Amide III frequencies for Ala-X peptides depend on the X amino acid size

Raman spectra of series of aqueous solutions of peptides containing two amino acids, glycine-X, alanine-X, and serine-X, where X is an uncharged amino acid, show that the amide III band shifts systematically to lower frequencies as the side chain of the X amino acid becomes larger. The range of this shift is about 20 cm-1, starting at 1275 cm-1 for alanine-glycine and moving to 1251 cm-1 for alanine-tryptophan, with a correlation coefficient of 0.93 with the mass of the X amino acid side chain for 10 peptides. The amide I frequencies remain constant as the X amino acid is changed. This shift may result from a change in the average conformational preference of the peptide, a change in vibrational coupling of the amide III modes with the X amino acid side chain, a change in molecular force constants, or a combination of these. These results present a test for computational methods.     

Genetic distances between Chinese populations calculated on gene frequencies of 38 loci

Genetic distances were calculated for Han subpopulations in different provinces, cities and au-tonomous regions and ethnic minorities in China by using gene frequency data of 38 loci, and genetic trees were con-structed. The results showed that, among both Han and ethnic minorities, there were two types, i.e. southern and northern Mongoloids, with Yangtze River as boundary. Therefore, both African origin theory and local origin theory about the modern man should answer the question; when did these two types separate and how did they develop. This paper also conclusively proved genetically that the Han subpopulations in different regions are genetically close to the lo-cal ethnic minorities, which indicates that much blood of ethnic minorities has mixed into Han, at the same time, some blood of Han also has mixed into the local ethnic minorities.     

Self-assembling peptides: sequence, secondary structure in solution and film formation

Peptides of alternating charge and hydrophobic amino acids have a tendency to adopt unusually stable beta-sheet structures that can form insoluble macroscopic aggregates under physiological conditions. In this study, analogues of a well-known self-assembling peptide, characterized by the same polar/nonpolar periodicity but with different residues, were designed to study the relationship between sequence, conformation in solution and film-forming capacity in saline solution. Peptide conformation, evaluated by circular dichroism, correlated with film forming capacity observed by inverted optical microscopy after addition of saline solution and subsequent drying. We found that polar/nonpolar periodicity of several analogues is not criterion enough to induce beta-sheet and thus film formation and that conformations different from beta-sheet also allow self-assemblage. Furthermore, addition of the short adhesive sequence RGD to a known self-assembling sequence was shown to not prevent the self-assembling process. This finding might prove useful for the design of biomimetic scaffolds. (c) 2008 Wiley Periodicals, Inc. Biopolymers 89: 906-915, 2008.This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com.     

The relationship between amide proton chemical shifts and secondary structure in proteins

Summary The parameters for HN chemical shift calculations of proteins have been determined using data from high-resolution crystal structures of 15 proteins. Employing these chemical shift calculations for HN protons, the observed secondary structure chemical shift trends of HN protons, i.e., upfield shifts on helix formation and downfield shifts on -sheet formation, are discussed. Our calculations suggest that the main reason for the difference in NH chemical shifts in helices and sheets is not an effect from the directly hydrogen-bonded carbonyl, which gives rise to downfield shifts in both cases, but arises from an additional upfield shift predicted in helices and originating in residues i-2 and i-3. The calculations also explain the well-known relationship between amide proton shifts and hydrogen-bond lengths. In addition, the HN chemical shifts of the distorted amphipathic helices of the GCN4 leucine zipper are calculated and used to characterise the solution structure of the helices. By comparing the calculated and experimental shifts, it is shown that in general the agreement is good between residues 15 and 28. The most interesting observation is that in the N-terminal half of the zipper, although both calculated and experimental shifts show clear periodicity, they are no longer in phase. This suggests that for the N-terminal half, in the true average solution structure the period of the helix coil is longer by roughly one residue compared to the NMR structures.     

NMR study of the structure of short-chain peptides in solution.

