1
|
Simm S, Einloft J, Mirus O, Schleiff E. 50 years of amino acid hydrophobicity scales: revisiting the capacity for peptide classification. Biol Res 2016; 49:31. [PMID: 27378087 PMCID: PMC4932767 DOI: 10.1186/s40659-016-0092-5] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 06/17/2016] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Physicochemical properties are frequently analyzed to characterize protein-sequences of known and unknown function. Especially the hydrophobicity of amino acids is often used for structural prediction or for the detection of membrane associated or embedded β-sheets and α-helices. For this purpose many scales classifying amino acids according to their physicochemical properties have been defined over the past decades. In parallel, several hydrophobicity parameters have been defined for calculation of peptide properties. We analyzed the performance of separating sequence pools using 98 hydrophobicity scales and five different hydrophobicity parameters, namely the overall hydrophobicity, the hydrophobic moment for detection of the α-helical and β-sheet membrane segments, the alternating hydrophobicity and the exact ß-strand score. RESULTS Most of the scales are capable of discriminating between transmembrane α-helices and transmembrane β-sheets, but assignment of peptides to pools of soluble peptides of different secondary structures is not achieved at the same quality. The separation capacity as measure of the discrimination between different structural elements is best by using the five different hydrophobicity parameters, but addition of the alternating hydrophobicity does not provide a large benefit. An in silico evolutionary approach shows that scales have limitation in separation capacity with a maximal threshold of 0.6 in general. We observed that scales derived from the evolutionary approach performed best in separating the different peptide pools when values for arginine and tyrosine were largely distinct from the value of glutamate. Finally, the separation of secondary structure pools via hydrophobicity can be supported by specific detectable patterns of four amino acids. CONCLUSION It could be assumed that the quality of separation capacity of a certain scale depends on the spacing of the hydrophobicity value of certain amino acids. Irrespective of the wealth of hydrophobicity scales a scale separating all different kinds of secondary structures or between soluble and transmembrane peptides does not exist reflecting that properties other than hydrophobicity affect secondary structure formation as well. Nevertheless, application of hydrophobicity scales allows distinguishing between peptides with transmembrane α-helices and β-sheets. Furthermore, the overall separation capacity score of 0.6 using different hydrophobicity parameters could be assisted by pattern search on the protein sequence level for specific peptides with a length of four amino acids.
Collapse
Affiliation(s)
- Stefan Simm
- />Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, Max von Laue Str. 9, 60438 Frankfurt/Main, Germany
| | - Jens Einloft
- />Molecular Bioinformatics, Cluster of Excellence Frankfurt “Macromolecular Complexes”, Institute of Computer Science, Faculty of Computer Science and Mathematics, Goethe-University Frankfurt, Robert-Mayer-Str. 11-15, 60325 Frankfurt/Main, Germany
| | - Oliver Mirus
- />Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, Max von Laue Str. 9, 60438 Frankfurt/Main, Germany
| | - Enrico Schleiff
- />Department of Biosciences, Molecular Cell Biology of Plants, Cluster of Excellence Frankfurt (CEF) and Buchmann Institute of Molecular Life Sciences (BMLS), Goethe University, Max von Laue Str. 9, 60438 Frankfurt/Main, Germany
| |
Collapse
|
2
|
Balazki P, Lindauer K, Einloft J, Ackermann J, Koch I. Erratum to: MONALISA for stochastic simulations of Petri net models of biochemical systems. BMC Bioinformatics 2015; 16:371. [PMID: 26542386 PMCID: PMC4636070 DOI: 10.1186/s12859-015-0725-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Pavel Balazki
- Department of Molecular Bioinformatics, Institute of Computer Science, Cluster of Excellence "Macromolecular Complexes", Johann Wolfgang Goethe-University Frankfurt am Main, Robert-Mayer-Straße 11-15, Frankfurt am Main, 60325, Germany. .,Sanofi Aventis Deutschland GmbH, Industriepark Höchst H831, Frankfurt am Main, 65926, Germany.
| | - Klaus Lindauer
- Sanofi Aventis Deutschland GmbH, Industriepark Höchst H831, Frankfurt am Main, 65926, Germany.
| | - Jens Einloft
- Department of Molecular Bioinformatics, Institute of Computer Science, Cluster of Excellence "Macromolecular Complexes", Johann Wolfgang Goethe-University Frankfurt am Main, Robert-Mayer-Straße 11-15, Frankfurt am Main, 60325, Germany.
| | - Jörg Ackermann
- Department of Molecular Bioinformatics, Institute of Computer Science, Cluster of Excellence "Macromolecular Complexes", Johann Wolfgang Goethe-University Frankfurt am Main, Robert-Mayer-Straße 11-15, Frankfurt am Main, 60325, Germany.
