Dynamics of dissolved organic <Superscript>14</Superscript>C in throughfall and soil solution of a Norway spruce forest

Dissolved organic carbon (DOC) is an important component of the C cycle in forest ecosystems, but dynamics and origin of DOC in throughfall and soil solution are yet poorly understood. In a 2-year study, we analyzed the radiocarbon signature of DOC in throughfall and soil solution beneath the Oa horizon and at 90 cm depth in a Norway spruce forest on a Podzol soil. A two-pool mixing model revealed that throughfall DOC comprised mainly biogenic C, i.e. recently fixed C, from canopy leaching and possibly other sources. The contribution of fossil DOC from atmospheric deposition to throughfall DOC was on average 6% with maxima of 8–11% during the dormant season. In soil solution from the Oa horizon, DO¹⁴C signature was highly dynamic (range from −8‰ to +103‰), but not correlated with DOC concentration. Radiocarbon signatures suggest that DOC beneath the Oa horizon originated mainly from occluded and mineral associated organic matter fractions of the Oa horizon rather than from the Oi or Oe horizon. Relatively old C was released in the rewetting phase following a drought period in the late summer of 2006. In contrast, the DO¹⁴C signature indicated the release of younger C throughout the humid year 2007. In soil solutions from 90 cm depth, DO¹⁴C signatures were also highly dynamic (−127‰ to +3‰) despite constantly low DOC concentrations. Similar to the Oa horizon, the lowest DO¹⁴C signature at 90 cm depth was found after the rewetting phase in the late summer of 2006. Because of the variation in the DO¹⁴C signatures at this depth, we conclude that DOC was not equilibrated with the surrounding soil, but also originated from overlaying soil horizons. The dynamics of DO¹⁴C in throughfall and soil solution suggest that the sources of DOC are highly variable in time. Extended drought periods likely have a strong influence on release and translocation of DOC from relatively old and possibly stabilized soil organic matter fractions. Temporal variations as well as the input of fossil DOC needs to be considered when calibrating DOC models based on DO¹⁴C signatures.     

Isotopic signature (<Superscript>15</Superscript>N/<Superscript>14</Superscript>N and <Superscript>13</Superscript>C/<Superscript>12</Superscript>C) confirms similarity of trophic niches of millipedes (Myriapoda,diplopoda) in a temperate deciduous forest

The species composition, abundance, and isotopic signature of millipedes (Myriapoda, Diplopoda) were investigated in seven biotopes of Kaluzhskie Zaseki State Nature Reserve. Nine Diplopoda species were found in total, and the local species diversity (within a sampling plot) reached seven species. The Diplopoda tissues were similar to the plant litter in the isotopic composition of nitrogen (δ¹⁵N was by 0.4‰ higher, on average), but were strongly enriched in heavy carbon (δ¹³C was by 4‰ higher, on average). Removal of mineral carbon from the cuticle reduced δ¹³C of Diplopoda by about 1.4‰ on average. Differences in the δ¹⁵N and δ¹³C values between the species did not exceed 2.5‰. Differences in the isotopic compositions of the considered species were small, and, it is impossible to distinguish particular trophic guilds in the Diplopoda community. Analysis of the published data confirmed that isotopic differentiation of millipedes was much less pronounced than in other investigated groups of soil animals. Hence, millipedes of the deciduous forest form a uniform trophic group.     

Conformational dependence of <Superscript>13</Superscript>C shielding and coupling constants for methionine methyl groups

