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Pajkos M, Dosztányi Z. Functions of intrinsically disordered proteins through evolutionary lenses. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 183:45-74. [PMID: 34656334 DOI: 10.1016/bs.pmbts.2021.06.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein sequences are the result of an evolutionary process that involves the balancing act of experimenting with novel mutations and selecting out those that have an undesirable functional outcome. In the case of globular proteins, the function relies on a well-defined conformation, therefore, there is a strong evolutionary pressure to preserve the structure. However, different evolutionary rules might apply for the group of intrinsically disordered regions and proteins (IDR/IDPs) that exist as an ensemble of fluctuating conformations. The function of IDRs can directly originate from their disordered state or arise through different types of molecular recognition processes. There is an amazing variety of ways IDRs can carry out their functions, and this is also reflected in their evolutionary properties. In this chapter we give an overview of the different types of evolutionary behavior of disordered proteins and associated functions in normal and disease settings.
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Affiliation(s)
- Mátyás Pajkos
- Department of Biochemistry, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Zsuzsanna Dosztányi
- Department of Biochemistry, ELTE Eötvös Loránd University, Budapest, Hungary.
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2
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Abstract
Background Protein sequence alignment analyses have become a crucial step for many bioinformatics studies during the past decades. Multiple sequence alignment (MSA) and pair-wise sequence alignment (PSA) are two major approaches in sequence alignment. Former benchmark studies revealed drawbacks of MSA methods on nucleotide sequence alignments. To test whether similar drawbacks also influence protein sequence alignment analyses, we propose a new benchmark framework for protein clustering based on cluster validity. This new framework directly reflects the biological ground truth of the application scenarios that adopt sequence alignments, and evaluates the alignment quality according to the achievement of the biological goal, rather than the comparison on sequence level only, which averts the biases introduced by alignment scores or manual alignment templates. Compared with former studies, we calculate the cluster validity score based on sequence distances instead of clustering results. This strategy could avoid the influence brought by different clustering methods thus make results more dependable. Results Results showed that PSA methods performed better than MSA methods on most of the BAliBASE benchmark datasets. Analyses on the 80 re-sampled benchmark datasets constructed by randomly choosing 90% of each dataset 10 times showed similar results. Conclusions These results validated that the drawbacks of MSA methods revealed in nucleotide level also existed in protein sequence alignment analyses and affect the accuracy of results. Electronic supplementary material The online version of this article (10.1186/s12859-018-2524-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yingying Wang
- Research Center for Biomedical Information Technology, Shenzhen Institutes of Advanced Technologies, Chinese Academy of Sciences, Shenzhen, China
| | - Hongyan Wu
- Research Center for Biomedical Information Technology, Shenzhen Institutes of Advanced Technologies, Chinese Academy of Sciences, Shenzhen, China.
| | - Yunpeng Cai
- Research Center for Biomedical Information Technology, Shenzhen Institutes of Advanced Technologies, Chinese Academy of Sciences, Shenzhen, China.
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Zhu JJ, Gao MX, Song XJ, Zhao L, Li YW, Hao ZH. Changes in bacterial diversity and composition in the faeces and colon of weaned piglets after feeding fermented soybean meal. J Med Microbiol 2018; 67:1181-1190. [PMID: 29923819 DOI: 10.1099/jmm.0.000766] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
PURPOSE The microbiota composition of faeces and colonic contents were analysed to investigate the mechaninsm by which fermented soybean meal improves intestinal microbial communities, growth and immunity in weaning piglets. METHODOLOGY Microbiota were investigated using16S rRNA gene sequencing and systematical bio-information Operational Taxonomic Units; α-diversity analyses indicated that fermented soybean meal increased bacterial species diversity. RESULTS The levels of Actinobacteria and Proteobacteia in faeces, and Firmicutes and Tenericutes in the colon, increased significantly in piglets fed fermented soybean meal (P<0.05). The relative abundance of Clostridium sensu stricto1, Lachnospira and Bacteoides had positive correlations with diarrhoea in the piglets. Lactobacillus, Blautia and Clostridium sensu stricto1 levels were correlated with increases in the average daily feed intake of piglets. Lactobacillus and Lachnospira also had positive relationships with IgM levels, and lymphocytes levels were increased relative to Clostridium sensu stricto1. Lymphocyte numbers also increased with higher levels of Blautia and decreased with Clostridium sensu stricto1. Increased levels of Blautia were also correlated with significant increases in white blood cells. CONCLUSION The significant differences in faecal and colonic bacteria were correlated with enhanced immunity and overall improved health in the weaning piglets.
