Two reaction pathways for transformation of high potential cytochrome b559 of PS II into the intermediate potential form

This study describes an analysis of different treatments that influence the relative content and the midpoint potential of HP Cyt b559 in PS II membrane fragments from higher plants. Two basically different types of irreversible modification effects are distinguished: the HP form of Cyt b559 is either predominantly affected when the heme group is oxidized (“O-type” effects) or when it is reduced (“R-type” effects). Transformation of HP Cyt b559 to lower potential redox forms (IP and LP forms) by the “O-type” mechanism is induced by high pH and detergent treatments. In this case the effects consist of a gradual decrease in the relative content of HP Cyt b559 while its midpoint potential remains unaffected. Transformation of HP Cyt b559 via an “R-type” mechanism is caused by a number of exogenous compounds denoted L: herbicides, ADRY reagents and tetraphenylboron. These compounds are postulated to bind to the PS II complex at a quinone binding site designated as Q_C which interacts with Cyt b559 and is clearly not the Q_B site. Binding of compounds L to the Q_C site when HP Cyt b559 is oxidized gives rise to a gradual decrease in the E_m of HP Cyt b559 with increasing concentration of L (up to 10 K_ox(L) values) while the relative content of HP Cyt b559 is unaffected. Higher concentrations of compounds L required for their binding to Q_C site when HP Cyt b559 is reduced (described by K_red(L)) induce a conversion of HP Cyt b559 to lower potential redox forms (“R-type” transformation). Two reaction pathways for transitions of Cyt b559 between the different protein conformations that are responsible for the HP and IP/LP redox forms are proposed and new insights into the functional regulation of Cyt b559 via the Q_C site are discussed.     

Melanization in the genus Propithecus Malagasey Lemur

Among the Lemurs of Madagascar the genus Propithecus contributes two species, but these are differentiated into numerous forms (subspecies and intermediates between them) which are essentially characterized by pelage coloration. The existence of certain “melanizing” forms among these intermediates permits us to examine the problem of the evolution of this genus in Madagascar, invoking a hypothesis to explain these chromatic variations. Hershkovitz's theory of “Metachromism” could easily fit the case of Propithecus. It would permit derivation of the light-coloured forms of the north, west and the south from a primitive form close to the dark-coloured Propithecus diadema of the southeast.     

Structure of a Prokaryotic Sodium Channel Pore Reveals Essential Gating Elements and an Outer Ion Binding Site Common to Eukaryotic Channels

Voltage-gated sodium channels (Na_Vs) are central elements of cellular excitation. Notwithstanding advances from recent bacterial Na_V (BacNa_V) structures, key questions about gating and ion selectivity remain. Here, we present a closed conformation of Na_VAe1p, a pore-only BacNa_V derived from Na_VAe1, a BacNa_V from the arsenite oxidizer Alkalilimnicola ehrlichei found in Mono Lake, California, that provides insight into both fundamental properties. The structure reveals a pore domain in which the pore-lining S6 helix connects to a helical cytoplasmic tail. Electrophysiological studies of full-length BacNa_Vs show that two elements defined by the Na_VAe1p structure, an S6 activation gate position and the cytoplasmic tail “neck”, are central to BacNa_V gating. The structure also reveals the selectivity filter ion entry site, termed the “outer ion” site. Comparison with mammalian voltage-gated calcium channel (Ca_V) selectivity filters, together with functional studies, shows that this site forms a previously unknown determinant of Ca_V high-affinity calcium binding. Our findings underscore commonalities between BacNa_Vs and eukaryotic voltage-gated channels and provide a framework for understanding gating and ion permeation in this superfamily.     