Methionine residues fulfill a broad range of roles in protein function related to conformational plasticity, ligand binding, and sensing/mediating the effects of oxidative stress. A high degree of internal mobility, intrinsic detection sensitivity of the methyl group, and low copy number have made methionine labeling a popular approach for NMR investigation of selectively labeled protein macromolecules. However, selective labeling approaches are subject to more limited information content. In order to optimize the information available from such studies, we have performed DFT calculations on model systems to evaluate the conformational dependence of ³ J _CSCC, ³ J _CSCH, and the isotropic shielding, σ_iso. Results have been compared with experimental data reported in the literature, as well as data obtained on [methyl-¹³C]methionine and on model compounds. These studies indicate that relative to oxygen, the presence of the sulfur atom in the coupling pathway results in a significantly smaller coupling constant, ³ J _CSCC/³ J _COCC ~ 0.7. It is further demonstrated that the ³ J _CSCH coupling constant depends primarily on the subtended CSCH dihedral angle, and secondarily on the CSCC dihedral angle. Comparison of theoretical shielding calculations with the experimental shift range of the methyl group for methionine residues in proteins supports the conclusion that the intra-residue conformationally-dependent shift perturbation is the dominant determinant of δ¹³Cε. Analysis of calmodulin data based on these calculations indicates that several residues adopt non-standard rotamers characterized by very large ~100° χ³ values. The utility of the δ¹³Cε as a basis for estimating the gauche/trans ratio for χ³ is evaluated, and physical and technical factors that limit the accuracy of both the NMR and crystallographic analyses are discussed.     

Deuterium isotope effects on <Superscript>15</Superscript>N backbone chemical shifts in proteins

Quantum mechanical calculations are presented that predict that one-bond deuterium isotope effects on the ¹⁵N chemical shift of backbone amides of proteins, ¹Δ¹⁵N(D), are sensitive to backbone conformation and hydrogen bonding. A quantitative empirical model for ¹Δ¹⁵N(D) including the backbone dihedral angles, Φ and Ψ, and the hydrogen bonding geometry is presented for glycine and amino acid residues with aliphatic side chains. The effect of hydrogen bonding is rationalized in part as an electric-field effect on the first derivative of the nuclear shielding with respect to N–H bond length. Another contributing factor is the effect of increased anharmonicity of the N–H stretching vibrational state upon hydrogen bonding, which results in an altered N–H/N–D equilibrium bond length ratio. The N–H stretching anharmonicity contribution falls off with the cosine of the N–H···O bond angle. For residues with uncharged side chains a very good prediction of isotope effects can be made. Thus, for proteins with known secondary structures, ¹Δ¹⁵N(D) can provide insights into hydrogen bonding geometries. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Stable carbon isotope ratios in Asian elephant collagen: implications for dietary studies

Summary Stable carbon isotope ratios in bone collagen have been used in a variety of dietary studies in modern and fossil animals, including humans. Inherent in the stable isotope technique is the assumption that the isotopic signature is a reflection of the diet and is persistent in collagen because this is a relatively inert protein. Carbon isotope analyses of bones from a southern Indian population of Asian elephant (Elephas maximus), a long-lived mammal that alternates seasonally between a predominantly C₃ (browse) and C₄ (grass) plant diet, showed two patterns that have important implications for dietary interpretation based on isotopic studies. Relative to the quantity of the two plant types consumed on average, the δ¹³C signal in collagen indicated that more carbon was incorporated from C₃ plants, possibly due to their higher protein contribution. There was a much greater variance in δ¹³C values of collagen in sub-adult (range -10.5‰ to-22.7‰, variance=14.51) compared to adult animals (range -16.0‰ to -20.3‰, variance=1.85) pointing to high collagen turnover rates and non-persistent isotopic signatures in younger, growing animals. It thus seems important to correct for any significant relative differences in nutritive value of food types and also consider the age of an animal before drawing definite conclusions about its diet from isotope ratios.     

Assigning large proteins in the solid state: a MAS NMR resonance assignment strategy using selectively and extensively <Superscript>13</Superscript>C-labelled proteins

In recent years, solid-state magic-angle spinning nuclear magnetic resonance spectroscopy (MAS NMR) has been growing into an important technique to study the structure of membrane proteins, amyloid fibrils and other protein preparations which do not form crystals or are insoluble. Currently, a key bottleneck is the assignment process due to the absence of the resolving power of proton chemical shifts. Particularly for large proteins (approximately >150 residues) it is difficult to obtain a full set of resonance assignments. In order to address this problem, we present an assignment method based upon samples prepared using [1,3-¹³C]- and [2-¹³C]-glycerol as the sole carbon source in the bacterial growth medium (so-called selectively and extensively labelled protein). Such samples give rise to higher quality spectra than uniformly [¹³C]-labelled protein samples, and have previously been used to obtain long-range restraints for use in structure calculations. Our method exploits the characteristic cross-peak patterns observed for the different amino acid types in ¹³C-¹³C correlation and 3D NCACX and NCOCX spectra. An in-depth analysis of the patterns and how they can be used to aid assignment is presented, using spectra of the chicken α-spectrin SH3 domain (62 residues), αB-crystallin (175 residues) and outer membrane protein G (OmpG, 281 residues) as examples. Using this procedure, over 90% of the Cα, Cβ, C′ and N resonances in the core domain of αB-crystallin and around 73% in the flanking domains could be assigned (excluding 24 residues at the extreme termini of the protein). Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

