Improved alignment of weakly homologous protein sequences using structural information

Protein sequence alignments can be unproved when at least oneof the proteins to be aligned has a known 3-D structure. Inthis work, geometrical constraints extracted from the targetfold are evaluated in independent units that deal with complementarystructural features. This information is used to set up mutationtables specific to the locally observed structural environments.The resulting partial evaluations are then combined linearlyinto a global function which is optimized by dynamic programming.Eventually, a score based on tertiary interactions can be usedas a selection criterion to discriminate among a set of suboptimalalignments. The relevance of the scores given by each unit istested on a representative set of protein families. Finally,a method for combining the different scores is described andits efficiency is evaluated on a few pairs of weakly homologousproteins.     

Structure-derived substitution matrices for alignment of distantly related sequences

Sequence alignment is a standard method to infer evolutionary,structural, and functional relationships among sequences. Thequality of alignments depends on the substitution matrix used.Here we derive matrices based on superimpositions from proteinpairs of similar structure, but of low or no sequence similarity.In a performance test the matrices are compared with 12 otherpreviously published matrices. It is found that the structure-derivedmatrices are applicable for comparisons of distantly relatedsequences. We investigate the influence of evolutionary relationshipsof protein pairs on the alignment accuracy.     

Sequence alignment of citrate synthase proteins using a multiple sequence alignment algorithm and multiple scoring matrices

The alignment of Escherichia coli citrate synthase to pig heartcitrate synthase and the multiple alignment of the known sequencesof the citrate synthase family of enzymes have been performedusing six different amino acid similarity scoring matrices anda large range of gap penalty ratios for insertions and deletionsof amino acids. The alignment studies have been performed asthe first step in a project aimed at homology modelling E.colicitrate synthase (a hexamer) from pig heart citrate synthase(a dimer) in a molecular modelling approach to the study ofmulti-subunit enzymes. The effects of several important variablesin producing realistic alignments have been investigated. Thedifference between multiple alignment of the family of enzymesversus simple pairwise alignment of the pig heart and E.coliproteins was explored. The effects of initial separate multiplealignments of the most highly related or most homologous speciesof the family of enzymes upon a subsequent pairwise alignmentbetween species was evaluated. The value of ‘fingerprinting’certain residues to bias the alignment in favour of matchingthose residues, as well as the worth of the computerized approachcompared to an intuitive alignment technique, were assessed.     

Applicability domains and accuracy of prediction of soft sensor models

Soft sensors are used to estimate process variables that are difficult to measure online. However, the predictive accuracy gradually decreases with changes in the state of chemical plants. Regression models can be updated, but if the model is updated with abnormal data, the predictive ability deteriorates. In practice, when the prediction error of an objective variable exceeds a threshold, an abnormal situation is detected. However, no effective method exists to decide this threshold. We have proposed a method to estimate the relationships between applicability domains and the accuracy of prediction of soft sensor models quantitatively. The larger the distances to models (DMs), the lower the estimated accuracy of prediction. Hence, the model between DMs and accuracy can separate variations in process variables and y‐analyzer fault. This method was applied to real industrial data. The fault detection ability of the proposed method was better than that of the traditional one. © 2010 American Institute of Chemical Engineers AIChE J, 2011     

Correlation of solubility data: IV. Prediction of solubilities of homologous and analogous long chain compounds in related solvents

A new method of correlation and prediction of solubility data for long chain compounds is described. It is based on the linear relationship between 1/T_a and 1/T_r derived from the freezing point depression equation. T_a and T_r represent temperatures in degrees Kelvin at which the mole % solubility of a compound, a, in a given solvent is the same as that of an analogous reference compound, r, in a related solvent. The validity of the method has been confirmed by applying it to the extensive literature data on the solubilities of saturated and unsaturated fatty acids. Four families of related solvents were examined: (a) benzene, hexane, cyclohexane, chlorobenzene,o-xylene and toluene; (b) acetone, butanone, ethyl acetate and butyl acetate; (c) isopropanol, 95% ethanol, butanol,p-dioxane and diethyl ether; and (d) carbon tetrachloride and 1,2-chloroethane. Complete solubility data for a compound can be predicted from the linear 1/T_a vs. 1/T_r plot based on the melting point and one experimental solubility determination. ARS, USDA.     

