Prediction of strong antigenic determinant of seminalplasmin and ribonuclease from the amino acid sequence

It has been reported earlier [Hopp, T.P. & Woods, K.R. (1981) Proc. Natl. Acad. Sci. US 78, 3824–3828] that the antigenic determinants of a protein can be delineated by examining the average local hydrophilicity values along the peptide chain. I have used this method to predict the strong antigenic determinants of two proteins, seminalplasmin and ribonuclease, of known sequence. In the former case, the N-terminal segment 1–14, and in the latter case the segments 27–38 and 80–86, are predicted to possess the antigenic determinants of the two proteins. Experimental verification already exists for the former case.     

Complete amino acid sequence of a subunit from rapeseed high molecular weight protein

A subunit (M, 15 600) from the high molecular weight protein from rapeseed was separated and isolated; its purity and homogeneity were ascertained. The subunit was cleaved with cyanogen bromide, trypsin, chymotrypsin, and Staphylococcus aureus V8 protease. The fragments were separated and isolated by polyacrylamide gel electrophoresis, gel filtration, column chromatography on Dowex 1 × 2, and paper electrophoresis. The amino acid compositions of the intact subunit and different fragments obtained from enzymatic and chemical cleavages were determined. The subunit and its fragments were sequenced by manual Edman method. The phenylthiohydantoin amino acids obtained after each step were identified by thin-layer chromatography and ultraviolet spectroscopy. The complete amino acid sequence of the subunit consisting of 125 amino acid residues has been established by the overlapping method.     

The value of short amino acid sequence matches for prediction of protein allergenicity.

Typically, genetically engineered crops contain traits encoded by one or a few newly expressed proteins. The allergenicity assessment of newly expressed proteins is an important component in the safety evaluation of genetically engineered plants. One aspect of this assessment involves sequence searches that compare the amino acid sequence of the protein to all known allergens. Analyses are performed to determine the potential for immunologically based cross-reactivity where IgE directed against a known allergen could bind to the protein and elicit a clinical reaction in sensitized individuals. Bioinformatic searches are designed to detect global sequence similarity and short contiguous amino acid sequence identity. It has been suggested that potential allergen cross-reactivity may be predicted by identifying matches as short as six to eight contiguous amino acids between the protein of interest and a known allergen. A series of analyses were performed, and match probabilities were calculated for different size peptides to determine if there was a scientifically justified search window size that identified allergen sequence characteristics. Four probability modeling methods were tested: (1) a mock protein and a mock allergen database, (2) a mock protein and genuine allergen database, (3) a genuine allergen and genuine protein database, and (4) a genuine allergen and genuine protein database combined with a correction for repeating peptides. These analyses indicated that searches for short amino acid sequence matches of eight amino acids or fewer to identify proteins as potential cross-reactive allergens is a product of chance and adds little value to allergy assessments for newly expressed proteins.     

Partial amino acid sequence of porcine elastase II

The partial amino acid sequence of porcine elastase II, isolated from crude trypsin Type II, was determined. The enzyme consists of two polypeptide chains, a light chain composed of 11 residues, and a heavy chain (M_r = 23 500) with four intrachain disulfide bridges; the two chains are held together by one interchain disulfide bond. Elastase II was fragmented into several peptides by chemical cleavages with CNBr at the two methionine residues, 99 and 180 (chymotrypsinogen numbering), and with hydroxylamine at the peptide bond following DIP-Ser¹⁹⁵. About 50% of the sequence was determined and the positions of 120 amino acids were located, including the light chain residues and most of the active site residues. The partial sequence shows 64% difference between porcine elastase II and elastase I and only 26% difference between porcine elastase II and bovine chymotrypsin B.     

