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- Bernsel, Andreas, et al.
(author)
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Prediction of membrane-protein topology from first principles
- 2008
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In: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 105:20, s. 7177-7181
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Journal article (peer-reviewed)abstract
- The current best membrane-protein topology-prediction methods are typically based on sequence statistics and contain hundreds of parameters that are optimized on known topologies of membrane proteins. However, because the insertion of transmembrane helices into the membrane is the outcome of molecular interactions among protein, lipids and water, it should be possible to predict topology by methods based directly on physical data, as proposed >20 years ago by Kyte and Doolittle. Here, we present two simple topology-prediction methods using a recently published experimental scale of position-specific amino acid contributions to the free energy of membrane insertion that perform on a par with the current best statistics-based topology predictors. This result suggests that prediction of membrane-protein topology and structure directly from first principles is an attainable goal, given the recently improved understanding of peptide recognition by the translocon.
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- Bernsel, Andreas, et al.
(author)
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TOPCONS : consensus prediction of membrane protein topology
- 2009
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In: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 37:Suppl. 2, s. W465-W468
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Journal article (peer-reviewed)abstract
- TOPCONS (http://topcons.net/) is a web server for consensus prediction of membrane protein topology. The underlying algorithm combines an arbitrary number of topology predictions into one consensus prediction and quantifies the reliability of the prediction based on the level of agreement between the underlying methods, both on the protein level and on the level of individual TM regions. Benchmarking the method shows that overall performance levels match the best available topology prediction methods, and for sequences with high reliability scores, performance is increased by approximately 10 percentage points. The web interface allows for constraining parts of the sequence to a known inside/outside location, and detailed results are displayed both graphically and in text format.
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- Ljungkvist, Göran, 1949, et al.
(author)
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Exploring a new method for the assessment of metal exposure by analysis of exhaled breath of welders
- 2022
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In: International Archives of Occupational and Environmental Health. - : Springer Science and Business Media LLC. - 0340-0131 .- 1432-1246. ; 95:6, s. 1255-1265
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Journal article (peer-reviewed)abstract
- Purpose Air monitoring has been the accepted exposure assessment of toxic metals from, e.g., welding, but a method characterizing the actual dose delivered to the lungs would be preferable. Sampling of particles in exhaled breath can be used for the biomonitoring of both endogenous biomarkers and markers of exposure. We have explored a new method for the sampling of metals in exhaled breath from the small airways in a study on welders. Methods Our method for particle sampling, Particles in Exhaled Air (PExA (R)), is based on particle counting and inertial impaction. We applied it on 19 stainless steel welders before and after a workday. In parallel, air monitoring of chromium, manganese and nickel was performed as well as blood sampling after work. Results Despite substantial exposure to welding fumes, we were unable to show any significant change in the metal content of exhaled particles after, compared with before, exposure. However, the significance might be obscured by a substantial analytical background noise, due to metal background in the sampling media and possible contamination during sampling, as an increase in the median metal contents were indicated. Conclusions If efforts to reduce background and contamination are successful, the PExA (R) method could be an important tool in the investigations of metals in exhaled breath, as the method collects particles from the small airways in contrast to other methods. In this paper, we discuss the discrepancy between our findings and results from studies, using the exhaled breath condensate (EBC) methodology.
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- Viklund, Håkan, 1974-
(author)
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Formalizing life : Towards an improved understanding of the sequence-structure relationship in alpha-helical transmembrane proteins
- 2007
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Doctoral thesis (other academic/artistic)abstract
- Genes coding for alpha-helical transmembrane proteins constitute roughly 25% of the total number of genes in a typical organism. As these proteins are vital parts of many biological processes, an improved understanding of them is important for achieving a better understanding of the mechanisms that constitute life.All proteins consist of an amino acid sequence that fold into a three-dimensional structure in order to perform its biological function. The work presented in this thesis is directed towards improving the understanding of the relationship between sequence and structure for alpha-helical transmembrane proteins. Specifically, five original methods for predicting the topology of alpha-helical transmembrane proteins have been developed: PRO-TMHMM, PRODIV-TMHMM, OCTOPUS, Toppred III and SCAMPI. A general conclusion from these studies is that approaches that use multiple sequence information achive the best prediction accuracy. Further, the properties of reentrant regions have been studied, both with respect to sequence and structure. One result of this study is an improved definition of the topological grammar of transmembrane proteins, which is used in OCTOPUS and shown to further improve topology prediction. Finally, Z-coordinates, an alternative system for representation of topological information for transmembrane proteins that is based on distance to the membrane center has been introduced, and a method for predicting Z-coordinates from amino acid sequence, Z-PRED, has been developed.
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