Online prediction of subcutaneous glucose concentration for type 1 diabetes using empirical models and frequency‐band separation

Online glucose prediction which can be used to provide important information of future glucose status is a key step to facilitate proactive management before glucose reaches undesirable concentrations. Based on frequency‐band separation (FS) and empirical modeling approaches, this article considers several important aspects of on‐line glucose prediction for subjects with type 1 diabetes mellitus. Three issues are of particular interest: (1) Can a global (or universal) model be developed from glucose data for a single subject and then used to make suitably accurate on‐line glucose predictions for other subjects? (2) Does a new FS approach based on data filtering provide more accurate models than standard modeling methods? (3) Does a new latent variable modeling method result in more accurate models than standard modeling methods? These and related issues are investigated by developing autoregressive models and autoregressive models with exogenous inputs based on clinical data for two groups of subjects. The alternative modeling approaches are evaluated with respect to on‐line short‐term prediction accuracy for prediction horizons of 30 and 60 min, using independent test data. © 2013 American Institute of Chemical Engineers AIChE J 60: 574–584, 2014     

Evaluation and improvements in the automatic alignment of protein sequences

The accuracy of protein sequence alignment obtained by applyinga commonly used global sequence comparison algorithm is assessed.Alignments based on the superposition of the three-dimensionalstructures are used as a standard for testing the automatic,sequence-based methods. Alignments obtained from the globalcomparison of five pairs of homologous protein sequences studiedgave 54% agreement overall for residues in secondary structures.The inclusion of information about the secondary structure ofone of the proteins in order to limit the number of gaps insertedin regions of secondary structure, improved this figure to 68%.A similarity score of greater than six standard deviation unitssuggests that an alignment which is greater than 75% correctwithin secondary structural regions can be obtained automaticallyfor the pair of sequences.     

SyGMa: combining expert knowledge and empirical scoring in the prediction of metabolites

Predictions of potential metabolites based on chemical structure are becoming increasingly important in drug discovery to guide medicinal chemistry efforts that address metabolic issues and to support experimental metabolite screening and identification. Herein we present a novel rule-based method, SyGMa (Systematic Generation of potential Metabolites), to predict the potential metabolites of a given parent structure. A set of reaction rules covering a broad range of phase 1 and phase 2 metabolism has been derived from metabolic reactions reported in the Metabolite Database to occur in humans. An empirical probability score is assigned to each rule representing the fraction of correctly predicted metabolites in the training database. This score is used to refine the rules and to rank predicted metabolites. The current rule set of SyGMa covers approximately 70 % of biotransformation reactions observed in humans. Evaluation of the rule-based predictions demonstrated a significant enrichment of true metabolites in the top of the ranking list: while in total, 68 % of all observed metabolites in an independent test set were reproduced by SyGMa, a large part, 30 % of the observed metabolites, were identified among the top three predictions. From a subset of cytochrome P450 specific metabolites, 84 % were reproduced overall, with 66 % in the top three predicted phase 1 metabolites. A similarity analysis of the reactions present in the database was performed to obtain an overview of the metabolic reactions predicted by SyGMa and to support ongoing efforts to extend the rules. Specific examples demonstrate the use of SyGMa in experimental metabolite identification and the application of SyGMa to suggest chemical modifications that improve the metabolic stability of compounds.     

Correlation of solubility data: III. The isopleth reference method for predicting solubility data for long chain homologous and analogous compounds

A new graphical method for correlating and predicting solubility data for homologous and analogous compounds is described. It complements the isotherm and isopleth methods which are applicable only to long chain homologous compounds. This method is based upon the linear relationship, derived from the approximate freezing point depression equation in which T and T′ are the primary freezing points of two analogous compounds at the same molar concentration in a given solvent. The basic assumption that ΔH′_f/ΔH_f remains essentially constant for homologous and analogous compounds in the same solvent over wide ranges of temperature was validated by construction of isopleth reference plots using both published and new experimental solubility data for a number of long chain fatty acids and fatty acid derivatives in a variety of solvents. Complete solubility data are reported for behenic, stearic, palmitic, heptadecanoic, brassidic, erucic, petroselaidic and petroselinic acid in acetone, methanol, toluene and isopropyl ether. Complete solubility data are also included for elaidic acid in acetone, toluene and isopropyl ether and oleic acid in isopropyl ether. Presented at the AOCS Meeting, San Francisco, April 1969. So. Utiliz. Res. Dev. Div., ARS, USDA.     