Studies of the Mo(V) Center of the Y343F Mutant of Human Sulfite Oxidase by Variable Frequency Pulsed EPR Spectroscopy

The Mo(V) forms of the Tyr343Phe (Y343F) mutant of human sulfite oxidase (SO) have been investigated by continuous wave (CW) and variable frequency pulsed EPR spectroscopies as a function of pH. The CW EPR spectrum recorded at low-pH (∼6.9) has g-values similar to those known for the low-pH form of the native vertebrate SO (original lpH form); however, unlike the spectrum of original lpH SO, it does not show any hyperfine splittings from a nearby exchangeable proton. The detailed electron spin echo (ESE) envelope modulation (ESEEM) and pulsed electron-nuclear double resonance (ENDOR) experiments also did not reveal any nearby protons that could belong to an exchangeable ligand at the molybdenum center. These results suggest that under low-pH conditions the active site of Y343F SO is in the “blocked” form, with the Mo(V) center coordinated by sulfate. With increasing pH the EPR signal from the “blocked” form decreases, while a signal similar to that of the original lpH form appears and becomes the dominant signal at pH >9. In addition, both the CW EPR and ESE-detected field-sweep spectra reveal a considerable contribution from a signal similar to that usually detected for the high-pH form of native vertebrate SO (original hpH form). The nearby exchangeable protons in both of the component forms observed at high-pH were studied by the ESEEM spectroscopy. These results indicate that the Y343F mutation increases the apparent pK_a of the transition from the lpH to hpH forms by ∼2 pH units.     

Crystal Structure of Glyceraldehyde-3-Phosphate Dehydrogenase 1 from Methicillin-Resistant Staphylococcus aureus MRSA252 Provides Novel Insights into Substrate Binding and Catalytic Mechanism

The dreaded pathogen Staphylococcus aureus is one of the causes of morbidity and mortality worldwide. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), one of the key glycolytic enzymes, is irreversibly oxidized under oxidative stress and is responsible for sustenance of the pathogen inside the host. With an aim to elucidate the catalytic mechanism and identification of intermediates involved, we describe in this study different crystal structures of GAPDH1 from methicillin-resistant S. aureus MRSA252 (SaGAPDH1) in apo and holo forms of wild type, thioacyl intermediate, and ternary complexes of active-site mutants with physiological substrate d-glyceraldehyde-3-phosphate (G3P) and coenzyme NAD⁺. A new phosphate recognition site, “new P_i” site, similar to that observed in GAPDH from Thermotoga maritima, is reported here, which is 3.40 Å away from the “classical P_i” site. Ternary complexes discussed are representatives of noncovalent Michaelis complexes in the ground state. d-G3P is bound to all the four subunits of C151S.NAD and C151G.NAD in more reactive hydrate (gem-di-ol) form. However, in C151S + H178N.NAD, the substrate is bound to two chains in aldehyde form and in gem-di-ol form to the other two. This work reports binding of d-G3P to the C151G mutant in an inverted manner for the very first time. The structure of the thiaocyl complex presented here is formed after the hydride transfer. The C3 phosphate of d-G3P is positioned at the “P_s” site in the ternary complexes but at the “new P_i” site in the thioacyl complex and C1-O1 bond points opposite to His178 disrupting the alignment between itself and NE2 of His178. A new conformation (Conformation I) of the 209-215 loop has also been identified, where the interaction between phosphate ion at the “new P_i” site and conserved Gly212 is lost. Altogether, inferences drawn from the kinetic analyses and crystal structures suggest the “flip-flop” model proposed for the enzyme mechanism.     

Mutations in Desmin's Carboxy-Terminal “Tail” Domain Severely Modify Filament and Network Mechanics

Inherited mutations in the gene coding for the intermediate filament protein desmin have been demonstrated to cause severe skeletal and cardiac myopathies. Unexpectedly, some of the mutated desmins, in particular those carrying single amino acid alterations in the non-α-helical carboxy-terminal domain (“tail”), have been demonstrated to form apparently normal filaments both in vitro and in transfected cells. Thus, it is not clear if filament properties are affected by these mutations at all. For this reason, we performed oscillatory shear experiments with six different desmin “tail” mutants in order to characterize the mesh size of filament networks and their strain stiffening properties. Moreover, we have carried out high-frequency oscillatory squeeze flow measurements to determine the bending stiffness of the respective filaments, characterized by the persistence length l_p. Interestingly, mesh size was not altered for the mutant filament networks, except for the mutant DesR454W, which apparently did not form proper filament networks. Also, the values for bending stiffness were in the same range for both the “tail” mutants (l_p = 1.0-2.0 μm) and the wild-type desmin (l_p = 1.1 ± 0.5 μm). However, most investigated desmin mutants exhibited a distinct reduction in strain stiffening compared to wild-type desmin and promoted nonaffine network deformation. Therefore, we conclude that the mutated amino acids affect intrafilamentous architecture and colloidal interactions along the filament in such a way that the response to applied strain is significantly altered.In order to explore the importance of the “tail” domain as such for filament network properties, we employed a “tail”-truncated desmin. Under standard conditions, it formed extended regular filaments, but failed to generate strain stiffening. Hence, these data strongly indicate that the “tail” domain is responsible for attractive filament-filament interactions. Moreover, these types of interactions may also be relevant to the network properties of the desmin cytoskeleton in patient muscle.     