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Affiliation(s)
- Jia-Jia Zhu
- 1Agricultural Bio-pharmaceutical Laboratory, Qingdao Agricultural University, Qingdao 266109, PR China
| | - Ming-Xing Gao
- 1Agricultural Bio-pharmaceutical Laboratory, Qingdao Agricultural University, Qingdao 266109, PR China
| | - Xiao-Jun Song
- 2Laboratory for Animal Nutrition and Immune Molecular Biology, College of Life Science, Qingdao Agricultural University, Qingdao 266109, PR China
| | - Li Zhao
- 1Agricultural Bio-pharmaceutical Laboratory, Qingdao Agricultural University, Qingdao 266109, PR China
| | - Yu-Wen Li
- 1Agricultural Bio-pharmaceutical Laboratory, Qingdao Agricultural University, Qingdao 266109, PR China
| | - Zhi-Hui Hao
- 1Agricultural Bio-pharmaceutical Laboratory, Qingdao Agricultural University, Qingdao 266109, PR China
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Eisinga R, Heskes T, Pelzer B, Te Grotenhuis M. Exact p-values for pairwise comparison of Friedman rank sums, with application to comparing classifiers. BMC Bioinformatics 2017; 18:68. [PMID: 28122501 PMCID: PMC5267387 DOI: 10.1186/s12859-017-1486-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2016] [Accepted: 01/11/2017] [Indexed: 12/21/2022] Open
Abstract
Background The Friedman rank sum test is a widely-used nonparametric method in computational biology. In addition to examining the overall null hypothesis of no significant difference among any of the rank sums, it is typically of interest to conduct pairwise comparison tests. Current approaches to such tests rely on large-sample approximations, due to the numerical complexity of computing the exact distribution. These approximate methods lead to inaccurate estimates in the tail of the distribution, which is most relevant for p-value calculation. Results We propose an efficient, combinatorial exact approach for calculating the probability mass distribution of the rank sum difference statistic for pairwise comparison of Friedman rank sums, and compare exact results with recommended asymptotic approximations. Whereas the chi-squared approximation performs inferiorly to exact computation overall, others, particularly the normal, perform well, except for the extreme tail. Hence exact calculation offers an improvement when small p-values occur following multiple testing correction. Exact inference also enhances the identification of significant differences whenever the observed values are close to the approximate critical value. We illustrate the proposed method in the context of biological machine learning, were Friedman rank sum difference tests are commonly used for the comparison of classifiers over multiple datasets. Conclusions We provide a computationally fast method to determine the exact p-value of the absolute rank sum difference of a pair of Friedman rank sums, making asymptotic tests obsolete. Calculation of exact p-values is easy to implement in statistical software and the implementation in R is provided in one of the Additional files and is also available at http://www.ru.nl/publish/pages/726696/friedmanrsd.zip. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1486-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rob Eisinga
- Department of Social Science Research Methods, Radboud University Nijmegen, PO Box 9104, , 6500 HE, Nijmegen, The Netherlands.
| | - Tom Heskes
- Institute for Computing and Information Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Ben Pelzer
- Department of Social Science Research Methods, Radboud University Nijmegen, PO Box 9104, , 6500 HE, Nijmegen, The Netherlands
| | - Manfred Te Grotenhuis
- Department of Social Science Research Methods, Radboud University Nijmegen, PO Box 9104, , 6500 HE, Nijmegen, The Netherlands
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Holbrook K, Subramanian C, Chotewutmontri P, Reddick LE, Wright S, Zhang H, Moncrief L, Bruce BD. Functional Analysis of Semi-conserved Transit Peptide Motifs and Mechanistic Implications in Precursor Targeting and Recognition. MOLECULAR PLANT 2016; 9:1286-1301. [PMID: 27378725 DOI: 10.1016/j.molp.2016.06.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 05/13/2016] [Accepted: 06/07/2016] [Indexed: 05/17/2023]
Abstract
Over 95% of plastid proteins are nuclear-encoded as their precursors containing an N-terminal extension known as the transit peptide (TP). Although highly variable, TPs direct the precursors through a conserved, posttranslational mechanism involving translocons in the outer (TOC) and inner envelope (TOC). The organelle import specificity is mediated by one or more components of the Toc complex. However, the high TP diversity creates a paradox on how the sequences can be specifically recognized. An emerging model of TP design is that they contain multiple loosely conserved motifs that are recognized at different steps in the targeting and transport process. Bioinformatics has demonstrated that many TPs contain semi-conserved physicochemical motifs, termed FGLK. In order to characterize FGLK motifs in TP recognition and import, we have analyzed two well-studied TPs from the precursor of RuBisCO small subunit (SStp) and ferredoxin (Fdtp). Both SStp and Fdtp contain two FGLK motifs. Analysis of large set mutations (∼85) in these two motifs using in vitro, in organello, and in vivo approaches support a model in which the FGLK domains mediate interaction with TOC34 and possibly other TOC components. In vivo import analysis suggests that multiple FGLK motifs are functionally redundant. Furthermore, we discuss how FGLK motifs are required for efficient precursor protein import and how these elements may permit a convergent function of this highly variable class of targeting sequences.