The electron-mediated spin–spin coupling constant J between the amide NH and the α-CH protons in the dipeptide fragment C^α? CO(NH? C^αH)R? C′ONH? C^α is dependent on the dihedral angle of rotation (Φ) around the N? C bond. Measurement of J in a series of zwitterionic dipeptides H₃N⁺? CHR₁? CONH? CHR₂? CO₂^? (which is conformationally similar to the dipeptide fragment) in TFA solution shows that J is independent of R₁, but dependent on the steric bulk of R₂. The data are interpreted in terms of a model that assumes that what we measure is an average value of J? a thermal average over all the possible rotamers. The groups R₁ and R₂ are, in most cases, sterically kept apart by the trans and planar amide bonds, and hence the independence of J of R₁. This model is consistent with the theoretical calculations done on the dipeptide fragment. The effect of the structural characteristics of the side chains (e.g., the effect of lengthening and branching the side chains) on the J values in dipeptides is discussed in the light of the existing results of theoretical calculations. Study of 〈J〉 values in tripeptides (C₆H₅CH₂OCONH? CHR₁? CONH? CHR₂? CO₂CH₃, essentially three linked peptide units) shows that electrostatic interaction between the two amide bonds modifies the potential energy surface and the 〈J〉 value of a dipeptide subunit in the tripeptides. Also in some cases, direct steric interaction between the two side chains in the two adjacent dipeptide subunits in the tripeptide affects the potential energy surfaces of the individual dipeptide subunits and hence the 〈J〉 values. The influence of the structural characteristics of the side chains of individual amino acids on structure formation at or beyond the dipeptide level is discussed at various points. The J(NH? ^αCH) values of CH₃CONH? CHR? CONH₂ and CH₃CONH? CHR? CO₂CH₃ with the same R are quite different for R = valine, leucine, phenylalanine, methionine, but equal for R = glycine. This, coupled with the fact that one of the carboxamide NH resonances has a chemical shift different from its counterpart in simple amides like CH₃CONH₂ and the other carboxamide NH has the same chemical shift as its counterpart in CH₃CONH₂, suggest the presence of a hydrogen bond in dipeptide CH₃CONH? CHR? CONH₂ with carboxamide NH as the donor. Theoretical evidence for two seven-membered hydrogen-bonded rings with the carboxamide NH as donor and the acetyl oxygen as acceptor is summarized. Our data cannot suggest the number of such hydrogen-bonded rings, nor can they conclude the relative proportion of these rings in a particular dipeptide. A discussion of the difficulty of interpretation is presented and the data are discussed under certain simplifying assumptions.     

Pressure response of amide one-bond J-couplings in model peptides and proteins

The pressure dependence of the one-bond indirect spin–spin coupling constants ¹ J _N–H was studied in the protected tetrapeptides Ac-Gly-Gly-Xxx-Ala-NH₂ (with Xxx being one of the 20 proteinogenic amino acids). The response of the ¹ J _N–H coupling constants is amino acid type specific, with an average increase of its magnitude by 0.6 Hz at 200 MPa. The variance of the pressure response is rather large, the largest pressure effect is observed for asparagine where the coupling constant becomes more negative by ?2.9 Hz at 200 MPa. The size of the J-coupling constant at high pressure is positively correlated with its low pressure value and the β-propensity, and negatively correlated with the amide proton shift and the first order nitrogen pressure coefficient and the electrostatic solvation free energy.     

Hydrolysis of primary amide groups in Asn/Gln-containing peptides

Peptides Boc-Ala-Asn/Gln-OH and Boc-Asn/Gln-Ala-OH were saponified with barium hydroxide to corresponding Asp/Glu-containing peptides. Under the conditions of saponification, Boc-Asn-Ala-OH additionally afforded Boc-Asp-OH, isopeptide Boc-Asp(Ala)-OH, and Boc-NHSuc > Ala-OH, with the third being the key intermediate in these transformations. Boc-Asp(OMe)-Ala-OMe underwent similar transformations under treatment with diazomethane or triethylamine. Saponification with barium hydroxide was accompanied by a high epimerization of N-terminal amino acid residues, whereas the products of the diazomethane treatment of Boc-Asp(OMe)-Ala-OMe had a low degree of epimerization.     

Identification of the TRH-like peptides pGlu-Glu-Pro amide and pGlu-Phe-Pro amide in rat thyroid: regulation by thyroid status.