Fine structure of spermatozoa in the blackspot sea bream Pagellus bogaraveo (Brünnich, 1768) with some considerations about the centriolar complex

Scanning and transmission electron microscopy were used to investigate the fine structure of the sperm of the sparid fish Pagellus bogaraveo.The spermatozoon of P. bogaraveo belongs, like that of the other sparid fish, to the teleostean “type I” spermatozoon with the flagellar axis insert perpendicular to the nuclear fossa. It has an ovoidal head, a short, cylindrically shaped midpiece and a long tail region. The nucleus reveals a deep invagination (nuclear fossa), in which the centriolar complex is located, and a satellite nuclear notch shaped like a golf club. The two centrioles are perpendicular to each other and show a conventional “9+0” pattern. The distal centriole is attached to the nuclear envelope by means of basal feet and radial fibers made of electron-dense material. Below the basal plate, plasma membrane pinches in, and the necklace, a specialized connection joining axonemal doublets to the plasma membrane, is visible. The short midpiece houses one mitochondrion. The flagellum is perpendicularly and eccentrically with respect to the nucleus and contains the conventional “9+2” axoneme.     

Dynamics of the glutamic acid 242 side chain in cytochrome c oxidase

In many cytochrome c oxidases glutamic acid 242 is required for proton transfer to the binuclear heme a₃/Cu_B site, and for proton pumping. When present, the side chain of Glu-242 is orientated “down” towards the proton-transferring D-pathway in all available crystal structures. A nonpolar cavity “above” Glu-242 is empty in these structures. Yet, proton transfer from Glu-242 to the binuclear site, and for proton-pumping, is well established, and the cavity has been proposed to at least transiently contain water molecules that would mediate proton transfer. Such proton transfer has been proposed to require isomerisation of the Glu-242 side chain into an “up” position pointing towards the cavity. Here, we have explored the molecular dynamics of the protonated Glu-242 side chain. We find that the “up” position is preferred energetically when the cavity contains four water molecules, but the “down” position is favoured with less water. We conclude that the cavity might be deficient in water in the crystal structures, possibly reflecting the “resting” state of the enzyme, and that the “up/down” equilibrium of Glu-242 may be coupled to the presence of active-site water molecules produced by O₂ reduction.     

An activation gating switch in Kv1.2 is localized to a threonine residue in the S2-S3 linker

The activation properties of Kv1.2 channels are highly variable, with reported half-activation (V_1/2) values ranging from ∼−40 mV to ∼+30 mV. Here we show that this arises because Kv1.2 channels occupy two distinct gating modes (“fast” and “slow”). “Slow” gating (τ_act = 90 ± 6 ms at +35 mV) was associated with a V_1/2 of activation of +16.6 ± 1.1 mV, whereas “fast” gating (τ_act = 4.5 ± 1.7 ms at +35 mV) was associated with a V_1/2 of activation of −18.8 ± 2.3 mV. It was possible to switch between gating modes by applying a prepulse, which suggested that channels activate to a single open state along separate “fast” and “slow” activation pathways. Using chimeras and point mutants between Kv1.2 and Kv1.5 channels, we determined that introduction of a positive charge at or around threonine 252 in the S2-S3 linker of Kv1.2 abolished “slow” activation gating. Furthermore, dialysis of the cytoplasm or excision of cell-attached patches from cells expressing Kv1.2 channels switched gating from “slow” to “fast”, suggesting involvement of cytoplasmic regulators. Collectively, these results demonstrate two modes of activation gating in Kv1.2 and specific residues in the S2-S3 linker that act as a switch between these modes.     

