The Subunit Interfaces of Weakly Associated Homodimeric Proteins

Dey, Sucharita; Pal, Arumay; Chakrabarti, Pinak; Janin, Joël

doi:10.1016/j.jmb.2010.02.020

Cited by 102 publications

(112 citation statements)

References 113 publications

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“…Here, m* is the number of amino acid classes for which p(i) 0, and n is the number of sequences in the alignment. Subsequently, the average entropy of the whole polypeptide chain calculated in this way was used to normalize S i , the value of which may depend on the choice of the aligned sequences, their number, and their diversity (68). Thus, S i Ͻ 1 implies a stronger conservation relative to the polypeptide as a whole.…”

Section: Methodsmentioning

confidence: 99%

“…In addition, we calculated the buried surface area for each amino acid residue contributing to the interface between two subunits in the crystallographic trimer (PDB entry 3OEQ) as well as between trimers in the hexamer model described above. Areaweighted average values S interf and S surf (Table 3) could then be calculated using the general equation from Dey et al (68),…”

Section: Methodsmentioning

confidence: 99%

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The Molecular Basis of Iron-induced Oligomerization of Frataxin and the Role of the Ferroxidation Reaction in Oligomerization

Söderberg

Rajan

Shkumatov

et al. 2013

Journal of Biological Chemistry

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Background: Iron-induced oligomerization of frataxin is still poorly understood. Results: The molecular basis of iron-induced oligomerization of yeast and bacterial frataxin is revealed. Catalyzed ferroxidation is required for correct oligomerization of Yfh1. Conclusion: Frataxin forms different oligomeric species at physiological conditions. Significance: Iron availability controls frataxin oligomerization, which in turn may control the processes that require iron delivery by frataxin.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

The Molecular Basis of Iron-induced Oligomerization of Frataxin and the Role of the Ferroxidation Reaction in Oligomerization

Söderberg

Rajan

Shkumatov

et al. 2013

Journal of Biological Chemistry

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show abstract

“…Those studies reveal that weak complexes (e.g. K D in the M range) have loosely packed interfaces that are smaller (by a factor of 2.4 on average) than in tight complexes (125).…”

Section: Structural Models Of Henipavirus N Tail -P Xd Complexes and mentioning

confidence: 99%

Characterization of the Interactions between the Nucleoprotein and the Phosphoprotein of Henipavirus

Habchi

Blangy

Mamelli

et al. 2011

Journal of Biological Chemistry

165

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The Henipavirus genome is encapsidated by the nucleoprotein (N) within a helical nucleocapsid that recruits the polymerase complex via the phosphoprotein (P). In a previous study, we reported that in henipaviruses, the N-terminal domain of the phosphoprotein and the C-terminal domain of the nucleoprotein (N TAIL ) are both intrinsically disordered. Here we show that Henipavirus N TAIL domains are also disordered in the context of full-length nucleoproteins. We also report the cloning, purification, and characterization of the C-terminal X domains (P XD ) of Henipavirus phosphoproteins. Using isothermal titration calorimetry, we show that N TAIL and P XD form a 1:1 stoichiometric complex that is stable under NaCl concentrations as high as 1 M and has a K D in the M range. Using far-UV circular dichroism and nuclear magnetic resonance, we show that P XD triggers an increase in the ␣-helical content of N TAIL . Using fluorescence spectroscopy, we show that P XD has no impact on the chemical environment of a Trp residue introduced at position 527 of the Henipavirus N TAIL domain, thus arguing for the lack of stable contacts between the C termini of N TAIL and P XD . Finally, we present a tentative structural model of the N TAIL -P XD interaction in which a short, order-prone region of N TAIL (␣-MoRE; amino acids 473-493) adopts an ␣-helical conformation and is embedded between helices ␣2 and ␣3 of P XD , leading to a relatively small interface dominated by hydrophobic contacts. The present results provide the first detailed experimental characterization of the N-P interaction in henipaviruses and designate the N TAIL -P XD interaction as a valuable target for rational antiviral approaches.

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“…The salient issue is that a gradient of different allelic classes can be expected between these extremes, and this is reflected in the wide range of interfacial surface areas observed in orthologous proteins in different lineages (Fig. 2), as well as in the widespread presence of "weak dimers" in nature (31). Dozens of studies have shown that dimeric interfaces can generally be obliterated with just one or two key amino acid substitutions (5,27,32).…”

Section: Significancementioning

confidence: 99%

Evolutionary diversification of the multimeric states of proteins

Lynch

2013

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

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Significance Rather than operating as single units, most proteins assemble as multimers, usually with all subunits derived from the same gene. In contrast to patterns of gene structure and genome organization, which typically exhibit substantial increases in complexity from unicellular to multicellular organisms, the structural complexity of orthologous proteins appears roughly constant over the tree of life. The interfaces of multimers also often shift dramatically over evolutionary time. To explain these observations, a model is presented for the stochastic origin of variation in the multimeric states of proteins via the joint processes of mutation, random genetic drift, and constant directional selection.

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The Subunit Interfaces of Weakly Associated Homodimeric Proteins

Cited by 102 publications

References 113 publications

The Molecular Basis of Iron-induced Oligomerization of Frataxin and the Role of the Ferroxidation Reaction in Oligomerization

The Molecular Basis of Iron-induced Oligomerization of Frataxin and the Role of the Ferroxidation Reaction in Oligomerization

Characterization of the Interactions between the Nucleoprotein and the Phosphoprotein of Henipavirus

Evolutionary diversification of the multimeric states of proteins

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