Birgit Eisenhaber | Agency of Science and Technology, Singapore (original) (raw)

Papers by Birgit Eisenhaber

Human Molecular Genetics, 2005

Mutations in the gene NYX, which encodes nyctalopin, lead to the retinal disorder congenital stat... more Mutations in the gene NYX, which encodes nyctalopin, lead to the retinal disorder congenital stationary night blindness which is characterised by defective night vision (nyctalopia) from birth. Nyctalopin is of unknown function but is predicted to be a secreted glycoprotein of the extracellular small leucine-rich repeat proteoglycan and protein (SLRP) family attached to the cell membrane in humans via a glycosylphosphatidylinositol (GPI) anchor but in mouse via a transmembrane domain. We investigated membrane association and attachment for human and mouse nyctalopin and show conclusively that human nyctalopin is a GPI anchored protein. Furthermore, the orthologous mouse protein, although it localises to the cell surface, is not GPI anchored. We also confirm both mouse and human nyctalopin are glycosylated.

Molecular cell, Jan 15, 2016

Cohesin is a ring-shaped protein complex that is capable of embracing DNA. Most of the ring circu... more Cohesin is a ring-shaped protein complex that is capable of embracing DNA. Most of the ring circumference is comprised of the anti-parallel intramolecular coiled coils of the Smc1 and Smc3 proteins, which connect globular head and hinge domains. Smc coiled coil arms contain multiple acetylated and ubiquitylated lysines. To investigate the role of these modifications, we substituted lysines for arginines to mimic the unmodified state and uncovered genetic interaction between the Smc arms. Using scanning force microscopy, we show that wild-type Smc arms associate with each other when the complex is not on DNA. Deacetylation of the Smc1/Smc3 dimers promotes arms' dissociation. Smc arginine mutants display loose packing of the Smc arms and, although they dimerize at the hinges, fail to connect the heads and associate with the DNA. Our findings highlight the importance of a "collapsed ring," or "rod," conformation of cohesin for its loading on the chromosomes.

Bioinformatics, 2004

Web-based servers implementing the DAS-TMfilter algorithm have been launched at three mirror site... more Web-based servers implementing the DAS-TMfilter algorithm have been launched at three mirror sites and their usage is described. The underlying computer program is an upgraded and modified version of the DAS-prediction method. The new server is designed to make distinction between protein sequences with and without transmembrane (TM) helices at a reasonably low rate of false positive prediction (∼1 among 100 unrelated queries) while the high efficiency of the original algorithm locating TM segments in queries is preserved (sensitivity of ∼95% among documented proteins with helical TM regions). Availability: The server operates at three mirror sites

Proteomics, Jun 1, 2004

In silico annotation techniques for post-translational modifications (PTMs) are important to gene... more In silico annotation techniques for post-translational modifications (PTMs) are important to generate biologically meaningful descriptions for sequences of experimentally uncharacterized proteins. Having previously contributed with predictors for lipid PTMs, we summarize our methodological experience. Rather than only looking for the sequence pattern in substrate sequences, a strategy aimed at creating a generalized model of substrate protein/enzyme interaction appears more appropriate since the number of known substrate sequences is small, and some of them are not sufficiently verified experimentally. Such a physical approach (in contrast to a mere textual analysis of substrate sequences) can also take into account other, heterogeneous biological data (mutations of substrate sequences, kinetic data, enzyme sequences/structures) with simple analytical expressions in the score function. Several lipid PTMs are encoded in the form of a small sequence region (with pronounced amino acid type preferences) that is connected to the substrate protein by a linker region with many conformationally flexible, hydrophilic residues. A score function composed of terms penalizing sequence properties known to be incompatible with productive substrate protein/enzyme complexes essentially unselects inappropriate queries. Also, we estimate the number of nonredundant sequences necessary for robust profile computation with statistical criteria, a number that is not reached in most cases of PTM prediction. Finally, we discuss the usage of evolutionary information in evaluating the functional importance of predicted PTMs in cases of motif conservation within sequence families.

