Selectivity and specificity of substrate binding in methionyl-tRNA synthetase

The accuracy of in vivo incorporation of amino acids during protein biosynthesis is controlled to a significant extent by aminoacyl-tRNA synthetases (aaRS). This paper describes the application of the HierDock computational method to study the molecular basis of amino acid binding to the Escherichia coli methionyl tRNA synthetase (MetRS). Starting with the protein structure from the MetRS cocrystal, the HierDock calculations predict the binding site of methionine in MetRS to a root mean square deviation in coordinates (CRMS) of 0.55 A for all the atoms, compared with the crystal structure. The MetRS conformation in the cocrystal structure shows good discrimination between cognate and the 19 noncognate amino acids. In addition, the calculated binding energies of a set of five methionine analogs show a good correlation (R(2) = 0.86) to the relative free energies of binding derived from the measured in vitro kinetic parameters, K(m) and k(cat). Starting with the crystal structure of MetRS without the methionine (apo-MetRS), the putative binding site of methionine was predicted. We demonstrate that even the apo-MetRS structure shows a preference for binding methionine compared with the 19 other natural amino acids. On comparing the calculated binding energies of the 20 natural amino acids for apo-MetRS with those for the cocrystal structure, we observe that the discrimination against the noncognate substrate increases dramatically in the second step of the physical binding process associated with the conformation change in the protein.     

An in vitro model to evaluate cell adhesion to metals used in implantation shows significant differences between palladium and gold or platinum

Adhesion of tissue cells to metallic implants is a major factor that is important for proper tissue integration. Adhesion of Swiss mouse 3T3 fibroblasts to gold, platinum and palladium surfaces was investigated. Immunofluorescence staining for the integrin subunits alphav and beta1 and the focal contact protein vinculin revealed that cells growing on gold and platinum expressed many focal contacts. In contrast, cells on palladium surfaces had reduced numbers of focal contacts shown by vinculin staining and failed to demonstrate expression of alphav and beta1 in focal contacts. Spread cell area was also significantly reduced on palladium than on other surfaces suggesting that cells on palladium were more weakly attached. This may be due to either a different molecular composition of focal contacts in cells grown on palladium surfaces or unusual microstructural properties of the palladium surface. This model is useful to evaluate adhesion of cells to different metal surfaces.     

Acoustic response properties of lagenar nerve fibers in the sleeper goby,<Emphasis Type="Italic"> Dormitator latifrons</Emphasis>

Auditory and vestibular functions of otolithic organs vary among vertebrate taxa. The saccule has been considered a major hearing organ in many fishes. However, little is known about the auditory role of the lagena in fishes. In this study we analyzed directional and frequency responses from single lagenar fibers of Dormitator latifrons to linear accelerations that simulate underwater acoustic particle motion. Characteristic frequencies of the lagenar fibers fell into two groups: 50 Hz and 80–125 Hz. We observed various temporal response patterns: strong phase-locking, double phase-locking, phase-locked bursting, and non-phase-locked bursting. Some bursting responses have not been previously observed in vertebrate otolithic nerve fibers. Lagenar fibers could respond to accelerations as small as 1.1 mm s^–2. Like saccular fibers, lagenar fibers were directionally responsive and decreased directional selectivity with stimulus level. Best response axes of the lagenar fibers clustered around the lagenar longitudinal axis in the horizontal plane, but distributed in a diversity of axes in the mid-sagittal plane, which generally reflect morphological polarizations of hair cells in the lagena. We conclude that the lagena of D. latifrons plays a role in sound localization in elevation, particularly at high stimulus intensities where responses of most saccular fibers are saturated.Abbreviations BRA best response axis/axes - BS best sensitivity - CF characteristic frequency - CV coefficient of variation - DI directionality index - ISIH inter-spike interval histogram - PSTH peri-stimulus time histogram - SR spontaneous rate     

