An Intriguing Controversy over Protein Structural Class Prediction

A recent report by Bahar et al. [(1997), Proteins 29, 172–185] indicates that the coupling effects among different amino acid components as originally formulated by K. C. Chou [(1995), Proteins 21, 319–344] are important for improving the prediction of protein structural classes. These authors have further proposed a compact lattice model to illuminate the physical insight contained in the component-coupled algorithm. However, a completely opposite result was concluded by Eisenhaber et al. [(1996), Proteins 25, 169–179], using a different dataset constructed according to their definition. To address such an intriguing controversy, tests were conducted by various approaches for the datasets from an objective database, the SCOP database [Murzin et al. (1995), J. Mol. Biol. 247, 536–540]. The results obtained by both self-consistency and jackknife tests indicate that the overall rates of correct prediction by the algorithm incorporating the coupling effect among different amino acid components are significantly higher than those by the algorithms without counting such an effect. This is fully consistent with the physical reality that the folding of a protein is the result of a collective interaction among its constituent amino acid residues, and hence the coupling effects of different amino acid components must be incorporated in order to improve the prediction quality. It was found by a revisiting the calculation procedures by Eisenhaber et al. that there was a conceptual mistake in constructing the structural class datasets and a systematic mistake in applying the component-coupled algorithm. These findings are informative for understanding and utilizing the component-coupled algorithm to study the structural classes of proteins.     

An improved method for large-scale purification of recombinant human glucagon

Glucagon was expressed inEscherichia coli as a fusion protein including the glucagon sequence [Ishizakiet al. (1992),Appl. Microbiol. Biotechnol.36, 483–486]. The high-level expression of a protein inE. coli often results in an insoluble aggregate called an inclusion body containing a fusion protein. In our previous report [Yoshikawaet al. (1992),J. Protein Chem. 11, 517–525], we solubilized this inclusion body by using guanidinium chloride. However, the existence of denaturant caused problems such as a low proteolytic activity for transforming the fusion protein into glucagon and complicated purification methods. We tried to improve the method to enable large-scale purification. At alkaline pH, the inclusion body could be solubilized to a high concentration and cleaved by amino acid-specific endopeptidases. By utilizing isoelectric precipitations as a new economical purification method for glucagon from intermediates, the glucagon obtained was shown to be over 99.5% pure by analytical RP-HPLC. The yield was almost equal that of our previous method, and the glucagon produced was chemically and biochemically equivalent to natural glucagon.     

Accuracy of Secondary Structure and Solvent Accessibility Predictions for a Clostridial Neurotoxin C-Fragment

Earlier studies used Rost and Sander's artificial neural network [(1993a), J. Mol. Biol. 232, 584–599] to predict the secondary structures [Lebeda and Olson (1994), Proteins 20, 293–300] and residue solvent accessibilities [Lebeda and Olson (1997), J. Protein Chem. 16, 607–618] of the clostridial neurotoxins. Because the X-ray crystal structure of the 50-kDa C-terminal half of the heavy chain of tetanus toxin was recently determined, this report evaluates the accuracy of these network-derived predictions. For this predominantly -strand-containing fragment, predictions, on a per-residue basis, for both secondary structure and solvent accessibility were about 70% accurate. A more flexible and realistic analysis based on overlapping segments yielded accuracies of over 80% for the three-state secondary structure and for the two-state accessibility predictions. Because the accuracies of these predictions are comparable to those made by Rost and Sander using a dataset of 126 nonhomologous globular proteins, our predictions provide a quantitative foundation for gauging the results when building by homology the structures of related proteins.     

An eigenvalue-eigenvector approach to predicting protein folding types

The accuracy of predicting protein folding types can be significantly enhanced by a recently developed algorithm in which the coupling effect among different amino acid components is taken into account [Chou and Zhang (1994)J. Biol. Chem. 269, 22014-22020]. However, in practical calculations using this powerful algorithm, one may sometimes face illconditioned matrices. To overcome such a difficulty, an effective eigenvalue-eigenvector approach is proposed. Furthermore, the new approach has been used to predict a recently constructed set of 76 proteins not included in the training set, and the accuracy of prediction is also much higher than those of other methods.     

Monte Carlo simulation studies on the prediction of protein folding types from amino acid composition.