| | - Ina Koch
- Department of Molecular Bioinformatics, Institute of Computer Science, Cluster of Excellence "Macromolecular Complexes", Johann Wolfgang Goethe-University Frankfurt am Main, Robert-Mayer-Straße 11-15, Frankfurt am Main, 60325, Germany.
| |
Collapse
|
3
|
Balazki P, Lindauer K, Einloft J, Ackermann J, Koch I. MONALISA for stochastic simulations of Petri net models of biochemical systems. BMC Bioinformatics 2015; 16:215. [PMID: 26156221 PMCID: PMC4496887 DOI: 10.1186/s12859-015-0596-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 03/10/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The concept of Petri nets (PN) is widely used in systems biology and allows modeling of complex biochemical systems like metabolic systems, signal transduction pathways, and gene expression networks. In particular, PN allows the topological analysis based on structural properties, which is important and useful when quantitative (kinetic) data are incomplete or unknown. Knowing the kinetic parameters, the simulation of time evolution of such models can help to study the dynamic behavior of the underlying system. If the number of involved entities (molecules) is low, a stochastic simulation should be preferred against the classical deterministic approach of solving ordinary differential equations. The Stochastic Simulation Algorithm (SSA) is a common method for such simulations. The combination of the qualitative and semi-quantitative PN modeling and stochastic analysis techniques provides a valuable approach in the field of systems biology. RESULTS Here, we describe the implementation of stochastic analysis in a PN environment. We extended MONALISA - an open-source software for creation, visualization and analysis of PN - by several stochastic simulation methods. The simulation module offers four simulation modes, among them the stochastic mode with constant firing rates and Gillespie's algorithm as exact and approximate versions. The simulator is operated by a user-friendly graphical interface and accepts input data such as concentrations and reaction rate constants that are common parameters in the biological context. The key features of the simulation module are visualization of simulation, interactive plotting, export of results into a text file, mathematical expressions for describing simulation parameters, and up to 500 parallel simulations of the same parameter sets. To illustrate the method we discuss a model for insulin receptor recycling as case study. CONCLUSIONS We present a software that combines the modeling power of Petri nets with stochastic simulation of dynamic processes in a user-friendly environment supported by an intuitive graphical interface. The program offers a valuable alternative to modeling, using ordinary differential equations, especially when simulating single-cell experiments with low molecule counts. The ability to use mathematical expressions provides an additional flexibility in describing the simulation parameters. The open-source distribution allows further extensions by third-party developers. The software is cross-platform and is licensed under the Artistic License 2.0.
Collapse
Affiliation(s)
- Pavel Balazki
- Department of Molecular Bioinformatics, Institute of Computer Science, Cluster of Excellence "Macromolecular Complexes", Johann Wolfgang Goethe-University Frankfurt am Main, Robert-Mayer-Straße 11-15, Frankfurt am Main, 60325, Germany. .,Sanofi Aventis Deutschland GmbH, Industriepark Höchst H831, Frankfurt am Main, 65926, Germany.
| | - Klaus Lindauer
- Sanofi Aventis Deutschland GmbH, Industriepark Höchst H831, Frankfurt am Main, 65926, Germany.
| | - Jens Einloft
- Department of Molecular Bioinformatics, Institute of Computer Science, Cluster of Excellence "Macromolecular Complexes", Johann Wolfgang Goethe-University Frankfurt am Main, Robert-Mayer-Straße 11-15, Frankfurt am Main, 60325, Germany.
| | - Jörg Ackermann
- Department of Molecular Bioinformatics, Institute of Computer Science, Cluster of Excellence "Macromolecular Complexes", Johann Wolfgang Goethe-University Frankfurt am Main, Robert-Mayer-Straße 11-15, Frankfurt am Main, 60325, Germany.
| | - Ina Koch
- Department of Molecular Bioinformatics, Institute of Computer Science, Cluster of Excellence "Macromolecular Complexes", Johann Wolfgang Goethe-University Frankfurt am Main, Robert-Mayer-Straße 11-15, Frankfurt am Main, 60325, Germany.