Exploring the origin of the ion selectivity of the KcsA potassium channel

The availability of structural information about biological ion channels provides an opportunity to gain a detailed understanding of the control of ion selectivity by biological systems. However, accomplishing this task by computer simulation approaches is very challenging. First, although the activation barriers for ion transport can be evaluated by microscopic simulations, it is hard to obtain accurate results by such approaches. Second, the selectivity is related to the actual ion current and not directly to the individual activation barriers. Thus, it is essential to simulate the ion currents and this cannot be accomplished at present by microscopic MD approaches. In order to address this challenge, we developed and refined an approach capable of evaluating ion current while still reflecting the realistic features of the given channel. Our method involves generation of semimacroscopic free energy surfaces for the channel/ions system and Brownian dynamics (BD) simulations of the corresponding ion current. In contrast to most alternative macroscopic models, our approach is able to reproduce the difference between the free energy surfaces of different ions and thus to address the selectivity problem. Our method is used in a study of the selectivity of the KcsA channel toward the K+ and Na+ ions. The BD simulations with the calculated free energy profiles produce an appreciable selectivity. To the best of our knowledge, this is the first time that the trend in the selectivity in the ion current is produced by a computer simulation approach. Nevertheless, the calculated selectivity is still smaller than its experimental estimate. Recognizing that the calculated profiles are not perfect, we examine how changes in these profiles can account for the observed selectivity. It is found that the origin of the selectivity is more complex than generally assumed. The observed selectivity can be reproduced by increasing the barrier at the exit and the entrance of the selectivity filter, but the necessary changes in the barrier approach the limit of the error in the PDLD/S-LRA calculations. Other options that can increase the selectivity are also considered, including the difference between the Na+...Na+ and K+...K+ interaction. However, this interesting effect does not appear to lead to a major difference in selectivity since the Na+ ions at the limit of strong interaction tend to move in a less concerted way than the K+ ions. Changes in the relative binding energies at the different binding sites are also not so effective in changing the selectivity. Finally, it is pointed out that using the calculated profiles as a starting point and forcing the model to satisfy different experimentally based constraints, should eventually provide more detailed understanding of the different complex factors involved in ion selectivity of biological channels.     

Identification of Ion-Selectivity Determinants in Heavy-Metal Transport P<Subscript>1B</Subscript>-type ATPases

P_1B-type ATPases transport a variety of metals (Cd²⁺, Zn²⁺, Pb²⁺, Co²⁺, Cu²⁺, Ag⁺, Cu⁺) across biomembranes. Characteristic sequences CP[C/H/S] in transmembrane fragment H6 were observed in the putative transporting metal site of the founding members of this subfamily (initially named CPx-ATPases). In spite of their importance for metal homeostasis and biotolerance, their mechanisms of ion selectivity are not understood. Studies of better-characterized P_II-type ATPases (Ca-ATPase and Na,K-ATPase) have identified three transmembrane segments that participate in ion binding and transport. Testing the hypothesis that metal specificity is determined by conserved amino acids located in the equivalent transmembrane segments of P_1B-type ATPases (H6, H7, and H8), 234 P_1B-ATPase protein sequences were analyzed. This showed that although H6 contains characteristic CPX or XPC sequences, conserved amino acids in H7 and H8 provide signature sequences that predict the metal selectivity in each of five P_1B-ATPase subgroups identified. These invariant amino acids contain diverse side chains (thiol, hydroxyl, carbonyl, amide, imidazolium) that can participate in transient metal coordination during transport and consequently determine the particular metal selectivity of each enzyme. Each subgroup shares additional structural characteristics such as the presence (or absence) of particular amino-terminal metal-binding domains and the number of putative transmembrane segments. These differences suggest unique functional characteristics for each subgroup in addition to their particular metal specificity.     

Horizontal Gene Transfer of “Prototype” Nramp in Bacteria

Eukaryotic Nramp genes encode divalent metal ion permeases important for nutrition and resistance to microbial infection. Bacterial homologs encode proton-dependent transporters of manganese (MntH), and other divalent metal ions. Bacterial MntH were classified in three homology groups (A, B, C) and MntH C further subdivided in C, C, C. The proteins from C. tepidum (MntH B) and E. faecalis (MntH C1, 2), divergent in sequence and hydropathy profile, conferred increased metal sensitivity when expressed in E. coli, suggesting conservation of divalent metal transport function in MntH B and C. Several genomic evidence suggest horizontal gene transfer (HGT) of mntH C genes: (i) The enterobacteria Wigglesworthia mntH C gene is linked to an Asn t-RNA, and its sequence most conserved with Gram positive bacteria homologs; (ii) all the C genes identified in oral streptococcaceae are associated with different potentially mobile DNA elements; (iii) Lactococcus lactis and Burkholderia mallei genomes contain an mntH gene prematurely terminated and a novel full-length mntH C gene; (iv) remarkable sequence relatedness between the unicellular alga C. reinhardtii prototype Nramp and some MntH C (e.g., Nostoc spp., Listeria spp.) suggests HGT between Eukarya and Bacteria. Other prototype Nramp genes (intronless, encoding proteins strongly conserved with MntH A and B proteins) identified in invertebrates represent a possible source for transfer of Nramp genes toward opportunistic bacteria. This study demonstrates complex evolution of MntH in Bacteria. It is proposed that prototype Nramp are ancestors of bacterial MntH C proteins, which could facilitate bacterial infection. Equally contributing authors (Etienne Richer and Pascal Courville).     