In the methodology development for statistical prediction of protein structures, the founders of different methods usually selected different sets of proteins to test their predicted results. Therefore, it is hard to make a fair comparison according to the results they reported. Even if the predictions by different methods are performed for the same set of proteins, there is still such a problem: a method better that the other for one set of proteins would not necessarily remain so when applied to another set of proteins. To tackle this problem, a Monte Carlo simulation method is proposed to establish an objective criterion to measure the accuracy of prediction for the protein folding type. Such an objective accuracy is actually corresponding to the asymptotical limit genereated during the Monte Carlo simulation process. Based on that, it has been found that the average objective accuracy for predicting the all-alpha, all-beta, alpha + beta, and alpha/beta proteins by the least Euclid's distance method (Nakashima, H., K. Nishikawa, and T. Ooi. 1986. J. Biochem. 99:152-162) is 73.0% and that by the least Minkowski's distance method (Chou, P.Y. 1989. Prediction in Protein Structure and the Principles of Protein Conformation. Plenum Press. New York. 549-586) is 70.9%, indicating that the former is better than the latter. However, according to the original reports, the latter claimed a rate of correct prediction with 79.7% but the former with only 70.2%, leading to a completely opposite conclusion. This indicates the necessity of establishing an objective criterion, and a comparison is meaningful only when it is based on the objective criterion. The simulation method and the idea developed here also can be applied to examine any other statistical prediction methods.     

Structure from NMR and molecular dynamics: Distance restraining inhibits motion in the essential subspace

Summary We address the question how well proteins can be modelled on the basis of NMR data, when these data are incorporated into the protein model using distance restraints in a molecular dynamics simulation. We found, using HPr as a model protein, that distance restraining freezes the essential motion of proteins, as defined by Amadei et al. [Amadei, A., Linssen, A.B.M. and Berendsen, H.J.C. (1993) Protein Struct. Funct. Genet., 17, 412–425]. We discuss how modelling protocols can be improved in order to solve this problem.     

What is pea legumin — Is it glycosylated?

Since there is some question as to whether or not legumin is glycosylated, this storage protein was isolated by various procedures from developing cotyledons of Pisum sativum L. supplied with [¹⁴C]-labeled glucosamine and analyzed by sodium dodecylsulfate-polyacrylamide gel electrophoresis. Legumin isolated by the classical method of Danielsson [(1949) Biochem. J. 44, 387–400] a procedure in which globulins extracted with a buffered salt solution are precipitated with ammonium sulfate (70% saturation) and legumin separated from vicilin by isoelectric precipitation, was labeled. The glucosamine incorporated into legumin was associated with low-molecular-weight polypeptides. In contrast, legumin isolated by the method of Casey [(1979) Biochem. J. 177, 509–520], a procedure where legumin is prepared by zonal isoelectric precipitation from globulins precipitated with 40–70% ammonium sulfate, was not labeled. However, the globulin fraction precipitated with 40% ammonium sulfate was labeled and the radioactive glucosamine was associated with low-molecular-weight polypeptides. Legumin isolated from protein bodies [Thomson et al. (1978) Aust. J. Plant Physiol. 5, 263–279] was not extensively labeled. However, the saltinsoluble fraction of protein body extracts was labeled and the radioactivity was associated with low-molecular-weight polypeptides. These results indicate that protein bodies contain a glycoprotein of low-molecular-weight that co-purifies with legumin isolated by the method of Danielsson but that is discarded when isolation methods developed more recently are used.     

Prediction of location of active sites in biologically active peptides

In a previous paper we demonstrated that the short-range compact regions in atrial natriuretic factor (-hANF) predicted by the average distance map (ADM) correspond to its active sites [Kikuchi,J. Protein Chem.11, 579–581 (1992)]. In the present paper we apply the same method to other bioactive peptides and peptidic enzyme inhibitors. We again observe that active sites in each peptide are contained in short-range compact regions predicted by the ADM for the peptide. This demonstrates that the ADM method predicts the possible location of active sites in biologically active peptides in general. The possibility of practical application of the present method to rational drug design is also discussed.     

