Conformational analysis of nucleic acids revisited: Curves+

We describe Curves+, a new nucleic acid conformational analysis program which is applicable to a wide range of nucleic acid structures, including those with up to four strands and with either canonical or modified bases and backbones. The program is algorithmically simpler and computationally much faster than the earlier Curves approach, although it still provides both helical and backbone parameters, including a curvilinear axis and parameters relating the position of the bases to this axis. It additionally provides a full analysis of groove widths and depths. Curves+ can also be used to analyse molecular dynamics trajectories. With the help of the accompanying program Canal, it is possible to produce a variety of graphical output including parameter variations along a given structure and time series or histograms of parameter variations during dynamics.     

Simplifying amino acid alphabets by means of a branch and bound algorithm and substitution matrices

MOTIVATION: Protein and DNA are generally represented by sequences of letters. In a number of circumstances simplified alphabets (where one or more letters would be represented by the same symbol) have proved their potential utility in several fields of bioinformatics including searching for patterns occurring at an unexpected rate, studying protein folding and finding consensus sequences in multiple alignments. The main issue addressed in this paper is the possibility of finding a general approach that would allow an exhaustive analysis of all the possible simplified alphabets, using substitution matrices like PAM and BLOSUM as a measure for scoring. RESULTS: The computational approach presented in this paper has led to a computer program called AlphaSimp (Alphabet Simplifier) that can perform an exhaustive analysis of the possible simplified amino acid alphabets, using a branch and bound algorithm together with standard or user-defined substitution matrices. The program returns a ranked list of the highest-scoring simplified alphabets. When the extent of the simplification is limited and the simplified alphabets are maintained above ten symbols the program is able to complete the analysis in minutes or even seconds on a personal computer. However, the performance becomes worse, taking up to several hours, for highly simplified alphabets. AVAILABILITY: AlphaSimp and other accessory programs are available at http://bioinformatics.cribi.unipd.it/alphasimp     

A simple electrostatic criterion for predicting the thermal stability of proteins

The enhancement of protein thermostability is an important issue for both basic science and biotechnology purposes. We have developed a thermostability criterion for a protein in terms of a quasi-electric dipole moment (contributed by its charged residues) defined for an electric charge distribution whose total charge is not zero. It was found that minimization of the modulus of this dipole moment increased its thermal stability, as demonstrated by surveying these values in pairs of mesostable-thermostable homologous proteins and in mutations described in the literature. The analysis of these observations provides criteria for thermostabilization of a protein, by computing its dipole profile. This profile is obtained by direct substitution of each amino acid of the sequence by either a positive, negative or neutral amino acid, followed by a recalculation of the dipole moment. As an experimental example, these criteria were applied to a beta-glucanase to enhance its thermal stability.     

Kinetics of tryptic hydrolysis as a probe of the structure of human plasma apolipoprotein A-II

As a model system to understand apolipoprotein structure-function and their relationships to proteolytic events, the kinetics of tryptic hydrolysis of apolipoprotein A-II (apo A-II) was investigated in solution and in association with phospholipid. The rates of appearance and identities of specific peptides were determined by reversed-phase high-performance liquid chromatography and amino acid analysis, respectively. For the kinetics of hydrolysis of apo A-II in solution, the carboxyl-terminal peptides of residues 55-77 and 56-77 appeared first, followed by peptides of residues 4-23, 29-39, 40-44 and 45-54, which appeared at nearly identical rates. The kinetics of hydrolysis of apo A-II associated with 1,2-dimyristoyl-sn-glycero-3-phosphocholine showed several differences. First, a 100-fold larger amount of trypsin was needed to obtain a similar rate of product formation; second, a new peptide appeared, eluting earlier than apo A-II but having a similar amino acid composition; and third, the relative rates of appearance of peptides were different. The secondary structure surrounding the bonds susceptible to trypsin cleavage was determined by several predictive algorithms. The lysine amino acid bonds were found to be in regions defined by a high helical amphipathic moment. The reduced susceptibility to tryptic hydrolysis of apo-II associated with phospholipid appears to be due to a higher free energy of stabilization of protein secondary structure. As a consequence, the lysine amino acid bonds are in folded regions of the protein where they are conformationally inaccessible to enzymatic hydrolysis. By use of structure-prediction methods, it is possible to designate which regions of apolipoproteins may be important in proteolysis.     