Methods in Molecular Biology, 2016

As biomolecular sequencing is becoming the main technique in life sciences, functional interpreta... more As biomolecular sequencing is becoming the main technique in life sciences, functional interpretation of sequences in terms of biomolecular mechanisms with in silico approaches is getting increasingly significant. Function prediction tools are most powerful for protein-coding sequences; yet, the concepts and technologies used for this purpose are not well reflected in bioinformatics textbooks. Notably, protein sequences typically consist of globular domains and non-globular segments. The two types of regions require cardinally different approaches for function prediction. Whereas the former are classic targets for homology-inspired function transfer based on remnant, yet statistically significant sequence similarity to other, characterized sequences, the latter type of regions are characterized by compositional bias or simple, repetitive patterns and require lexical analysis and/or empirical sequence pattern-function correlations. The recipe for function prediction recommends first to find all types of non-globular segments and, then, to subject the remaining query sequence to sequence similarity searches. We provide an updated description of the ANNOTATOR software environment as an advanced example of a software platform that facilitates protein sequence-based function prediction.

Journal of Structural Biology, 2016

The ability of bacteria to combat oxidative stress is imperative for their survival. The Alkyl hy... more The ability of bacteria to combat oxidative stress is imperative for their survival. The Alkyl hydroperoxide Reductase (AhpR) system, composed of the AhpC and AhpF proteins, is one of the dominant antioxidant defense systems required for scavenging hydrogen peroxide and organic peroxide. Therefore, it is necessary to understand the mechanism of the AhpR ensemble formation. In previous studies, we were able to elucidate conformational flexibility of Escherichia coli AhpF during the catalytic cycle and its binding site, the N-terminal domain (NTD), to AhpC. We proposed the novel binding and release mechanism of EcAhpC-AhpF, which is mediated by the well defined redox-state linked conformational changes associated with the C-terminal tail and active site regions of EcAhpC. Here, we have proceeded further to elucidate the solution structure of E. coli AhpC and the stable ensemble formation with EcAhpF using size-exclusion chromatography (SEC), dynamic light scattering (DLS) and small angle X-ray scattering (SAXS) techniques. The EcAhpC-AhpF complex structure with a stoichiometry of AhpC10:AhpF2 reveals that dimeric EcAhpF in its extended conformation enables the NTD disulphide centers to come in close proximity to the redox-active disulphide centers of EcAhpC, and provides an efficient electron transfer. Furthermore, the significance of the C-terminal tail of EcAhpC in ensemble formation is elucidated. SAXS data-based modeling revealed the flexible C-terminal tail of EcAhpC in solution, and its exposed nature, making it possible to contact the NTD of EcAhpF for stable complex formation.

Journal of Molecular Biology, Apr 5, 2002

N-terminal N-myristoylation is a lipid anchor modi®cation of eukaryotic and viral proteins target... more N-terminal N-myristoylation is a lipid anchor modi®cation of eukaryotic and viral proteins targeting them to membrane locations, thus changing the cellular function of modi®ed proteins. Protein myristoylation is critical in many pathways; e.g. in signal transduction, apoptosis, or alternative extracellular protein export. The myristoyl-CoA:protein N-myristoyltransferase (NMT) recognizes the sequence motif of appropriate substrate proteins at the N terminus and attaches the lipid moiety to the absolutely required N-terminal glycine residue. Reliable recognition of capacity for N-terminal myristoylation from the substrate protein sequence alone is desirable for proteome-wide function annotation projects but the existing PROSITE motif is not practical, since it produces huge numbers of false positive and even some false negative predictions.