1-<Superscript>13</Superscript>C amino acid selective labeling in a <Superscript>2</Superscript>H<Superscript>15</Superscript>N background for NMR studies of large proteins

Isotope labeling by residue type (LBRT) has long been an important tool for resonance assignments at the limit where other approaches, such as triple-resonance experiments or NOESY methods do not succeed in yielding complete assignments. While LBRT has become less important for small proteins it can be the method of last resort for completing assignments of the most challenging protein systems. Here we present an approach where LBRT is achieved by adding protonated ¹⁴N amino acids that are ¹³C labeled at the carbonyl position to a medium for uniform deuteration and ¹⁵N labeling. This has three important benefits over conventional ¹⁵N LBRT in a deuterated back ground: (1) selective TROSY-HNCO cross peaks can be observed with high sensitivity for amino-acid pairs connected by the labeling, and the amide proton of the residue following the ¹³C labeled amino acid is very sharp since its alpha position is deuterated, (2) the ¹³C label at the carbonyl position is less prone to scrambling than the ¹⁵N at the α-amino position, and (3) the peaks for the 1-¹³C labeled amino acids can be identified easily from the large intensity reduction in the ¹H-¹⁵N TROSY-HSQC spectrum for some residues that do not significantly scramble nitrogens, such as alanine and tyrosine. This approach is cost effective and has been successfully applied to proteins larger than 40 kDa. Electronic Supplementary Material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

<Superscript>13</Superscript>C-detected NMR experiments for measuring chemical shifts and coupling constants in nucleic acid bases

The paper presents a set of two-dimensional experiments that utilize direct ¹³C detection to provide proton–carbon, carbon–carbon and carbon–nitrogen correlations in the bases of nucleic acids. The set includes a ¹³C-detected proton–carbon correlation experiment for the measurement of ¹³C–¹³C couplings, the CaCb experiment for correlating two quaternary carbons, the HCaCb experiment for the ¹³C–¹³C correlations in cases where one of the carbons has a proton attached, the HCC-TOCSY experiment for correlating a proton with a network of coupled carbons, and a ¹³C-detected ¹³C–¹⁵N correlation experiment for detecting the nitrogen nuclei that cannot be detected via protons. The IPAP procedure is used for extracting the carbon–carbon couplings and/or carbon decoupling in the direct dimension, while the S³E procedure is preferred in the indirect dimension of the carbon–nitrogen experiment to obtain the value of the coupling constant. The experiments supply accurate values of ¹³C and ¹⁵N chemical shifts and carbon–carbon and carbon–nitrogen coupling constants. These values can help to reveal structural features of nucleic acids either directly or via induced changes when the sample is dissolved in oriented media. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Natural Abundance of <Superscript>15</Superscript>N in Nitrogen-Limited Forests and Tundra Can Estimate Nitrogen Cycling Through Mycorrhizal Fungi: A Review