Evaluation of Alternate Isotope-Coded Derivatization Assay (AIDA) in the LC–MS/MS analysis of aldehydes in exhaled breath condensate

We present the application of a novel isotope dilution method, named Alternate Isotope-Coded Derivatization Assay (AIDA), to the quantitative analysis of hydrazone derivatives of malondialdehyde (MDA) and 4-hydroxynonenal (4-HNE) in exhaled breath condensate (EBC) samples using liquid chromatography–tandem mass spectrometry. AIDA is based on the alternate derivatization of the analyte(s) with reagents that are available in two pure isotopic forms, respectively “light” and “heavy”, by using light-derivatized standards for the quantification of the heavy-derivatized analytes, and vice versa. To this purpose, 2,4-dinitro-3,5,6-trideuterophenylhydrazine (d₃-DNPH) has been synthesized and used as “heavy” reagent in combination with commercial “light” DNPH. Using the AIDA method, any unknown concentration of the analyte in the matrix can be calculated without the need of a calibration curve. An external calibration method has been also investigated for comparative purpose. The stability of DNPH and d₃-DNPH derivatives was verified by excluding any exchange of hydrazones with each other. In the range of concentrations of biological interest, e.g., 2–40 nM for MDA and 0.5–10 nM for 4-HNE, the derivatization reactions of MDA and 4-HNE with DNPH and d₃-DNPH showed overlapping kinetics and comparable yields. The MS response of both DNPH and d₃-DNPH hydrazones was similar. The precision of AIDA, calculated as %RSD, was within 3.2–8% for MDA and 4.5–11% for 4-HNE. Accuracy was tested by analyzing a spiked EBC pool sample and acceptable results (accuracy within 98–108% for MDA and 93–114% for 4-HNE) were obtained by AIDA after subtraction of the blank, which was not negligible. The results of quantitative analysis of MDA and 4-HNE in EBC samples obtained by AIDA assay with four analyses per sample were in good agreement with those obtained by external calibration method on the same samples.     

Bidesmoside triterpenoid glycosides from Stauntonia chinensis and relationship to anti-inflammation

Ten triterpenoid glycosides, yemuoside YM_26-35 (1-9 and 12), were isolated from a traditional Chinese medicine known as “Ye Mu Gua” (Stauntonia chinensis DC.) along with two known ones, kalopanax saponin C (10) and sieboldianoside A (11). Their structures, as elucidated by spectroscopic analyses and chemical methods, were either penta-saccharidic or hexa-saccharidic bidesmoside triterpenoid glycosides. To help explain the clinical applications of “Ye Mu Gua” for its anti-inflammatory effects, the inhibitory activity on the release of inflammatory mediators (nitric oxide, TNF-α and IL-6) of 1-12 and the related aglycone, hederagenin (13), was evaluated in vitro. It was found that compound 13, but not 1-12, exhibited significant inhibitory activity. The abundant triterpenoid glycosides in “Ye Mu Gua” might therefore be transformed into their respective aglycones, and thus inhibit the release of inflammatory factors in vivo. This could then account for the clinical value of “Ye Mu Gua” as regards anti-inflammatory effects. This proposed explanation of how “Ye Mu Gua” may have an effect is similar to the concept of prodrugs for chemical drugs which could be extended to some traditional medicines. That is, the major components might be biologically active not directly, but via biochemical transformation in vivo. Hence, we propose a “traditional medicine’s prodrug characteristic” concept.     

The Pragian-Emsian conodont successions of the Barrandian area: search of an alternative to the GSSP polygnathid-based correlation concept

Six Pragian-Emsian boundary sections in the Barrandian area, western of Prague, provided evidence of well detectable entries of Latericriodus fauna probably at the earliest Emsian beds (particularly Latericriodus bilatericrescens gracilis Bultynck). The chance to find icriodontid conodonts increases with latest part of Praha Fm., which is apparently of Emsian age, whereas polygnathids are sparsely preserved to absent. The high icriodontid/polygnathid ratio links together all these Barrandian sections, although their open-sea depositional environments range widely from deep troughs with rapid calciturbidite accumulation (Pod Barrandovem section) to relatively starving slope environments on elevations (Na Po?árech sections). The reports on polygnathid occurrences around the Pragian-Emsian boundary beds of the Barrandian area are much biased by poor reproducibility of the results (the conodonts cannot be found again) as well as by different levels where they were randomly found and/or by major taxonomic problems with the “kitabicus” and “dehiscens” definitions and their stratigraphic use. Apart from the GSSP in the Zinzilban Gorge (Uzbekistan) and its “kitabicus” boundary, the newly introduced “gracilis” biostratigraphic-marker concept preserves the major volume of the Pragian and respects also approximately the base of the traditional Emsian. These “gracilis” entries are clustered around the dark-colored “graptolite-bearing interval” beds, which largely form a prominent lithological marker within the latest, light gray-colored Dvorce-Prokop Limestone of the Barrandian area. This “gracilis” biostratigraphic marker has a promising correlation potential relative to Spanish and Moroccan sections.     