重组蛋白药物C末端不同长度氨基酸序列的质谱分析

目的:基于本实验室已建立的溴化氰裂解蛋白质C末端方法结合优化后的质谱检测技术,对C末端长度分别为2~37个氨基酸,相对分子质量在200~5000的8个重组蛋白药物进行检测。方法:(1)针对重组蛋白药物的不同状态(SDS-PAGE、干粉或溶液)分别进行C末端胶内或溶液裂解;(2)质谱检测,正离子方式,雾化气为氮气,碰撞气体为氩气。源温80℃,锥孔电压50 V,MCP检测器电压为2.15 kV。结果:8个重组蛋白药物的C末端全部成功检测出,且基本为基峰。结论:建立的重组蛋白药物C末端测序联用方法应用于实际药物的检测具有很高的实用价值和学术意义。     

Complete amino acid sequence of fin whale growth hormone

The complete amino acid sequence of growth hormone from fin whale pituitary has been determined. It consists of 190 amino acid residues with two disulfide bridges formed by residues 52–163 and 180–188. The sequence identity with sei whale, bovine, ovine and human growth hormone is 90%, 91%, 90% and 68%, respectively.     

LC-MS/MS法对融合蛋白FP3的氨基酸全序列测定

运用液质联用、两种串联质谱对融合蛋白FP3的氨基酸全序列测定, 确证其一级结构。将样品还原烷基化后, 通过胰蛋白酶酶解蛋白, PNGase F去除多肽混合物中糖肽的糖基化, 将去糖后的总肽用于液质联用系统, 通过液相分离后, 运用Q-TOF和线性离子阱两种串联质谱测定各个肽段的b, y碎片离子, 分析测定融合蛋白FP3的氨基酸全序列。通过LC-ESI-Q-TOF完成了融合蛋白FP3的76%氨基酸序列测定, 通过LC-ESI-Trap完成余下24%氨基酸序列测定。液质联用、串联质谱法测定蛋白质氨基酸序列快速、灵敏、准确, 是对重组蛋白结构分析和确证的重要手段。     

Primary structure of rat spermidine synthase: an example of refining the cDNA-derived amino acid sequence.

The primary structure of rat spermidine synthase having the N-terminal acetylated methionine and 98.7% homology with that of the mouse enzyme is presented using a limited amount of the homogeneous enzyme. The study strategy was principally to compare the molecular masses of liberated peptides determined by three specific cleavage methods with those expected from known cDNA-derived amino acid sequences of mouse and human enzymes using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI TOF-MS). The cleavage methods involved two enzymatic methods using lysylendopeptidase and arginylendopeptidase, and a chemical method for cleaving at the cysteine residue using 2-nitro-5-thiocyanobenzoic acid. Their usefulness was clearly demonstrated. Column-switching semimicro reversed-phase HPLC, which permits application of the entire reaction mixture, was useful for collecting a small amount of peptides containing the N-terminal amino acid, to confirm acetylation of the N-terminal methionine by MALDI TOF-MS. It was necessary in this approach to examine the amino acid sequence of certain peptides. The Edman method was used for the sequence analysis, and this will be replaced by an improved MALDI TOF-MS now available in a few laboratories.     

Complete amino acid sequence of a VLDV-type neurophysin from ostrich differs markedly from known mammalian neurophysins

The neurohypophyseal hormones vasopressin and oxytocin are known to be synthesized in eutherian mammals as part of larger precursors containing either MSEL-or VLDV-neurophysins. A neurophysin has been isolated from ostrich neurohypophyses and shown by partial amino acid sequence determination to be related to mammalian VLDV-neurophysin. The present report describes the complete amino acid sequence of this ostrich neurophysin containing 93 residues. This amino acid sequence, the first reported in birds, differs in a remarkable manner from its mammalian homolog. Indeed, it contains a large number of substitutions, including one insertion, distributed throughout the polypeptide chain when compared to known VLDV-neurophysins. Whereas many of these substitutions are localized inside the so-called constant region of the neurophysin, the highest variation can be found in the COOH-terminal region.     