The hyphae of ectomycorrhizal and ericoid mycorrhizal fungi proliferate in nitrogen (N)-limited forests and tundra where the availability of inorganic N is low; under these conditions the most common fungal species are those capable of protein degradation that can supply their host plants with organic N. Although it is widely understood that these symbiotic fungi supply N to their host plants, the transfer is difficult to quantify in the field. A novel approach uses the natural ¹⁵N:¹⁴N ratios (expressed as δ¹⁵N values) in plants, soils, and mycorrhizal fungi to estimate the fraction of N in symbiotic trees and shrubs that enters through mycorrhizal fungi. This calculation is possible because mycorrhizal fungi discriminate against ¹⁵N when they create compounds for transfer to plants; host plants are depleted in ¹⁵N, whereas mycorrhizal fungi are enriched in ¹⁵N. The amount of carbon (C) supplied to these fungi can be stoichiometrically calculated from the fraction of plant N derived from the symbiosis, the N demand of the plants, the fungal C:N ratio, and the fraction of N retained in the fungi. Up to a third of C allocated belowground, or 20% of net primary production, is used to support ectomycorrhizal fungi. As anthropogenic N inputs increase, the C allocation to fungi decreases and plant δ¹⁵N increases. Careful analyses of δ¹⁵N patterns in systems dominated by ectomycorrhizal and ericoid mycorrhizal symbioses may reveal the ecosystem-scale effects of alterations in the plant–mycorrhizal symbioses caused by shifts in climate and N deposition. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Effects of growth and tissue type on the kinetics of <Superscript>13</Superscript>C and <Superscript>15</Superscript>N incorporation in a rapidly growing ectotherm

The use of stable isotopes to investigate animal diets, habitat use, and trophic level requires understanding the rate at which animals incorporate the ¹³C and ¹⁵N from their diets and the factors that determine the magnitude of the difference in isotopic composition between the animal’s diet and that of its tissues. We determined the contribution of growth and catabolic turnover to the rate of ¹³C and ¹⁵N incorporation into several tissues that can be sampled non-invasively (skin, scute, whole blood, red blood cells, and plasma solutes) in two age classes of a rapidly growing ectotherm (loggerhead turtles, Caretta caretta). We found significant differences in C and N incorporation rates and isotopic discrimination factors (Δ¹³C = δ¹³C_tissues − δ¹³C_diet and Δ¹⁵N = δ¹⁵N_tissues − δ¹⁵N_diet) among tissues and between age classes. Growth explained from 26 to 100% of the total rate of incorporation in hatchling turtles and from 15 to 52% of the total rate of incorporation in juvenile turtles. Because growth contributed significantly to the rate of isotopic incorporation, variation in rates among tissues was lower than reported in previous studies. The contribution of growth can homogenize the rate of isotopic incorporation and limit the application of stable isotopes to identify dietary changes at contrasting time scales and to determine the timing of diet shifts. The isotopic discrimination factor of nitrogen ranged from −0.64 to 1.77‰ in the turtles’ tissues. These values are lower than the commonly assumed average 3.4‰ discrimination factors reported for whole body and muscle isotopic analyses. The increasing reliance on non-invasive and non-destructive sampling in animal isotopic ecology requires that we recognize and understand why different tissues differ in isotopic discrimination factors.     

A simplified recipe for assigning amide NMR signals using combinatorial <Superscript>14</Superscript>N amino acid inverse-labeling

Assignment of backbone amide proton resonances is one of the most time-consuming stages of any protein NMR study when the protein samples behave non-ideally. A robust and convenient NMR procedure for analyzing spectra of marginal-to-low quality is helpful for high-throughput structure determination. The ¹⁴N selective- and inverse-labeling method is a candidate solution. Here, we present a simplified protocol for assigning protein backbone amide NMR signals. When ¹⁴N inversely labeled residues are present in a protein, their backbone NH cross peaks vanish from the protein’s ¹H–¹⁵N HSQC spectrum, and thus, their chemical shifts can be readily identified by a process of elimination. Some metabolically related amino acids, for example, Ile, Leu, and Val, cannot be individually incorporated but can be inversely labeled together. We optimized and simplified the protocol and M9-based medium formula for the ¹⁴N selective- and inverse-labeling method without any additives. Our approach should be cost-effective, because the method could be additively applied stepwise, even when the proteins of interest were found to be non-ideal.     

Application of <Superscript>13</Superscript>C mineral carbon for assessment of the primary production of organic matter in aquatic environments

The possibility of measuring the rates of light and dark CO₂ assimilation using ¹³C carbonate was demonstrated on Lake Kichier (Marii El). The application of methods utilizing the stable ¹³C and the radioactive ¹⁴C isotopes resulted in comparable values of the rates of light and dark CO₂ fixation. Due to its absolute environmental safety, the method with ¹³C mineral carbon can be recommended as an alternative to radioisotope methods for qualitative measurements of CO₂ fixation rates in aquatic ecosystems.     

