The structure of BRMS1 nuclear export signal and SNX6 interacting region reveals a hexamer formed by antiparallel coiled coils

Perturbation of BRMS1 interactome reveals pathways that impact metastasis

Breast Cancer Metastasis Suppressor 1 (BRMS1) expression is associated with longer patient survival in multiple cancer types. Understanding BRMS1 functionality will provide insights into both mechanism of action and will enhance potential therapeutic development. In this study, we confirmed that the C-terminus of BRMS1 is critical for metastasis suppression and hypothesized that critical protein interactions in this region would explain its function. Phosphorylation status at S237 regulates BRMS1 protein interactions related to a variety of biological processes, phenotypes [cell cycle (e.g., CDKN2A), DNA repair (e.g., BRCA1)], and metastasis [(e.g., TCF2 and POLE2)]. Presence of S237 also directly decreased MDA-MB-231 breast carcinoma migration in vitro and metastases in vivo. The results add significantly to our understanding of how BRMS1 interactions with Sin3/HDAC complexes regulate metastasis and expand insights into BRMS1's molecular role, as they demonstrate BRMS1 C-terminus involvement in distinct protein-protein interactions.

The isolated C-terminal nuclear localization sequence of the breast cancer metastasis suppressor 1 is disordered

BRMS1 is a 246-residue-long protein belonging to the family of metastasis suppressors. It is a predominantly nuclear protein, although it can also function in the cytoplasm. At its C terminus, it has a region that is predicted to be a nuclear localization sequence (NLS); this region, NLS2, is necessary for metastasis suppression. We have studied in vitro and in silico the conformational preferences in aqueous solution of a peptide (NLS2-pep) that comprises the NLS2 of BRMS1, to test whether it has a preferred conformation that could be responsible for its function. Our spectroscopic (far-UV circular dichroism, DOSY-NMR and 2D-NMR) and computational (all-atom molecular dynamics) results indicate that NLS2-pep was disordered in aqueous solution. Furthermore, it did not acquire a structure even when experiments were performed in a more hydrophobic environment, such as the one provided by 2,2,2-trifluoroethanol (TFE). The hydrodynamic radius of the peptide in water was identical to that of a random-coil sequence, in agreement with both our molecular simulations and other theoretical predictions. Thus, we suggest that NLS2 is a disordered region, with non pre-formed structure, that participates in metastasis suppression.

Structural insights into the assembly of the histone deacetylase-associated Sin3L/Rpd3L corepressor complex

Acetylation is correlated with chromatin decondensation and transcriptional activation, but its regulation by histone deacetylase (HDAC)-bearing corepressor complexes is poorly understood. Here, we describe the mechanism of assembly of the mammalian Sin3L/Rpd3L complex facilitated by Sds3, a conserved subunit deemed critical for proper assembly. Sds3 engages a globular, helical region of the HDAC interaction domain (HID) of the scaffolding protein Sin3A through a bipartite motif comprising a helix and an adjacent extended segment. Sds3 dimerizes through not only one of the predicted coiled-coil motifs but also, the segment preceding it, forming an ∼ 150-Å-long antiparallel dimer. Contrary to previous findings in yeast, Sin3A rather than Sds3 functions in recruiting HDAC1 into the complex by engaging the latter through a highly conserved segment adjacent to the helical HID subdomain. In the resulting model for the ternary complex, the two copies of the HDACs are situated distally and dynamically because of a natively unstructured linker connecting the dimerization domain and the Sin3A interaction domain of Sds3; these features contrast with the static organization described previously for the NuRD (nucleosome remodeling and deacetylase) complex. The Sds3 linker features several conserved basic residues that could potentially maintain the complex on chromatin by nonspecific interactions with DNA after initial recruitment by sequence-specific DNA-binding repressors.

Probing coiled-coil assembly by paramagnetic NMR spectroscopy

Here a new method to determine the orientation of coiled-coil peptide motifs is described.