Comparative approach to correction of annotated gene starts in complete bacterial genomes

A method for refining the beginnings of genes and a search for shifts of the reading frame is proposed. The method is based on a comparison of nucleotide and amino acid sequences of homologous genes of related organisms. The algorithm is based on the fact that the rate of changes in the protein-coding regions of the genome is substantially lower than that of noncoding regions. A modification of the Smith-Waterman algorithm is proposed, which makes it possible to align the amino acid sequences obtained by formal translation of the starting nucleotide sequences by taking into account a possible shift of the reading frame. The algorithm has been implemented in the package of ORTOLOGATOR-GeneCorrector programs. Testing the program showed that the approach enables one to detect a wrong annotation of the beginnings in 1% of genes (even in well-studied organisms such as Escherichia coli) and identify several (approximately 10) shifts of the open reading frame. Thus, the algorithm can be used at both the initial and final stages of analysis of the genome.     

Generation and evaluation of dimension-reduced amino acid parameter representations by artificial neural networks

In order to process data of proteins, a numerical representation for an amino acid is often necessary. Many suitable parameters can be derived from experiments or statistical analysis of databases. To ensure a fast and efficient use of these sources of information, a reduction and extraction of relevant information out of these parameters is a basic need. In this approach established methods like principal component analysis (PCA) are supplemented by a method based on symmetric neural networks. Two different parameter representations of amino acids are reduced from five and seven dimensions, respectively, to one, two, three, or four dimensions by using a symmetric neural network approach alternatively with one or three hidden layers. It is possible to create general reduced parameter representations for amino acids. To demonstrate the ability of this approach, these reduced sets of parameters are applied for the ab initio prediction of protein secondary structure from primary structure only. Artificial neural networks are implemented and trained with a diverse representation of 430 proteins out of the PDB. An essentially faster training and also prediction without a decrease in accuracy is obtained for the reduced parameter representations in comparison with the complete set of parameters. The method is transferable to other amino acids or even other molecular building blocks, like nucleic acids, and therefore represents a general approach.Electronic Supplementary Material available.     

Peptide sequencing program

A computer program has been devised to automate rationalizationof peptide fragmentation patterns. The program systematicallygenerates all possible linear amino acid sequences which mightbe attributable to a peptide with a known amino acid composition.The generated sequences are then searched to find those thatmost closely match the spectrum of an unknown sequence. Received on March 10, 1986; accepted on March 24, 1986     

cDNA sequence and deduced amino acid sequence of the precursor of the 37-kDa inner envelope membrane polypeptide from spinach chloroplasts. Its transit peptide contains an amphiphilic alpha-helix as the only detectable structural element

We present the nucleotide sequence and the deduced amino acid sequence of a cDNA clone that encodes the entire precursor of the 37-kDa inner envelope membrane protein from spinach chloroplasts. The precursor protein consists of 344 amino acids (Mr 38,976). In vitro processing followed by radiosequence analysis of the in vitro transcribed and translated precursor protein revealed that its transit peptide consists of only 21 amino acid residues. The transit peptide has the potential to form an amphiphilic alpha-helix with a strong hydrophobic moment. It is speculated that this structural element represents an ancestral envelope-targeting domain. The in vitro synthesized precursor protein is directed to the chloroplasts and it is inserted into the envelope membrane in an ATP-dependent manner. The mature protein (323 amino acid residues, Mr 36,830) has a moderate hydrophobicity and contains only one membrane-spanning segment which is located at the C-terminus and possibly anchors the protein within the envelope membrane.     

The hydrophobic moment and its use in the classification of amphiphilic structures (review)

Amphiphilic alpha-helices play a major role in membrane dependent processes and are manifested in the primary structure of a protein by the periodic appearance of hydrophobic residues. Based on these periodic sequences, the hydrophobic moment was introduced, , which essentially treats the hydrophobicity of amino acid residues as a two-dimensional vector sum and provides a measure of amphiphilicity within regular repeat structures. To identify putative amphiphilic alpha-helix forming sequences, hydrophobic moment analysis assumes an amino acid residue periodicity of 100 and scans protein primary structures to find the 11-residue window with maximal . Taken with the window's mean hydrophobicity, , hydrophobic moment plot analysis uses the coordinate pair, [, ] to classify alpha-helices as either surface active, globular or transmembrane. More recently, this latter analysis has been extended to recognize candidate oblique orientated alpha-helices. Here, the hydrophobic moment is reviewed and data to query the logic of using a fixed window length and a fixed residue angular periodicity in hydrophobic moment analysis are provided. In addition, problems associated with the use of such analysis to predict alpha-helix structure/function relationships are considered.     

