SUMMARY: Every protein family has a set of characteristic secondary structures. However, due to individual variations, a single structure is not enough to represent the whole family. OverProt can create a secondary structure consensus, showing the general fold of the family as well as its variation. Our server provides precomputed results for all CATH superfamilies and user-defined computations, visualized by an interactive viewer, which shows the secondary structure element type, length, frequency of occurrence, spatial variability and β-connectivity. AVAILABILITY AND IMPLEMENTATION: OverProt Server is freely available at https://overprot.ncbr.muni.cz. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

• MeSH
• Consensus MeSH
• Computers MeSH
• Proteins * chemistry   MeSH
• Protein Structure, Secondary MeSH
• Software * MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Names of Substances
• Proteins * MeSH

SUMMARY: Secondary structures provide a deep insight into the protein architecture. They can serve for comparison between individual protein family members. The most straightforward way how to deal with protein secondary structure is its visualization using 2D diagrams. Several software tools for the generation of 2D diagrams were developed. Unfortunately, they create 2D diagrams based on only a single protein. Therefore, 2D diagrams of two proteins from one family markedly differ. For this reason, we developed the 2DProts database, which contains secondary structure 2D diagrams for all domains from the CATH and all proteins from PDB databases. These 2D diagrams are generated based on a whole protein family, and they also consider information about the 3D arrangement of secondary structure elements. Moreover, 2DProts database contains multiple 2D diagrams, which provide an overview of a whole protein family's secondary structures. 2DProts is updated weekly and is integrated into CATH. AVAILABILITY AND IMPLEMENTATION: Freely accessible at https://2dprots.ncbr.muni.cz. The web interface was implemented in JavaScript. The database was implemented in Python. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

• MeSH
• Databases, Factual MeSH
• Proteins * chemistry   MeSH
• Protein Structure, Secondary MeSH
• Software * MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Names of Substances
• Proteins * MeSH

Secondary structure elements (SSEs) are inherent parts of protein structures, and their arrangement is characteristic for each protein family. Therefore, annotation of SSEs can facilitate orientation in the vast number of homologous structures which is now available for many protein families. It also provides a way to identify and annotate the key regions, like active sites and channels, and subsequently answer the key research questions, such as understanding of molecular function and its variability.This chapter introduces the concept of SSE annotation and describes the workflow for obtaining SSE annotation for the members of a selected protein family using program SecStrAnnotator.

• Keywords
• Annotation, Protein domain, Protein family, SecStrAnnotator, Secondary structure, Secondary structure assignment, Secondary structure elements, Structural alignment,
• MeSH
• Algorithms MeSH
• Amino Acid Motifs * MeSH
• Molecular Sequence Annotation methods   MeSH
• Catalytic Domain genetics   MeSH
• Proteins chemistry   genetics   MeSH
• Software MeSH
• Computational Biology methods   MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Names of Substances
• Proteins MeSH

SUMMARY: We present the cpPredictor webserver that implements a novel template-based method for prediction of secondary structure of RNA. The method outperforms available prediction methods as it uses RNA structures of related molecules, either predicted or experimentally identified, as structural templates. The server aims at three major tasks: i) prediction of RNA secondary structures that are difficult to predict by available methods, ii) characterization of uncharacterized RNAs as compatible or incompatible with a chosen template structure and iii) an identification of the most relevant structure among different candidate structures of a single RNA ambiguously predicted by available methods. The web server is accompanied with a comprehensive documentation. AVAILABILITY AND IMPLEMENTATION: The web server is freely available at http://cppredictor.elixir-czech.cz/. The source code of the cpPredictor algorithm is freely available from the webserver under the Apache License, Version 2.0.

• MeSH
• Algorithms MeSH
• Internet MeSH
• Nucleic Acid Conformation * MeSH
• RNA MeSH
• Protein Structure, Secondary MeSH
• Sequence Analysis, RNA MeSH
• Software * MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Names of Substances
• RNA MeSH

Raman spectra of the elastinlike polypentapeptide poly(GVGVP) were measured in H(2)O and D(2)O as solutions and, after increasing the temperature, as suspensions and sediments. In addition, spectra of the polypentapeptide in the solutions of increasing concentration and in the solid state were also investigated by gradually evaporating the water. Significant changes in band frequencies, intensities, and shapes were found for selected Raman bands in the measured spectra, particularly for the C-H stretching, the glycine CH(2) wagging, and some amide vibrations. The C-H stretching vibrations are influenced predominantly by the presence of water, the glycine CH(2) wagging vibrations are associated with conformational transitions. Three possible types of poly(GVGVP)s in the presence of water were indicated: polymer chains in a relatively extended state in the solution, a beta-spiral structure in the suspension, and irregularly bent chains in the sediment.