The prediction of adhesion between polymer matrices and silane-treated glass surfaces in filled composites

Extending the database and the analysis of work reported earlier, the practical adhesion between a glass filler, modified by various silane coupling agents, and different polymeric matrices is measured and compared with predictions based on a generalized thermodynamic criterion. The criterion used is the magnitude of the (negative) molar Gibbs free energy of mixing, (-ΔGmix)_0.5, for a pseudo-solution consisting of equal molar amounts of the repeat units of the polymer matrix and the organo-functional group of the silane coupling agent. It is computed using the group contribution method of UNIFAC, in which molar volumes, molar areas, and molar interaction energies are constructed from contributions of the functional groups which make up the molecules of the solution. Measurements leading to the values of the adhesion strength are carried out using the singleparticle composite method, in which a rectangular polymer specimen containing a single silane-treated glass bead is subjected to increasing uni-axial tensile stress until interfacial failure, as observed using a microscope, occurs at one of the poles of the sphere. Earlier work reported a good correlation between the local stress at the pole computed from such measurements and the value of (-ΔG _mix)_0.5 computed using UNIFAC for ten different organo-silane-modified spheres imbedded in a poly(vinyl butyral) matrix. The present work extends the database to two additional matrices, viz. poly(methyl methacrylate) and poly(ethyl methacrylate). In addition, elastic fracture-mechanics theory is used to deduce specific adhesion energies in all cases. The relative values of the latter are all found to be in good correlation with the predictive thermodynamic criterion.     

Feature-based prediction of non-classical and leaderless protein secretion

We present a sequence-based method, SecretomeP, for the prediction of mammalian secretory proteins targeted to the non-classical secretory pathway, i.e. proteins without an N-terminal signal peptide. So far only a limited number of proteins have been shown experimentally to enter the non-classical secretory pathway. These are mainly fibroblast growth factors, interleukins and galectins found in the extracellular matrix. We have discovered that certain pathway-independent features are shared among secreted proteins. The method presented here is also capable of predicting (signal peptide-containing) secretory proteins where only the mature part of the protein has been annotated or cases where the signal peptide remains uncleaved. By scanning the entire human proteome we identified new proteins potentially undergoing non-classical secretion. Predictions can be made at http://www.cbs.dtu.dk/services/SecretomeP.     

Analysis of amino acid indices and mutation matrices for sequence comparison and structure prediction of proteins

An amino acid index is a set of 20 numerical values representingany of the different physicochemical and biochemical propertiesof amino adds. As a follow-up to the previous study, we haveincreased the size of the database, which currently contains402 published indices, and re-performed the single-linkage clusteranalysis. The results basically confirmed the previous findings.Another important feature of amino acids that can be representednumerically is the similarity between them. Thus, a similaritymatrix, also called a mutation matrix, is a set of 20x20 numericalvalues used for protein sequence alignments and similarity searches.We have collected 42 published matrices, performed hierarchicalcluster analyses and identified several clusters correspondingto the nature of the data set and the method used for constructingthe mutation matrix. Further, we have tried to reproduce eachmutation matrix by the combination of amino acid indices inorder to understand which properties of amino acids are reflectedmost. There was a relationship between the PAM units of Dayhoff'smutation matrix and the volume and hydrophobicity of amino adds.The database of 402 amino acid indices and 42 amino acid mutationmatrices is made publicly available on the Internet.     

Heats of mixing for homologous series of ketones and their prediction from group interaction theory and the congruence principle

Heats of mixing for 12 binary systems of ketones at several temperatures are reported. Application of an extension of the congruence principle and the group interaction theory is studied, for these data. A graphical procedure for prediction of heats of mixing data is proposed     

Effect of crystallographic orientation on transparency of alumina prepared using magnetic alignment and SPS

Transparent polycrystalline alumina was developed over many years because its attractive properties are expected to find applications in many fields. Crystallographic orientation is one of the effective ways to improve transparency in birefringent ceramics such as alumina, because birefringence at grain boundaries can be suppressed by the alignment of optical axis. Fabrication of high-transparency alumina with an oriented c-axis and fine microstructure can be attained by slip casting in a strong magnetic field, followed by spark plasma sintering at 1150?°C for 20?min. The real in-line transmittance of the textured alumina with a thickness of 0.80?mm was 70% at λ?=?640?nm, which was higher than that of randomly-oriented alumina. The c-axis orientation reduced the actual difference of the refractive index and suppressed remarkably the birefringence.     

