An ensemble method for multi-type Gram-negative bacterial secreted protein prediction by integrating different PSSM-based features

In Gram-negative bacteria, a wide range of proteins are secreted by highly specialized secretion systems. These secreted proteins play essential roles in the response of bacteria to their environment and also in several physiological processes such as adhesion, pathogenicity, adaptation and survival. Therefore, identifying secreted proteins in Gram-negative bacteria may assist in understanding the secretion mechanism and development of new antimicrobial strategies. Considering that a single-feature model is less likely to comprehensively cover this information, three kinds of feature models were used in this paper to represent protein samples by composition analysis, correlation analysis and smoothing encoding method on position-specific scoring matrix profiles. A support vector machine-based ensemble method with these hybrid features was developed to predict multi-type Gram-negative bacterial secreted proteins. Finally, our method achieves overall accuracies of 97.09% and 96.51% using an independent dataset test and jackknife test on a public test dataset, which are 3.49% and 2.32% higher, respectively, than results obtained by other methods. These results show the effectiveness and stability of the proposed ensemble method. It is anticipated that our method will provide useful information for further research on bacterial secreted proteins and secreted systems.     

A trans-ortho asymmetrically di-strapped metalloporphyrin integrating three key structural features of ligand in heme

Heme responsible for the dioxygen fixation, transport and conversion is a metalloporphyrin complex highly dependent on its diverse geometry of ligand. In this work, a trans-ortho-di-strapped zinc porphyrin with dome-like deformation was synthesized by thermodynamically controlling the formation of trans-precursor of porphyrinogen. Its single-crystal structure demonstrated that the asymmetric treatment of porphyrin achieves three goals of creating two secondary coordination sphere (SCS) bulks, maintaining a unique dome deformation, and making atomic out-of-plane deviation. In this way, this metallic complex integrates at least three key features of the pocket structure, the differentiated axial ligations, and the ring distortion, making it an ideal heme analog.     

Prediction of 2-hydroxyisobutyrylation sites by integrating multiple sequence features with ensemble support vector machine

Lysine 2-hydroxyisobutyrylation (K_hib) is a new type of histone mark, which has been found to affect the association between histone and DNA. To better understand the molecular mechanism of K_hib, it is important to identify 2-hydroxyisobutyrylated substrates and their corresponding K_hib sites accurately. In this study, a novel bioinformatics tool named KhibPred is proposed to predict K_hib sites in human HeLa cells. Three kinds of effective features, the composition of k-spaced amino acid pairs, binary encoding and amino acid factors, are incorporated to encode K_hib sites. Moreover, an ensemble support vector machine is employed to overcome the imbalanced problem in the prediction. As illustrated by 10-fold cross-validation, the performance of KhibPred achieves a satisfactory performance with an area under receiver operating characteristic curve of 0.7937. Therefore, KhibPred can be a useful tool for predicting protein K_hib sites. Feature analysis shows that the polarity factor features play significant roles in the prediction of K_hib sites. The conclusions derived from this study might provide useful insights for in-depth investigation into the molecular mechanisms of K_hib.     

A novel protein refolding method integrating ion exchange chromatography with artificial molecular chaperone

Artificial molecular chaperone （AMC） and ion exchange chromatography （IEC） were integrated, thus a new refolding method, artificial molecular chaperone-ion exchange chromatography （AMC-IEC） was developed. Compared with AMC and IEC, the activity recovery of lysozyme obtained by AMC-IEC was much higher in the investigated range of initial protein concentrations, and the results show that AMC-IEC is very efficient for protein refolding at high concentrations. When the initial concentration of lysozyme is 180 mg/mL, its activity recovery obtained by AMC-IEC is still as high as 76.6%, while the activity recoveries obtained by AMC and IEC are 45.6% and 42.4%, respectively.     

