Predicting properties of intrinsically unstructured proteins

Bright, Joanne N.; Woolf, Thomas B.; Hoh, Jan H.

doi:10.1016/s0079-6107(01)00012-8

Cited by 75 publications

(83 citation statements)

References 110 publications

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“…Moreover, Yamada et al demonstrate that regions of FG-domains can be globularly compact (cohesive) and extended (repulsive) depending on their low charge and high charge content, respectively. This is in agreement with predictions (Bright et al, 2001) that intrinsically unstructured proteins can exhibit polyampholytic behavior (i.e., charged polymers consisting of both positively and negatively charged groups).…”

Section: Discussionsupporting

confidence: 92%

Converging on the function of intrinsically disordered nucleoporins in the nuclear pore complex

Peleg

Lim

2010

Biological Chemistry

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Several biological mechanisms involve proteins or proteinaceous components that are intrinsically disordered. A case in point pertains to the nuclear pore complex (NPC), which regulates molecular transport between the nucleus and the cytoplasm. NPC functionality is dependent on unfolded domains rich in Phe-Gly (FG) repeats (i.e., FG-domains) that collectively act to promote or hinder cargo translocation. To a large extent, our understanding of FG-domain behavior is limited to in vitro investigations given the difficulty to resolve them directly in the NPC. Nevertheless, recent findings indicate a collective convergence towards rationalizing FG-domain function. This review aims to glean further insight into this fascinating problem by taking an objective look at the boundary conditions and contextual details underpinning FG-domain behavior in the NPC. Here, we treat the FG-domains as being commensurate with polymeric chains to address ambiguities such as for instance, how FG-domains tethered to the central channel of the NPC would behave differently as compared with their free-floating counterparts in solution. By bringing such fundamental questions to the fore, this review seeks to illuminate the importance of how such parameters can hold influence over the structure-function relation of intrinsically disordered proteins in the NPC and beyond.

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Section: Discussionsupporting

confidence: 92%

Converging on the function of intrinsically disordered nucleoporins in the nuclear pore complex

Peleg

Lim

2010

Biological Chemistry

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“…Immunolabeling did not occur in TauRD fibrils (F) and trypsindigested hTau40 fibrils (E), which both lack the N-terminal end of hTau40. and has a diameter (≈2-5 nm) similar to many cytoplasmic proteins, one can assume that the AFM stylus mimics unspecific electrostatic interactions of proteins with Tau fibrils (24). Compared with "naked" TauRD fibrils devoid of the fuzzy coat, the AFM stylus shows lower adhesion to hTau40 fibrils surrounded by a fuzzy coat.…”

Section: Resultsmentioning

confidence: 99%

“…The adhesion of the negatively charged, hydrophilic AFM stylus to the fuzzy coat can mimic interactions between Tau fibrils and negatively charged hydrophilic biomolecules (24), such as tubulin (≈4-5 nm in diameter), the main interaction partner of Tau (27,28). At pH 7.4, the AFM stylus adhered at ≈20 pN to hTau40 fibrils independent of the ion concentration (Fig.…”

Section: Stiffness Of the Fuzzy Coat Depends On Electrolyte Concentramentioning

confidence: 92%

The fuzzy coat of pathological human Tau fibrils is a two-layered polyelectrolyte brush

Wegmann

Medalsy

Mandelkow

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

162

178

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The structure and properties of amyloid-like Tau fibrils accumulating in neurodegenerative diseases have been debated for decades. Although the core of Tau fibrils assembles from short β-strands, the properties of the much longer unstructured Tau domains protruding from the fibril core remain largely obscure. Applying immunogold transmission EM, and force-volume atomic force microscopy (AFM), we imaged human Tau fibrils at high resolution and simultaneously mapped their mechanical and adhesive properties. Tau fibrils showed a ≈16-nm-thick fuzzy coat that resembles a two-layered polyelectrolyte brush, which is formed by the unstructured short C-terminal and long N-terminal Tau domains. The mechanical and adhesive properties of the fuzzy coat are modulated by electrolytes and pH, and thus by the cellular environment. These unique properties of the fuzzy coat help in understanding how Tau fibrils disturb cellular interactions and accumulate in neurofibrillary tangles.protein aggregation | Alzheimer's disease | paired helical filaments