Microenvironmental Influences on Metastasis Suppressor Expression and Function during a Metastatic Cell's Journey

Metastasis is the process of primary tumor cells breaking away and colonizing distant secondary sites. In order for a tumor cell growing in one microenvironment to travel to, and flourish in, a secondary environment, it must survive a series of events termed the metastatic cascade. Before departing the primary tumor, cells acquire genetic and epigenetic changes that endow them with properties not usually associated with related normal differentiated cells. Those cells also induce a subset of bone marrow-derived stem cells to mobilize and establish pre-metastatic niches [1]. Many tumor cells undergo epithelial-to-mesenchymal transition (EMT), where they transiently acquire morphologic changes, reduced requirements for cell-cell contact and become more invasive [2]. Invasive tumor cells eventually enter the circulatory (hematogenous) or lymphatic systems or travel across body cavities. In transit, tumor cells must resist anoikis, survive sheer forces and evade detection by the immune system. For blood-borne metastases, surviving cells then arrest or adhere to endothelial linings before either proliferating or extravasating. Eventually, tumor cells complete the process by proliferating to form a macroscopic mass [3].Up to 90 % of all cancer related morbidity and mortality can be attributed to metastasis. Surgery manages to ablate most primary tumors, especially when combined with chemotherapy and radiation. But if cells have disseminated, survival rates drop precipitously. While multiple parameters of the primary tumor are predictive of local or distant relapse, biopsies remain an imperfect science. The introduction of molecular and other biomarkers [4, 5] continue to improve the accuracy of prognosis. However, the invasive procedure introduces new complications for the patient. Likewise, the heterogeneity of any tumor population [3, 6, 7] means that sampling error (i.e., since it is impractical to examine the entire tumor) necessitates further improvements.In the case of breast cancer, for example, women diagnosed with stage I diseases (i.e., no evidence of invasion through a basement membrane) still have a ~30 % likelihood of developing distant metastases [8]. Many physicians and patients opt for additional chemotherapy in order to "mop up" cells that have disseminated and have the potential to grow into macroscopic metastases. This means that ~ 70 % of patients receive unnecessary therapy, which has undesirable side effects. Therefore, improving prognostic capability is highly desirable.Recent advances allow profiling of primary tumor DNA sequences and gene expression patterns to define a so-called metastatic signature [9-11], which can be predictive of patient outcome. However, the genetic changes that a tumor cell must undergo to survive the initial events of the metastatic cascade and colonize a second location belie a plasticity that may not be adequately captured in a sampling of heterogeneous tumors. In order to tailor or personalize patient treatments, a more accurate assessment of the genetic profile in the metastases is needed. Biopsy of each individual metastasis is not practical, safe, nor particularly cost-effective. In recent years, there has been a resurrection of the notion to do a 'liquid biopsy,' which essentially involves sampling of circulating tumor cells (CTC) and/or cell free nucleic acids (cfDNA, including microRNA (miRNA)) present in blood and lymph [12-16].The rationale for liquid biopsy is that tumors shed cells and/or genetic fragments into the circulation, theoretically making the blood representative of not only the primary tumor but also distant metastases. Logically, one would predict that the proportion of CTC and/or cfDNA would be proportionate to the likelihood of developing metastases [14]. While a linear relationship does not exist, the information within CTC or cfDNA is beginning to show great promise for enabling a global snapshot of the disease. However, the CTC and cfDNA are present at extremely low levels. Nonetheless, newer technologies capture enough material to enrich and sequence the patient's DNA or quantification of some biomarkers.Among the biomarkers showing great promise are metastasis suppressors which, by definition, block a tumor cell's ability to complete the metastatic process without prohibiting primary tumor growth [17]. Since the discovery of the first metastasis suppressor, Nm23, more than 30 have been functionally characterized. They function at various stages of the metastatic cascade, but their mechanisms of action, for the most part, remain ill-defined. Deciphering the molecular interactions of functional metastasis suppressors may provide insights for targeted therapies when these regulators cease to function and result in metastatic disease.In this brief review, we summarize what is known about the various metastasis suppressors and their functions at individual steps of the metastatic cascade (Table 1). Some of the subdivisions are rather arbitrary in nature, since many metastasis suppressors affect more than one step in the metastatic cascade. Nonetheless what emerges is a realization that metastasis suppressors are intimately associated with the microenvironments in which cancer cells find themselves [18].

POODLE: tools predicting intrinsically disordered regions of amino acid sequence

Protein intrinsic disorder, a widespread phenomenon characterized by a lack of stable three-dimensional structure, is thought to play an important role in protein function. In the last decade, dozens of computational methods for predicting intrinsic disorder from amino acid sequences have been developed. They are widely used by structural biologists not only for analyzing the biological function of intrinsic disorder but also for finding flexible regions that possibly hinder successful crystallization of the full-length protein. In this chapter, I introduce Prediction Of Order and Disorder by machine LEarning (POODLE), which is a series of programs accurately predicting intrinsic disorder. After giving the theoretical background for predicting intrinsic disorder, I give a detailed guide to using POODLE. I then also briefly introduce a case study where using POODLE for functional analyses of protein disorder led to a novel biological findings.