Reactivity-selectivity correlations: I. The reactivity of alkyl aryl sulfates towards papain and ficin

A series of alkyl aryl sulfates has been investigated as inhibitors of papain and ficin activity. The results show that the percentage of residual enzymatic activity depends on several factors, including the solvolytic reactivity of the alkylating agent. It is possible to correlate the reactivities of the sulfates with a selectivity parameter which is based on product ratio results. The resulting correlations indicate that the reactivity-selectivity principle is applicable to this system. It is shown, however, from the results of amino acid analyses that specific methylation of active-site cysteine or histidine residues is not effective with the enzymes in the native or denatured state. This phenomenon contrasts with reported work on methyl p-nitrobenzenesulfonate in which extensive methylation of papain in the denatured state was observed. The finding that the nonspecific methylation of the enzymes by the alkyl aryl sulfates leads to inhibition of enzymic activity is discussed in terms of conformational and other effects.     

Screening mutant mice for inborn errors of metabolism

We described our methods of screening mice for inborn errors of metabolism including metabolic storage diseases, disorders of amino acid metabolism, and organic acidemias. Our screening program consisted of histopathology, quantitative serum amino acid analysis, and urinary organic acid analysis. In this preliminary study, we tested mice representing 28 different mutations whose clinical signs suggested a possible metabolic disorder. We documented the normal values for mouse serum amino acids and urinary organic acids. No mutant tested had relevant or consistent biochemical abnormalities as determined by our screening tests. Some mutants showed histopathology as described previously. However, we were unable to confirm the histopathology described originally for the shambling mutant.     

A statistical view of FMRFamide neuropeptide diversity

FMRFamide-like peptide (FLP) amino acid sequences have been collected and statistically analyzed. FLP amino acid composition as a function of position in the peptide is graphically presented for several major phyla. Results of total amino acid composition and frequencies of pairs of FLP amino acids have been computed and compared with corresponding values from the entire GenBank protein sequence database. The data for pairwise distributions of amino acids should help in future structure-function studies of FLPs. To aid in future peptide discovery, a computer program and search protocol was developed to identify FLPs from the GenBank protein database without the use of keywords.     

On the primary structure of human plasminogen and plasmin. Purification and characterization of cyanogen-bromide fragments.

Most of the cyanogen bromide fragments obtained from human plasminogen and plasmin have been purified using combinations of gel filtration and ion-exchange chromatography. The purified fragments have been characterized by molecular weight determination (dodecyl sulphate electrophoresis), amino acid analysis, carbohydrate analysis and direct NH2-terminal amino acid sequence determination. Since some of the purified fragments were compounds with uncompletely cleaved methionyl bonds it was possible to clarify the organization of most of the cyanogen bromide fragments in the plasminogen molecule. The fragment containing the arginyl-valyl bond cleaved during the second step of the activation process is further identified. It is also shown that the microheterogeneity that normally exists in human plasminogen probably has its origin in several sites. One such site is situated in the light (B) chain of plasmin, while another is situated in the carboxyterminal part of the heavy (A) chain. Neither of these sites seems to contain sialic acid.     

Are proteins ideal mixtures of amino acids? Analysis of energy parameter sets

Various existing derivations of the effective potentials of mean force for the two-body interactions between amino acid side chains in proteins are reviewed and compared to each other. The differences between different parameter sets can be traced to the reference state used to define the zero of energy. Depending on the reference state, the transfer free energy or other pseudo-one-body contributions can be present to various extents in two-body parameter sets. It is, however, possible to compare various derivations directly by concentrating on the "excess" energy-a term that describes the difference between a real protein and an ideal solution of amino acids. Furthermore, the number of protein structures available for analysis allows one to check the consistency of the derivation and the errors by comparing parameters derived from various subsets of the whole database. It is shown that pair interaction preferences are very consistent throughout the database. Independently derived parameter sets have correlation coefficients on the order of 0.8, with the mean difference between equivalent entries of 0.1 kT. Also, the low-quality (low resolution, little or no refinement) structures show similar regularities. There are, however, large differences between interaction parameters derived on the basis of crystallographic structures and structures obtained by the NMR refinement. The origin of the latter difference is not yet understood.     