Effect of amino acid sequence on transdermal iontophoretic peptide delivery

The objective of this study was to investigate the effect of amino acid sequence on the transdermal delivery of peptides by iontophoresis. Structurally related, cationic tripeptides based on the residues at positions (i) 6–8 in LHRH (Ac-X-Leu-Arg-NH₂) and (ii) 3–5 in octreotide (Ac-X-dTrp-Lys-NH₂) were studied. Iontophoretic transport experiments were conducted using porcine skin in vitro to investigate the dependence of flux on peptide concentration. Co-iontophoresis of acetaminophen enabled deconvolution of the contributions of electromigration (EM) and electroosmosis (EO) and the calculation of an electroosmotic inhibition factor (IF). A two-fold increase in donor peptide concentration increased iontophoretic flux for most peptides, and electroosmotic inhibition for dNal-containing tripeptides. The improvement in transport and the impact on the EM and EO components were peptide-specific. A reduction in the number of competing ions in the formulation significantly increased transport and, specifically, the EM contribution; it also increased IF of compounds with a propensity to interact with the membrane. No monotonic dependence of flux on either molecular weight or lipophilicity was observed. Iontophoretic peptide transport could not be rationalized in terms of either peptide molecular weight or computational 2D estimates of lipophilicity. Data suggest that a more complex three-dimensional approach is required to develop structure permeation relationships governing iontophoretic peptide delivery.     

Deoxyribonucleic acid sequence effects on molecular structure

The deoxyribonucleic acid (DNA) duplex shows polymorphism depending on the base sequence and the environment. The base sequence dependent variations in conformational properties of the synthesized oligonucleotides are studied by X-ray analysis and several physico-chemical techniques. The possible structures in solution were proposed by molecular dynamics (MD) simulation. 1) The several oligonucleotides which include the adenine or adenine-thiamine tract, have unique conformational characteristics with the base sequence dependent property. The junction-model structure for DNA bending was proposed by the combined method of nuclear magnetic resonance (NMR) observations and MD calculation. 2) The two different hydrogen bonding schemes of inosine-adenine base-pairing, anti/anti and anti/syn forms, are adopted in B-DNA structure. The preference of these forms depends on the base sequence. The MD calculation could offer the models consistent with NMR evidence. 3) Oligonucleotides containing cyclonucleosides with a high-anti (intermediate between anti and syn) glycosidic conformation adopt left-handed double-helical structures. A suitable model of this left-handed duplex was proposed by calculation with energy minimization.     

Prediction of γ‐turns from amino acid sequences

Abstract: We predicted γ‐turns from amino acid sequences using the first‐order Markov chain theory and enlarged representative data sets corresponding to protein chains selected from the Protein Data Bank (PDB). The following data sets were used for training and deriving the probability values: (1) an initial data set containing 315 protein chains comprising 904 γ‐turns and (2) a later data set in order to include new entries in the PDB, containing 434 protein chains and comprising 1053 γ‐turns. By excluding 93 protein chains that were common to these two training data sets, we generated two mutually exclusive data sets containing 222 and 341 protein chains for testing our predictions. Applying amino acid probability values derived from training data sets on to testing data sets yielded overall prediction accuracies in the range 54–57%. We recommend the use of probability values derived from the data set comprising 315 protein chains that represents more γ‐turns and also provides better predictions.     

Complete amino acid sequence of arachin subunit of molecular weight 21000

A subunit of molecular weight 21 000 from arachin, the major peanut protein, was isolated in pure form and primary structure was determined. The subunit was fragmented with CNBr, trypsin, and NBS; the fragments were separated and isolated by PAGE, gel filtration, Dowex treatment, and paper electrophoresis, and Edman degradation on each fragment, including the intact subunit, was performed. The PTH-amino acids thus obtained were identified by UV spectroscopy and TLC. The complete sequence of 176 residues was established by overlapping technique.     

搀假穿山甲中蛋白质与氨基酸破坏程度的测定

目的报道搀假穿山甲中蛋白质与氨基酸破坏程度.方法采用聚酰胺薄层色谱法、定氮法与氨基酸分析仪测定法,对穿山甲和搀假穿山甲中蛋白质和氨基酸进行测定.结果聚酰胺薄层色谱法显示搀假穿山甲中化学成分已发生变化,定氮与氨基酸测定表明搀假穿山甲中蛋白质与氨基酸破坏严重.结论搀假穿山甲应按假药论处.     

