@article {18695,
	title = {Avid interactions underlie the Lys63-linked polyubiquitin binding specificities observed for UBA domains},
	journal = {Nature Structural \& Molecular Biology},
	volume = {16},
	year = {2009},
	month = {2009///},
	pages = {883 - 889},
	abstract = {Ubiquitin (denoted Ub) receptor proteins as a group must contain a diverse set of binding specificities to distinguish the many forms of polyubiquitin (polyUb) signals. Previous studies suggested that the large class of ubiquitin-associated (UBA) domains contains members with intrinsic specificity for Lys63-linked polyUb or Lys48-linked polyUb, thus explaining how UBA-containing proteins can mediate diverse signaling events. Here we show that previously observed Lys63-polyUb selectivity in UBA domains is the result of an artifact in which the dimeric fusion partner, glutathione S-transferase (GST), positions two UBAs for higher affinity, avid interactions with Lys63-polyUb, but not with Lys48-polyUb. Freed from GST, these UBAs are either nonselective or prefer Lys48-polyUb. Accordingly, NMR experiments reveal no Lys63-polyUb{\textendash}specific binding epitopes for these UBAs. We reexamine previous conclusions based on GST-UBAs and present an alternative model for how UBAs achieve a diverse range of linkage specificities.},
	keywords = {apoptosis, basic cellular processes, Biochemistry, biophysics, cell biology, cell cycle, cell surface proteins, cell-cell interactions, checkpoints, chromatin, chromatin remodeling, chromatin structure, content, DNA recombination, DNA repair, DNA replication, Gene expression, Genetics, intracellular signaling, journal, macromolecules, mechanism, membrane processes, molecular, molecular basis of disease, molecular biology, molecular interactions, multi-component complexes, nature publishing group, nature structural molecular biology, nucleic acids, protein degradation, protein folding, protein processing, Proteins, regulation of transcription, regulation of translation, RNA, RNA processing, RNAi, signal transduction, single molecule studies, structure and function of proteins, transcription, translation},
	isbn = {1545-9993},
	doi = {10.1038/nsmb.1637},
	url = {http://www.nature.com/nsmb/journal/v16/n8/abs/nsmb.1637.html},
	author = {Sims,Joshua J. and Haririnia,Aydin and Dickinson,Bryan C. and Fushman, David and Cohen,Robert E.}
}
@article {12888,
	title = {Microbial oceanography in a sea of opportunity},
	journal = {Nature},
	volume = {459},
	year = {2009},
	month = {2009/05/13/},
	pages = {180 - 184},
	abstract = {Plankton use solar energy to drive the nutrient cycles that make the planet habitable for larger organisms. We can now explore the diversity and functions of plankton using genomics, revealing the gene repertoires associated with survival in the oceans. Such studies will help us to appreciate the sensitivity of ocean systems and of the ocean{\textquoteright}s response to climate change, improving the predictive power of climate models.},
	keywords = {Astronomy, astrophysics, Biochemistry, Bioinformatics, Biology, biotechnology, cancer, cell cycle, cell signalling, climate change, Computational Biology, development, developmental biology, DNA, drug discovery, earth science, ecology, environmental science, Evolution, evolutionary biology, functional genomics, Genetics, Genomics, geophysics, immunology, interdisciplinary science, life, marine biology, materials science, medical research, medicine, metabolomics, molecular biology, molecular interactions, nanotechnology, Nature, neurobiology, neuroscience, palaeobiology, pharmacology, Physics, proteomics, quantum physics, RNA, Science, science news, science policy, signal transduction, structural biology, systems biology, transcriptomics},
	isbn = {0028-0836},
	doi = {10.1038/nature08056},
	url = {http://www.nature.com/nature/journal/v459/n7244/abs/nature08056.html},
	author = {Bowler,Chris and Karl,David M. and Rita R Colwell}
}
@article {18717,
	title = {Structural Biology: Analysis of {\textquoteright}downhill{\textquoteright} protein folding; Analysis of protein-folding cooperativity (Reply)},
	journal = {Nature},
	volume = {445},
	year = {2007},
	month = {2007/02/15/},
	pages = {E17-E18 - E17-E18},
	abstract = {Ferguson et al. and Zhou and Bai criticize the quality of our nuclear magnetic resonance (NMR) data and atom-by-atom analysis of global {\textquoteright}downhill{\textquoteright} folding, also claiming that the data are compatible with two-state folding.},
	keywords = {Astronomy, astrophysics, Biochemistry, Bioinformatics, Biology, biotechnology, cancer, cell cycle, cell signalling., climate change, Computational Biology, development, developmental biology, DNA, drug discovery, earth science, ecology, environmental science, Evolution, evolutionary biology, functional genomics, Genetics, Genomics, geophysics, immunology, interdisciplinary science, life, marine biology, materials science, medical research, medicine, metabolomics, molecular biology, molecular interactions, nanotechnology, Nature, neurobiology, neuroscience, palaeobiology, pharmacology, Physics, proteomics, quantum physics, RNA, Science, science news, science policy, signal transduction, structural biology, systems biology, transcriptomics},
	isbn = {0028-0836},
	doi = {10.1038/nature05645},
	url = {http://www.nature.com/nature/journal/v445/n7129/full/nature05645.html?lang=en},
	author = {Sadqi,Mourad and Fushman, David and Mu{\~n}oz,Victor}
}
@article {18699,
	title = {Diverse polyubiquitin interaction properties of ubiquitin-associated domains},
	journal = {Nature Structural \& Molecular Biology},
	volume = {12},
	year = {2005},
	month = {2005///},
	pages = {708 - 714},
	abstract = {The ubiquitin-associated (UBA) domain occurs frequently in proteins involved in ubiquitin-dependent signaling pathways. Although polyubiquitin chain binding is considered to be a defining feature of the UBA domain family, the generality of this property has not been established. Here we have surveyed the polyubiquitin interaction properties of 30 UBA domains, including 16 of 17 occurrences in budding yeast. The UBA domains sort into four classes that include linkage-selective polyubiquitin binders and domains that bind different chains (and monoubiquitin) in a nondiscriminatory manner; one notable class (30\%) did not bind any ubiquitin ligand surveyed. The properties of a given UBA domain are conserved from yeast to mammals. Their functional relevance is further suggested by the ability of an ectopic UBA domain to alter the specificity of a deubiquitylating enzyme in a predictable manner. Conversely, non-UBA sequences can modulate the interaction properties of a UBA domain.},
	keywords = {apoptosis, basic cellular processes, Biochemistry, biophysics, cell biology, cell cycle, cell surface proteins, cell-cell interactions, checkpoints, chromatin, chromatin remodeling, chromatin structure, content, DNA recombination, DNA repair, DNA replication, Gene expression, Genetics, intracellular signaling, journal, macromolecules, mechanism, membrane processes, molecular, molecular basis of disease, molecular biology, molecular interactions, multi-component complexes, nature publishing group, nature structural molecular biology, nucleic acids, protein degradation, protein folding, protein processing, Proteins, regulation of transcription, regulation of translation, RNA, RNA processing, RNAi, signal transduction, single molecule studies, structure and function of proteins, transcription, translation},
	isbn = {1545-9993},
	doi = {10.1038/nsmb962},
	url = {http://www.nature.com/nsmb/journal/v12/n8/full/nsmb962.html},
	author = {Raasi,Shahri and Varadan,Ranjani and Fushman, David and Pickart,Cecile M.}
}