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Affiliation(s)
- Kristen Holbrook
- Department of Biochemistry, Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Chitra Subramanian
- Graduate Program in Plant Physiology and Genetics, University of Tennessee, Knoxville, TN 37996, USA
| | | | - L Evan Reddick
- Department of Biochemistry, Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Sarah Wright
- Department of Botany, University of Tennessee, Knoxville, TN 37996, USA
| | - Huixia Zhang
- Department of Biochemistry, Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Lily Moncrief
- Department of Biochemistry, Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Barry D Bruce
- Department of Biochemistry, Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA; Graduate Program in Plant Physiology and Genetics, University of Tennessee, Knoxville, TN 37996, USA; Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37996, USA.
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Lange J, Wyrwicz LS, Vriend G. KMAD: knowledge-based multiple sequence alignment for intrinsically disordered proteins. ACTA ACUST UNITED AC 2015; 32:932-6. [PMID: 26568635 PMCID: PMC4803389 DOI: 10.1093/bioinformatics/btv663] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 11/09/2015] [Indexed: 12/16/2022]
Abstract
Summary: Intrinsically disordered proteins (IDPs) lack tertiary structure and thus differ from globular proteins in terms of their sequence–structure–function relations. IDPs have lower sequence conservation, different types of active sites and a different distribution of functionally important regions, which altogether make their multiple sequence alignment (MSA) difficult. The KMAD MSA software has been written specifically for the alignment and annotation of IDPs. It augments the substitution matrix with knowledge about post-translational modifications, functional domains and short linear motifs. Results: MSAs produced with KMAD describe well-conserved features among IDPs, tend to agree well with biological intuition, and are a good basis for designing new experiments to shed light on this large, understudied class of proteins. Availability and implementation: KMAD web server is accessible at http://www.cmbi.ru.nl/kmad/. A standalone version is freely available. Contact: vriend@cmbi.ru.nl
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Affiliation(s)
- Joanna Lange
- Laboratory of Bioinformatics and Biostatistics, M. Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland and Laboratory of Bioinformatics and Biostatistics, M. Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland and
| | - Lucjan S Wyrwicz
- Laboratory of Bioinformatics and Biostatistics, M. Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland and
| | - Gert Vriend
- CMBI Radboudumc, 6525 GA, Nijmegen, The Netherlands
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Pais FSM, Ruy PDC, Oliveira G, Coimbra RS. Assessing the efficiency of multiple sequence alignment programs. Algorithms Mol Biol 2014; 9:4. [PMID: 24602402 PMCID: PMC4015676 DOI: 10.1186/1748-7188-9-4] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 02/22/2014] [Indexed: 12/17/2022] Open
Abstract
Background Multiple sequence alignment (MSA) is an extremely useful tool for molecular and evolutionary biology and there are several programs and algorithms available for this purpose. Although previous studies have compared the alignment accuracy of different MSA programs, their computational time and memory usage have not been systematically evaluated. Given the unprecedented amount of data produced by next generation deep sequencing platforms, and increasing demand for large-scale data analysis, it is imperative to optimize the application of software. Therefore, a balance between alignment accuracy and computational cost has become a critical indicator of the most suitable MSA program. We compared both accuracy and cost of nine popular MSA programs, namely CLUSTALW, CLUSTAL OMEGA, DIALIGN-TX, MAFFT, MUSCLE, POA, Probalign, Probcons and T-Coffee, against the benchmark alignment dataset BAliBASE and discuss the relevance of some implementations embedded in each program’s algorithm. Accuracy of alignment was calculated with the two standard scoring functions provided by BAliBASE, the sum-of-pairs and total-column scores, and computational costs were determined by collecting peak memory usage and time of execution. Results Our results indicate that mostly the consistency-based programs Probcons, T-Coffee, Probalign and MAFFT outperformed the other programs in accuracy. Whenever sequences with large N/C terminal extensions were present in the BAliBASE suite, Probalign, MAFFT and also CLUSTAL OMEGA outperformed Probcons and T-Coffee. The drawback of these programs is that they are more memory-greedy and slower than POA, CLUSTALW, DIALIGN-TX, and MUSCLE. CLUSTALW and MUSCLE were the fastest programs, being CLUSTALW the least RAM memory demanding program. Conclusions Based on the results presented herein, all four programs Probcons, T-Coffee, Probalign and MAFFT are well recommended for better accuracy of multiple sequence alignments. T-Coffee and recent versions of MAFFT can deliver faster and reliable alignments, which are specially suited for larger datasets than those encountered in the BAliBASE suite, if multi-core computers are available. In fact, parallelization of alignments for multi-core computers should probably be addressed by more programs in a near future, which will certainly improve performance significantly.