Prediction of protein function in the absence of significant sequence similarity

Tremendous progress in DNA sequencing has yielded the genomes of a host of important organisms. The utilisation of these resources requires understanding of the function of each gene. Standard methods of functional assignment involve sequence alignment to a gene of known function; however such methods often fail to find any significant matches. Here we discuss a number of recent alternative methods that may be of use when sequence alignment fails. Function can be defined in a number of ways including E.C. number and MIPS and KEGG functional classes. Phylogenetic profiles show the pattern of presence or absence of a protein between genomes. Protein-protein interactions can be identified by searching for interacting pairs of proteins that are fused to a single protein chain in another organism. The gene neighbour method uses the observation that if the genes that encode two proteins are close on a chromosome, the proteins tend to be functionally related. More general methods use sequence properties such as amino acid composition, mean hydrophobicity, predicted secondary structure and post-translational modification sites. Data mining methods devise rules in the form of IF...THEN statements that make predictions of function using sequence based attributes, predicted secondary structure and sequence similarity. Finally, structural features can be used, after modelling the structure of a protein from its sequence or solving its structure. Protein fold class can be strongly indicative of function, while other structural features, such as secondary structure content, cleft size and 3D structural motifs are also useful.     

Amino acid sequence of UP1, an hnRNP-derived single-stranded nucleic acid binding protein from calf thymus

The UP1 single-stranded nucleic acid binding protein from calf thymus (Herrick, G. & Alberts, B.M. (1976) J. Biol. Chem. 251, 2124–2132) has recently been shown to be a proteolytic fragment derived from the A₁ heterogeneous nuclear ribonucleoprotein (hnRNP)(Pandolfo et al. (1985) Nucleic Acids Res. 13, 6577–6590). The NH₂-terminus of the 22 162 dalton UP1 protein appears to be blocked, which suggests that UP1 represents the NH₂-terminal two thirds of this 32 000 dalton hnRNP protein. The complete amino acid sequence for UP1 was derived from automated sequencing of peptides that were purified by HPLC from digests with trypsin, chymotrypsin, Staphylococcus aureus protease, endoproteinase Lys-C, and cyanogen bromide. Trichloroacetic acid precipitation followed by enzymatic digestion in 2 M urea proved to be the best approach for generating UP1 peptides. By carboxymethylating after, rather than before, digestion it was possible to avoid problems associated with the insolubility of the carboxymethylated UP1. All of the resulting peptides in amounts varying from 2 to 15 nmol were coupled to aminopolystyrene prior to solid-phase sequencing. Using these methods, no difficulties were encountered in assigning glutamic acid residues or in completely sequencing peptides that contained up to 25–30 residues. The relative ease with which the UP1 protein was sequenced, requiring only about a year to complete, and the comparatively modest amount of protein required, less than 5 mg, attests to the usefulness of water soluble carbodiimide coupling and solid-phase sequencing for determining the primary structures of proteins. In addition to serving as a basis for determining structural relationships among various mammalian single-stranded nucleic acid binding proteins, the amino acid sequence of UP1 reveals that the A₁ hnRNP protein contains a region of internal sequence homology that apparently corresponds to two independent nucleic acid binding sites.     

Prediction of drug solubility from structure

The aqueous solubility of a drug is an important factor affecting its bioavailability. Numerous computational methods have been developed for the prediction of aqueous solubility from a compound's structure. A review is provided of the methodology and quality of results for the most useful procedures including the model implemented in the QikProp program. Viable methods now exist for predictions with less than 1 log unit uncertainty, which is adequate for prescreening synthetic candidates or design of combinatorial libraries. Further progress with predictive methods would require an experimental database of highly accurate solubilities for a large, diverse collection of drug-like molecules.