J Mol Biol, 2002

Myristoylation by the myristoyl-CoA:protein N-myristoyltransferase (NMT) is an important lipid an... more Myristoylation by the myristoyl-CoA:protein N-myristoyltransferase (NMT) is an important lipid anchor modification of eukaryotic and viral proteins. Automated prediction of N-terminal N-myristoylation from the substrate protein sequence alone is necessary for large-scale sequence annotation projects but it requires a low rate of false positive hits in addition to a sufficient sensitivity.Our previous analysis of substrate protein sequence variability, NMT sequences and 3D structures has revealed motif properties in addition to the known PROSITE motif that are utilized in a new predictor described here. The composite prediction function (with separate ad hoc parameterization (a) for queries from non-fungal eukaryotes and their viruses and (b) for sequences from fungal species) consists of terms evaluating amino acid type preferences at sequences positions close to the N terminus as well as terms penalizing deviations from the physical property pattern of amino acid side-chains encoded in multi-residue correlation within the motif sequence. The algorithm has been validated with a self-consistency and two jack-knife tests for the learning set as well as with kinetic data for model substrates. The sensitivity in recognizing documented NMT substrates is above 95 % for both taxon-specific versions. The corresponding rate of false positive prediction (for sequences with an N-terminal glycine residue) is close to 0.5 %; thus, the technique is applicable for large-scale automated sequence database annotation. The predictor is available as public WWW-server with the URL http://mendel.imp.univie.ac.at/myristate/. Additionally, we propose a version of the predictor that identifies a number of proteolytic protein processing sites at internal glycine residues and that evaluates possible N-terminal myristoylation of the protein fragments.A scan of public protein databases revealed new potential NMT targets for which the myristoyl modification may be of critical importance for biological function. Among others, the list includes kinases, phosphatases, proteasomal regulatory subunit 4, kinase interacting proteins KIP1/KIP2, protozoan flagellar proteins, homologues of mitochondrial translocase TOM40, of the neuronal calcium sensor NCS-1 and of the cytochrome c-type heme lyase CCHL. Analyses of complete eukaryote genomes indicate that about 0.5 % of all encoded proteins are apparent NMT substrates except for a higher fraction in Arabidopsis thaliana (∼0.8 %).

J Mol Biol, 2002

N-terminal N-myristoylation is a lipid anchor modification of eukaryotic and viral proteins targe... more N-terminal N-myristoylation is a lipid anchor modification of eukaryotic and viral proteins targeting them to membrane locations, thus changing the cellular function of modified proteins. Protein myristoylation is critical in many pathways; e.g. in signal transduction, apoptosis, or alternative extracellular protein export. The myristoyl-CoA:protein N-myristoyltransferase (NMT) recognizes the sequence motif of appropriate substrate proteins at the N terminus and attaches the lipid moiety to the absolutely required N-terminal glycine residue. Reliable recognition of capacity for N-terminal myristoylation from the substrate protein sequence alone is desirable for proteome-wide function annotation projects but the existing PROSITE motif is not practical, since it produces huge numbers of false positive and even some false negative predictions.As a first step towards a new prediction method, it is necessary to refine the sequence motif coding for N-terminal N-myristoylation. Relying on the in-depth study of the amino acid sequence variability of substrate proteins, on binding site analyses in X-ray structures or 3D homology models for NMTs from various taxa, and on consideration of biochemical data extracted from the scientific literature, we found indications that, at least within a complete substrate protein, the N-terminal 17 protein residues experience different types of variability restrictions. We identified three motif regions: region 1 (positions 1-6) fitting the binding pocket; region 2 (positions 7-10) interacting with the NMT’s surface at the mouth of the catalytic cavity; and region 3 (positions 11-17) comprising a hydrophilic linker. Each region was characterized by physical requirements to single sequence positions or groups of positions regarding volume, polarity, backbone flexibility and other typical properties of amino acids (http://mendel.imp.univie.ac.at/myristate/). These specificity differences are confined partly to taxonomic ranges and are proposed for the design of NMT inhibitors in pathogenic fungal and protozoan systems including Aspergillus fumigatus, Leishmania major, Trypanosoma cruzi, Trypanosoma brucei, Giardia intestinalis, Entamoeba histolytica, Pneumocystis carinii, Strongyloides stercoralis and Schistosoma mansoni. An exhaustive search for NMT-homologues led to the discovery of two putative entomopoxviral NMTs.