Influence of pore residues on permeation properties in the Kv2.1 potassium channel. Evidence for a selective functional interaction of K+ with the outer vestibule

The Kv2.1 potassium channel contains a lysine in the outer vestibule (position 356) that markedly reduces open channel sensitivity to changes in external [K(+)]. To investigate the mechanism underlying this effect, we examined the influence of this outer vestibule lysine on three measures of K(+) and Na(+) permeation. Permeability ratio measurements, measurements of the lowest [K(+)] required for interaction with the selectivity filter, and measurements of macroscopic K(+) and Na(+) conductance, were all consistent with the same conclusion: that the outer vestibule lysine in Kv2.1 interferes with the ability of K(+) to enter or exit the extracellular side of the selectivity filter. In contrast to its influence on K(+) permeation properties, Lys 356 appeared to be without effect on Na(+) permeation. This suggests that Lys 356 limited K(+) flux by interfering with a selective K(+) binding site. Combined with permeation studies, results from additional mutagenesis near the external entrance to the selectivity filter indicated that this site was located external to, and independent from, the selectivity filter. Protonation of a naturally occurring histidine in the same outer vestibule location in the Kv1.5 potassium channel produced similar effects on K(+) permeation properties. Together, these results indicate that a selective, functional K(+) binding site (e.g., local energy minimum) exists in the outer vestibule of voltage-gated K(+) channels. We suggest that this site is the location of K(+) hydration/dehydration postulated to exist based on the structural studies of KcsA. Finally, neutralization of position 356 enhanced outward K(+) current magnitude, but did not influence the ability of internal K(+) to enter the pore. These data indicate that in Kv2.1, exit of K(+) from the selectivity filter, rather than entry of internal K(+) into the channel, limits outward current magnitude. We discuss the implications of these findings in relation to the structural basis of channel conductance in different K(+) channels.     

Asymmetric temporal properties in the receptive field of retinal transient amacrine cells

The speed of signal conduction is a factor determining the temporal properties of individual neurons and neuronal networks. We observed very different conduction velocities within the receptive field of fast-type On-Off transient amacrine cells in carp retina cells, which are tightly coupled to each other via gap junctions. The fastest speeds were found in the dorsal area of the receptive fields, on average five times faster than those detected within the ventral area. The asymmetry was similar in the On- and Off-part of the responses, thus being independent of the pathway, pointing to the existence of a functional mechanism within the recorded cells themselves. Nonetheless, the spatial decay of the graded-voltage photoresponse within the receptive field was found to be symmetrical, with the amplitude center of the receptive field being displaced to the faster side from the minimum-latency location. A sample of the orientation of varicosity-laden polyaxons in neurobiotin-injected cells supported the model, revealing that approximately 75% of these processes were directed dorsally from the origin cells. Based on these results, we modeled the velocity asymmetry and the displacement of amplitude center by adding a contribution of an asymmetric polyaxonal inhibition to the network. Due to the asymmetry in the conduction velocity, the time delay of a light response is proposed to depend on the origin of the photostimulus movement, a potentially important mechanism underlying direction selectivity within the inner retina.     

Effect of different metal ions on the oxidative damage and antioxidant capacity of hyaluronic acid

Degradation and the antioxidative effect of Na-, Zn-, Co-, Cu-, and Mn-hyaluronic acid (HA) associates were studied. Our findings revealed the protective effect of certain counterions against ROS-induced HA degradation. We could also separate the antioxidative effect of certain counterions from that of the HA by examining the effect of the counterions in their free ionic forms. The result showed that metal ions with altering oxidative status (Co(2+), Cu(2+), Mn(2+)) proved to be effective in themselves or their effect added to that of HA when HA was also effective. Moreover, the effects of Co-HA against z.rad;O(2)(-) and of Mn-HA against ONOO(-) as well as the synergic effect of Zn-HA associates where Zn(2+) is of fixed oxidative status were attributed to the structure-stabilizing complex formed between certain counterions and HA. Our examination also concerned the influence of HA associates on the indirect antioxidation related to Fe(2+) chelating. The individual effects of Zn(2+), Co(2+), and Cu(2+) were only detectable, which could be explained by the competitive displacement of ferrous from its binding site.