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Sobolev BN, Veselovsky AV, Poroikov VV. Prediction of protein post-translational modifications: main trends and methods. RUSSIAN CHEMICAL REVIEWS 2014. [DOI: 10.1070/rc2014v083n02abeh004377] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Davey NE, Cowan JL, Shields DC, Gibson TJ, Coldwell MJ, Edwards RJ. SLiMPrints: conservation-based discovery of functional motif fingerprints in intrinsically disordered protein regions. Nucleic Acids Res 2012; 40:10628-41. [PMID: 22977176 PMCID: PMC3510515 DOI: 10.1093/nar/gks854] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Large portions of higher eukaryotic proteomes are intrinsically disordered, and abundant evidence suggests that these unstructured regions of proteins are rich in regulatory interaction interfaces. A major class of disordered interaction interfaces are the compact and degenerate modules known as short linear motifs (SLiMs). As a result of the difficulties associated with the experimental identification and validation of SLiMs, our understanding of these modules is limited, advocating the use of computational methods to focus experimental discovery. This article evaluates the use of evolutionary conservation as a discriminatory technique for motif discovery. A statistical framework is introduced to assess the significance of relatively conserved residues, quantifying the likelihood a residue will have a particular level of conservation given the conservation of the surrounding residues. The framework is expanded to assess the significance of groupings of conserved residues, a metric that forms the basis of SLiMPrints (short linear motif fingerprints), a de novo motif discovery tool. SLiMPrints identifies relatively overconstrained proximal groupings of residues within intrinsically disordered regions, indicative of putatively functional motifs. Finally, the human proteome is analysed to create a set of highly conserved putative motif instances, including a novel site on translation initiation factor eIF2A that may regulate translation through binding of eIF4E.
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Affiliation(s)
- Norman E Davey
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Baden-Württemberg 69117, Germany.
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Astakhova TV, Lobanov MN, Poverennaya IV, Roytberg MA, Yacovlev VV. Verification of the PREFAB alignment database. Biophysics (Nagoya-shi) 2012. [DOI: 10.1134/s0006350912020030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Weatheritt RJ, Luck K, Petsalaki E, Davey NE, Gibson TJ. The identification of short linear motif-mediated interfaces within the human interactome. ACTA ACUST UNITED AC 2012; 28:976-82. [PMID: 22328783 PMCID: PMC3315716 DOI: 10.1093/bioinformatics/bts072] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
MOTIVATION Eukaryotic proteins are highly modular, containing multiple interaction interfaces that mediate binding to a network of regulators and effectors. Recent advances in high-throughput proteomics have rapidly expanded the number of known protein-protein interactions (PPIs); however, the molecular basis for the majority of these interactions remains to be elucidated. There has been a growing appreciation of the importance of a subset of these PPIs, namely those mediated by short linear motifs (SLiMs), particularly the canonical and ubiquitous SH2, SH3 and PDZ domain-binding motifs. However, these motif classes represent only a small fraction of known SLiMs and outside these examples little effort has been made, either bioinformatically or experimentally, to discover the full complement of motif instances. RESULTS In this article, interaction data are analysed to identify and characterize an important subset of PPIs, those involving SLiMs binding to globular domains. To do this, we introduce iELM, a method to identify interactions mediated by SLiMs and add molecular details of the interaction interfaces to both interacting proteins. The method identifies SLiM-mediated interfaces from PPI data by searching for known SLiM-domain pairs. This approach was applied to the human interactome to identify a set of high-confidence putative SLiM-mediated PPIs. AVAILABILITY iELM is freely available at http://elmint.embl.de CONTACT toby.gibson@embl.de SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- R J Weatheritt
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
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Uncovering new substrates for Aurora A kinase. EMBO Rep 2010; 11:977-84. [PMID: 21072059 DOI: 10.1038/embor.2010.171] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2010] [Revised: 09/20/2010] [Accepted: 10/01/2010] [Indexed: 12/23/2022] Open
Abstract
Aurora A is a serine/threonine kinase that is essential for a wide variety of cell-cycle-related events, but only a small number of its substrates are known. We present and validate a strategy by which to identify Aurora A substrates and their phosphorylation sites. We developed a computational approach integrating various types of biological information to generate a list of 90 potential Aurora substrates, with a prediction accuracy of about 80%. We also demonstrated the specific phosphorylation of NUSAP (nucleolar and spindle-associated protein) by Aurora A in vivo. Our results provide a means by which to develop an understanding of Aurora A function and suggest unexpected roles for this kinase.