Mcm10 self-association is mediated by an N-terminal coiled-coil domain

Minichromosome maintenance protein 10 (Mcm10) is an essential eukaryotic DNA-binding replication factor thought to serve as a scaffold to coordinate enzymatic activities within the replisome. Mcm10 appears to function as an oligomer rather than in its monomeric form (or rather than as a monomer). However, various orthologs have been found to contain 1, 2, 3, 4, or 6 subunits and thus, this issue has remained controversial. Here, we show that self-association of Xenopus laevis Mcm10 is mediated by a conserved coiled-coil (CC) motif within the N-terminal domain (NTD). Crystallographic analysis of the CC at 2.4 Å resolution revealed a three-helix bundle, consistent with the formation of both dimeric and trimeric Mcm10 CCs in solution. Mutation of the side chains at the subunit interface disrupted in vitro dimerization of both the CC and the NTD as monitored by analytical ultracentrifugation. In addition, the same mutations also impeded self-interaction of the full-length protein in vivo, as measured by yeast-two hybrid assays. We conclude that Mcm10 likely forms dimers or trimers to promote its diverse functions during DNA replication.

BRMS151-98 and BRMS151-84 are crystal oligomeric coiled coils with different oligomerization states, which behave as disordered protein fragments in solution

The breast cancer metastasis suppressor 1 (BRMS1) gene suppresses metastasis without affecting the primary tumor growth. Cellular localization of BRMS1 appears to be important for exerting its effects on metastasis inhibition. We recently described a nucleo-cytoplasmic shuttling for BRMS1 and identified a nuclear export signal within the N-terminal coiled coil. The structure of these regions shows an antiparallel coiled coil capable of oligomerizing, which compromises the accessibility to the nuclear export signal consensus residues. We have studied the structural and biophysical features of this region to further understand the contribution of the N-terminal coiled coil to the biological function of BRMS1. We have observed that residues 85 to 98 might be important in defining the oligomerization state of the BRMS1 N-terminal coiled coil. The fragments are mainly disordered in solution, with evidence of residual structure. In addition, we report the presence of a conformational dynamic equilibrium (oligomeric folded species ↔ oligomeric unfolded) in solution in the BRMS1 N-terminal coiled coil that might facilitate the nuclear export of BRMS1 to the cytoplasm.

Role of breast cancer metastasis suppressor 1 in digestive system neoplasms

Breast cancer metastasis suppressor 1 (BRMS1) is a tumor metastasis suppressor discovered in breast carcinoma cells in 2000. It can reduce the metastasis potential of tumor cells without affecting the growth of orthotopic tumor. BRMS1 is lowly expressed or not at all in metastases of melanoma, bladder carcinoma, pheochromocytoma, ovarian cancer, non-small cell lung cancer, endometrial cancer, nasal and paranasal sinus carcinoma. Malignant tumors have become one of the most serious diseases endangering human health, and digestive system neoplasms are the most common malignant tumors in China. Elucidation of the role of BRMS1 will certainly provide a potential theoretical basis for the molecular diagnosis, targeted therapy, and prognosis evaluation of tumor metastases. In this review, we will summarize recent progress in understanding the role of BRMS1 in digestive system neoplasms.

Contribution of DEAF1 structural domains to the interaction with the breast cancer oncogene LMO4

The proteins LMO4 and DEAF1 contribute to the proliferation of mammary epithelial cells. During breast cancer LMO4 is upregulated, affecting its interaction with other protein partners. This may set cells on a path to tumour formation. LMO4 and DEAF1 interact, but it is unknown how they cooperate to regulate cell proliferation. In this study, we identify a specific LMO4-binding domain in DEAF1. This domain contains an unstructured region that directly contacts LMO4, and a coiled coil that contains the DEAF1 nuclear export signal (NES). The coiled coil region can form tetramers and has the typical properties of a coiled coil domain. Using a simple cell-based assay, we show that LMO4 modulates the activity of the DEAF NES, causing nuclear accumulation of a construct containing the LMO4-interaction region of DEAF1.