Journal of Bioinformatics and Computational Biology, 2015

Next-generation sequencing advances are rapidly expanding the number of human mutations to be ana... more Next-generation sequencing advances are rapidly expanding the number of human mutations to be analyzed for causative roles in genetic disorders. Our Human Protein Mutation Viewer (HPMV) is intended to explore the biomolecular mechanistic significance of non-synonymous human mutations in protein-coding genomic regions. The tool helps to assess whether protein mutations affect the occurrence of sequence-architectural features (globular domains, targeting signals, post-translational modification sites, etc.). As input, HPMV accepts protein mutations - as UniProt accessions with mutations (e.g. HGVS nomenclature), genome coordinates, or FASTA sequences. As output, HPMV provides an interactive cartoon showing the mutations in relation to elements of the sequence architecture. A large variety of protein sequence architectural features were selected for their particular relevance to mutation interpretation. Clicking a sequence feature in the cartoon expands a tree view of additional information including multiple sequence alignments of conserved domains and a simple 3D viewer mapping the mutation to known PDB structures, if available. The cartoon is also correlated with a multiple sequence alignment of similar sequences from other organisms. In cases where a mutation is likely to have a straightforward interpretation (e.g. a point mutation disrupting a well-understood targeting signal), this interpretation is suggested. The interactive cartoon can be downloaded as standalone viewer in Java jar format to be saved and viewed later with only a standard Java runtime environment. The HPMV website is: http://hpmv.bii.a-star.edu.sg/ .

Molecular Machines Involved in Peroxisome Biogenesis and Maintenance, 2014

Computational studies based on high-throughput experimental datasets, some of which were even not... more Computational studies based on high-throughput experimental datasets, some of which were even not generated in the context of peroxisome research, have considerably shaped the understanding of the peroxisomal proteome. Most importantly, this research revealed to a considerable extent how the total peroxisomal proteome is composed and what is its network and pathway structure. Computational prediction tools have been instrumental for finding proteins that are imported into peroxisomes via canonical import mechanisms. Based on sequence homology considerations, functions of many experimentally uncharacterized proteins have been suggested and subsequently verified experimentally. As an example, the case of peroxisomal proteases is analyzed in detail.

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, 2004

Proteomics, 2004

In silico annotation techniques for post-translational modifications (PTMs) are important to gene... more In silico annotation techniques for post-translational modifications (PTMs) are important to generate biologically meaningful descriptions for sequences of experimentally uncharacterized proteins. Having previously contributed with predictors for lipid PTMs, we summarize our methodological experience. Rather than only looking for the sequence pattern in substrate sequences, a strategy aimed at creating a generalized model of substrate protein/enzyme interaction appears more appropriate since the number of known substrate sequences is small, and some of them are not sufficiently verified experimentally. Such a physical approach (in contrast to a mere textual analysis of substrate sequences) can also take into account other, heterogeneous biological data (mutations of substrate sequences, kinetic data, enzyme sequences/structures) with simple analytical expressions in the score function. Several lipid PTMs are encoded in the form of a small sequence region (with pronounced amino acid ...

Genome Biology, 2007

Proteins of the ring between ring fingers (RBR)-domain family are characterized by three groups o... more Proteins of the ring between ring fingers (RBR)-domain family are characterized by three groups of specifically clustered (typically eight) cysteine and histidine residues. Whereas the aminoterminal ring domain (N-RING) binds two zinc ions and folds into a classical cross-brace ring finger, the carboxy-terminal ring domain (C-RING) involves only one zinc ion. The threedimensional structure of the central ring domain, the IBR domain, is still unsolved. About 400 genes coding for RBR proteins have been identified in the genomes of uni-and multicellular eukaryotes and some of their viruses, but the family has not been found in archaea or bacteria. The RBR proteins are classified into 15 major subfamilies (besides some orphan cases) by the phylogenetic relationships of the RBR segments and the conservation of their sequence architecture. The RBR domain mediates protein-protein interactions and a subset of RBR proteins has been shown to function as E3 ubiquitin ligases. RBR proteins have attracted interest because of their involvement in diseases such as parkinsonism, dementia with Lewy bodies, and Alzheimer's disease, and in susceptibility to some intracellular bacterial pathogens. Here, we present an overview of the RBR-domain containing proteins and their subcellular localization, additional domains, function, specificity, and regulation.