SiteBinder: an improved approach for comparing multiple protein structural motifs

There is a paramount need to develop new techniques and tools that will extract as much information as possible from the ever growing repository of protein 3D structures. We report here on the development of a software tool for the multiple superimposition of large sets of protein structural motifs. Our superimposition methodology performs a systematic search for the atom pairing that provides the best fit. During this search, the RMSD values for all chemically relevant pairings are calculated by quaternion algebra. The number of evaluated pairings is markedly decreased by using PDB annotations for atoms. This approach guarantees that the best fit will be found and can be applied even when sequence similarity is low or does not exist at all. We have implemented this methodology in the Web application SiteBinder, which is able to process up to thousands of protein structural motifs in a very short time, and which provides an intuitive and user-friendly interface. Our benchmarking analysis has shown the robustness, efficiency, and versatility of our methodology and its implementation by the successful superimposition of 1000 experimentally determined structures for each of 32 eukaryotic linear motifs. We also demonstrate the applicability of SiteBinder using three case studies. We first compared the structures of 61 PA-IIL sugar binding sites containing nine different sugars, and we found that the sugar binding sites of PA-IIL and its mutants have a conserved structure despite their binding different sugars. We then superimposed over 300 zinc finger central motifs and revealed that the molecular structure in the vicinity of the Zn atom is highly conserved. Finally, we superimposed 12 BH3 domains from pro-apoptotic proteins. Our findings come to support the hypothesis that there is a structural basis for the functional segregation of BH3-only proteins into activators and enablers.     

Improving protein structural class prediction using novel combined sequence information and predicted secondary structural features

Protein structural class prediction solely from protein sequences is a challenging problem in bioinformatics. Numerous efficient methods have been proposed for protein structural class prediction, but challenges remain. Using novel combined sequence information coupled with predicted secondary structural features (PSSF), we proposed a novel scheme to improve prediction of protein structural classes. Given an amino acid sequence, we first transformed it into a reduced amino acid sequence and calculated its word frequencies and word position features to combine novel sequence information. Then we added the PSSF to the combine sequence information to predict protein structural classes. The proposed method was tested on four benchmark datasets in low homology and achieved the overall prediction accuracies of 83.1%, 87.0%, 94.5%, and 85.2%, respectively. The comparison with existing methods demonstrates that the overall improvements range from 2.3% to 27.5%, which indicates that the proposed method is more efficient, especially for low-homology amino acid sequences.     

Correlations between designability and various structural characteristics of protein lattice models

Using six kinds of lattice types (4 x 4, 5 x 5, and 6 x 6 square lattices; 3 x 3 x 3 cubic lattice; and 2+3+4+3+2 and 4+5+6+5+4 triangular lattices), three different size alphabets (HP, HNUP, and 20 letters), and two energy functions, the designability of protein structures is calculated based on random samplings of structures and common biased sampling (CBS) of protein sequence space. Then three quantities stability (average energy gap), foldability, and partnum of the structure, which are defined to elucidate the designability, are calculated. The authors find that whatever the type of lattice, alphabet size, and energy function used, there will be an emergence of highly designable (preferred) structure. For all cases considered, the local interactions reduce degeneracy and make the designability higher. The designability is sensitive to the lattice type, alphabet size, energy function, and sampling method of the sequence space. Compared with the random sampling method, both the CBS and the Metropolis Monte Carlo sampling methods make the designability higher. The correlation coefficients between the designability, stability, and foldability are mostly larger than 0.5, which demonstrate that they have strong correlation relationship. But the correlation relationship between the designability and the partnum is not so strong because the partnum is independent of the energy. The results are useful in practical use of the designability principle, such as to predict the protein tertiary structure.     

Sums of ranking differences and inversion numbers for method discrimination

Héberger and colleagues [Trends Anal Chem 2010;29:101–109; J Chemometrics 2011;25:151–158] have introduced the sum of ranking differences as a measure for comparing models or methods and have demonstrated its applicability in a variety of settings. The sum of ranking differences is closely related to another distance measure for permutations, namely, the inversion number. In this note, we describe the inversion number along with some of its distributional properties and draw comparisons with the sum of ranking differences for model comparison. Copyright © 2013 John Wiley & Sons, Ltd.     