基于卷积神经网络的大肠杆菌启动子预测

目的 基于位点特异性打分矩阵（position-specific scoring matrices,PSSM）的预测模型已经取得了良好的效果,基于PSSM的各种优化方法也在不断发展,但准确率相对较低,为了进一步提高预测准确率,本文基于卷积神经网络（convolutional neural networks,CNN）算法做了进一步研究。方法 采用PSSM将启动子序列处理成数值矩阵,通过CNN算法进行分类。大肠杆菌K-12（Escherichia coli K-12,E.coli K-12,下文简称大肠杆菌）的Sigma38、Sigma54和Sigma70 3种启动子序列被作为正集,编码（Coding）区和非编码（Non-coding）区的序列为负集。结果 在预测大肠杆菌启动子的二分类中,准确率达到99%,启动子预测的成功率接近100%;在对Sigma38、Sigma54、Sigma70 3种启动子的三分类中,预测准确率为98%,并且针对每一种序列的预测准确率均可以达到98%以上。最后,本文以Sigma38、Sigma54、Sigma70 3种启动子分别和Coding区或者Non-coding区序列做四分类,预测得到的准确性为0.98,对3种Sigma启动子均衡样本的十交叉检验预测精度均可以达到0.95以上,海明距离为0.016,Kappa系数为0.97。结论 相较于支持向量机（support vector machine,SVM）等其他分类算法,CNN分类算法更具优势,并且基于CNN的分类优势,编码方式亦可以得到简化。     

Prediction of the secondary structure content of globular proteins based on structural classes

The prediction of the secondary structure content (-helix and-strand content) of a globular protein may play an important complementary role in the prediction of the protein's structure. We propose a new prediction algorithm based on Chou's database [Chou (1995),Proteins Struct. Fund Genet. 21, 319]. The new algorithm is an improved multiple linear regression method, taking the nonlinear and coupling terms of the frequencies of different amino acids into account. The prediction is also based on the structural classes of proteins. A resubstitution examination for the algorithm shows that the average errors are 0.040 and 0.033 for the prediction of-helix content and-strand content, respectively. The examination of cross-validation, the jackknife analysis, shows that the average errors are 0.051 and 0.044 for the prediction of-helix content and-strand content, respectively. Both examinations indicate the self-consistency and the extrapolative effectiveness of the new algorithm. Compared with the other methods available currently, our method has the merits of simplicity and convenience for use, as well as a high prediction accuracy. By incorporating the prediction of the structural classes, the only input of our method is the amino acid composition of the protein to be predicted.     

Band-selective 3D NOESY-TOCSY: Measurement of through-space correlations between aliphatic protons of membrane peptides and proteins in non-deuterated detergents

Summary Recently the use of band-selective excitation to obtain ¹H 2D NMR spectra of membrane peptides and proteins in non-deuterated detergents has been demonstrated [Seigneuret, M. and Levy, D. (1995) J. Biomol. NMR, 5, 345–352]. A limitation of the method was the inability to obtain through-space correlation between aliphatic protons. Here, a 3D F3-band-selective NOESY-TOCSY experiment is described that allows such correlations to be observed in the presence of an excess of non-deuterated detergent. Application to the measurement of proximities between aliphatic protons of the membrane peptide mastoparan X solubilized in non-deuterated n-octylglucoside is presented. With this additional experiment, it is now possible to obtain the same amount of structural constraints on membrane peptides and protein in non-deuterated detergent as in deuterated detergent and therefore to perform complete structural studies.     

Expression, Purification, Characterization, and X-Ray Analysis of Selenomethionine 215 Variant of Leukocyte Collagenase

Matrix metalloproteinases belong to the superfamily of metzincins containing, besides a similar topology and a strictly conserved zinc environment, a 1,4-tight turn with a strictly conserved methionine residue at position three (the so called Met-turn [Bode et al. (1993) FEBS 331, 134–140; Stöcker et al. (1995) Protein Sci. 4, 823–840]. The distal S–CH₃ moiety of this methionine residue forms the hydrophobic basement of the three His residues liganding the catalytic zinc ion. To assess the importance of this methionine, we have expressed the catalytic domain of neutrophil collagenase (rHNC, residues Met80–Gly242) in the methionine auxotrophic Escherichia coli strain B834[DE3](hsd metB), with the two methionine residues replaced by Selenomethionine. Complete replacement was confirmed by amino acid analysis and electrospray mass spectrometry. The folded and purified enzyme retained its catalytic activity, but showed modifications which are reflected in changed kinetic parameters. The Met215SeMet substitution caused a decrease in conformational stability upon urea denaturation. The X-ray crystal structure of this Selenomethionine rHNC was virtually identical to that of the wild-type catalytic domain except for a very faint local disturbance around the sulfur-seleno substitution site.     

