Protein Oligomerization: How and Why

Ali, Mayssam H.; Imperiali, Barbara

doi:10.1002/chin.200547270

Cited by 83 publications

(111 citation statements)

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“…This article is a PNAS Direct Submission. 1 To whom correspondence may be addressed. E-mail: jagesh@hms.harvard.edu or galit@ hms.harvard.edu.…”

Section: Resultsmentioning

confidence: 99%

“…systems biology | FCS | mathematical model H omo-oligomerization, the formation of a protein complex out of identical components, is extremely common in nature; in Escherichia coli it is estimated that 35% of proteins form homo-oligomers (1), with an average of four subunits per complex. In yeast and human cells many transcription factors undergo homo-oligomerization, which has been shown to be crucial for their function (2).…”

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Activation and control of p53 tetramerization in individual living cells

Gaglia

Guan

Shah

et al. 2013

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

108

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Homo-oligomerization is found in many biological systems and has been extensively studied in vitro. However, our ability to quantify and understand oligomerization processes in cells is still limited. We used fluorescence correlation spectroscopy and mathematical modeling to measure the dynamics of the tetramers formed by the tumor suppressor protein p53 in single living cells. Previous in vitro studies suggested that in basal conditions all p53 molecules are bound in dimers. We found that in resting cells p53 is present in a mix of oligomeric states with a large cell-to-cell variation. After DNA damage, p53 molecules in all cells rapidly assemble into tetramers before p53 protein levels increase. We developed a model to understand the connection between p53 accumulation and tetramerization. We found that the rapid increase in p53 tetramers requires a combination of active tetramerization and protein stabilization, however tetramerization alone is sufficient to activate p53 transcriptional targets. This suggests triggering tetramerization as a mechanism for activating the p53 pathway in cancer cells. Many other transcription factors homo-oligomerize, and our approach provides a unique way for probing the dynamics and functional consequences of oligomerization.H omo-oligomerization, the formation of a protein complex out of identical components, is extremely common in nature; in Escherichia coli it is estimated that 35% of proteins form homo-oligomers (1), with an average of four subunits per complex. In yeast and human cells many transcription factors undergo homo-oligomerization, which has been shown to be crucial for their function (2). The molecular dynamics of oligomerization have been studied for some proteins in vitro, but no study has quantified a discrete number of oligomers in a dynamic oligomerization process in live single cells. Here we focus on the homo-tetramers formed by the tumor suppressor p53 and quantify the fraction, dynamics, and function of homo-oligomers in single living cells in response to DNA damage.p53 is a stress-response transcription factor that orchestrates cell fate decisions such as cell-cycle arrest, senescence, and apoptosis. Tetramerization of p53 is required for its direct binding to DNA (3,4). Mutations in the p53 tetramerization domain (326-356 aa) lead to a reduction in, or loss of, its transcriptional activity in cells (5) and were shown to cause early cancer onset, known as Li-Fraumeni syndrome (6, 7).In in vitro studies, p53 first assembles into homo-dimers with a K d of ∼1 nM (8), and these dimers then come together in tetramers with a K d of ∼100 nM-1 μM (8-11). The K d of tetramerization in vitro can be lowered by specific posttranslational modifications (10-12). Based on these measurements and the estimated p53 concentration in cells of 140 nM (13), it has been proposed that p53 should be primarily dimeric in basal conditions and that it forms tetramers in stressed conditions (14). However, there is currently no direct experimental evidence for this in cells.We used...

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“…This article is a PNAS Direct Submission. 1 To whom correspondence may be addressed. E-mail: jagesh@hms.harvard.edu or galit@ hms.harvard.edu.…”

Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 99%

Activation and control of p53 tetramerization in individual living cells

Gaglia

Guan

Shah

et al. 2013

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

108

View full text Add to dashboard Cite

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“…For example, functional proteins can be produced more efficiently when several short sequences are synthesized, since single disabling transcriptional or translational errors affect a part, as compared to an entire single chain protein. 1,2 Lower organisms, with less complex quality control mechanisms, in fact, seem to exploit the use of multimeric assemblies more frequently. 1 Likewise, it may be easier to tailor the properties of oligomeric complexes to the demands of evolution by mutation of an oligomeric subunit rather than a domain within a single chain protein.…”