Human Molecular Genetics, 2005

Mutations in the gene NYX, which encodes nyctalopin, lead to the retinal disorder congenital stat... more Mutations in the gene NYX, which encodes nyctalopin, lead to the retinal disorder congenital stationary night blindness which is characterised by defective night vision (nyctalopia) from birth. Nyctalopin is of unknown function but is predicted to be a secreted glycoprotein of the extracellular small leucine-rich repeat proteoglycan and protein (SLRP) family attached to the cell membrane in humans via a glycosylphosphatidylinositol (GPI) anchor but in mouse via a transmembrane domain. We investigated membrane association and attachment for human and mouse nyctalopin and show conclusively that human nyctalopin is a GPI anchored protein. Furthermore, the orthologous mouse protein, although it localises to the cell surface, is not GPI anchored. We also confirm both mouse and human nyctalopin are glycosylated.

Molecular cell, Jan 15, 2016

Cohesin is a ring-shaped protein complex that is capable of embracing DNA. Most of the ring circu... more Cohesin is a ring-shaped protein complex that is capable of embracing DNA. Most of the ring circumference is comprised of the anti-parallel intramolecular coiled coils of the Smc1 and Smc3 proteins, which connect globular head and hinge domains. Smc coiled coil arms contain multiple acetylated and ubiquitylated lysines. To investigate the role of these modifications, we substituted lysines for arginines to mimic the unmodified state and uncovered genetic interaction between the Smc arms. Using scanning force microscopy, we show that wild-type Smc arms associate with each other when the complex is not on DNA. Deacetylation of the Smc1/Smc3 dimers promotes arms' dissociation. Smc arginine mutants display loose packing of the Smc arms and, although they dimerize at the hinges, fail to connect the heads and associate with the DNA. Our findings highlight the importance of a "collapsed ring," or "rod," conformation of cohesin for its loading on the chromosomes.

Bioinformatics, 2004

Web-based servers implementing the DAS-TMfilter algorithm have been launched at three mirror site... more Web-based servers implementing the DAS-TMfilter algorithm have been launched at three mirror sites and their usage is described. The underlying computer program is an upgraded and modified version of the DAS-prediction method. The new server is designed to make distinction between protein sequences with and without transmembrane (TM) helices at a reasonably low rate of false positive prediction (∼1 among 100 unrelated queries) while the high efficiency of the original algorithm locating TM segments in queries is preserved (sensitivity of ∼95% among documented proteins with helical TM regions). Availability: The server operates at three mirror sites

Proteomics, Jun 1, 2004

In silico annotation techniques for post-translational modifications (PTMs) are important to gene... more In silico annotation techniques for post-translational modifications (PTMs) are important to generate biologically meaningful descriptions for sequences of experimentally uncharacterized proteins. Having previously contributed with predictors for lipid PTMs, we summarize our methodological experience. Rather than only looking for the sequence pattern in substrate sequences, a strategy aimed at creating a generalized model of substrate protein/enzyme interaction appears more appropriate since the number of known substrate sequences is small, and some of them are not sufficiently verified experimentally. Such a physical approach (in contrast to a mere textual analysis of substrate sequences) can also take into account other, heterogeneous biological data (mutations of substrate sequences, kinetic data, enzyme sequences/structures) with simple analytical expressions in the score function. Several lipid PTMs are encoded in the form of a small sequence region (with pronounced amino acid type preferences) that is connected to the substrate protein by a linker region with many conformationally flexible, hydrophilic residues. A score function composed of terms penalizing sequence properties known to be incompatible with productive substrate protein/enzyme complexes essentially unselects inappropriate queries. Also, we estimate the number of nonredundant sequences necessary for robust profile computation with statistical criteria, a number that is not reached in most cases of PTM prediction. Finally, we discuss the usage of evolutionary information in evaluating the functional importance of predicted PTMs in cases of motif conservation within sequence families.