• MeSH
• Elastin chemistry   MeSH
• Models, Molecular MeSH
• Oligopeptides chemistry   MeSH
• Peptides chemistry   MeSH
• Spectrum Analysis, Raman MeSH
• Protein Structure, Secondary MeSH
• Thermodynamics MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Names of Substances
• Elastin MeSH
• glycyl-valyl-glycyl-valyl-proline MeSH Browser
• Oligopeptides MeSH
• Peptides MeSH

The relationship between the fractions of protein secondary structural components as determined from X-ray crystallographic data by the procedures of Kabsch and Sander (KS) and of Levitt and Greer (LG) is analyzed by neural network analysis of these two tabulations of literature data. A linear relationship between the KS and LG reductions of X-ray data to secondary structure descriptors is demonstrated by a regression analysis of the relationships between these sets of structural parameters. Back-propagation neural network analysis was then used to derive equations for determination of the most probable fractions of beta-sheet, bend, turn, and "other" conformations given the fraction of alpha-helix in a globular protein. The deviation of the X-ray values for beta-sheet from that determined with these equations was shown to have a variance that exponentially decreased with increasing fraction of alpha-helix. A second neural network analysis showed that knowledge of both the alpha-helical and beta-sheet fractions in a protein significantly reduces the uncertainty in prediction of the other components of the secondary structure. These analyses provide insight into the nature of the data sets derived from crystal structures. Since these complications of crystal structure data are commonly used as reference information for quantitative evaluation of spectra (for example, FTIR, Raman, and electronic or vibrational circular dichroism) in terms of secondary structure, such internal correlations in the reference sets may have significant effects on the stability of spectroscopic analyses derived from them.

• MeSH
• X-Ray Diffraction MeSH
• Mathematics MeSH
• Neural Networks, Computer MeSH
• Probability MeSH
• Proteins chemistry   MeSH
• Protein Structure, Secondary * MeSH
• Publication type
• Journal Article MeSH
• Research Support, U.S. Gov't, Non-P.H.S. MeSH
• Research Support, U.S. Gov't, P.H.S. MeSH
• Comparative Study MeSH
• Names of Substances
• Proteins MeSH

BACKGROUND: Protein function is determined by many factors, namely by its constitution, spatial arrangement, and dynamic behavior. Studying these factors helps the biochemists and biologists to better understand the protein behavior and to design proteins with modified properties. One of the most common approaches to these studies is to compare the protein structure with other molecules and to reveal similarities and differences in their polypeptide chains. RESULTS: We support the comparison process by proposing a new visualization technique that bridges the gap between traditionally used 1D and 3D representations. By introducing the information about mutual positions of protein chains into the 1D sequential representation the users are able to observe the spatial differences between the proteins without any occlusion commonly present in 3D view. Our representation is designed to serve namely for comparison of multiple proteins or a set of time steps of molecular dynamics simulation. CONCLUSIONS: The novel representation is demonstrated on two usage scenarios. The first scenario aims to compare a set of proteins from the family of cytochromes P450 where the position of the secondary structures has a significant impact on the substrate channeling. The second scenario focuses on the protein flexibility when by comparing a set of time steps our representation helps to reveal the most dynamically changing parts of the protein chain.

• Keywords
• Molecular sequence analysis, Molecular structure and function, Molecular visualization,
• MeSH
• Algorithms MeSH
• Models, Molecular MeSH
• Proteins chemistry   MeSH
• Protein Structure, Secondary * MeSH
• Amino Acid Sequence MeSH
• Sequence Alignment MeSH
• Molecular Dynamics Simulation * MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• Proteins MeSH

BACKGROUND: Visualization of RNA secondary structures is a complex task, and, especially in the case of large RNA structures where the expected layout is largely habitual, the existing visualization tools often fail to produce suitable visualizations. This led us to the idea to use existing layouts as templates for the visualization of new RNAs similarly to how templates are used in homology-based structure prediction. RESULTS: This article introduces Traveler, a software tool enabling visualization of a target RNA secondary structure using an existing layout of a sufficiently similar RNA structure as a template. Traveler is based on an algorithm which converts the target and template structures into corresponding tree representations and utilizes tree edit distance coupled with layout modification operations to transform the template layout into the target one. Traveler thus accepts a pair of secondary structures and a template layout and outputs a layout for the target structure. CONCLUSIONS: Traveler is a command-line open source tool able to quickly generate layouts for even the largest RNA structures in the presence of a sufficiently similar layout. It is available at http://github.com/davidhoksza/traveler .