Morphometric analysis of Tremadocian (earliest Ordovician) kirkocystid mitrates (Echinodermata, Stylophora) from the Taebaeksan Basin, Korea

Abundant isolated remains of stylophoran echinoderms (cornutes and mitrates) are reported for the first time in the late Tremadocian (Asaphellus Zone) Tumugol Formation of Korea. Mitrate remains include numerous adorals of Kirkocystidae. Several new important anatomical features have been observed on these adorals, as an internal calcitic layer that is associated to s₂ and possibly also to the palmar complex. This observation suggests that the palmar complex would be present not only in mitrocystitid mitrates, but also in peltocystitids. For the first time, several morphometric analyses have been undertaken based on isolated kirkocystid adorals, so as to explore the morphological diversity displayed by Korean adorals, but also in order to compare their morphology with that of other Gondwanan kirkocystids. Morphometric analyses indicate the occurrence of two contrasted morphologies within Korean adorals (morphotypes A and B), and of three distinct morphologies within European and North African forms (“Anatifopsis”, “Balanocystites”, and “escandei” morphotypes). Comparison of Korean adorals with those from Europe and North Africa shows that: (1) morphotypes B and “Anatifopsis” are equivalent; consequently, the two Korean specimens referred to morphotype B are assigned to the genus Anatifopsis; (2) morphology of most Korean adorals, which belong to morphotype A, is clearly distinct from that of all other described kirkocystids from Europe and North Africa. The small size, juvenile morphology, and great morphological variability observed in the morphotype A of the Korean adorals are suggestive of possible heterochronic processes (peramorphosis).     

Crystal Structure of a Symmetric Football-Shaped GroEL:GroES2-ATP14 Complex Determined at 3.8 Å Reveals Rearrangement between Two GroEL Rings

The chaperonin GroEL is an essential chaperone that assists in protein folding with the aid of GroES and ATP. GroEL forms a double-ring structure, and both rings can bind GroES in the presence of ATP. Recent progress on the GroEL mechanism has revealed the importance of a symmetric 1:2 GroEL:GroES₂ complex (the “football”-shaped complex) as a critical intermediate during the functional GroEL cycle. We determined the crystal structure of the football GroEL:GroES₂-ATP₁₄ complex from Escherichia coli at 3.8 Å, using a GroEL mutant that is extremely defective in ATP hydrolysis. The overall structure of the football complex resembled the GroES-bound GroEL ring of the asymmetric 1:1 GroEL:GroES complex (the “bullet” complex). However, the two GroES-bound GroEL rings form a modified interface by an ~ 7° rotation about the 7-fold axis. As a result, the inter-ring contacts between the two GroEL rings in the football complex differed from those in the bullet complex. The differences provide a structural basis for the apparently impaired inter-ring negative cooperativity observed in several biochemical analyses.     

A Balanced Ratio of Proteins from Gene G and Frameshift-Extended Gene GT Is Required for Phage Lambda Tail Assembly

In bacteriophage λ, the overlapping open reading frames G and T are expressed by a programmed translational frameshift similar to that of the gag-pol genes of many retroviruses to produce the proteins gpG and gpGT. An analogous frameshift is widely conserved among other dsDNA tailed phages in their corresponding “G” and “GT” tail genes even in the absence of detectable sequence homology. The longer protein gpGT is known to be essential for tail assembly, but the requirement for the shorter gpG remained unclear because mutations in gene G affect both proteins. A plasmid system that can direct the efficient synthesis of tails was created and used to show that gpG and gpGT are both essential for correct tail assembly. Phage complementation assays under conditions where levels of plasmid-expressed gpG or gpGT could be altered independently revealed that the correct molar ratio of these two related proteins, normally determined by the efficiency of the frameshift, is also crucial for efficient assembly of functional tails. Finally, the physical connection between the G and T domains of gpGT, a consequence of the frameshift mechanism of protein expression, appears to be important for efficient tail assembly.     

