Core Promoter Regions of Antisense and Long Intergenic Non-Coding RNAs.

RNA polymerase II (POL II) is responsible for the transcription of messenger RNAs (mRNAs) and long non-coding RNAs (lncRNAs). Previously, we have shown the evolutionary invariance of the structural features of DNA in the POL II core promoters of the precursors of mRNAs. In this work, we have analyzed the POL II core promoters of the precursors of lncRNAs in Homo sapiens and Mus musculus genomes. Structural analysis of nucleotide sequences in positions -50, +30 bp in relation to the TSS have shown the extremely heterogeneous 3D structure that includes two singular regions - hexanucleotide "INR" around the TSS and octanucleotide "TATA-box" at around ~-28 bp upstream. Thus, the 3D structure of core promoters of lncRNA resembles the architecture of the core promoters of mRNAs; however, textual analysis revealed differences between promoters of lncRNAs and promoters of mRNAs, which lies in their textual characteristics; namely, the informational entropy at each position of the nucleotide text of lncRNA core promoters (by the exception of singular regions) is significantly higher than that of the mRNA core promoters. Another distinguishing feature of lncRNA is the extremely rare occurrence in the TATA box of octanucleotides with the consensus sequence. These textual differences can significantly affect the efficiency of the transcription of lncRNAs.

Structural attributes of nucleotide sequences in promoter regions of supercoiling-sensitive genes: how to relate microarray expression data with genomic sequences.

The level of supercoiling in the chromosome can affect gene expression. To clarify the basis of supercoiling sensitivity, we analyzed the structural features of nucleotide sequences in the vicinity of promoters for the genes with expression enhanced and decreased in response to loss of chromosomal supercoiling in Escherichia coli. Fourier analysis of promoter sequences for supercoiling-sensitive genes reveals the tendency in selection of sequences with helical periodicities close to 10nt for relaxation-induced genes and to 11nt for relaxation-repressed genes. The helical periodicities in the subsets of promoters recognized by RNA polymerase with different sigma factors were also studied. A special procedure was developed for the study of correlations between the intensities of periodicities in promoter sequences and the expression levels of corresponding genes. Significant correlations of expression with the AT content and with AT periodicities about 10, 11, and 50nt indicate their role in regulation of supercoiling-sensitive genes.

Numeric analysis of reversibility of classic movement equations and constructive criteria of estimating quality of molecular dynamic simulations.

The fundamental criteria of the quality of molecular dynamics (MD) simulation represent a pivotal challenge, especially in the case of MD simulations of large systems (in particular, proteins).This work presents a simple theoretical analysis of time reversibility in classical mechanics that has allowed us to formulate a number of constructive criteria for evaluating the quality of the trajectories, generated in MD simulations. The results of testing the criteria on the structures of eight small proteins are presented. The criteria can be useful for solving different MD problems, such as: choosing the most appropriate thermostats for a MD system under study, the methods for sampling conformations, etc.Communicated by Ramaswamy H. Sarma.

Structural coordinates: A novel approach to predict protein backbone conformation.

MOTIVATION: Local protein structure is usually described via classifying each peptide to a unique class from a set of pre-defined structures. These classifications may differ in the number of structural classes, the length of peptides, or class attribution criteria. Most methods that predict the local structure of a protein from its sequence first rely on some classification and only then proceed to the 3D conformation assessment. However, most classification methods rely on homologous proteins' existence, unavoidably lose information by attributing a peptide to a single class or suffer from a suboptimal choice of the representative classes. RESULTS: To alleviate the above challenges, we propose a method that constructs a peptide's structural representation from the sequence, reflecting its similarity to several basic representative structures. For 5-mer peptides and 16 representative structures, we achieved the Q16 classification accuracy of 67.9%, which is higher than what is currently reported in the literature. Our prediction method does not utilize information about protein homologues but relies only on the amino acids' physicochemical properties and the resolved structures' statistics. We also show that the 3D coordinates of a peptide can be uniquely recovered from its structural coordinates, and show the required conditions under various geometric constraints.

Reconstruction of genuine pair-wise sequence alignment.