A method for the structural determination of cannabichromene metabolites by mass spectrometry

Ready identification of hydroxy metabolites of cannabichromene (CBC) by mass spectrometry of their trimethylsilyl derivatives is prevented by the dominant fragmentation to give a substituted chromenyl ion; this suppresses ions diagnostic of the position of metabolic hydroxylation. To overcome this difficulty, metabolites were hydrogenated over a rhodium/alumina catalyst to reduce the double bond responsible for chromenyl ion formation and to redirect the fragmentation to the site of metabolic attack. This resulted in the production of abundant diagnostic fragment ions enabling all monohydroxy-CBCs to be readily identified.     

A CIEF‐LIF method for simultaneous analysis of multiple protein kinases and screening of inhibitors

Here, a CIEF‐LIF method for multiple protein kinase simultaneous analysis and inhibitors throughput screening with fast rate and low cost is presented. Comparing with CZE, CIEF‐LIF exhibited great focusing ability and high separation efficiency for substrate and phosphorylated peptides, and is applicable for multiple kinases simultaneous analysis regardless of their substrate peptides compositions and charge statuses. Thus, highly sensitive analysis for cyclic adenosine 3’, 5’‐monophosphate‐dependent protein kinase (PKA) and cyclin‐dependent kinase 1 (CDK1) was achieved in CIEF‐LIF analysis with detection sensitivity up to 1.25 mU/μL and 0.4 mU/μL, respectively, two magnitudes higher than that of CZE and comparable with that in nanomaterials or green fluorescent protein‐based kinase assay. Moreover, the inhibition effect of inhibitors on multiple kinases could be simultaneously readout in a single electrophoretic run, with half maximal inhibitory concentration of H‐89 for PKA and Ro‐3306 for CDK1 calculated as 37.0 and 35.9 nM, respectively, consistent with literatures reported. The CIEF‐LIF also exhibited strong anti‐interference ability in human breast cancer cell lysates analysis and simulators such as forskolin and 3‐isobutyl‐1‐methylxantine assessment. Therefore, CIEF‐LIF is desirable for future biological application and clinical diagnostics and drug discovery.     

A facile and efficient method for the incorporation of multiple unnatural amino acids into a single protein

One stone, two birds: Here, we have developed a simple and efficient method for the incorporation of multiple unnatural amino acids in a single protein. This single protein exhibited two different novel functionalities acquired from the genetically incorporated unnatural amino acids, which is an interesting and not an inherent property of the protein.     

A more general method for ranking the enrichment of alloying elements in passivation films

The corrosion of alloys is often characterized by an enrichment of one or other of the alloying elements within the surface oxide or even within the underlying metallic phase. For some three decades the measurement of such surface enrichment has been one of the most important contributions made by XPS to corrosion science. X‐ray photoelectron spectroscopy permits the composition of the oxide film to be distinguished from that of the metallic surface underlying the oxide so that both can be determined independently. In the mid‐1970s these measurements were crucial in showing that the selective enrichment of chromium in the electrochemical passivation of stainless steel occurred by selective dissolution of iron, and not by selective oxidation of chromium. Measurements of this type are important also in active corrosion, where there is no stable oxide film, as in studies of dealloying phenomena. The literature now contains numerous cases, many published by one of us (K.A.) based on studies of novel alloys produced in the Institute for Materials Research at Sendai. Typically, measurements are made for a series of binary compositions A_xB_y ranging from A‐rich to B‐rich alloys, in media that reflect the intended use of the alloy. The results are normally produced in the form of plots of cation composition Aⁿ⁺/(Aⁿ⁺ + B^m+) against bulk composition A/(A + B) or, in the case of dealloying, as A_surface/(A_surface + B_surface) against the bulk composition. Although graphical representation is useful in giving the full picture of the alloy's behaviour, it is not so useful in cataloguing or indexing performance. In this paper we suggest a means to give a rank or performance index as a single number that will characterize the behaviour of the alloy over a wide range of composition for a given medium or exposure condition. The rank number does not imply that any particular mechanism of enrichment is in operation; in various cases of corrosion it might occur by selective precipitation (FeOOH on steels, CuO on cupronickels), by selective dissolution (dezincification of brass) or by preferential incorporation of ions in a passivating oxide or oxyhydroxide (Cr³⁺ on stainless steels). Although the rank has no mechanistic implications, it is useful within a known class of mechanistic behaviour for indicating the magnitude of the effect and thus for enabling an XPS measurement to be indicative of wanted, or unwanted, behaviour. For example, the rank number could be useful in indicating, perhaps from a single alloy composition, whether a degree of passivation is likely to be achieved for that mix of metallic elements. Copyright © 2004 John Wiley & Sons, Ltd.     