Habitat use and activity influence thermoregulation in a tropical lizard, Ameiva exsul

We examined the contributions of alterations in daily activity and behavioral selection of microhabitat to thermoregulation in a population of the lizard, Ameiva exsul (Teiidae), by combining data on lizard activity with data on the availability of sun-shade patches and operative temperatures (T_e). By comparing T_e distributions predicted by “no thermoregulation” and “only thermoregulation” hypotheses to those predicted by random use of thermal habitat, we assessed the relative contributions of microhabitat selection and daily activity to regulation of body temperature (T_b). Over the course of a day lizards maintained T_b very close to optimal temperature (T_sel) despite T_es that deviated substantially from T_sel. Data demonstrating a unimodal daily activity pattern reject the hypothesis of uniform activity throughout the day. Also, lizard activity was not positively correlated with the proportion of T_es within T_sel nor negatively correlated with the absolute deviation of available T_e from T_sel (d_e) (“only thermoregulation”). Microsite use by A. exsul deviated significantly from predictions of the “no thermoregulation” hypothesis, but our data could not reject predictions of the “only thermoregulation” hypothesis that lizards would use sun-shade patches relative to the proportion of microsites where T_e is within T_sel. Also, lizards appeared to actively select sunlit and partially shaded microsites at different times of day. Thus, despite thermal constraints imposed by the habitat, A. exsul maintained high and relatively constant T_bs throughout its daily activity period and thermoregulated effectively. This appears to be generally representative of West Indian species of Ameiva.     

Point mutations in firefly luciferase C-domain demonstrate its significance in green color of bioluminescence

Firefly luciferase is a two-domain enzyme that catalyzes the bioluminescent reaction of firefly luciferin oxidation. Color of the emitted light depends on the structure of the enzyme, yet the exact color-tuning mechanism remains unknown by now, and the role of the C-domain in it is rarely discussed, because a very few color-shifting mutations in the C-domain were described. Recently we reported a strong red-shifting mutation E457K in the C-domain; the bioluminescence spectra of this enzyme were independent of temperature or pH. In the present study we investigated the role of the residue E457 in the enzyme using the Luciola mingrelica luciferase with a thermostabilized N-domain as a parent enzyme for site-directed mutagenesis. We obtained a set of mutants and studied their catalytic properties, thermal stability and bioluminescence spectra. Experimental spectra were represented as a sum of two components (bioluminescence spectra of putative “red” and “green” emitters); λ_max of these components were constant for all the mutants, but the ratio of these emitters was defined by temperature and mutations in the C-domain. We suggest that each emitter is stabilized by a specific conformation of the active site; thus, enzymes with two forms of the active site coexist in the reactive media. The rigid structure of the C-domain is crucial for maintaining the conformation corresponding to the “green” emitter. We presume that the emitters are the keto- and enol forms of oxyluciferin.     

Probing the metal ion selectivity in methionine aminopeptidase via changes in the luminescence properties of the enzyme bound europium ion

We report herein, for the first time, that Europium ion (Eu³⁺) binds to the “apo” form of Escherichia coli methionine aminopeptidase (EcMetAP), and such binding results in the activation of the enzyme as well as enhancement in the luminescence intensity of the metal ion. Due to competitive displacement of the enzyme-bound Eu³⁺ by different metal ions, we could determine the binding affinities of both “activating” and “non-activating” metal ions for the enzyme via fluorescence spectroscopy. The experimental data revealed that among all metal ions, Fe²⁺ exhibited the highest binding affinity for the enzyme, supporting the notion that it serves as the physiological metal ion for the enzyme. However, the enzyme-metal binding data did not adhere to the Irving-William series. On accounting for the binding affinity vis a vis the catalytic efficiency of the enzyme for different metal ions, it appears evident that that the “coordination states” and the relative softness” of metal ions are the major determinants in facilitating the EcMetAP catalyzed reaction.