Section: Introductionmentioning

confidence: 99%

“…1 Likewise, it may be easier to tailor the properties of oligomeric complexes to the demands of evolution by mutation of an oligomeric subunit rather than a domain within a single chain protein. Associations between subunits of an oligomeric complex also provide additional means of regulating different biological functions 2 and a means of enhancing affinity in receptor interactions, as they often do in multimeric lectins. 3,4 For these reasons, knowledge of the geometry of subunit assembly is important for understanding structure-function relationships and protein surface properties.…”

Section: Introductionmentioning

confidence: 99%

Three‐dimensional structure of the weakly associated protein homodimer SeR13 using RDCs and paramagnetic surface mapping

et al. 2010

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The traditional NMR-based method for determining oligomeric protein structure usually involves distinguishing and assigning intra-and intersubunit NOEs. This task becomes challenging when determining symmetric homo-dimer structures because NOE cross-peaks from a given pair of protons occur at the same position whether intra-or intersubunit in origin. While there are isotope-filtering strategies for distinguishing intra from intermolecular NOE interactions in these cases, they are laborious and often prove ineffectual in cases of weak dimers, where observation of intermolecular NOEs is rare. Here, we present an efficient procedure for weak dimer structure determination based on residual dipolar couplings (RDCs), chemical shift changes upon dilution, and paramagnetic surface perturbations. This procedure is applied to the Northeast Structural Genomics Consortium protein target, SeR13, a negatively charged Staphylococcus epidermidis dimeric protein (K d 3.4 6 1.4 mM) composed of 86 amino acids. A structure determination for the monomeric form using traditional NMR methods is presented, followed by a dimer structure determination using docking under orientation constraints from RDCs data, and scoring under residue pair potentials and shape-based predictions of RDCs. Validation using paramagnetic surface perturbation and chemical shift perturbation data acquired on sample dilution is also presented. The general utility of the dimer structure determination procedure and the possible relevance of SeR13 dimer formation are discussed.

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“…Inside the cells, proteins rarely act alone, but interact instead with each other, assembled in complexes either homooligomeric (2) or formed by several different components. The design of ligands with the capacity to modulate protein-protein interactions is a current pursuit in drug discovery (3).…”

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confidence: 99%

Stability and structural recovery of the tetramerization domain of p53-R337H mutant induced by a designed templating ligand

Gordo

Martos

Santos

et al. 2008

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

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Protein p53 is a transcription factor crucial for cell cycle and genome integrity. It is able to induce both cell arrest when DNA is damaged and the expression of DNA repair machinery. When the damage is irreversible, it triggers apoptosis. Indeed, the protein, which is a homotetramer, is mutated in most human cancers. For instance, the inherited mutation p53-R337H results in destabilization of the tetramer and, consequently, leads to an organism prone to tumor setup. We describe herein a rational designed molecule capable of holding together the four monomers of the mutated p53-R337H protein, recovering the tetramer integrity as in the wild-type structure. Two ligand molecules, based on a conical calix[4]arene with four cationic guanidiniomethyl groups at the wider edge (upper rim) and hydrophobic loops at the narrower edge (lower rim), fit nicely and cooperatively into the hydrophobic clefts between two of the monomers at each side of the protein and keep the tetrameric structure, like molecular templates, by both ion-pair and hydrophobic interactions. We found a good agreement between the structure of the complex and the nature of the interactions involved by a combination of theory (molecular dynamics) and experiments (circular dichroism, differential scanning calorimetry and 1 H saturation transfer difference NMR). molecular recognition ͉ multivalent calix[4]arene ligands ͉ oligoprotein stabilization ͉ protein-protein interactions

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Protein Oligomerization: How and Why

Abstract: For Abstract see ChemInform Abstract in Full Text.

Cited by 83 publications

References 1 publication

Activation and control of p53 tetramerization in individual living cells

Activation and control of p53 tetramerization in individual living cells

Three‐dimensional structure of the weakly associated protein homodimer SeR13 using RDCs and paramagnetic surface mapping

Stability and structural recovery of the tetramerization domain of p53-R337H mutant induced by a designed templating ligand

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