Intrinsically disordered proteins: lessons from colicins

Hecht, Oliver; Macdonald, Colin; Moore, Geoffrey R.

doi:10.1042/bst20120198

Cited by 6 publications

(7 citation statements)

References 36 publications

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“…This global value, however, hides the complex dynamics of the isolated T-domain. Results presented here and elsewhere ( 14 , 23 , 24 , 60 ) point to the TABS region, with its aromatic groups, as the driver for compaction. More precisely, NMR chemical shift analysis suggests that residues 62–67 form a β -structure in the isolated T-domain ( 24 ), which is in harmony with predictions ( 14 ).…”

Section: Discussionsupporting

confidence: 58%

The Two-State Prehensile Tail of the Antibacterial Toxin Colicin N

Johnson

Solovyova

Hecht

et al. 2017

Biophysical Journal

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Intrinsically disordered regions within proteins are critical elements in many biomolecular interactions and signaling pathways. Antibacterial toxins of the colicin family, which could provide new antibiotic functions against resistant bacteria, contain disordered N-terminal translocation domains (T-domains) that are essential for receptor binding and the penetration of the Escherichia coli outer membrane. Here we investigate the conformational behavior of the T-domain of colicin N (ColN-T) to understand why such domains are widespread in toxins that target Gram-negative bacteria. Like some other intrinsically disordered proteins in the solution state of the protein, ColN-T shows dual recognition, initially interacting with other domains of the same colicin N molecule and later, during cell killing, binding to two different receptors, OmpF and TolA, in the target bacterium. ColN-T is invisible in the high-resolution x-ray model and yet accounts for 90 of the toxin’s 387 amino acid residues. To reveal its solution structure that underlies such a dynamic and complex system, we carried out mutagenic, biochemical, hydrodynamic and structural studies using analytical ultracentrifugation, NMR, and small-angle x-ray scattering on full-length ColN and its fragments. The structure was accurately modeled from small-angle x-ray scattering data by treating ColN as a flexible system, namely by the ensemble optimization method, which enables a distribution of conformations to be included in the final model. The results reveal, to our knowledge, for the first time the dynamic structure of a colicin T-domain. ColN-T is in dynamic equilibrium between a compact form, showing specific self-recognition and resistance to proteolysis, and an extended form, which most likely allows for effective receptor binding.

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Section: Discussionsupporting

confidence: 58%

The Two-State Prehensile Tail of the Antibacterial Toxin Colicin N

Johnson

Solovyova

Hecht

et al. 2017

Biophysical Journal

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“…Some of these recent reviews are dedicated to specific proteins, such as myelin basic protein (191), measles virus nucleoprotein and phosphoprotein (192), HIV-1 Vif protein (193), p53 (194), α-synuclein (195)(196)(197)(198), the genome-linked protein VPg of plant viruses (199), CP12 (200), HMGA (201), EWS-FLI1 fusion protein (202), Hox transcription factor (203), and CBP/p300 (204), to name a few. Other reviews talk about roles of intrinsic disorder in various classes and families of IDPs or protein complexes (e.g., colicins (205), cell cycle regulators p21 and p27 (206,207), neurofilamets (208), LEA proteins (209), steroid hormone receptors (210), protein Ser/Thr phosphatase-1-interacting proteins (211), histone proteins (212), HSF transcription factor family (213), GRASS proteins (214), the nuclear pore complex (215,216), extracellular matrix (217), 14-3-3 interaction network 218…”

Section: Intrinsically Disordered Proteins Idps 261 Conceptmentioning

confidence: 99%

The triple power of D³: Protein intrinsic disorder in degenerative diseases

Uversky¹

2014

Front Biosci

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This review is an update of an article published four years ago (Uversky V.N. (2009) Intrinsically disordered proteins in neurodegenerative diseases: another illustration of the D² concept. Frontiers in Bioscience 14, 5188-5238). The major goal of this review is to show the interconnections between intrinsically disordered proteins (IDPs) and human neurodegeneration. This brings to existence a new D³ concept: protein intrinsic Disorder in neuroDegenerative Diseases. An important aspect of the D³ concept is that it deals with three D³'s, emphasizing that intrinsically Disordered proteins are abundantly found in various neuroDegenerative Diseases (the first D³), that these IDPs provoke neuroDegeneration due to their Dysfunctionality (the second D³), and that neuroDegeneration-related IDPs are often controlled by other Disordered proteins (the third D³).

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“…where and are adjustable constants to consider specific denaturation profiles. The general tendency described in (9) dictates that the rate at which urea or GdnHCl denatures protein is constant. Fully denatured systems are reached at a particular concentration ⋆ .…”

Section: Full Analytical Solution To Ezm For Linear Denaturation Profmentioning

confidence: 99%

“…A large class of proteins known as intrinsically disordered proteins (IDPs) is one of the most outstanding examples of this category. IDPs can show a high level of biological activity even if the protein is in one of the states associated with the disordered ensemble [6][7][8][9]. The transition from → has been, accordingly, a subject of intense research.…”

Section: Introductionmentioning

confidence: 99%

Exact Solution to the Extended Zwanzig Model for Quasi-Sigmoidal Chemically Induced Denaturation Profiles: Specific Heat and Configurational Entropy

Aguilar-Pineda

Olivares‐Quiroz

2014

International Journal of Statistical Mechanics

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Temperature and chemically induced denaturation comprise two of the most characteristic mechanisms to achieve the passage from the native stateNto any of the unstructured statesDjin the denatured ensemble in proteins and peptides. In this work we present a full analytical solution for the configurational partition function𝒵qsof a homopolymer chain poly-X in the extended Zwanzig model (EZM) for a quasisigmoidal denaturation profile. This solution is built up from an EZM exact solution in the case where the fractionαof native contacts follows exact linear dependence on denaturant’s concentrationζ; thus an analytical solution for𝒵Lin the case of an exact linear denaturation profile is also provided. A recently established connection between the numberνof potential nonnative conformations per residue and temperature-independent helical propensityωcomplements the model in order to identify specific proteinogenic poly-X chains, where X represents any of the twenty naturally occurring aminoacid residues. From𝒵qs, equilibrium thermodynamic potentials like entropy𝒮and average internal energy〈E〉and thermodynamic susceptibilities like specific heatC𝓋are calculated for poly-valine (poly-V) and poly-alanine (poly-A) chains. The influence of the rate at which native contacts denature as function ofζon thermodynamic stability is also discussed.

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Intrinsically disordered proteins: lessons from colicins

Cited by 6 publications

References 36 publications

The Two-State Prehensile Tail of the Antibacterial Toxin Colicin N

The Two-State Prehensile Tail of the Antibacterial Toxin Colicin N

The triple power of D³: Protein intrinsic disorder in degenerative diseases

Exact Solution to the Extended Zwanzig Model for Quasi-Sigmoidal Chemically Induced Denaturation Profiles: Specific Heat and Configurational Entropy

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