| 1. |
- Björkholm, Patrik, et al.
(författare)
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Comparative analysis and unification of domain-domain interaction networks
- 2009
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Ingår i: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811. ; 25:22, s. 3020-5
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Tidskriftsartikel (refereegranskat)abstract
- MOTIVATION: Certain protein domains are known to preferentially interact with other domains. Several approaches have been proposed to predict domain-domain interactions, and over nine datasets are available. Our aim is to analyse the coverage and quality of the existing resources, as well as the extent of their overlap. With this knowledge, we have the opportunity to merge individual domain interaction networks to construct a comprehensive and reliable database. RESULTS: In this article we introduce a new approach towards comparing domain-domain interaction networks. This approach is used to compare nine predicted domain and protein interaction networks. The networks were used to generate a database of unified domain interactions, UniDomInt. Each interaction in the dataset is scored according to the benchmarked reliability of the sources. The performance of UniDomInt is an improvement compared to the underlying source networks and to another composite resource, Domine. AVAILABILITY: http://sonnhammer.sbc.su.se/download/UniDomInt/
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| 2. |
- Björkholm, Patrik, et al.
(författare)
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Identification of novel sphingolipid-binding motifs in mammalian membrane proteins
- 2014
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Ingår i: Biochimica et Biophysica Acta - Biomembranes. - : Elsevier BV. - 0005-2736 .- 1879-2642. ; 1838:8, s. 2066-2070
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Tidskriftsartikel (refereegranskat)abstract
- Specific interactions between transmembrane proteins and sphingolipids is a poorly understood phenomenon, and only a couple of instances have been identified. The best characterized example is the sphingolipid-binding motif VXXTLXXIY found in the transmembrane helix of the vesicular transport protein p24. Here, we have used a simple motif-probability algorithm (MOPRO) to identify proteins that contain putative sphingolipid-binding motifs in a dataset comprising proteomes from mammalian organisms. From these motif-containing candidate proteins, four with different numbers of transmembrane helices were selected for experimental study: i) major histocompatibility complex II Q alpha chain subtype (DQA1), ii) GPI-attachment protein 1 (GAA1), iii) tetraspanin-7 TSN7, and iv), metabotropic glutamate receptor 2 (GRM2). These candidates were subjected to photo-affinity labeling using radiolabeled sphingolipids, confirming all four candidate proteins as sphingolipid-binding proteins. The sphingolipid-binding motifs are enriched in the 7TM family of G-protein coupled receptors, predominantly in transmembrane helix 6. The ability of the motif-containing candidate proteins to bind sphingolipids with high specificity opens new perspectives on their respective regulation and function.
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| 3. |
- Björkholm, Patrik, et al.
(författare)
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Identification of novel sphingolipid-binding motifs in mammalian membrane proteins
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Specific interactions between transmembrane proteins and sphingolipids is a poorly understood phenomenon, and only a couple of instances have been identified. The best characterized example is the sphingolipid-binding motif VXXTLXXIY found in the transmembrane helix of the vesicular transport protein p24. Here, we have used a simple motif- probability algorithm (MOPRO) to identify proteins that contain putative sphingolipid-binding motifs in a dataset comprising full proteomes from mammalian organisms. Four selected candidate proteins all tested positive for sphingolipid binding in a photoaffinity assay. The putative sphingolipid-binding motifs are noticeably enriched in the 7TM family of G-protein coupled receptors, predominantly in transmembrane helix 6.
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| 4. |
- Björkholm, Patrik, et al.
(författare)
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Mitochondrial genomes are retained by selective constraints on protein targeting
- 2015
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 112:33, s. 10154-10161
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Tidskriftsartikel (refereegranskat)abstract
- Mitochondria are energy-producing organelles in eukaryotic cells considered to be of bacterial origin. The mitochondrial genome has evolved under selection for minimization of gene content, yet it is not known why not all mitochondrial genes have been transferred to the nuclear genome. Here, we predict that hydrophobic membrane proteins encoded by the mitochondrial genomes would be recognized by the signal recognition particle and targeted to the endoplasmic reticulum if they were nuclear-encoded and translated in the cytoplasm. Expression of the mitochondrially encoded proteins Cytochrome oxidase subunit 1, Apocytochrome b, and ATP synthase subunit 6 in the cytoplasm of HeLa cells confirms export to the endoplasmic reticulum. To examine the extent to which the mitochondrial proteome is driven by selective constraints within the eukaryotic cell, we investigated the occurrence of mitochondrial protein domains in bacteria and eukaryotes. The accessory protein domains of the oxidative phosphorylation system are unique to mitochondria, indicating the evolution of new protein folds. Most of the identified domains in the accessory proteins of the ribosome are also found in eukaryotic proteins of other functions and locations. Overall, one-third of the protein domains identified in mitochondrial proteins are only rarely found in bacteria. We conclude that the mitochondrial genome has been maintained to ensure the correct localization of highly hydrophobic membrane proteins. Taken together, the results suggest that selective constraints on the eukaryotic cell have played a major role in modulating the evolution of the mitochondrial genome and proteome.
