Building proteins from C alpha coordinates using the dihedral probability grid Monte Carlo method.

Dihedral probability grid Monte Carlo (DPG-MC) is a general-purpose method of conformational sampling that can be applied to many problems in peptide and protein modeling. Here we present the DPG-MC method and apply it to predicting complete protein structures from C alpha coordinates. This is useful in such endeavors as homology modeling, protein structure prediction from lattice simulations, or fitting protein structures to X-ray crystallographic data. It also serves as an example of how DPG-MC can be applied to systems with geometric constraints. The conformational propensities for individual residues are used to guide conformational searches as the protein is built from the amino-terminus to the carboxyl-terminus. Results for a number of proteins show that both the backbone and side chain can be accurately modeled using DPG-MC. Backbone atoms are generally predicted with RMS errors of about 0.5 A (compared to X-ray crystal structure coordinates) and all atoms are predicted to an RMS error of 1.7 A or better.     

用于蛋白质同源模建及三维结构预测的结构比较方法

继前面的工作把测试蛋白从三族扩大到十一族,寻求联配参数的普适“缺省值“;比较不同的主链曲率和挠率的计算方法,进一步确认主链的折红红分几何刻划方法的有效性;寻找有效的可变缺失突变惩罚函数的形式。结果表明,编制的蛋白质多重联配软件系统是满意的,可用于蛋白质三维结构预测。     

VIP in cerebrospinal fluid of patients with multiple sclerosis

The concentration of VIP was measured radioimmunochemically in cerebrospinal fluid (CSF) from 14 healthy volunteers and from 22 patients with multiple sclerosis. Significantly lower levels of VIP was obtained in the patients (18 +/- 3 pmol/l) than in controls (37 +/- 4 pmol/l). There was no correlation between the level of VIP in CSF and other CSF parameters such as albumin. IgG or cell content; nor between VIP concentration and the physical handicap or neuropsychiatric symptoms. There was a trend towards lower values of VIP in patients with steadily progressing rather than intermittent course of the disease but the difference between the groups was not significant.     

Total nitrogen and phosphorus balance sheet in a typic ustochrept soil under intensive cropping and fertilizer use

Summary Balance sheets were computed for total nitrogen and phosphorus in plough layer (0–15 cm) of a Typic Ustochrept soil under continuous multiple cropping for seven years (1971–72 to 1977–78) with a fixed rotation of pearl millet (Pennisetum typhoideum L.) wheat (Triticum aestivum L.) (Vigna sinensis Savi.) The treatments considered of soil test-based rates of N, P and K, applied both singly and in combinations together with farm yard manure, sulphur and zinc superimposed over optimum rates (100%) of NPK. Heavy, losses of N (762–899 kg ha⁻¹) occurred in the plots which received high rates of Nviz. 150% of recommended NPK and 100% NPK plus FYM. Application of N alone accelerated N losses whereas addition of P, PK, PKS to N minimised such losses. Enrichment of P (66 to 198 kg ha⁻¹) occurred in all phosphate-treated plots. A marginal net decrease (29–54 kg ha⁻¹) in P levels was observed in control and N alone treatments.     

Opiate binding properties of naturally occurring N- and C-terminus modified beta-endorphins

Beta-endorphin is further processed within the pituitary and brain by either N-terminal acetylation, carboxy-terminal proteolysis, or both. These naturally occurring analogues are stored intracellularly and, in some tissues, represent the majority of beta-endorphin immunoreactivity detected by antisera. It is therefore critical to determine their relative potencies at the opiate receptor. This study demonstrates that cleavage of the C-terminus tetrapeptide brings about a 10-fold decrease in opiate binding potency of either camel or human beta-endorphin. N-Acetylation, on the other hand, causes over a thousand fold loss in opiate potency rendering the peptide effectively inactive. Since unmodified beta-endorphin is approximately equipotent at multiple opiate receptors, we tested for possible differential shifts towards mu or delta-type receptors which may result from the modification. Our results show no change in selectivity, but simply an overall loss of potency.     

Multiple forms of phycoerythrin-545 from Cryptomonas maculata

Three multiple phycoerythrin-545 forms were purified from crude extracts of Cryptomonas maculata by preparative isoelectric focusing. The phycoerythrin forms are charge isomers with isoelectric points at 7.83, 5.05 and 4.84. The multiple pigment forms have similar molecular weights of 44500 daltons and are composed of subunits of unequal size in a 1:1 stoichiometry with molecular weights of () 9900 and () 15700 daltons, twice. The proposed quarternary structure of the native pigments is ()₂()₂.The charge differences of the phycoerthrins are caused by a charge heterogeneity of the light subunits, as revealed by urea gel electrophoresis. The chains of pigment form pI 7.83 had a greater electrophoretic mobility than those subunits of the acidic pigment forms pI 5.05 and pI 4.84.The phycoerythrin forms have an absorption spectrum with similar absorption maxima at 544 nm, but differ in the position of the long wavelength shoulders lying at 555 and 557 nm in the negatively charged pigment forms and at 560 nm for the phycoerythrin form with a pI at 7.83.The fluorescence emission spectra coincide in their asymmetrical shape with shoulders at about 620 nm; they slightly differ int he position of the emission maxima at 586 nm for the phycoerythrins with pIs at 4.84 and 5.05 and at 584 nm for phycoerythrin with pI at 7.83.Abbreviations PC phycocyanin - PE phycoerythrin - pI isoelectric point - SDS sodium dodecyl sulphate     

Properties of auxin binding sites in different subcellular fractions from maize coleoptiles

In-vitro binding of labeled auxins to sedimentable particles was tested in subcellular fractions from homogenates of maize (Zea mays L.) coleoptiles. The material was fractionated by differential centrifugation or on sucrose density gradients. It was confirmed that the major saturable binding activity (site I) for 1-naphthyl[1-¹⁴C]acetic acid is associated with vesicles derived from the endoplasmatic reticulum. A second type of specific auxin binding (site II) could be distinguished by several criteria, e.g. by the low affinity towards phenylacetic acid. The particles carrying site II could be clearly separated from markers of the endoplasmatic reticulum, the plasmalemma, the mitochondria and the nuclei, while their density as well as sedimentation velocity correlated with particle-bound acid phosphatase, indicating a localization at the tonoplast. In contrast to site I, binding at site II was hardly affected by a supernatant factor and by sulfhydryl groups. However, the specificity pattern of site II towards auxins and auxin analogs was very similar to that of site I tested in the presence of supernatant factor. The existence of a third auxin receptor localized in plasma membrane-rich gradient fractions was indicated by a preferential in-vitro binding of 2,4-dichlorophenoxyacetic acid.Abbreviations 1-NAA 1-naphthyl acetic acid - 2-NAA 2-naphthyl acetic acid - IAA 3-indolyl acetic acid - PAA phenyl acetic acid - 2,4-D 2,4-D-dichlorophenoxy acetic acid - D-2,4-DP dichlorophenoxy isopropionic acid - NPA 1-N-naphthyl phthalamic acid - ER endoplasmatic reticulum - SF supernatant factor