| |
Collapse
|
4
|
Simm S, Fragkostefanakis S, Paul P, Keller M, Einloft J, Scharf KD, Schleiff E. Identification and Expression Analysis of Ribosome Biogenesis Factor Co-orthologs in Solanum lycopersicum. Bioinform Biol Insights 2015; 9:1-17. [PMID: 25698879 PMCID: PMC4325683 DOI: 10.4137/bbi.s20751] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 11/17/2014] [Accepted: 11/21/2014] [Indexed: 12/12/2022] Open
Abstract
Ribosome biogenesis involves a large inventory of proteinaceous and RNA cofactors. More than 250 ribosome biogenesis factors (RBFs) have been described in yeast. These factors are involved in multiple aspects like rRNA processing, folding, and modification as well as in ribosomal protein (RP) assembly. Considering the importance of RBFs for particular developmental processes, we examined the complexity of RBF and RP (co-)orthologs by bioinformatic assignment in 14 different plant species and expression profiling in the model crop Solanum lycopersicum. Assigning (co-)orthologs to each RBF revealed that at least 25% of all predicted RBFs are encoded by more than one gene. At first we realized that the occurrence of multiple RBF co-orthologs is not globally correlated to the existence of multiple RP co-orthologs. The transcript abundance of genes coding for predicted RBFs and RPs in leaves and anthers of S. lycopersicum was determined by next generation sequencing (NGS). In combination with existing expression profiles, we can conclude that co-orthologs of RBFs by large account for a preferential function in different tissue or at distinct developmental stages. This notion is supported by the differential expression of selected RBFs during male gametophyte development. In addition, co-regulated clusters of RBF and RP coding genes have been observed. The relevance of these results is discussed.
Collapse
Affiliation(s)
- Stefan Simm
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, Frankfurt/Main, Germany. ; Cluster of Excellence Frankfurt, Goethe University, Frankfurt/Main, Germany
| | - Sotirios Fragkostefanakis
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, Frankfurt/Main, Germany. ; Cluster of Excellence Frankfurt, Goethe University, Frankfurt/Main, Germany
| | - Puneet Paul
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, Frankfurt/Main, Germany
| | - Mario Keller
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, Frankfurt/Main, Germany
| | - Jens Einloft
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, Frankfurt/Main, Germany
| | - Klaus-Dieter Scharf
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, Frankfurt/Main, Germany
| | - Enrico Schleiff
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, Frankfurt/Main, Germany. ; Center of Membrane Proteomics, Goethe University, Frankfurt/Main, Germany. ; Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, Frankfurt/Main, Germany
| |
Collapse
|
5
|
Abstract
SUMMARY Structural modeling of biochemical networks enables qualitative as well as quantitative analysis of those networks. Automated network decomposition into functional modules is a crucial point in network analysis. Although there exist approaches for the analysis of networks, there is no open source tool available that combines editing, visualization and the computation of steady-state functional modules. We introduce a new tool called MonaLisa, which combines computation and visualization of functional modules as well as an editor for biochemical Petri nets. The analysis techniques allow for network decomposition into functional modules, for example t-invariants (elementary modes), maximal common transition sets, minimal cut sets and t-clusters. The graphical user interface provides various functionalities to construct and modify networks as well as to visualize the results of the analysis. AVAILABILITY AND IMPLEMENTATION MonaLisa is licensed under the Artistic License 2.0. It is freely available at http://www.bioinformatik.uni-frankfurt.de/software.html. MonaLisa requires at least Java 6 and runs under Linux, Microsoft Windows and Mac OS.
Collapse
Affiliation(s)
- Jens Einloft
- Molecular Bioinformatics Group, Institute of Computer Science, Faculty of Computer Science and Mathematics, Cluster of Excellence Frankfurt 'Macromolecular Complexes', Robert-Mayer-Strasse 11-15, Frankfurt am Main, Germany
| | | | | | | |
Collapse
|
6
|
Ackermann J, Einloft J, Nöthen J, Koch I. Reduction techniques for network validation in systems biology. J Theor Biol 2012; 315:71-80. [PMID: 22982289 DOI: 10.1016/j.jtbi.2012.08.042] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Revised: 08/27/2012] [Accepted: 08/29/2012] [Indexed: 10/27/2022]
Abstract
The rapidly increasing amount of experimental biological data enables the development of large and complex, often genome-scale models of molecular systems. The simulation and analysis of these computer models of metabolism, signal transduction, and gene regulation are standard applications in systems biology, but size and complexity of the networks limit the feasibility of many methods. Reduction of networks provides a hierarchical view of complex networks and gives insight knowledge into their coarse-grained structural properties. Although network reduction has been extensively studied in computer science, adaptation and exploration of these concepts are still lacking for the analysis of biochemical reaction systems. Using the Petri net formalism, we describe two local network structures, common transition pairs and minimal transition invariants. We apply these two structural elements for network reduction. The reduction preserves the CTI-property (covered by transition invariants), which is an important feature for completeness of biological models. We demonstrate this concept for a selection of metabolic networks including a benchmark network of Saccharomyces cerevisiae whose straightforward treatment is not yet feasible even on modern supercomputers.
Collapse
Affiliation(s)
- J Ackermann
- Department of Molecular Bioinformatics, Johann Wolfgang Goethe-University Frankfurt am Main, Institute of Computer Science, Robert-Mayer-Str. 11-15, 60325 Frankfurt am Main, Germany
| | | | | | | |
Collapse
|