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Aniba MR, Poch O, Thompson JD. Issues in bioinformatics benchmarking: the case study of multiple sequence alignment. Nucleic Acids Res 2010; 38:7353-63. [PMID: 20639539 PMCID: PMC2995051 DOI: 10.1093/nar/gkq625] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2010] [Revised: 06/10/2010] [Accepted: 06/29/2010] [Indexed: 11/13/2022] Open
Abstract
The post-genomic era presents many new challenges for the field of bioinformatics. Novel computational approaches are now being developed to handle the large, complex and noisy datasets produced by high throughput technologies. Objective evaluation of these methods is essential (i) to assure high quality, (ii) to identify strong and weak points of the algorithms, (iii) to measure the improvements introduced by new methods and (iv) to enable non-specialists to choose an appropriate tool. Here, we discuss the development of formal benchmarks, designed to represent the current problems encountered in the bioinformatics field. We consider several criteria for building good benchmarks and the advantages to be gained when they are used intelligently. To illustrate these principles, we present a more detailed discussion of benchmarks for multiple alignments of protein sequences. As in many other domains, significant progress has been achieved in the multiple alignment field and the datasets have become progressively more challenging as the existing algorithms have evolved. Finally, we propose directions for future developments that will ensure that the bioinformatics benchmarks correspond to the challenges posed by the high throughput data.
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Affiliation(s)
- Mohamed Radhouene Aniba
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Department of Structural Biology and Genomics, Institut National de la Santé et de la Recherche Médicale (INSERM), U596, The Centre National de la Recherche Scientifique (CNRS), UMR7104, F-67400 Illkirch and Université de Strasbourg, F-67000 Strasbourg, France
| | - Olivier Poch
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Department of Structural Biology and Genomics, Institut National de la Santé et de la Recherche Médicale (INSERM), U596, The Centre National de la Recherche Scientifique (CNRS), UMR7104, F-67400 Illkirch and Université de Strasbourg, F-67000 Strasbourg, France
| | - Julie D. Thompson
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Department of Structural Biology and Genomics, Institut National de la Santé et de la Recherche Médicale (INSERM), U596, The Centre National de la Recherche Scientifique (CNRS), UMR7104, F-67400 Illkirch and Université de Strasbourg, F-67000 Strasbourg, France
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Aucher W, Becker E, Ma E, Miron S, Martel A, Ochsenbein F, Marsolier-Kergoat MC, Guerois R. A strategy for interaction site prediction between phospho-binding modules and their partners identified from proteomic data. Mol Cell Proteomics 2010; 9:2745-59. [PMID: 20733106 DOI: 10.1074/mcp.m110.003319] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Small and large scale proteomic technologies are providing a wealth of potential interactions between proteins bearing phospho-recognition modules and their substrates. Resulting interaction maps reveal such a dense network of interactions that the functional dissection and understanding of these networks often require to break specific interactions while keeping the rest intact. Here, we developed a computational strategy, called STRIP, to predict the precise interaction site involved in an interaction with a phospho-recognition module. The method was validated by a two-hybrid screen carried out using the ForkHead Associated (FHA)1 domain of Rad53, a key protein of Saccharomyces cerevisiae DNA checkpoint, as a bait. In this screen we detected 11 partners, including Cdc7 and Cdc45, essential components of the DNA replication machinery. FHA domains are phospho-threonine binding modules and the threonines involved in both interactions could be predicted using the STRIP strategy. The threonines T484 and T189 in Cdc7 and Cdc45, respectively, were mutated and loss of binding could be monitored experimentally with the full-length proteins. The method was further tested for the analysis of 63 known Rad53 binding partners and provided several key insights regarding the threonines likely involved in these interactions. The STRIP method relies on a combination of conservation, phosphorylation likelihood, and binding specificity criteria and can be accessed via a web interface at http://biodev.extra.cea.fr/strip/.