Probing membrane protein orientation and structure using fast magic-angle-spinning solid-state NMR

One and two-dimensional solid-state NMR experiments are discussed that permit probing local structure and overall molecular conformation of membrane-embedded polypeptides under Magic Angle Spinning. The functional dependence of a series of anisotropic recoupling schemes is analyzed using theoretical and numerical methods. These studies lead to the construction of a set of polarization dephasing or transfer units that probe local backbone conformation and overall molecular orientation within the same NMR experiment. Experimental results are shown for a randomly oriented peptide and for two model membrane–peptides reconstituted into lipid bilayers and oriented on polymer films according to a method proposed by Bechinger etal. [J. Am. Chem. Soc., 124, (2002), 1146–1147].     

Prediction of probable pathways of folding in globular proteins

A method is described for the prediction of probable folding pathways of globular proteins, based on the analysis of distance maps. It is applicable to proteins of unknown spatial structure but known amino acid sequence as well as to proteins of known structure. It is based on an objective procedure for the determination of the boundary of compact regions that contain high densities of interresidue contacts on the distance map of a globular protein. The procedure can be used both with contact maps derived from a known three-dimensional protein structure and with predicted contact maps computed by means of a statistical procedure from the amino acid sequence alone. The computed contact map can also be used to predict the location of compact short-range structures, viz. -helices and -turns, thereby complementing other statistical predictive procedures. The method provides an objective basis for the derivation of a theoretically predicted pathway of protein folding, proposed by us earlier [Tanaka and Scheraga (1977) Macromolecules10, 291–304; Némethy and Scheraga (1979) Proc. Natl. Acad. Sci., U.S.A.76, 6050–6054].     

Purification and characterization of a 60-kDa protein from oat, formerly known as a TCP1-related chaperone

Recently, Mummertet al. [Nature 363, 644–648 (1993)] isolated a proposed TCP1-related chaperone. Here we report several findings concerning the protein which they sequenced. Two similar N-terminal sequences were obtained from this abundant 60-kDa protein. Internal sequences were also acquired by protease digestion. Initially it was believed the protein was able to completely inhibit citrate synthase aggregation, but later purifications demonstrated that the 60-kDa polypeptide lacked both chaperone activity and the previously reported kinase activity [Grimmet al., Planta 178, 199–206 (1989)]. It is now our belief that this protein is neither a chaperone nor a kinase.     

Improved frequency resolution in multidimensional constant-time experiments by multidimensional Bayesian analysis

Summary The resolution of spectral frequencies in NMR data obtained from discrete Fourier transformation (DFT) along D constant-time dimensions can be improved significantly through extrapolation of the D-dimensional free induction decay (FID) by multidimensional Bayesian analysis. Starting from Bayesian probability theory for parameter estimation and model detection of one-dimensional time-domain data [Bretthorst, (1990) J. Magn. Reson., 88, 533–551; 552–570; 571–595], a theory for the D-dimensional case has been developed and implemented in an algorithm called BAMBAM (BAyesian Model Building Algorithm in Multidimensions). BAMBAM finds the most probable sinusoidal model to account for the systematic portion of any D-dimensional stationary FID. According to the parameters estimated by the algorithm, the FID is extrapolated in D dimensions prior to apodization and Fourier transformation. Multidimensional Bayesian analysis allows for the detection of signals not resolved by the DFT alone or even by sequential one-dimensional extrapolation from mirror-image linear prediction prior to the DFT. The procedure has been tested with a theoretical two-dimensional dataset and with four-dimensional HN(CO)CAHA (Kay et al. (1992) J. Magn. Reson., 98, 443–450) data from a small protein (8 kDa) where BAMBAM was applied to the ¹³C and H constant-time dimensions.To whom correspondence should be addressed.     