In many applications, the algorithmically obtained alignment ideally should restore the "golden standard" (GS) alignment, which superimposes positions originating from the same position of the common ancestor of the compared sequences. The average similarity between the algorithmically obtained and GS alignments ("the quality") is an important characteristic of an alignment algorithm. We proposed to determine the quality of an algorithm, using sequences that were artificially generated in accordance with an appropriate evolution model; the approach was applied to the global version of the Smith-Waterman algorithm (SWA). The quality of SWA is between 97% (for a PAM distance of 60) and 70% (for a PAM distance of 300). The percentage of identical aligned residues is the same for algorithmic and GS alignments. The total length of indels in algorithmic alignments is less than in the GS-mainly due to a substantial decrease in the number of indels in algorithmic alignments.

Study and prediction of secondary structure for membrane proteins.

In this paper we present a novel approach to membrane protein secondary structure prediction based on the statistical stepwise discriminant analysis method. A new aspect of our approach is the possibility to derive physical-chemical properties that may affect the formation of membrane protein secondary structure. The certain physical-chemical properties of protein chains can be used to clarify the formation of the secondary structure types under consideration. Another aspect of our approach is that the results of multiple sequence alignment, or the other kinds of sequence alignment, are not used in the frame of the method. Using our approach, we predicted the formation of three main secondary structure types (alpha-helix, beta-structure and coil) with high accuracy, that is Q(3) = 76%. Predicting the formation of alpha-helix and non-alpha-helix states we reached the accuracy which was measured as Q(2) = 86%. Also we have identified certain protein chain properties that affect the formation of membrane protein secondary structure. These protein properties include hydrophobic properties of amino acid residues, presence of Gly, Ala and Val amino acids, and the location of protein chain end.

Omnipresence of the polyproline II helix in fibrous and globular proteins.

Left-handed helical conformation of a polypeptide chain (PPII) is the third type of the protein backbone structure. This conformation universally exists in fibrous, globular proteins, and biologically active peptides. It has unique physical and chemical properties determining a wide range of biological functions, from the protein folding to the tissue differentiation. New examples of the structure have been appearing in spite of difficulties in their detection and investigation. The annotation and prediction of the PPII was also a challenging task. Recently, many PPII motifs with new and/or unexpected functions are being accumulated in databases. In this review we describe the major structural and dynamic forms of PPII, the diversity of its functions, and the role in different biological processes.

A tetrapeptide-based method for polyproline II-type secondary structure prediction.

We describe a new method for polyproline II-type (PPII) secondary structure prediction based on tetrapeptide conformation properties using data obtained from all globular proteins in the Protein Data Bank (PDB). This is the first method for PPII prediction with a relatively high level of accuracy (approximately 60%). Our method uses only frequencies of different conformations among oligopeptides without any additional parameters. We also attempted to predict alpha-helices and beta-strands using the same approach. We find that the application of our method reveals interrelation between sequence and structure even for very short oligopeptides (tetrapeptides).

Analysis of forces that determine helix formation in alpha-proteins.

A model for prediction of alpha-helical regions in amino acid sequences has been tested on the mainly-alpha protein structure class. The modeling represents the construction of a continuous hypothetical alpha-helical conformation for the whole protein chain, and was performed using molecular mechanics tools. The positive prediction of alpha-helical and non-alpha-helical pentapeptide fragments of the proteins is 79%. The model considers only local interactions in the polypeptide chain without the influence of the tertiary structure. It was shown that the local interaction defines the alpha-helical conformation for 85% of the native alpha-helical regions. The relative energy contributions to the energy of the model were analyzed with the finding that the van der Waals component determines the formation of alpha-helices. Hydrogen bonds remain at constant energy independently whether alpha-helix or non-alpha-helix occurs in the native protein, and do not determine the location of helical regions. In contrast to existing methods, this approach additionally permits the prediction of conformations of side chains. The model suggests the correct values for ~60% of all chi-angles of alpha-helical residues.

Use of molecular mechanics for secondary structure prediction. Is it possible to reveal alpha-helix?

A new approach to predicting protein standard conformations is suggested. The idea consists in modeling by molecular mechanics tools a continuous alpha-helical conformation for the whole protein. The profile of energy along the model alpha-helix reveals minima corresponding to real alpha-helical segments in the native protein. The 3/10-helices and beta-turns including a local alpha-helical conformation may be detected as well. All alpha-helical segments in the test sample are delineated; mean residue by residue accuracy Q(3alpha) is 79%. This non-statistical approach can shed light on the physical grounds of alpha-helix formation.