Rat thyroid contains thyrotropin-releasing hormone (TRH) and TRH-like peptides which react with TRH antisera. We have identified the TRH-like peptides in the thyroid and examined whether their levels are influenced by thyroid status. The peptides were extracted from the thyroid glands of five hyperthyroid rats and purified by ion-exchange chromatography on SP-Sephadex C25 and reversed-phase high performance liquid chromatography. The principal TRH-immunoreactive component exhibited the same retention on HPLC as synthetic pGlu-Glu-Pro amide and a secondary component corresponded to synthetic pGlu-Phe-Pro amide. In agreement with these assignments the main peptide was shown to be acidic when chromatographed on DEAE-Sephadex A25 and the second peptide neutral. The levels of TRH and TRH-like peptides in the thyroid were investigated in hyper-, hypo- and euthyroid rats. Hyperthyroidism was induced by chronic subcutaneous administration of triiodothyronine (T3) and hypothyroidism was produced by addition of propylthiouracil (PTU) to the drinking water. The amounts of the peptides were determined by radioimmunoassay with a TRH-antiserum, carried out after extraction from the tissues and purification by ion exchange chromatography. The mean concentration of TRH-like peptides in the thyroids of the hyperthyroid rats was 95.5+/-25.5 pmol/g, the mean concentration in the hypothyroid rats was 11.7+/-3.4 pmol/g, and in the euthyroid rats 17.6+/-3.2 pmol/g. The concentrations of TRH were less influenced by thyroid status: the values in hyper-, hypo- and euthyroid rats were 47.5+/-9.4, 42.1+/-6.3, and 17.2+/-1.6 pmol/g respectively. The results show that the levels of the TRH-like peptides in rat thyroid are highly sensitive to thyroid status, suggesting a possible involvement in thyroid regulation.     

昆虫抗菌肽和抗真菌肽结构与功能的关系及分子设计

在对GenBank和EMBL数据库中登录的昆虫抗微生物肽 (antimicrobial peptide, AMP), 即昆虫抗菌肽 (antibacterial peptide) 和抗真菌肽 (antifungal peptide, AFP) 进行归类整理的基础上,对天蚕素族(cecropins )抗菌肽结构与功能的关系及人工改造的分子设计策略,特别是对目前新发现的一些昆虫抗真菌肽的已知结构与功能关系的研究进展、存在问题等进行了简要介绍和分析,为从事昆虫抗微生物肽的理论研究和发展新型抗生素药物提供了必要的信息。     

半边莲营养器官结构与生态环境的关系

利用石蜡切片和光学显微镜,对半边莲的营养器官进行形态解剖学研究。结果表明:半边莲根和茎的次生结构不发达;地上茎表现为根的特征:茎皮层所占比例较大,茎中有明显的内皮层,内皮层上具凯氏带;根的皮层和茎的髓具通气组织,裂生型分泌道存在于茎的皮层;叶的气孔高于表皮,气孔只在上表皮有分布,叶尖具水孔。半边莲的形态结构特征表现出对水生生活的高度适应。对半边莲的系统位置也作了简单探讨。     

Relation of spatial and temporal frequencies to vernier acuity

Vernier thresholds were measured with a pair of vertical sinusoidal gratings of one and a half cycles as targets. The amplitude was weighted by a one-dimensional Gaussian and contrast was set one log unit above contrast threshold. The vernier thresholds were estimated with the method of constant stimuli. Temporal frequency effects were introduced by movement of the vernier targets. It was found that vernier thresholds expressed in phase angle were unchanged in the effective range of spatial frequencies provided that the temporal frequency and the visibility were unchanged, and that thresholds deteriorated by increasing the temporal frequency. It is suggested that the detection of relative phase may be involved in the discrimination of vernier offsets and that it may be mediated by a sustained unit. Three possible types of mechanisms, edge-localization processes, orientation-selective units and phase-sensitive units, were considered in relation to vernier acuity.     

The hydrolysis of primary amide groups in Asn/Gln-containing peptides

Peptides Boc-Ala-Asn/Gln-OH and Boc-Asn/Gln-Ala-OH were saponified with barium hydroxide to corresponding Asp/Glu-containing peptides. Under the conditions of saponification, Boc-Asn-Ala-OH additionally afforded Boc-Asp-OH, isopeptide Boc-Asp(Ala)-OH, and Boc-NHSuc>Ala-OH, with the third being the key intermediate in these transformations. Boc-Asp(OMe)-Ala-OMe underwent similar transformations under treatment with diazomethane or triethylamine. Saponification with barium hydroxide was accompanied by a high epimerization ofN-terminal amino acid residues, whereas the products of the diazomethane treatment of Boc-Asp(OMe)-Ala-OMe had a low degree of epimerization.