Theoretical prediction of tie-chain concentration and its characterization using postyield response

In the past, relative tie-chain concentration has been semiquantitatively characterized by infrared dichroism on a stretched sample and from brittle fracture strenght. The probability of tie-molecule formation has also been theoretically estimated from chain dimensions and the semicrystalline morphology of the polymers. In this article the probability of tie-chain formation of monodisperse and homogeneous single-site ethylene copolymers has been estimated over a range of densities and molecular weights using the model proposed by Huang and Brown. The relative tie-chain concentration is obtained by multiplying tie-chain probability with the volume fraction crystallinity of polymer. A modified rubber elasticity theory is applied to calculate the concentration of chain links between junction points (crystallites) of the INSITE technology polymers (ITPs) from measured rubber modulus. It is expected that the chain-link concentration should relate to the tie-chain concentration. The calculated rubber modulus, or the chain-links concentration, of the ITPs increases with an increase in density in the 0.865 to 0.910 g/cc range and did not change significantly in the density range of about 0.91 g/cc to 0.954 g/cc. Normalized rubber modulus and relative tie-chain concentration data shows that the relative tie-chain concentration predicated by Huang and Brown model and measured using the modified rubber elasticity theory are quantitatively similar below 0.01 g/cc density. However, above 0.91 g/cc density, the measured rubber modulus is influenced by additional tie-chain formation during deformation due to breakdown of crystallities and, hence, the discrepancy exists between the two methods of estimating relative tie-chain concentration. © 1996 John Wiley & Sons, Inc.     

Recognition of hormones by membrane potential and circular dichroism of immobilized protein membranes

The shifts in membrane potential, caused by the injection of hormones into a permeation cell, were measured using immobilized (entrapped) serum albumin and γ-globulin membranes. The effective fixed charge density was estimated to increase after the injection of estradiol and testosterone in both albumin and γ-globulin membranes, while the charge density was estimated to decrease after the injection of progesterone in the γ-globulin membranes. Because the change in the charge density originates from the conformational change of proteins in the membranes, the change in the circular dichroism induced by the hormones was measured in the membranes. The α-helix content in both albumin and γ-globulin membranes was found from the circular dichroism measurements to increase when estradiol and testosterone was bound to the proteins, while the α-helix content in the albumin membrane decreased on the binding of progesterone. Some discrepancy was found between the conformational change of the proteins in the membranes detected by the membrane potential measurements and the circular dichroism measurements. This is explained by the fact that the circular dichroism measurements do not directly contribute to the change in the charge density induced by the binding of hormones to proteins in the membranes. © 1997 John Wiley & Sons, Inc. J Appl Polym Sci 65:251–259, 1997     

Analysis of RNA phage fr coat protein assembly by insertion, deletion and substitution mutagenesis

A structure-function analysis of the icosahedral RNA bacteriophagefr coat protein (CP) assembly was undertaken using linker-insertion,deletion and substitution mutagenesis. Mutations were specificallyintroduced into either pre-existing or artificially createdrestriction enzyme sites within fr CP gene expressed in Escherichiacoli from a recombinant plasmid. This directs synthesis of wildtype protein that undergoes self-assembly and forms capsid-likeparticles indistinguishable morphologically and immunologicallyfrom native phage particles. A series of fr CP variants containingsequence alterations in the regions which are (i) exposed onthe external surface of capsid or (ii) located on the contactingareas between CP subunits were obtained and their assembly propertiesinvestigated. The majority of mutants demonstrated reductionof assembly ability and formed either CP dimers (mutations atresidues 2, 10, 63 or 129) or both dimer and capsid structures(residue 2 or 69). The exceptions were variants demonstratingnormal assembly and containing insertions at residues 2, 50or 129 of thefr CP. A third type of assembled structure wasformed by a variant with a single amino acid substitution I104T.The aA-helix region (residues 97-111) is particularly sensitiveto mutation and any alteration in this region decreases accumulationof mutant protein in E.coli. The relative contributions of particularfr CP domains in maintenance of capsid structural integrityas well as the possible capsid assembly mechanism are discussed.