| 1. |
- Hedin, Linnea E., et al.
(författare)
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An Introduction to Membrane Proteins
- 2011
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Ingår i: Journal of Proteome Research. - : American Chemical Society (ACS). - 1535-3893 .- 1535-3907. ; 10:8, s. 3324-3331
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Tidskriftsartikel (refereegranskat)abstract
- alpha-Helical membrane proteins are important for many biological functions. Due to physicochemical constraints, the structures of membrane proteins differ from the structure of soluble proteins. Historically, membrane protein structures were assumed to be more or less two-dimensional, consisting of long, straight, membrane-spanning parallel helices packed against each other. However, during the past decade, a number of the new membrane protein structures cast doubt on this notion. Today, it is evident that the structures of many membrane proteins are equally complex as for many soluble proteins. Here, we review this development and discuss the consequences for our understanding of membrane protein biogenesis, folding, evolution, and bioinformatics.
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| 2. |
- Hedin, Linnea E, 1981-
(författare)
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Intra- and intermolecular interactions in proteins : Studies of marginally hydrophobic transmembrane alpha-helices and protein-protein interactions.
- 2010
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Most of the processes in a living cell are carried out by proteins. Depending on the needs of the cell, different proteins will interact and form the molecular machines demanded for the moment. A subset of proteins called integral membrane proteins are responsible for the interchange of matter and information across the biological membrane, the lipid bilayer enveloping and defining the cell. Most of these proteins are co-translationally integrated into the membrane by the Sec translocation machinery. This thesis addresses two questions that have emerged during the last decade. The first concerns membrane proteins: a number of α-helices have been observed to span the membrane in the obtained three-dimensional structures even though these helices are predicted not to be hydrophobic enough to be recognized by the translocon for integration. We show for a number of these marginally hydrophobic protein segments that they indeed do not insert well outside of their native context, but that their local sequence context can improve the level of integration mediated by the translocon. We also find that many of these helices are overlapped by more hydrophobic segments. We propose, supported by experimental results, that the latter are initially integrated into the membrane, followed by post-translational structural rearrangements. Finally, we investigate whether the integration of the marginally hydrophobic TMHs of the lactose permease of Escherichia coli is facilitated by the formation of hairpin structures. However our combined efforts of computational simulations and experimental investigations find no evidence for this. The second question addressed in this thesis is that of the interpretation of the large datasets on which proteins that interact with each other in a cell. We have analyzed the results from several large-scale investigations concerning protein interactions in yeast and draw conclusions regarding the biases, strengths and weaknesses of these datasets and the methods used to obtain them.
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| 3. |
- Hedin, Linnea E., et al.
(författare)
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Membrane Insertion of Marginally Hydrophobic Transmembrane Helices Depends on Sequence Context
- 2010
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Ingår i: Journal of Molecular Biology. - : Elsevier BV. - 0022-2836 .- 1089-8638. ; 396:1, s. 221-229
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Tidskriftsartikel (refereegranskat)abstract
- In mammalian cells, most integral membrane proteins are initially inserted into the endoplasmic reticulum membrane by the so-called Sec61 translocon. However, recent predictions suggest that many transmembrane helices (TMHs) in multispanning membrane proteins are not sufficiently hydrophobic to be recognized as such by the translocon. In this study, we have screened 16 marginally hydrophobic TMHs from membrane proteins of known three-dimensional structure. Indeed, most of these TMHs do not insert efficiently into the endoplasmic reticulum membrane by themselves. To test if loops or TMHs immediately upstream or downstream of a marginally hydrophobic helix might influence the insertion efficiency, insertion of marginally hydrophobic helices was also studied in the presence of their neighboring loops and helices. The results show that flanking loops and nearest-neighbor TMHs are sufficient to ensure the insertion of many marginally hydrophobic helices. However, for at least two of the marginally hydrophobic helices, the local interactions are not enough, indicating that post-insertional rearrangements are involved in the folding of these proteins.
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| 4. |
- Kauko, Anni, et al.
(författare)
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Repositioning of transmembrane alpha-helices during membrane protein folding
- 2010
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Ingår i: Journal of Molecular Biology. - : Elsevier BV. - 0022-2836 .- 1089-8638. ; 397:1, s. 190-201
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Tidskriftsartikel (refereegranskat)abstract
- We have determined the optimal placement of individual transmembrane helices in the Pyrococcus horikoshii Glt(Ph) glutamate transporter homolog in the membrane. The results are in close agreement with theoretical predictions based on hydrophobicity, but do not, in general, match the known three-dimensional structure, suggesting that transmembrane helices can be repositioned relative to the membrane during folding and oligomerization. Theoretical analysis of a database of membrane protein structures provides additional support for this idea. These observations raise new challenges for the structure prediction of membrane proteins and suggest that the classical two-stage model often used to describe membrane protein folding needs to be modified.
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| 5. |
- Vereshchaga, Yana, et al.
(författare)
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Insertion Properties of Marginally Hydrophobic Helices in the LacY Lactose Permease Transporter
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Transmembrane helices are generally believed to be recognized individually by the translocon based on theirhydrophobicity, but it has been proposed that they could also be recognized as pairs of helices. The fact thatmost transmembrane helices are individually clearly hydrophobic seems to support separate helix insertion,but there are important exceptions where the helices are only borderline hydrophilic, at least according tosequence-based prediction. Conrming these patterns and characterizing their role for insertion of helices isan important part in deciphering membrane protein insertion and folding. Here, we use a combination ofsequence bioinformatics, simplied physical modeling, and experiments to investigate whether helices in theLacY lactose permease transporter are recognized by the translocon, and if not whether helix-helix interactionsmight stabilize their insertion. From the experimentally determined biological hydrophobicity scale, ve out of thetwelve transmembrane segments of LacY are predicted to have low spontaneous insertion, which is qualitativelyconrmed in a simplied simulation model using an implicit membrane environment as well as experimentallyin vitro. For some pairs a small, but signicant, increase in insertion eciency was seen both in the simulationsand in the in vitro system. However, the overall insertion eciency is only marginally increased when pairsof borderline hydrophobic helices are co-inserted, which suggests that translocon-mediated membrane insertionpredominantly recognizes individual helices. It also seems to imply that stabilization of marginally hydrophobichelices - at least for LacY - is a collective eect in the nal folded membrane protein, rather than caused by favorable interactions and hairpin formation during insertion.
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