Assignment of paramagnetic <Superscript>15</Superscript>N-HSQC spectra by heteronuclear exchange spectroscopy

Paramagnetic metal ions in proteins provide a rich source of structural information, but the resonance assignments required to extract the information can be challenging. Here we demonstrate that paramagnetically shifted ¹⁵N-HSQC cross-peaks can be assigned using N_Z-exchange spectroscopy under conditions in which the paramagnetic form of the protein is in dynamic equilibrium with its diamagnetic form. Even slow exchange of specifically bound metal ions may be detected within the long lifetime of ¹⁵N longitudinal magnetization of large proteins at high magnetic fields. Alternatively, the exchange can be accelerated using an excess of metal ions. In the resulting exchange spectra, paramagnetic ¹⁵N resonances become visible for residues that are not directly observed in a conventional ¹⁵N-HSQC spectrum due to paramagnetic ¹H^N broadening. The experiments are illustrated by the 30 kDa lanthanide-binding ɛ186/θ complex of DNA polymerase III in the presence of sub-stoichiometric amounts of Dy³⁺ or a mixture of Dy³⁺ and La³⁺.     

An enclosed-chamber labeling system for the safe <Superscript>14</Superscript>C-enrichment of phytochemicals in plant cell suspension cultures

Summary Various plant secondary products have been implicated in the promotion of good health or the prevention of disease in humans, but little is known about the way they are absorbed in the gut, or in which tissues they are deposited throughout the body. While these issues could be studied if the phytochemicals were isotopically labeled, generating labeled molecules often is problematic because many compounds of interest can be synthesized only in planta at present. In order to generale ¹⁴C-labeled phytochemicals of high radioactive enrichment, we developed an enclosed-chamber labeling system in which cell suspension cultures can be safely and efficiently grown when supplied with ¹⁴C-enriched precursors. The system is designed to hold culture flasks within a clear, polyacrylic compartment that is affixed to the top of a rotary shaker. The flow-through gas exchange nature of the system allows for O₂ replenishment and complete capture of respired ¹⁴CO₂ throughout the entire period of cell culture. Air is circulated internally with the aid of a small fan, and chamber air temperature is monitored continuously with an internal temperature probe and data logger. Production runs of 12–14 d with Vaccinium pahalae (ohelo berry) and Vitis vinifera (grape) suspension cultures, using [¹⁴C]sucrose as the carbon source, demonstrated a 20–23% efficiency of ¹⁴C incorporation into the flavonoid-rich fractions. Further studies with ohelo cell cultures showed that flavonoids were produced with either sucrose or glucose as the carbohydrate source, although flavonoid productivity (measured as anthocyanins) was higher with sucrose. This comprehensive chamber system should have broad applicability with numerous cell types and can be used to generate a wide array of labeled phytochemicals.     

Density functional calculations of chemical shielding of backbone <Superscript>15</Superscript>N in helical residues of protein G

We performed density functional calculations of backbone ¹⁵N chemical shielding tensors in selected helical residues of protein G. Here we describe a computationally efficient methodology to include most of the important effects in the calculation of chemical shieldings of backbone ¹⁵N. We analyzed the role of long-range intra-protein electrostatic interactions by comparing models with different complexity in vacuum and in charge field. Our results show that the dipole moment of the α-helix can cause significant deshielding of ¹⁵N; therefore, it needs to be considered when calculating ¹⁵N chemical shielding. We found that it is important to include interactions with the side chains that are close in space when the charged form for ionizable side chains is adopted in the calculation. We also illustrate how the ionization state of these side chains can affect the chemical shielding tensor elements. Chemical shielding calculations using a 8-residue fragment model in vacuum and adopting the charged form of ionizable side chains yield a generally good agreement with experimental data.     

