Affiliation: Stockholm University
- Network analysis of metabolic enzyme evolution in Escherichia coliSara Light
Stockholm Bioinformatics Center, Department of Biochemistry and Biophysics, Stockholm Center for Physics, Astronomy and Biotechnology, Stockholm University, Stockholm SE 10691, Sweden
BMC Bioinformatics 5:15. 2004..We here investigate the evolution of the metabolism in E. coli viewed as a single network using EcoCyc...
- Preferential attachment in the evolution of metabolic networksSara Light
Stockholm Bioinformatics Center, Department of Biochemistry and Biophyhsics, AlbaNova University Center, Stockholm University, Stockholm SE 10691, Sweden
BMC Genomics 6:159. 2005..In networks which have evolved through preferential attachment older nodes should have a higher average connectivity than younger nodes. Here we have investigated preferential attachment in the context of metabolic networks...
- What properties characterize the hub proteins of the protein-protein interaction network of Saccharomyces cerevisiae?Diana Ekman
Stockholm Bioinformatics Center, Stockholm University, Stockholm, Sweden
Genome Biol 7:R45. 2006..Therefore, we have investigated what differentiates hubs from non-hubs and static hubs (party hubs) from dynamic hubs (date hubs) in the protein-protein interaction network of Saccharomyces cerevisiae...
- Quantitative assessment of the structural bias in protein-protein interaction assaysAsa K Björklund
Department of Biochemistry and Biophysics, Center for Biological Membrane Research Stockholm Bioinformatics Center, Stockholm University, Stockholm, Sweden
Proteomics 8:4657-67. 2008..Most importantly, we show that there are method-specific biases in PPI experiments. Thus, care should be taken before drawing strong conclusions based on a single dataset...
- Improved production of membrane proteins in Escherichia coli by selective codon substitutionsMorten H H Nørholm
Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE 106 91 Stockholm, Sweden Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Alle 6, DK 2970 Hørsholm, Denmark Electronic address
FEBS Lett 587:2352-8. 2013..We conclude that coding sequences can be re-wired for high-level protein expression by selective engineering of the 5' coding sequence with synonymous codons, thus circumventing the need to consider whole sequence optimization. ..
- Nebulin: a study of protein repeat evolutionAsa K Björklund
Center for Biological Membrane Research, Stockholm Bioinformatics Center, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
J Mol Biol 402:38-51. 2010..In fact, segmental duplications are found three to six times more often in long repeated genes than expected by chance...
- Long indels are disordered: a study of disorder and indels in homologous eukaryotic proteinsSara Light
Science for Life Laboratory, Stockholm University, Solna, Sweden
Biochim Biophys Acta 1834:890-7. 2013..This article is part of a Special Issue entitled: The emerging dynamic view of proteins: Protein plasticity in allostery, evolution and self-assembly...
- The evolution of filamin-a protein domain repeat perspectiveSara Light
Center for Biomembrane Research, Department of Biochemistry and Biophysics, Science for Life Laboratory, Bioinformatics Infrastructure for Life Sciences, Stockholm University, SE 17121 Solna, Sweden
J Struct Biol 179:289-98. 2012..Given that invertebrate integrin shows more similarity to the weaker filamin binder, integrin β3, it is possible that the distance between integrin-binding domains is not as crucial for invertebrate filamins as for vertebrates...
- Domain rearrangements in protein evolutionAsa K Björklund
Stockholm Bioinformatics Center, Stockholm University, SE 10691 Stockholm, Sweden
J Mol Biol 353:911-23. 2005..Finally, the evolution of multi-domain proteins is exemplified by a closer study of the evolution of two protein families, non-receptor tyrosine kinases and RhoGEFs...
- The impact of splicing on protein domain architectureSara Light
Science for Life Laboratory, Stockholm University, Box 1031 SE 171 21 Solna, Sweden
Curr Opin Struct Biol 23:451-8. 2013..Here, we review the state of the art methods for identification of functional isoforms and present a summary of what is known, thus far, about alternative splicing with regard to protein domain architectures...
- Manipulating the genetic code for membrane protein production: what have we learnt so far?Morten H H Nørholm
Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE 106 91, Sweden
Biochim Biophys Acta 1818:1091-6. 2012..This article is part of a Special Issue entitled: Protein Folding in Membranes...
- Evolution after gene duplication: models, mechanisms, sequences, systems, and organismsChristian Roth
Department of Molecular Biology, University of Wyoming, Laramie, Wyoming 82071, USA
J Exp Zool B Mol Dev Evol 308:58-73. 2007..single gene duplication. Lastly, the role that these processes may have played in driving speciation is examined...