• Keywords
• RNA secondary structure, Software tool, Template-based modeling, Visualization,
• MeSH
• Algorithms MeSH
• Nucleic Acid Conformation MeSH
• RNA chemistry   MeSH
• Software * MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• RNA MeSH

Decorin binding proteins (Dbps) mediate attachment of spirochetes in host organisms during the early stages of Lyme disease infection. Previously, different binding mechanisms of Dbps to glycosaminoglycans have been elucidated for the pathogenic species Borrelia burgdorferi sensu stricto and B. afzelii. We are investigating various European Borrelia spirochetes and their interactions at the atomic level using NMR. We report preparative scale recombinant expression of uniformly stable isotope enriched B. afzelii DbpA in Escherichia coli, its chromatographic purification, and solution NMR assignments of its backbone and sidechain 1H, 13C, and 15N atoms. This data was used to predict secondary structure propensity, which we compared to the North American B. burgdorferi sensu stricto and European B. garinii DbpA for which solution NMR structures had been determined previously. Backbone dynamics of DbpA from B. afzelii were elucidated from spin relaxation and heteronuclear NOE experiments. NMR-based secondary structure analysis together with the backbone dynamics characterization provided a first look into structural differences of B. afzelii DbpA compared to the North American species and will serve as the basis for further investigation of how these changes affect interactions with host components.

• Keywords
• Borrelia afzelii, Decorin-binding proteins, NMR resonance assignment,
• MeSH
• Adhesins, Bacterial chemistry   MeSH
• Bacterial Proteins * metabolism   MeSH
• Borrelia burgdorferi Group * chemistry   MeSH
• Nuclear Magnetic Resonance, Biomolecular MeSH
• Protein Structure, Secondary MeSH
• Amino Acid Sequence MeSH
• Publication type
• Journal Article MeSH
• Geographicals
• Europe MeSH
• Names of Substances
• Adhesins, Bacterial MeSH
• Bacterial Proteins * MeSH

Methods of artificial evolution such as SELEX and in vitro selection have made it possible to isolate RNA and DNA motifs with a wide range of functions from large random sequence libraries. Once the primary sequence of a functional motif is known, the sequence space around it can be comprehensively explored using a combination of random mutagenesis and selection. However, methods to explore the sequence space of a secondary structure are not as well characterized. Here we address this question by describing a method to construct libraries in a single synthesis which are enriched for sequences with the potential to form a specific secondary structure, such as that of an aptamer, ribozyme, or deoxyribozyme. Although interactions such as base pairs cannot be encoded in a library using conventional DNA synthesizers, it is possible to modulate the probability that two positions will have the potential to pair by biasing the nucleotide composition at these positions. Here we show how to maximize this probability for each of the possible ways to encode a pair (in this study defined as A-U or U-A or C-G or G-C or G.U or U.G). We then use these optimized coding schemes to calculate the number of different variants of model stems and secondary structures expected to occur in a library for a series of structures in which the number of pairs and the extent of conservation of unpaired positions is systematically varied. Our calculations reveal a tradeoff between maximizing the probability of forming a pair and maximizing the number of possible variants of a desired secondary structure that can occur in the library. They also indicate that the optimal coding strategy for a library depends on the complexity of the motif being characterized. Because this approach provides a simple way to generate libraries enriched for sequences with the potential to form a specific secondary structure, we anticipate that it should be useful for the optimization and structural characterization of functional nucleic acid motifs.

• Keywords
• DNA, RNA, SELEX, aptamer, artificial evolution, deoxyribozyme, in vitro selection, nucleic acids, ribozyme, secondary structure, synthetic biology,
• MeSH
• Aptamers, Nucleotide genetics   MeSH
• DNA, Catalytic genetics   MeSH
• Gene Library * MeSH
• Nucleic Acid Conformation MeSH
• Mutagenesis MeSH
• Nucleotide Motifs genetics   MeSH
• Inverted Repeat Sequences genetics   MeSH
• Base Pairing MeSH
• Probability MeSH
• Directed Molecular Evolution methods   MeSH
• RNA, Catalytic genetics   MeSH
• Synthetic Biology methods   MeSH
• In Vitro Techniques MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• Aptamers, Nucleotide MeSH
• DNA, Catalytic MeSH
• RNA, Catalytic MeSH