Carbon fluxes to the soil in a mature temperate forest assessed by <Superscript>13</Superscript>C isotope tracing

Photosynthetic carbon uptake and respiratory C release from soil are major components of the global carbon balance. The use of ¹³C depleted CO₂ (¹³C = –30) in a free air CO₂ enrichment experiment in a mature deciduous forest permitted us to trace the carbon transfer from tree crowns to the rhizosphere of 100–120 years old trees. During the first season of CO₂ enrichment the CO₂ released from soil originated substantially from concurrent assimilation. The small contribution of recent carbon in fine roots suggests a much slower fine root turnover than is often assumed.¹³C abundance in soil air correlated best with temperature data taken from 4 to 10 days before air sampling time and is thus rapidly available for root and rhizosphere respiration. The spatial variability of ¹³C in soil air showed relationships to above ground tree types such as conifers versus broad-leaved trees. Considering the complexity and strong overlap of roots from different individuals in a forest, this finding opens an exciting new possibility of associating respiration with different species. What might be seen as signal noise does in fact contain valuable information on the spatial heterogeneity of tree-soil interaction.     

Foliar and fungal <Superscript>15</Superscript> N:<Superscript>14</Superscript> N ratios reflect development of mycorrhizae and nitrogen supply during primary succession: testing analytical models

Nitrogen isotopes (¹⁵N/¹⁴N ratios, expressed as δ¹⁵N values) are useful markers of the mycorrhizal role in plant nitrogen supply because discrimination against ¹⁵N during creation of transfer compounds within mycorrhizal fungi decreases the ¹⁵N/¹⁴N in plants (low δ¹⁵N) and increases the ¹⁵N/¹⁴N of the fungi (high δ¹⁵N). Analytical models of ¹⁵N distribution would be helpful in interpreting δ¹⁵N patterns in fungi and plants. To compare different analytical models, we measured nitrogen isotope patterns in soils, saprotrophic fungi, ectomycorrhizal fungi, and plants with different mycorrhizal habits on a glacier foreland exposed during the last 100 years of glacial retreat and on adjacent non-glaciated terrain. Since plants during early primary succession may have only limited access to propagules of mycorrhizal fungi, we hypothesized that mycorrhizal plants would initially be similar to nonmycorrhizal plants in δ¹⁵N and then decrease, if mycorrhizal colonization were an important factor influencing plant δ¹⁵N. As hypothesized, plants with different mycorrhizal habits initially showed similar δ¹⁵N values (−4 to −6‰ relative to the standard of atmospheric N₂ at 0‰), corresponding to low mycorrhizal colonization in all plant species and an absence of ectomycorrhizal sporocarps. In later successional stages where ectomycorrhizal sporocarps were present, most ectomycorrhizal and ericoid mycorrhizal plants declined by 5–6‰ in δ¹⁵N, suggesting transfer of ¹⁵N-depleted N from fungi to plants. The values recorded (−8 to −11‰) are among the lowest yet observed in vascular plants. In contrast, the δ¹⁵N of nonmycorrhizal plants and arbuscular mycorrhizal plants declined only slightly or not at all. On the forefront, most ectomycorrhizal and saprotrophic fungi were similar in δ¹⁵N (−1 to −3‰), but the host-specific ectomycorrhizal fungus Cortinarius tenebricus had values of up to 7‰. Plants, fungi and soil were at least 4‰ higher in δ¹⁵N from the mature site than in recently exposed sites. On both the forefront and the mature site, host-specific ectomycorrhizal fungi had higher δ¹⁵N values than ectomycorrhizal fungi with a broad host range. From these isotopic patterns, we conclude:(1) large enrichments in ¹⁵N of many ectomycorrhizal fungi relative to co-occurring ectomycorrhizal plants are best explained by treating the plant-fungal-soil system as a closed system with a discrimination against ¹⁵N of 8–10‰ during transfer from fungi to plants, (2) based on models of ¹⁵N mass balance, ericoid and ectomycorrhizal fungi retain up to two-thirds of the N in the plant-mycorrhizal system under the N-limited conditions at forefront sites, (3) sporocarps are probably enriched in ¹⁵N by an additional 3‰ relative to available nitrogen, and (4) host-specific ectomycorrhizal fungi may transfer more N to plant hosts than non-host-specific ectomycorrhizal fungi. Our study confirms that nitrogen isotopes are a powerful tool for probing nitrogen dynamics between mycorrhizal fungi and associated plants.     