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“…More novel is the possibility that gp17 and other large subunit terminase proteins may belong to a class of recently described intrinsically unstructured proteins (40,41). Some of the properties of gp17 suggest that it fits criteria for inclusion in this class; thus, gp17 1) is implicated in a critical regulatory stage of phage development (DNA packaging); 2) interacts with multiple proteins, including gp16, gp20, gp32, and gp55 (17) and presumably DNA; 3) binds and hydrolyzes ATP; 4) is highly susceptible to proteolysis; and 5) exists in multiple interconvertible conformational states.…”

Section: Discussionmentioning

confidence: 99%

Isolation and Characterization of T4 Bacteriophage gp17 Terminase, a Large Subunit Multimer with Enhanced ATPase Activity

Baumann

Black

2003

Journal of Biological Chemistry

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Phage T4 terminase is a two-subunit enzyme that binds to the prohead portal protein and cuts and packages a headful of concatameric DNA. To characterize the T4 terminase large subunit, gp17 (70 kDa), gene 17 was cloned and expressed as a chitin-binding fusion protein.Following cleavage and release of gp17 from chitin, two additional column steps completed purification. The purification yielded (i) homogeneous soluble gp17 highly active in in vitro DNA packaging (ϳ10% efficiency, >10 8 phage/ml of extract); (ii) gp17 lacking endonuclease and contaminating protease activities; and (iii) a DNA-independent ATPase activity stimulated >100-fold by the terminase small subunit, gp16 (18 kDa), and modestly by portal gp20 and single-stranded binding protein gp32 multimers. Analyses revealed a preparation of highly active and slightly active gp17 forms, and the latter could be removed by immunoprecipitation using antiserum raised against a denatured form of the gp17 protein, leaving a terminase with the increased specific activity (ϳ400 ATPs/gp17 monomer/min) required for DNA packaging. Analysis of gp17 complexes separated from gp16 on glycerol gradients showed that a prolonged enhanced ATPase activity persisted after exposure to gp16, suggesting that constant interaction of the two proteins may not be required during packaging. Many dsDNA1 bacteriophage require the activity of two "terminase" proteins to cut and package concatameric DNA into assembled phage proheads. In T4, the gp16 (small subunit) and gp17 (large subunit) terminase proteins are essential proteins for DNA packaging. (Similar proteins are gpA and gpNu1 in phage, gp18 and gp19 in phage T7/T3, gp2 and gp3 in phage P22, and gp3 and gp16 in phage 29.) As generally found among these phage terminases, the T4 small subunit confers the specific DNA-binding/association properties (1-3). The large subunit contains the prohead-binding and putative DNAtranslocating ATPase activities (3-7). However, because the measured in vitro ATPase activities of isolated terminase proteins (8, 9) have been low in comparison with measured rates of ATP consumption in packaging (10, 11), the identification of terminases as DNA-translocating ATPases has been problematic. What is clear is that packaging is ATP-driven and involves the cooperation of the DNA-associated terminase proteins with the prohead-associated portal vertex protein (7, 12, 13) in phage T4, gp20.The T4 terminase large subunit protein, gp17, has proven difficult to purify because of the protein's limited solubility and toxicity to host cells (14). Coexpression with the gp16 small subunit reduces toxicity; thus, gp17 could be purified with gp16 in low amounts from a temperature-induced expression vector (4). A vector that makes gp17 with a 20-amino acid OmpT leader peptide results in low amounts of uninduced, soluble, and active protein, whereas the overexpressed protein is insoluble and inactive and resists renaturation (15). A His-tagged gp17 protein was also overexpressed and showed similar problems in protein solubi...

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Predicting properties of intrinsically unstructured proteins

Cited by 75 publications

References 110 publications

Converging on the function of intrinsically disordered nucleoporins in the nuclear pore complex

Converging on the function of intrinsically disordered nucleoporins in the nuclear pore complex

The fuzzy coat of pathological human Tau fibrils is a two-layered polyelectrolyte brush

Isolation and Characterization of T4 Bacteriophage gp17 Terminase, a Large Subunit Multimer with Enhanced ATPase Activity

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