ProSTRIP: A method to find similar structural repeats in three-dimensional protein structures

The occurrence of similar structural repeats in a protein structure has evolved through gene duplication. These repeats act as a structural building block and form more than one compact structural and functional unit called a repeat domain. The protein families comprising similar structural repeats are mainly involved in protein–protein interactions as well as binding to other ligand molecules. The identification of internal sequence repeats in the primary structure is not sufficient for the analysis of structural repeats. Thus, a new method called ProSTRIP has been developed using dynamic programming to find the similar structural repeats in a three-dimensional protein structure. The detection of these repeats is made by calculating the protein backbone Cα angles. An internet computing server is also created by implementing this method and enables graphical visualization of the results. It can be freely accessed at http://cluster.physics.iisc.ernet.in/prostrip/.     

AquaBridge: A novel method for systematic search of structural water molecules within the protein active sites

We have developed a novel method for calculation of the water bridges that can be formed in the active sites of proteins in the absence or in the presence of small‐molecule ligands. We tested its efficiency on a representative set of human ATP‐binding proteins, and show that the docking accuracy of ligands can be substantially improved when water bridges are included in the modeling of protein–ligand interactions. Our analysis of binding pocket hydration can be a useful addition to the in silico approaches of Drug Design. © 2015 Wiley Periodicals, Inc.     

A novel feature representation method based on Chou's pseudo amino acid composition for protein structural class prediction

During last few decades accurate determination of protein structural class using a fast and suitable computational method has been a challenging problem in protein science. In this context a meaningful representation of a protein sample plays a key role in achieving higher prediction accuracy. In this paper based on the concept of Chou's pseudo amino acid composition (Chou, K.C., 2001. Proteins 43, 246-255), a new feature representation method is introduced which is composed of the amino acid composition information, the amphiphilic correlation factors and the spectral characteristics of the protein. Thus the sample of a protein is represented by a set of discrete components which incorporate both the sequence order and the length effect. On the basis of such a statistical framework a simple radial basis function network based classifier is introduced to predict protein structural class. A set of exhaustive simulation studies demonstrates high success rate of classification using the self-consistency and jackknife test on the benchmark datasets.     

Synthesis, electrical properties, and structural features of copper-containing chalcogenide films produced by the chemical deposition method

Multicomponent copper-containing CuI-AsI₃-As₂Se₃ and CuI-Sb₃I-As₂Se₃ chalcogenide films were produced by chemical deposition from solutions of chalcogenide glasses in n-butylamine and their electrical conductivity was studied. It was shown that the electrical properties of chalcogenide glasses and films based on these glasses have the same values within experimental error. It was found sing Mossbauer spectroscopy that antimony atoms are in the Sb(III) state in the environment of three selenium atoms, and copper ions in the Cu(I) state and are surrounded by iodine atoms. The chalcogenide films can be used to fabricate ion-selective electrodes sensitive to copper cations.