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Affiliation(s)
- Willy Aucher
- Laboratoire du Métabolisme de l'ADN et Réponses aux Génotoxiques, Gif-sur-Yvette F-91191, France
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15
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Gould CM, Diella F, Via A, Puntervoll P, Gemünd C, Chabanis-Davidson S, Michael S, Sayadi A, Bryne JC, Chica C, Seiler M, Davey NE, Haslam N, Weatheritt RJ, Budd A, Hughes T, Pas J, Rychlewski L, Travé G, Aasland R, Helmer-Citterich M, Linding R, Gibson TJ. ELM: the status of the 2010 eukaryotic linear motif resource. Nucleic Acids Res 2009; 38:D167-80. [PMID: 19920119 PMCID: PMC2808914 DOI: 10.1093/nar/gkp1016] [Citation(s) in RCA: 204] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Linear motifs are short segments of multidomain proteins that provide regulatory functions independently of protein tertiary structure. Much of intracellular signalling passes through protein modifications at linear motifs. Many thousands of linear motif instances, most notably phosphorylation sites, have now been reported. Although clearly very abundant, linear motifs are difficult to predict de novo in protein sequences due to the difficulty of obtaining robust statistical assessments. The ELM resource at http://elm.eu.org/ provides an expanding knowledge base, currently covering 146 known motifs, with annotation that includes >1300 experimentally reported instances. ELM is also an exploratory tool for suggesting new candidates of known linear motifs in proteins of interest. Information about protein domains, protein structure and native disorder, cellular and taxonomic contexts is used to reduce or deprecate false positive matches. Results are graphically displayed in a 'Bar Code' format, which also displays known instances from homologous proteins through a novel 'Instance Mapper' protocol based on PHI-BLAST. ELM server output provides links to the ELM annotation as well as to a number of remote resources. Using the links, researchers can explore the motifs, proteins, complex structures and associated literature to evaluate whether candidate motifs might be worth experimental investigation.
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Affiliation(s)
- Cathryn M Gould
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
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Gibson TJ. Cell regulation: determined to signal discrete cooperation. Trends Biochem Sci 2009; 34:471-82. [PMID: 19744855 DOI: 10.1016/j.tibs.2009.06.007] [Citation(s) in RCA: 131] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2009] [Revised: 06/02/2009] [Accepted: 06/04/2009] [Indexed: 11/25/2022]
Abstract
Do kinases cascade? How well is cell regulation understood? What are the best ways to model regulatory systems? Attempts to answer such questions can have bearings on the way in which research is conducted. Fortunately there are recurring themes in regulatory processes from many different cellular contexts, which might provide useful guidance. Three principles seem to be almost universal: regulatory interactions are cooperative; regulatory decisions are made by large dynamic protein complexes; and regulation is intricately networked. A fourth principle, although not universal, is remarkably common: regulatory proteins are actively placed where they are needed. Here, I argue that the true nature of cell signalling and our perceptions of it are in a state of discord. This raises the question: Are our misconceptions detrimental to progress in biomedical science?
