1H, 13C and 15N random coil NMR chemical shifts of the common amino acids. I. Investigations of nearest-neighbor effects

Summary In this study we report on the ¹H, ¹³C and ¹⁵N NMR chemical shifts for the random coil state and nearest-neighbor sequence effects measured from the protected linear hexapeptide Gly-Gly-X-Y-Gly-Gly (where X and Y are any of the 20 common amino acids). We present data for a set of 40 peptides (of the possible 400) including Gly-Gly-X-Ala-Gly-Gly and Gly-Gly-X-Pro-Gly-Gly, measured under identical aqueous conditions. Because all spectra were collected under identical experimental conditions, the data from the Gly-Gly-X-Ala-Gly-Gly series provide a complete and internally consistent set of ¹H, ¹³C and ¹⁵N random coil chemical shifts for all 20 common amino acids. In addition, studies were also conducted into nearest-neighbor effects on the random coil shift arising from a variety of X and Y positional substitutions. Comparisons between the chemical shift measurements obtained from Gly-Gly-X-Ala-Gly-Gly and Gly-Gly-X-Pro-Gly-Gly reveal significant systematic shift differences arising from the presence of proline in the peptide sequence. Similarly, measurements of the chemical shift changes occurring for both alanine and proline (i.e., the residues in the Y position) are found to depend strougly on the type of amino acid substituted into the X position. These data lend support to the hypothesis that sequence effects play a significant role in determining peptide and protein chemical shifts.     

C, N CP MAS and high resolution multinuclear NMR study of methyl

Carbon (C) and nitrogen (N) metabolism of the hermatypic coral Acropora pulchra and its symbiotic algae (zooxanthellae) was investigated using ¹³C and ¹⁵N isotope tracers. A. pulchra was incubated in seawater containing ¹³C-labeled bicarbonate and ¹⁵N-labeled nitrate (NO₃⁻) for 24 h (pulse period), and subsequently ¹³C and ¹⁵N isotopic ratios of the host coral and the zooxanthellae were followed in ¹³C- and ¹⁵N-free seawater for 2 weeks (chase period). Under our experimental condition of NO₃⁻ (12 μM), C and N were absorbed by the coral-algal symbiotic system with the C:N ratio of 23 during the pulse period. Taking account of concentration dependence of NO₃⁻ uptake rates determined by a separate experiment, C:N uptake ratios under supposed in situ NO₃⁻ conditions (< 1.0 μM) would be > 3.0 times higher, if the photosynthetic rate did not change. During the pulse period, more than half of the absorbed ¹³C and ¹⁵N appeared in the host fraction in organic forms. ¹³C:¹⁵N ratio at the end of the pulse period was similar between the host and the algal fraction, suggesting that algal photosynthetic products were translocated to the host. It is also implied that C:N ratios of the translocated products change depending on N availability for the zooxanthellae. During the chase period, atom % excess (APE) ¹⁵N of the zooxanthellae constantly declined, while that of the host slightly increased. Consequently, APE ¹⁵N of the both fractions appeared to approach a common steady state value, suggesting that ¹⁵N was recycled within the coral-algal symbiotic system. As for C, > 86% of C photosynthetically fixed by the zooxanthellae accumulated in the host at the end of the pulse period, and had a turnover time of ca. 20 days for the host C pool during the following chase period. C:N ratios of organic matter newly synthesized with NO₃⁻ exponentially declined and converged into 5.7 and 4.5 for the host and the zooxanthellae, respectively. This suggests that organic compounds of high C:N ratios such as lipids and carbohydrates were selectively consumed more rapidly than those of low C:N ratios such as proteins and nucleic acids.     

Translocation and conservation of organic nitrogen within the coral-zooxanthella symbiotic system of Acropora pulchra, as demonstrated by dual isotope-labeling techniques