Methods in Molecular Biology, 2016

As biomolecular sequencing is becoming the main technique in life sciences, functional interpreta... more As biomolecular sequencing is becoming the main technique in life sciences, functional interpretation of sequences in terms of biomolecular mechanisms with in silico approaches is getting increasingly significant. Function prediction tools are most powerful for protein-coding sequences; yet, the concepts and technologies used for this purpose are not well reflected in bioinformatics textbooks. Notably, protein sequences typically consist of globular domains and non-globular segments. The two types of regions require cardinally different approaches for function prediction. Whereas the former are classic targets for homology-inspired function transfer based on remnant, yet statistically significant sequence similarity to other, characterized sequences, the latter type of regions are characterized by compositional bias or simple, repetitive patterns and require lexical analysis and/or empirical sequence pattern-function correlations. The recipe for function prediction recommends first to find all types of non-globular segments and, then, to subject the remaining query sequence to sequence similarity searches. We provide an updated description of the ANNOTATOR software environment as an advanced example of a software platform that facilitates protein sequence-based function prediction.

Journal of Structural Biology, 2016

The ability of bacteria to combat oxidative stress is imperative for their survival. The Alkyl hy... more The ability of bacteria to combat oxidative stress is imperative for their survival. The Alkyl hydroperoxide Reductase (AhpR) system, composed of the AhpC and AhpF proteins, is one of the dominant antioxidant defense systems required for scavenging hydrogen peroxide and organic peroxide. Therefore, it is necessary to understand the mechanism of the AhpR ensemble formation. In previous studies, we were able to elucidate conformational flexibility of Escherichia coli AhpF during the catalytic cycle and its binding site, the N-terminal domain (NTD), to AhpC. We proposed the novel binding and release mechanism of EcAhpC-AhpF, which is mediated by the well defined redox-state linked conformational changes associated with the C-terminal tail and active site regions of EcAhpC. Here, we have proceeded further to elucidate the solution structure of E. coli AhpC and the stable ensemble formation with EcAhpF using size-exclusion chromatography (SEC), dynamic light scattering (DLS) and small angle X-ray scattering (SAXS) techniques. The EcAhpC-AhpF complex structure with a stoichiometry of AhpC10:AhpF2 reveals that dimeric EcAhpF in its extended conformation enables the NTD disulphide centers to come in close proximity to the redox-active disulphide centers of EcAhpC, and provides an efficient electron transfer. Furthermore, the significance of the C-terminal tail of EcAhpC in ensemble formation is elucidated. SAXS data-based modeling revealed the flexible C-terminal tail of EcAhpC in solution, and its exposed nature, making it possible to contact the NTD of EcAhpF for stable complex formation.

Journal of Molecular Biology, Apr 5, 2002

N-terminal N-myristoylation is a lipid anchor modi®cation of eukaryotic and viral proteins target... more N-terminal N-myristoylation is a lipid anchor modi®cation of eukaryotic and viral proteins targeting them to membrane locations, thus changing the cellular function of modi®ed proteins. Protein myristoylation is critical in many pathways; e.g. in signal transduction, apoptosis, or alternative extracellular protein export. The myristoyl-CoA:protein N-myristoyltransferase (NMT) recognizes the sequence motif of appropriate substrate proteins at the N terminus and attaches the lipid moiety to the absolutely required N-terminal glycine residue. Reliable recognition of capacity for N-terminal myristoylation from the substrate protein sequence alone is desirable for proteome-wide function annotation projects but the existing PROSITE motif is not practical, since it produces huge numbers of false positive and even some false negative predictions.