Alternatingly twisted ß-hairpins and nonglycine residues in the disallowed II' region of the Ramachandran plot.

The structure of the SH3 domain of α-spectrin (PDB code 1SHG) features Asn47 in the II' area of the Ramachandran plot, which as a rule admits only glycine residues, and this phenomenon still awaits its explanation. Here, we undertook a computational study of this particular case by means of molecular dynamics and bioinformatics approaches. We found that the region of the SH3 domain in the vicinity of Asn47 remains relatively stable during denaturing molecular dynamics simulations of the entire domain and of its parts. This increased stability may be connected with the dynamic hydrogen bonding that is susceptible to targeted in silico mutations of Arg49. Bioinformatics analysis indicated that Asn47 is in the ß-turn of a distinctive structural fragment we called 'alternatingly twisted ß-hairpin.' Fragments of similar conformation are quite abundant in a nonredundant set of PDB chains and are distinguished from ordinary ß-hairpins by some surplus of glycine in their ß-turns, lack of certain interpeptide hydrogen bonds, and an increased chirality index. Thus, the disallowed conformation of residues other than glycine is realized in the ß-turns of alternatingly twisted ß-hairpins.

Comparative analysis of the quality of a global algorithm and a local algorithm for alignment of two sequences.

BACKGROUND: Algorithms of sequence alignment are the key instruments for computer-assisted studies of biopolymers. Obviously, it is important to take into account the "quality" of the obtained alignments, i.e. how closely the algorithms manage to restore the "gold standard" alignment (GS-alignment), which superimposes positions originating from the same position in the common ancestor of the compared sequences. As an approximation of the GS-alignment, a 3D-alignment is commonly used not quite reasonably. Among the currently used algorithms of a pair-wise alignment, the best quality is achieved by using the algorithm of optimal alignment based on affine penalties for deletions (the Smith-Waterman algorithm). Nevertheless, the expedience of using local or global versions of the algorithm has not been studied. RESULTS: Using model series of amino acid sequence pairs, we studied the relative "quality" of results produced by local and global alignments versus (1) the relative length of similar parts of the sequences (their "cores") and their nonhomologous parts, and (2) relative positions of the core regions in the compared sequences. We obtained numerical values of the average quality (measured as accuracy and confidence) of the global alignment method and the local alignment method for evolutionary distances between homologous sequence parts from 30 to 240 PAM and for the core length making from 10% to 70% of the total length of the sequences for all possible positions of homologous sequence parts relative to the centers of the sequences. CONCLUSION: We revealed criteria allowing to specify conditions of preferred applicability for the local and the global alignment algorithms depending on positions and relative lengths of the cores and nonhomologous parts of the sequences to be aligned. It was demonstrated that when the core part of one sequence was positioned above the core of the other sequence, the global algorithm was more stable at longer evolutionary distances and larger nonhomologous parts than the local algorithm. On the contrary, when the cores were positioned asymmetrically, the local algorithm was more stable at longer evolutionary distances and larger nonhomologous parts than the global algorithm. This opens a possibility for creation of a combined method allowing generation of more accurate alignments.

A novel model system for design of biomaterials based on recombinant analogs of spider silk proteins.

Spider dragline silk possesses impressive mechanical and biochemical properties. It is synthesized by a couple of major ampullate glands in spiders and comprises of two major structural proteins--spidroins 1 and 2. The relationship between structure and mechanical properties of spider silk is not well understood. Here, we modeled the complete process of the spider silk assembly using two new recombinant analogs of spidroins 1 and 2. The artificial genes sequence of the hydrophobic core regions of spidroin 1 and 2 have been designed using computer analysis of existing databases and mathematical modeling. Both proteins were expressed in Pichia pastoris and purified using a cation exchange chromatography. Despite the absence of hydrophilic N- and C-termini, both purified proteins spontaneously formed the nanofibrils and round micelles of about 1 microm in aqueous solutions. The electron microscopy study has revealed the helical structure of a nanofibril with a repeating motif of 40 nm. Using the electrospinning, the thin films with an antiparallel beta-sheet structure were produced. In summary, we were able to obtain artificial structures with characteristics that are perspective for further biomedical applications, such as producing three-dimensional matrices for tissue engineering and drug delivery.