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| 5. |
- Björkholm, Patrik, 1981-
(författare)
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Protein Interactions from the Molecular to the Domain Level
- 2014
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The basic unit of life is the cell, from single-cell bacteria to the largest creatures on the planet. All cells have DNA, which contains the blueprint for proteins. This information is transported in the form of messenger RNA from the genome to ribosomes where proteins are produced. Proteins are the main functional constituents of the cell, they usually have one or several functions and are the main actors in almost all essential biological processes. Proteins are what make the cell alive. Proteins are found as solitary units or as part of large complexes. Proteins can be found in all parts of the cell, the most common place being the cytoplasm, a central space in all cells. They are also commonly found integrated into or attached to various membranes.Membranes define the cell architecture. Proteins integrated into the membrane have a wide number of responsibilities: they are the gatekeepers of the cell, they secrete cellular waste products, and many of them are receptors and enzymes.The main focus of this thesis is the study of protein interactions, from the molecular level up to the protein domain level.In paper I use reoccurring local protein structures to try and predict what sections of a protein interacts with another part using only sequence information. In papers II and III we use a randomization approach on a membrane protein motif that we know interacts with a sphingomyelin lipid to find other candidate proteins that interact with sphingolipids. These are then experimentally verified as sphingolipid-binding. In the last paper, paper IV, we look at how protein domain interaction networks overlap and can be evaluated.
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| 6. |
- Björkholm, Patrik, et al.
(författare)
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Using multi-data hidden Markov models trained on local neighborhoods of protein structure to predict residue-residue contacts
- 2009
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Ingår i: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811. ; 25:10, s. 1264-1270
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Tidskriftsartikel (refereegranskat)abstract
- Motivation: Correct prediction of residue-residue contacts in proteins that lack good templates with known structure would take ab initio protein structure prediction a large step forward. The lack of correct contacts, and in particular long-range contacts, is considered the main reason why these methods often fail. Results: We propose a novel hidden Markov model (HMM)based method for predicting residue-residue contacts from protein sequences using as training data homologous sequences, predicted secondary structure and a library of local neighborhoods (local descriptors of protein structure). The library consists of recurring structural entities incorporating short-, medium- and long-range interactions and is general enough to reassemble the cores of nearly all proteins in the PDB. The method is tested on an external test set of 606 domains with no significant sequence similarity to the training set as well as 151 domains with SCOP folds not present in the training set. Considering the top 0.2 . L predictions (L = sequence length), our HMMs obtained an accuracy of 22.8% for long-range interactions in new fold targets, and an average accuracy of 28.6% for long-, medium- and short- range contacts. This is a significant performance increase over currently available methods when comparing against results published in the literature.
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| 7. |
- Björkholm, Patrik, et al.
(författare)
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Why mitochondria need a genome revisited
- 2017
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Ingår i: FEBS Letters. - : WILEY-BLACKWELL. - 0014-5793 .- 1873-3468. ; 591:1, s. 65-75
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Tidskriftsartikel (refereegranskat)abstract
- In this paper, we experimentally address the debate about why functional transfer of mitochondrial genes to the nucleus has been halted in some organismal groups and why cytosolic expression of mitochondrial proteins has proven remarkably difficult. By expressing all 13 human mitochondrial-encoded genes with strong mitochondrial-targeting sequences in the cytosol of human cells, we show that all proteins, except ATP8, are transported to the endoplasmic reticulum (ER). These results confirm and extend previous findings based on three mitochondrial genes lacking mitochondrial-targeting sequences that also were relocated to the ER during cytosolic expression. We conclude that subcellular protein targeting constitutes a major barrier to functional transfer of mitochondrial genes to the nuclear genome.
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| 8. |
- Botelho, Salomé Calado, et al.
(författare)
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TIM23-mediated insertion of transmembrane alpha-helices into the mitochondrial inner membrane
- 2011
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Ingår i: EMBO Journal. - : Wiley. - 0261-4189 .- 1460-2075. ; 30:6, s. 1003-1011
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Tidskriftsartikel (refereegranskat)abstract
- While overall hydrophobicity is generally recognized as the main characteristic of transmembrane (TM) alpha-helices, the only membrane system for which there are detailed quantitative data on how different amino acids contribute to the overall efficiency of membrane insertion is the endoplasmic reticulum (ER) of eukaryotic cells. Here, we provide comparable data for TIM23-mediated membrane protein insertion into the inner mitochondrial membrane of yeast cells. We find that hydrophobicity and the location of polar and aromatic residues are strong determinants of membrane insertion. These results parallel what has been found previously for the ER. However, we see striking differences between the effects elicited by charged residues flanking the TM segments when comparing the mitochondrial inner membrane and the ER, pointing to an unanticipated difference between the two insertion systems.
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| 9. |
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| 10. |
- Contreras, F.-Xabier, et al.
(författare)
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Molecular recognition of a single sphingolipid species by a protein's transmembrane domain
- 2012
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 481:7382, s. 525-529
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Tidskriftsartikel (refereegranskat)abstract
- Functioning and processing of membrane proteins critically depend on the way their transmembrane segments are embedded in the membrane. Sphingolipids are structural components of membranes and can also act as intracellular second messengers. Not much is known of sphingolipids binding to transmembrane domains (TMDs) of proteins within the hydrophobic bilayer, and how this could affect protein function. Here we show a direct and highly specific interaction of exclusively one sphingomyelin species, SM 18, with the TMD of the COPI machinery protein p24 (ref. 2). Strikingly, the interaction depends on both the headgroup and the backbone of the sphingolipid, and on a signature sequence (VXXTLXXIY) within the TMD. Molecular dynamics simulations show a close interaction of SM 18 with the TMD. We suggest a role of SM 18 in regulating the equilibrium between an inactive monomeric and an active oligomeric state of the p24 protein, which in turn regulates COPI-dependent transport. Bioinformatic analyses predict that the signature sequence represents a conserved sphingolipid-binding cavity in a variety of mammalian membrane proteins. Thus, in addition to a function as second messengers, sphingolipids can act as cofactors to regulate the function of transmembrane proteins. Our discovery of an unprecedented specificity of interaction of a TMD with an individual sphingolipid species adds to our understanding of why biological membranes are assembled from such a large variety of different lipids.
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