J Mol Biol, 2002

Myristoylation by the myristoyl-CoA:protein N-myristoyltransferase (NMT) is an important lipid an... more Myristoylation by the myristoyl-CoA:protein N-myristoyltransferase (NMT) is an important lipid anchor modification of eukaryotic and viral proteins. Automated prediction of N-terminal N-myristoylation from the substrate protein sequence alone is necessary for large-scale sequence annotation projects but it requires a low rate of false positive hits in addition to a sufficient sensitivity.Our previous analysis of substrate protein sequence variability, NMT sequences and 3D structures has revealed motif properties in addition to the known PROSITE motif that are utilized in a new predictor described here. The composite prediction function (with separate ad hoc parameterization (a) for queries from non-fungal eukaryotes and their viruses and (b) for sequences from fungal species) consists of terms evaluating amino acid type preferences at sequences positions close to the N terminus as well as terms penalizing deviations from the physical property pattern of amino acid side-chains encoded in multi-residue correlation within the motif sequence. The algorithm has been validated with a self-consistency and two jack-knife tests for the learning set as well as with kinetic data for model substrates. The sensitivity in recognizing documented NMT substrates is above 95 % for both taxon-specific versions. The corresponding rate of false positive prediction (for sequences with an N-terminal glycine residue) is close to 0.5 %; thus, the technique is applicable for large-scale automated sequence database annotation. The predictor is available as public WWW-server with the URL http://mendel.imp.univie.ac.at/myristate/. Additionally, we propose a version of the predictor that identifies a number of proteolytic protein processing sites at internal glycine residues and that evaluates possible N-terminal myristoylation of the protein fragments.A scan of public protein databases revealed new potential NMT targets for which the myristoyl modification may be of critical importance for biological function. Among others, the list includes kinases, phosphatases, proteasomal regulatory subunit 4, kinase interacting proteins KIP1/KIP2, protozoan flagellar proteins, homologues of mitochondrial translocase TOM40, of the neuronal calcium sensor NCS-1 and of the cytochrome c-type heme lyase CCHL. Analyses of complete eukaryote genomes indicate that about 0.5 % of all encoded proteins are apparent NMT substrates except for a higher fraction in Arabidopsis thaliana (∼0.8 %).

J Mol Biol, 2002

N-terminal N-myristoylation is a lipid anchor modification of eukaryotic and viral proteins targe... more N-terminal N-myristoylation is a lipid anchor modification of eukaryotic and viral proteins targeting them to membrane locations, thus changing the cellular function of modified proteins. Protein myristoylation is critical in many pathways; e.g. in signal transduction, apoptosis, or alternative extracellular protein export. The myristoyl-CoA:protein N-myristoyltransferase (NMT) recognizes the sequence motif of appropriate substrate proteins at the N terminus and attaches the lipid moiety to the absolutely required N-terminal glycine residue. Reliable recognition of capacity for N-terminal myristoylation from the substrate protein sequence alone is desirable for proteome-wide function annotation projects but the existing PROSITE motif is not practical, since it produces huge numbers of false positive and even some false negative predictions.As a first step towards a new prediction method, it is necessary to refine the sequence motif coding for N-terminal N-myristoylation. Relying on the in-depth study of the amino acid sequence variability of substrate proteins, on binding site analyses in X-ray structures or 3D homology models for NMTs from various taxa, and on consideration of biochemical data extracted from the scientific literature, we found indications that, at least within a complete substrate protein, the N-terminal 17 protein residues experience different types of variability restrictions. We identified three motif regions: region 1 (positions 1-6) fitting the binding pocket; region 2 (positions 7-10) interacting with the NMT’s surface at the mouth of the catalytic cavity; and region 3 (positions 11-17) comprising a hydrophilic linker. Each region was characterized by physical requirements to single sequence positions or groups of positions regarding volume, polarity, backbone flexibility and other typical properties of amino acids (http://mendel.imp.univie.ac.at/myristate/). These specificity differences are confined partly to taxonomic ranges and are proposed for the design of NMT inhibitors in pathogenic fungal and protozoan systems including Aspergillus fumigatus, Leishmania major, Trypanosoma cruzi, Trypanosoma brucei, Giardia intestinalis, Entamoeba histolytica, Pneumocystis carinii, Strongyloides stercoralis and Schistosoma mansoni. An exhaustive search for NMT-homologues led to the discovery of two putative entomopoxviral NMTs.