Simultaneous determination of methionine and total homocysteine in human plasma by gas chromatography–mass spectrometry

A gas chromatographic–mass spectrometric method for the simultaneous determination of methionine and total homocysteine in human plasma is described. dl-[²H₄]Methionine and dl-[²H₈]homocystine were used as internal standards. The method involved reduction of the disulfide bond with dithiothreitol, purification by cation-exchange chromatography using a BondElut SCX cartridge and derivatization with isobutyl chlorocarbonate in water–ethanol–pyridine. Quantitation was performed by selected-ion monitoring of the quasi-molecular ions of N(O,S)-isobutyloxycarbonyl ethyl ester (IBC-OEt) derivatives for methionine and [²H₄]methionine, respectively, and the fragment ions ([M+H–COOisoBu–COOEt]⁺) for IBC-OEt derivatives for homocysteine and [²H₄]homocysteine, respectively. The sensitivity, specificity, accuracy and precision of the method were demonstrated to be satisfactory for measuring concentrations of methionine and total homocysteine in human plasma.     

Platinum(II) and palladium(II) complexes with 2-Acetyl pyridine 4N-ethyl thiosemicarbazone able to overcome the cis-Platin resistance. Structure, antibacterial activity and DNA strand breakage

The reactions of Pd(II) and Pt(II) with 2-Acetyl Pyridine N(4)-Ethyl-Thiosemicarbazones, HAc4Et and 2-Acetyl Pyridine N(4)-1-(2-pyridyl)-piperazinyl Thiosemicarbazone, HAc4PiPiz and 2-Formyl Pyridine N(4)-1-(2-pyridyl)-piperazinyl Thiosemicarbazone, HFo4PiPiz afforded the complexes, [Pd(Ac4Et)], 1, [Pd(HAc4Et)₂]Cl₂, 2 and [Pd(Ac4Et)₂], 3[Pt(Ac4Et)], 4, [Pt(HAc4Et)₂]Cl₂, 5, [Pt(Ac4Et)₂], 6 and [Pd(Fo4PipePiz)Cl], 7, [Pd(Fo4PipePiz)₂], 8, [Pd(Ac4PipePiz)Cl], 9 and [Pd(Ac4PipePiz)₂], 10. The crystal structure of the complex [Pt(Ac4Et)₂], 6 has been solved. The platinum(II) atom is in a square planar environment surrounded by two cis nitrogen atoms and two cis sulfur atoms. The ligands are not equivalent, one being tridentate with (N,N,S) donation, the other being monodentate using only the sulfur atom to coordinate to the metal. The tridentate ligand shows a Z, E, Z configuration while the monodentate ligand shows an E, E, Z. Inter-molecular hydrogen bonds stabilize the structure, while the crystal packing is determined by –, and Pt – C interactions. The antibacterial effect of Pd(II) and Pt(II) complexes were studied in vitro. The complexes were found to have effect on Gram(+) bacteria, while the same complexes showed no bactericidal effect on Gram(–) bacteria. The effect of the Pd(II) and Pt(II) complexes on the in vitro DNA strand breakage was studied by agarose gel electrophoresis. The complexes 1-6 were found to exhibit a cytotoxic potency in a very low micromolar range and to be able to overcome the cisplatin resistance of A2780/Cp8 cells (Kovala-Demertzi et al. 2000).     

Beiträge zur Kenntnis von Rumex. XIII

Ohne ZusammenfassungBeiträge: I. Fedde Repert.26, 177 (1929); II. 1. c.27, 385–391 (1930); III. 1. c.29, 246–248 (1931); IV. 1. c.33, 353–363 (1934); V. 1. c.38, 49–55 (1935); VI. 1. e.39, 169–173 (1936); VII. 1. c.40, 294–301 (1936); VIII. 1. c.49, 1–4 (1940); IX. Candollea11, 229–241 (1948); X. Österr. Bot. Zeitschr.99, 523–527 (1952); XI. 1. c.100, 669–670 (1953); XII. Leaflets of Western Botany7, 133–152 (1954).     

Use of the Cadzow procedure in 2D NMR for the reduction of t1 noise

Summary A data processing approach is proposed for reducing the t₁ noise observed in multidimensional NMR spectra. This method is based on the use of the Cadzow procedure [Cadzow, J.A. (1988) IEEE Trans. Acous. Speech Signal Proc., 36, 49–62], and is demonstrated to be efficient for simulated cases as well as real experiments.