The influence of protein coding sequences on protein folding rates of all-β proteins

It is currently believed that the protein folding rate is related to the protein structures and its amino acid sequence. However, few studies have been done on the problem that whether the protein folding rate is influenced by its corresponding mRNA sequence. In this paper, we analyzed the possible relationship between the protein folding rates and the corresponding mRNA sequences. The content of guanine and cytosine (GC content) of palindromes in protein coding sequence was introduced as a new parameter and added in the Gromiha's model of predicting protein folding rates to inspect its effect in protein folding process. The multiple linear regression analysis and jack-knife test show that the new parameter is significant. The linear correlation coefficient between the experimental and the predicted values of the protein folding rates increased significantly from 0.96 to 0.99, and the population variance decreased from 0.50 to 0.24 compared with Gromiha's results. The results show that the GC content of palindromes in the corresponding protein coding sequence really influences the protein folding rate. Further analysis indicates that this kind of effect mostly comes from the synonymous codon usage and from the information of palindrome structure itself, but not from the translation information from codons to amino acids.     

Disordered regions in elongation factors EF1A in the three superkingdoms of life

A new criterion proposed for classification of the living world is based on the ability of the protein amino acid sequence to form disordered regions, appearing as loops in the 3D structure. The approach used fundamentally differs from the approaches based on comparisons of certain RNA or protein sequences of different organisms. Introduction of any new structural-functional criterion that could resolve the evolutionary relationships between the main groups of origin organisms is of interest in itself, as megasystematics and macrophylogeny lack informative criteria despite the apparent abundance of molecular characteristics. The specialized program FoldUnfold was used to search for disordered regions in the elongation factors EF1A (EFs). The reliability of loop prediction was verified against five EFs with the structures known from X-ray analysis. It was demonstrated with the example of several dozens of typical representatives of the living world that the program predicts extra loops in addition to two linkers between three structural domains in EFs. Besides the effector loop, contained in all EFs, six loops were detected at maximum. Of them, three loops (A, B, and C) are in domain I, one (D) is in domain II, and two (E and F) are in domain III. Moreover, all six loops are never present in the same EF. The EF signatures were determined for each of the superkingdoms of life. Each superkingdom displayed variations in the number of loops and their location within the EF domains. Not only the presence of a particular loop was important in the analysis, but also the specificity of its amino acid sequence. As the total number of predicted loops in EFs increases with the increasing complexity of organisms, the following evolutionary role was postulated for the loops. Following the principle of thrifty inventiveness, nature operates with different universal inserts (loops), adapting their number, location within the EF domains, and amino acid composition so that the protein performs specialized functions—single in protozoa and several in higher organisms.     

Specificity in the genetic code. The role of nucleotide base-amino acid interaction

The mechanism of the unique and specific association of a given amino acid to its t-RNA is investigated by theoretical methods. Several possible schemes are proposed to explain specificity. The physical forces which act within these mechanisms are illustrated by the computer simulation of probable interactions between glycine and nucleotide bases and base pairs. It is demonstrated that glycine has direct and selective affinities for the nucleotide bases and that these interactions are principally determined by the polar groups. Energies have been calculated for the interaction of glycine with several base pairs. From these, the possibility that specificity arises through direct complexing of an amino acid with its anticodon is evaluated.     

Estimation of primary sequence homology from amino acid composition of evolutionary related proteins

The amino acid compositions of many of the known sequenced proteins were compared to determine if a relationship exists between the amino acid composition and the amount of sequence homology of these proteins. For this purpose, a function, the composition divergence, was defined. A computer program based on relatively simple assumptions has been successfully used to simulate the data distribution found in comparing composition divergence with the sequence dissimilarity. From this characterization of known proteins, it is possible to predict the sequence homology of unsequenced proteins, based on amino acid composition comparisons. The power and limitations of this technique are discussed.