Journal of Bioinformatics and Computational Biology, 2015

Next-generation sequencing advances are rapidly expanding the number of human mutations to be ana... more Next-generation sequencing advances are rapidly expanding the number of human mutations to be analyzed for causative roles in genetic disorders. Our Human Protein Mutation Viewer (HPMV) is intended to explore the biomolecular mechanistic significance of non-synonymous human mutations in protein-coding genomic regions. The tool helps to assess whether protein mutations affect the occurrence of sequence-architectural features (globular domains, targeting signals, post-translational modification sites, etc.). As input, HPMV accepts protein mutations - as UniProt accessions with mutations (e.g. HGVS nomenclature), genome coordinates, or FASTA sequences. As output, HPMV provides an interactive cartoon showing the mutations in relation to elements of the sequence architecture. A large variety of protein sequence architectural features were selected for their particular relevance to mutation interpretation. Clicking a sequence feature in the cartoon expands a tree view of additional information including multiple sequence alignments of conserved domains and a simple 3D viewer mapping the mutation to known PDB structures, if available. The cartoon is also correlated with a multiple sequence alignment of similar sequences from other organisms. In cases where a mutation is likely to have a straightforward interpretation (e.g. a point mutation disrupting a well-understood targeting signal), this interpretation is suggested. The interactive cartoon can be downloaded as standalone viewer in Java jar format to be saved and viewed later with only a standard Java runtime environment. The HPMV website is: http://hpmv.bii.a-star.edu.sg/ .

Molecular Machines Involved in Peroxisome Biogenesis and Maintenance, 2014

Computational studies based on high-throughput experimental datasets, some of which were even not... more Computational studies based on high-throughput experimental datasets, some of which were even not generated in the context of peroxisome research, have considerably shaped the understanding of the peroxisomal proteome. Most importantly, this research revealed to a considerable extent how the total peroxisomal proteome is composed and what is its network and pathway structure. Computational prediction tools have been instrumental for finding proteins that are imported into peroxisomes via canonical import mechanisms. Based on sequence homology considerations, functions of many experimentally uncharacterized proteins have been suggested and subsequently verified experimentally. As an example, the case of peroxisomal proteases is analyzed in detail.

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, 2004

Proteomics, 2004

In silico annotation techniques for post-translational modifications (PTMs) are important to gene... more In silico annotation techniques for post-translational modifications (PTMs) are important to generate biologically meaningful descriptions for sequences of experimentally uncharacterized proteins. Having previously contributed with predictors for lipid PTMs, we summarize our methodological experience. Rather than only looking for the sequence pattern in substrate sequences, a strategy aimed at creating a generalized model of substrate protein/enzyme interaction appears more appropriate since the number of known substrate sequences is small, and some of them are not sufficiently verified experimentally. Such a physical approach (in contrast to a mere textual analysis of substrate sequences) can also take into account other, heterogeneous biological data (mutations of substrate sequences, kinetic data, enzyme sequences/structures) with simple analytical expressions in the score function. Several lipid PTMs are encoded in the form of a small sequence region (with pronounced amino acid ...

Genome Biology, 2007

Proteins of the ring between ring fingers (RBR)-domain family are characterized by three groups o... more Proteins of the ring between ring fingers (RBR)-domain family are characterized by three groups of specifically clustered (typically eight) cysteine and histidine residues. Whereas the aminoterminal ring domain (N-RING) binds two zinc ions and folds into a classical cross-brace ring finger, the carboxy-terminal ring domain (C-RING) involves only one zinc ion. The threedimensional structure of the central ring domain, the IBR domain, is still unsolved. About 400 genes coding for RBR proteins have been identified in the genomes of uni-and multicellular eukaryotes and some of their viruses, but the family has not been found in archaea or bacteria. The RBR proteins are classified into 15 major subfamilies (besides some orphan cases) by the phylogenetic relationships of the RBR segments and the conservation of their sequence architecture. The RBR domain mediates protein-protein interactions and a subset of RBR proteins has been shown to function as E3 ubiquitin ligases. RBR proteins have attracted interest because of their involvement in diseases such as parkinsonism, dementia with Lewy bodies, and Alzheimer's disease, and in susceptibility to some intracellular bacterial pathogens. Here, we present an overview of the RBR-domain containing proteins and their subcellular localization, additional domains, function, specificity, and regulation.