for the folded, partially folded (K_f), and fully unfolded (K_u) conformations of these molecules. A general nonspecific, delocalized ion binding model was developed and applied to the analysis of the metal ion concentration dependence of individual two‐state unfolding transitions. Trivalent Co(NH₃) was found to associate with the fully folded and partially unfolded pseudoknotted forms of these RNAs with a K_f of 5–8 × 10⁴ M⁻¹ in a background of 0.10 M K⁺, or 3‐ to 5‐fold larger than the K_f obtained for two model RNA hairpins and hairpin unfolding intermediates, and ≈ 40–50‐fold larger than K_f for Mg²⁺. The magnitude of K_f was found to be strongly dependent on the monovalent salt concentration in a manner qualitatively consistent with polyelectrolyte theory, with K_f reaching 1.2 × 10⁵ M⁻¹ in 50 mM K⁺. Two RNA hairpins were found to have affinities for Co(NH₃) and Ru(NH₃) of 1–2 ×10⁴ M⁻¹, or ≈ 15‐fold larger than the K_f of ∼ 1000 M⁻¹ observed for Mg²⁺. Additionally, the K_u of 4,800 M⁻¹ for the trivalent ligands is ≈ 8‐fold larger than the K_u of 600 M⁻¹ observed for Mg²⁺. These findings suggest that the T2 and T4 gene 32 mRNA pseudoknots possess a site(s) for Mg²⁺ and Co(NH₃) binding of significantly higher affinity than a “duplexlike” delocalized ion binding site that is strongly linked to the thermodynamic stability of these molecules. Imino proton perturbation nmr spectroscopy suggests that this site(s) lies near the base of the pseudoknot stem S2, near a patch of high negative electrostatic potential associated with the region where the single loop L1 adenosine crosses the major groove of stem S2. © 1999 John Wiley & Sons, Inc. Biopoly 50: 443–458, 1999     

Electron transport is the functional limitation of photosynthesis in field-grown Pima cotton plants at high temperature

Restrictions to photosynthesis can limit plant growth at high temperature in a variety of ways. In addition to increasing photorespiration, moderately high temperatures (35–42 °C) can cause direct injury to the photosynthetic apparatus. Both carbon metabolism and thylakoid reactions have been suggested as the primary site of injury at these temperatures. In the present study this issue was addressed by first characterizing leaf temperature dynamics in Pima cotton (Gossypium barbadense) grown under irrigation in the US desert south‐west. It was found that cotton leaves repeatedly reached temperatures above 40 °C and could fluctuate as much as 8 or 10 °C in a matter of seconds. Laboratory studies revealed a maximum photosynthetic rate at 30–33 °C that declined by 22% at 45 °C. The majority of the inhibition persisted upon return to 30 °C. The mechanism of this limitation was assessed by measuring the response of photosynthesis to CO₂ in the laboratory. The first time a cotton leaf (grown at 30 °C) was exposed to 45 °C, photosynthetic electron transport was stimulated (at high CO₂) because of an increased flux through the photorespiratory pathway. However, upon cooling back to 30 °C, photosynthetic electron transport was inhibited and fell substantially below the level measured before the heat treatment. In the field, the response of assimilation (A) to various internal levels of CO₂ (C_i) revealed that photosynthesis was limited by ribulose‐1,5‐bisphosphate (RuBP) regeneration at normal levels of CO₂ (presumably because of limitations in thylakoid reactions needed to support RuBP regeneration). There was no evidence of a ribulose‐1,5‐bisphosphate carboxylase/oxygenase (Rubisco) limitation at air levels of CO₂ and at no point on any of 30 A–C_i curves measured on leaves at temperatures from 28 to 39 °C was RuBP regeneration capacity measured to be in substantial excess of the capacity of Rubisco to use RuBP. It is therefore concluded that photosynthesis in field‐grown Pima cotton leaves is functionally limited by photosynthetic electron transport and RuBP regeneration capacity, not Rubisco activity.     

Interactive effects of elevated CO2 and temperature on water transport inponderosa pine

Many studies report that water flux through trees declines in response to elevated CO₂, but this response may be modified by exposure to increased temperatures. To determine whether elevated CO₂ and temperature interact to affect hydraulic conductivity, we grew ponderosa pine seedlings for 24 wk in growth chambers with one of four atmospheric CO₂ concentrations (350, 550, 750, and 1100 ppm) and either a low (15°C nights, 25°C days) or high (20°C nights, 30°C days) temperature treatment. Vapor pressure deficits were also higher in the elevated temperature treatment. Seedling biomass increased with CO₂ concentration but was not affected by temperature. Root : shoot ratio was unaffected by CO₂ and temperature. Leaf : sapwood area ratio (A_L/A_S) declined in response to elevated temperature but was not influenced by CO₂. Larger tracheid diameters at elevated temperature caused an increase in xylem-specific hydraulic conductivity (K_S). The increase in K_S and decrease in A_L/A_S led to higher leaf-specific hydraulic conductivity (K_L) at elevated temperature. Stomatal conductance (g_S) was correlated with K_L across all treatments. Neither K_S, K_L, nor g_S were affected by elevated CO₂ concentrations. High K_L in response to elevated temperature may support increased transpiration or reduce the incidence of xylem cavitation in ponderosa pine in future, warmer climates.     

The effects of development at sub-optimal growth temperatures on photosynthetic capacity and susceptibility to chilling-dependent photoinhibition in Zea mays

When plants of Zea mays L. cv. LG11 that have been grown at optimal temperatures are transferred to chilling temperatures (0–12°C) photoinhibition of photosynthetic CO₂ assimilation can occur. This study examines how growth at sub-optimal temperatures alters both photosynthetic capacity and resistance to chilling-dependent photoinhibition. Plants of Z. mays cv. LG11 were grown in controlled environments at 14, 17, 20 and 25°C. As a measure of the capacity for photosynthesis under light limiting conditions, the maximum quantum yields of CO₂ assimilation (φ^a.c) and O₂ evolution (φ^a.o) were determined for the laminae of the second leaves at photon fluxes of 50–150 μmol m^-2s^-1. To determine photosynthetic capacity at photon fluxes approaching light saturation, rates of CO₂ uptake (A₁₅₀₀) and O₂ evolution (A₁₅₀₀) were determined in a photon flux of 1500 μmol m^-2s^-1. In leaves developed at 14°C, φ and φ were 26 and 43%, respectively, of the values for leaves grown at 25°C. Leaves grown at 17°C showed intermediate reductions in φ and φ, whilst leaves developed at 20°C showed no significant differences from those grown at 25°C. Similar patterns of decrease were observed for A₁₅₀₀ and A_1500.0 with decreasing growth temperature. Leaves developed at 25°C showed higher rates of CO₂ assimilation at all light levels and measurement temperatures in comparison to leaves developed at 17 and 14°C. A greater reduction in A₁₅₀₀ relative to A_1500.0 with decreasing growth temperature was attributed to increased stomatal limitation. Exposure of leaves to 800–1000 μmol m^-2 s^-1 when plant temperature was depressed to ca 6.5°C produced a photoinhibition of photosynthetic CO₂ assimilation in all leaves. However, in leaves developed at 17°C the decrease in A₁₅₀₀ following this chilling treatment was only 25% compared to 90% in leaves developed at 25°C. Recovery following chilling was completed earlier in leaves developed at 17°C. The results suggest that growth at sub-optimal temperatures induces increased tolerance to exposure to high light at chilling temperatures. This is offset by the large loss in photosynthetic capacity imposed by leaf development at sub-optimal temperatures.