An intraresidual i(HCA)CO(CA)NH experiment for the assignment of main-chain resonances in <Superscript>15</Superscript>N, <Superscript>13</Superscript>C labeled proteins

An improved pulse sequence, intraresidual i(HCA)CO(CA)NH, is described for establishing solely ¹³C′(i), ¹⁵N(i), ¹H^N(i) connectivities in uniformly ¹⁵N/¹³C-labeled proteins. In comparison to the “out-and-back” style intra-HN(CA)CO experiment, the new pulse sequence offers at least two-fold higher experimental resolution in the ¹³C′ dimension and on average 1.6 times higher sensitivity especially for residues in α-helices. Performance of the new experiment was tested on a small globular protein ubiquitin and an intrinsically unfolded 110-residue cancer/testis antigen CT16/PAGE5. Use of intraresidual i(HCA)CO(CA)NH experiment in combination with the established HNCO experiment was crucial for the assignment of highly disordered CT16.     

Fast Assignment of <Superscript>15</Superscript>N-HSQC Peaks using High-Resolution 3D HNcocaNH Experiments with Non-Uniform Sampling

We describe an efficient NMR triple resonance approach for fast assignment of backbone amide resonance peaks in the ¹⁵N-HSQC spectrum. The exceptionally high resolutions achieved in the 3D HncocaNH and hNcocaNH experiments together with non-uniform sampling facilitate error-free sequential connection of backbone amides. Data required for the complete backbone amide assignment of the 56-residue protein GB1 domain were obtained in 14 h. Data analysis was vastly streamlined using a ‘backbone NH walk’ method to determine sequential connectivities without the need for ¹³C chemical shifts comparison. Amino acid residues in the sequentially connected NH chains are classified into two groups by a simple variation of the NMR pulse sequence, and the resulting ‘ZeBra’ stripe patterns are useful for mapping these chains to the protein sequence. In addition to resolving ambiguous assignments derived from conventional backbone experiments, this approach can be employed to rapidly assign small proteins or flexible regions in larger proteins, and to transfer assignments to mutant proteins or proteins in different ligand-binding states.     

Modulation of the reaction cycle of the Na<Superscript>+</Superscript>:Ca<Superscript>2+</Superscript>, K<Superscript>+</Superscript> exchanger

Ca²⁺ concentration in retinal photoreceptor rod outer segment (OS) strongly affects the generator potential kinetics and the receptor light adaptation. The response to intense light stimuli delivered in the dark produce potential changes exceeding 40 mV: since the Ca²⁺ extrusion in the OS is entirely controlled by the Na⁺:Ca²⁺, K⁺ exchanger, it is important to assess how the exchanger ion transport rate is affected by the voltage and, in general, by intracellular factors. It is indeed known that the cardiac Na⁺:Ca²⁺ exchanger is regulated by Mg-ATP via a still unknown metabolic pathway. In the present work, the Na⁺:Ca²⁺, K⁺ exchanger regulation was investigated in isolated OS, recorded in whole-cell configuration, using ionic conditions that activated maximally the exchanger in both forward and reverse mode. In all species examined (amphibia: Rana esculenta and Ambystoma mexicanum; reptilia: Gecko gecko), the forward (reverse) exchange current increased about linearly for negative (positive) voltages and exhibited outward (inward) rectification for positive (negative) voltages. Since hyperpolarisation increases Ca²⁺ extrusion rate, the recovery of the dark level of Ca²⁺ (and, in turn, of the generator potential) after intense light stimuli results accelerated. Mg-ATP increased the size of forward and reverse exchange current by a factor of ∼2.3 and ∼2.6, respectively, without modifying their voltage dependence. This indicates that Mg-ATP regulates the number of active exchanger sites and/or the exchanger turnover number, although via an unknown mechanism. Proceedings of the XVIII Congress of the Italian Society of Pure and Applied Biophysics (SIBPA), Palermo, Sicily, September 2006.