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Affiliation(s)
- Toby J Gibson
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
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Chica C, Diella F, Gibson TJ. Evidence for the concerted evolution between short linear protein motifs and their flanking regions. PLoS One 2009; 4:e6052. [PMID: 19584925 PMCID: PMC2702822 DOI: 10.1371/journal.pone.0006052] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2009] [Accepted: 04/16/2009] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Linear motifs are short modules of protein sequences that play a crucial role in mediating and regulating many protein-protein interactions. The function of linear motifs strongly depends on the context, e.g. functional instances mainly occur inside flexible regions that are accessible for interaction. Sometimes linear motifs appear as isolated islands of conservation in multiple sequence alignments. However, they also occur in larger blocks of sequence conservation, suggesting an active role for the neighbouring amino acids. RESULTS The evolution of regions flanking 116 functional linear motif instances was studied. The conservation of the amino acid sequence and order/disorder tendency of those regions was related to presence/absence of the instance. For the majority of the analysed instances, the pairs of sequences conserving the linear motif were also observed to maintain a similar local structural tendency and/or to have higher local sequence conservation when compared to pairs of sequences where one is missing the linear motif. Furthermore, those instances have a higher chance to co-evolve with the neighbouring residues in comparison to the distant ones. Those findings are supported by examples where the regulation of the linear motif-mediated interaction has been shown to depend on the modifications (e.g. phosphorylation) at neighbouring positions or is thought to benefit from the binding versatility of disordered regions. CONCLUSION The results suggest that flanking regions are relevant for linear motif-mediated interactions, both at the structural and sequence level. More interestingly, they indicate that the prediction of linear motif instances can be enriched with contextual information by performing a sequence analysis similar to the one presented here. This can facilitate the understanding of the role of these predicted instances in determining the protein function inside the broader context of the cellular network where they arise.
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Affiliation(s)
- Claudia Chica
- Structural and Computational Biology Unit, EMBL Heidelberg, Heidelberg, Germany.
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Davey NE, Shields DC, Edwards RJ. Masking residues using context-specific evolutionary conservation significantly improves short linear motif discovery. ACTA ACUST UNITED AC 2009; 25:443-50. [PMID: 19136552 DOI: 10.1093/bioinformatics/btn664] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
MOTIVATION Short linear motifs (SLiMs) are important mediators of protein-protein interactions. Their short and degenerate nature presents a challenge for computational discovery. We sought to improve SLiM discovery by incorporating evolutionary information, since SLiMs are more conserved than surrounding residues. RESULTS We have developed a new method that assesses the evolutionary signal of a residue in its sequence and structural context. Under-conserved residues are masked out prior to SLiM discovery, allowing incorporation into the existing statistical model employed by SLiMFinder. The method shows considerable robustness in terms of both the conservation score used for individual residues and the size of the sequence neighbourhood. Optimal parameters significantly improve return of known functional motifs from benchmarking data, raising the return of significant validated SLiMs from typical human interaction datasets from 20% to 60%, while retaining the high level of stringency needed for application to real biological data. The success of this regime indicates that it could be of general benefit to computational annotation and prediction of protein function at the sequence level. AVAILABILITY All data and tools in this article are available at http://bioware.ucd.ie/~slimdisc/slimfinder/conmasking/.
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Affiliation(s)
- Norman E Davey
- UCD Complex and Adaptive Systems Laboratory, UCD Conway Institute of Biomolecular and Biomedical Sciences, University College Dublin, Dublin 4, Ireland
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Chica C, Labarga A, Gould CM, López R, Gibson TJ. A tree-based conservation scoring method for short linear motifs in multiple alignments of protein sequences. BMC Bioinformatics 2008; 9:229. [PMID: 18460207 PMCID: PMC2396637 DOI: 10.1186/1471-2105-9-229] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2007] [Accepted: 05/06/2008] [Indexed: 12/16/2022] Open
Abstract
Background The structure of many eukaryotic cell regulatory proteins is highly modular. They are assembled from globular domains, segments of natively disordered polypeptides and short linear motifs. The latter are involved in protein interactions and formation of regulatory complexes. The function of such proteins, which may be difficult to define, is the aggregate of the subfunctions of the modules. It is therefore desirable to efficiently predict linear motifs with some degree of accuracy, yet sequence database searches return results that are not significant. Results We have developed a method for scoring the conservation of linear motif instances. It requires only primary sequence-derived information (e.g. multiple alignment and sequence tree) and takes into account the degenerate nature of linear motif patterns. On our benchmarking, the method accurately scores 86% of the known positive instances, while distinguishing them from random matches in 78% of the cases. The conservation score is implemented as a real time application designed to be integrated into other tools. It is currently accessible via a Web Service or through a graphical interface. Conclusion The conservation score improves the prediction of linear motifs, by discarding those matches that are unlikely to be functional because they have not been conserved during the evolution of the protein sequences. It is especially useful for instances in non-structured regions of the proteins, where a domain masking filtering strategy is not applicable.
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Affiliation(s)
- Claudia Chica
- EMBL Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
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