Carbon (C) and nitrogen (N) metabolism of the hermatypic coral Acropora pulchra and its symbiotic algae (zooxanthellae) was investigated using ¹³C and ¹⁵N isotope tracers. A. pulchra was incubated in seawater containing ¹³C-labeled bicarbonate and ¹⁵N-labeled nitrate (NO₃⁻) for 24 h (pulse period), and subsequently ¹³C and ¹⁵N isotopic ratios of the host coral and the zooxanthellae were followed in ¹³C- and ¹⁵N-free seawater for 2 weeks (chase period). Under our experimental condition of NO₃⁻ (12 μM), C and N were absorbed by the coral-algal symbiotic system with the C:N ratio of 23 during the pulse period. Taking account of concentration dependence of NO₃⁻ uptake rates determined by a separate experiment, C:N uptake ratios under supposed in situ NO₃⁻ conditions (< 1.0 μM) would be > 3.0 times higher, if the photosynthetic rate did not change. During the pulse period, more than half of the absorbed ¹³C and ¹⁵N appeared in the host fraction in organic forms. ¹³C:¹⁵N ratio at the end of the pulse period was similar between the host and the algal fraction, suggesting that algal photosynthetic products were translocated to the host. It is also implied that C:N ratios of the translocated products change depending on N availability for the zooxanthellae. During the chase period, atom % excess (APE) ¹⁵N of the zooxanthellae constantly declined, while that of the host slightly increased. Consequently, APE ¹⁵N of the both fractions appeared to approach a common steady state value, suggesting that ¹⁵N was recycled within the coral-algal symbiotic system. As for C, > 86% of C photosynthetically fixed by the zooxanthellae accumulated in the host at the end of the pulse period, and had a turnover time of ca. 20 days for the host C pool during the following chase period. C:N ratios of organic matter newly synthesized with NO₃⁻ exponentially declined and converged into 5.7 and 4.5 for the host and the zooxanthellae, respectively. This suggests that organic compounds of high C:N ratios such as lipids and carbohydrates were selectively consumed more rapidly than those of low C:N ratios such as proteins and nucleic acids.     

Effect of lipid removal on carbon and nitrogen stable isotope ratios in crustacean tissues

The analysis of tissue's naturally occurring stable carbon and nitrogen isotope ratios is a useful tool to delineate trophic relationships. However, the interpretation of δ¹³C and δ¹⁵N is complicated by the influence of multiple factors such as the tissue-specific lipid content. The aim of this work was to evaluate the effects of lipid extraction on δ¹³C and δ¹⁵N compositions in muscle, hepatopancreas and gonads of a marine decapod crustacean, the spider crab Maja brachydactyla. Samples were analyzed for stable isotopes before and after lipid removal, using a derived Soxhlet extraction method. Differences in δ¹³C and δ¹⁵N were measured among tissues before and after treatment. Lipid extraction of muscle did not have a significant effect on either δ¹³C or δ¹⁵N. By contrast, ecologically significant shifts for both carbon and nitrogen stable isotopes ratios (+ 2.9 ± 0.8‰ for δ¹³C, and + 1.2 ± 0.7‰ for δ¹⁵N) were noticed in the hepatopancreas. In regard to gonads, lipid extraction led to a shift only on δ¹³C (+ 1.3 ± 0.3‰). Finally, the derived Soxhlet extraction method removed the lipid influence for δ¹³C, and had an effect on δ¹⁵N composition for lipid-rich samples. We recommend this treatment for carbon stable isotope studies on decapod crustacean lipid-rich tissues.     

The role of irregular unit,GAAS, on the secondary structure of Bombyx mori silk fibroin studied with 13C CP/MAS NMR and wide-angle X-ray scattering

Bombyx mori silk fibroin is a fibrous protein whose fiber is extremely strong and tough, although it is produced by the silkworm at room temperature and from an aqueous solution. The primary structure is mainly Ala-Gly alternative copolypeptide, but Gly-Ala-Ala-Ser units appear frequently and periodically. Thus, this study aims at elucidating the role of such Gly-Ala-Ala-Ser units on the secondary structure. The sequential model peptides containing Gly-Ala-Ala-Ser units selected from the primary structure of B. mori silk fibroin were synthesized, and their secondary structure was studied with (13)C CP/MAS NMR and wide-angle X-ray scattering. The (13)C isotope labeling of the peptides and the (13)C conformation-dependent chemical shifts were used for the purpose. The Ala-Ala units take antiparallel beta-sheet structure locally, and the introduction of one Ala-Ala unit in (Ala-Gly)(15) chain promotes dramatical structural changes from silk I (repeated beta-turn type II structure) to silk II (antiparallel beta-sheet structure). Thus, the presence of Ala-Ala units in B. mori silk fibroin chain will be one of the inducing factors of the structural transition for silk fiber formation. The role of Tyr residue in the peptide chain was also studied and clarified to induce "locally nonordered structure."