Molecular recognition, which is the process of biological macromolecules interacting with each other or various small molecules with a high specificity and affinity to form a specific complex, constitutes the basis of all processes in living organisms. Proteins, an important class of biological macromolecules, realize their functions through binding to themselves or other molecules. A detailed understanding of the protein–ligand interactions is therefore central to understanding biology at the molecular level. Moreover, knowledge of the mechanisms responsible for the protein-ligand recognition and binding will also facilitate the discovery, design, and development of drugs. In the present review, first, the physicochemical mechanisms underlying protein–ligand binding, including the binding kinetics, thermodynamic concepts and relationships, and binding driving forces, are introduced and rationalized. Next, three currently existing protein-ligand binding models—the “lock-and-key”, “induced fit”, and “conformational selection”—are described and their underlying thermodynamic mechanisms are discussed. Finally, the methods available for investigating protein–ligand binding affinity, including experimental and theoretical/computational approaches, are introduced, and their advantages, disadvantages, and challenges are discussed.

Lysine-specific demethylase 1 (LSD1) exerts pathway-specific activity in animal development and has been linked to several high-risk cancers. Here, we report that LSD1 is an integral component of the Mi-2/nucleosome remodeling and deacetylase (NuRD) complex. Transcriptional target analysis revealed that the LSD1/NuRD complexes regulate several cellular signaling pathways including TGFbeta1 signaling pathway that are critically involved in cell proliferation, survival, and epithelial-to-mesenchymal transition. We demonstrated that LSD1 inhibits the invasion of breast cancer cells in vitro and suppresses breast cancer metastatic potential in vivo. We found that LSD1 is downregulated in breast carcinomas and that its level of expression is negatively correlated with that of TGFbeta1. Our data provide a molecular basis for the interplay of histone demethylation and deacetylation in chromatin remodeling. By enlisting LSD1, the NuRD complex expands its chromatin remodeling capacity to include ATPase, histone deacetylase, and histone demethylase.

SOX genes encode a family of high-mobility group transcription factors that play critical roles in organogenesis. The functional specificity of different SOX proteins and the tissue specificity of a particular SOX factor are largely determined by the differential partnership of SOX transcription factors with other transcription regulators, many of which have not yet been discovered. Virtually all members of the SOX family have been found to be deregulated in a wide variety of tumors. However, little is known about the cellular and molecular behaviors involved in the oncogenic potential of SOX proteins. Using cell culture experiments, tissue analysis, molecular profiling, and animal studies, we report here that SOX2 promotes cell proliferation and tumorigenesis by facilitating the G 1 /S transition and through its transcription regulation of the CCND1 gene in breast cancer cells. In addition, we identified ␤-catenin as the transcription partner for SOX2 and demonstrated that SOX2 and ␤-catenin act in synergy in the transcription regulation of CCND1 in breast cancer cells. Our experiments not only determined a role for SOX2 in mammary tumorigenesis but also revealed another activity of the multifunctional protein, ␤-catenin.The SOX 2 gene family encodes a group of transcription factors that are characterized by a highly conserved high-mobility group (HMG) domain (1-3). These genes are found throughout the animal kingdom, are expressed in a restricted spatial-temporal pattern, and play critical roles in stem cell biology, organogenesis, and animal development (3, 4). For example, overexpression of Sox2 in mouse neural stem cells blocks their differentiation, and inhibition of Sox2 in these cells causes their premature exit from the cell cycle and differentiation into neurons(5). Depletion of Sox2 by RNA interference blocks the proliferation of neural stem-like cells and causes them to differentiate into neurons(6).Recently, a number of links have been found between SOX transcription factors and human cancers (7). For instance, SOX2 has been found to be an immunogenic antigen in 41% of small cell lung cancer patients (8) and in 29% of meningioma patients (9). Immunohistochemistry results suggest that SOX2 is involved in later events of carcinogenesis, such as invasion and metastasis of pancreatic intraepithelial neoplasia (10). SOX2 may also be involved in gastric carcinogenesis (11) and may be amplified in prostate cancers (12). Furthermore, SOX2 expression has been observed in 43% of basal cell-like breast carcinomas and was found to be strongly correlated with CK5/6, EGFR, and vimentin immunoreactivity, suggesting that SOX2 may play a role in conferring a less differentiated phenotype in these tumors (13).How SOX2 exerts its oncogenic potential is currently unknown. SOX proteins including SOX2 bind to specific DNA sequences (C(T/A)TTG(T/A)(T/A)) by means of their HMG domains in functioning as transcription factors to activate or repress target gene expression (2, 3). It is currently accepted that SOX proteins the...

Essential for embryonic development, the polycomb group protein enhancer of zeste homolog 2 (EZH2) is overexpressed in breast and prostate cancers and is implicated in the growth and aggression of the tumors. The tumorigenic mechanism underlying EZH2 overexpression is largely unknown. It is believed that EZH2 exerts its biological activity as a transcription repressor. However, we report here that EZH2 functions in gene transcriptional activation in breast cancer cells. We show that EZH2 transactivates genes that are commonly targeted by estrogen and Wnt signaling pathways. We demonstrated that EZH2 physically interacts directly with estrogen receptor ␣ and ␤-catenin, thus connecting the estrogen and Wnt signaling circuitries, functionally enhances gene transactivation by estrogen and Wnt pathways, and phenotypically promotes cell cycle progression. In addition, we identified the transactivation activity of EZH2 in its two N-terminal domains and demonstrated that these structures serve as platforms to connect transcription factors and the Mediator complex. Our experiments indicated that EZH2 is a dual function transcription regulator with a dynamic activity, and we provide a mechanism for EZH2 in tumorigenesis.Initially discovered as epigenetic silencers during embryogenesis, polycomb group (PcG) proteins have been implicated in development and differentiation (34). The biological activities of PcG proteins are expanding and now include the regulation of various adult processes, such as lymphopoiesis, Xinactivation, and cell proliferation, and several PcG genes have been implicated in tumorigenesis (3,5).Initial suggestions that EZH2 is involved in cell proliferation came from the observation that EZH2 is preferentially expressed in proliferating, but not resting, mantle cell lymphoma cells (53). Subsequently, EZH2 was found to be overexpressed in metastatic prostate cancer, and knockdown of EZH2 expression inhibited cell proliferation (52). It was also observed that the EZH2 level directly correlates with the aggressiveness of breast cancer, and forced EZH2 expression in immortalized human mammary epithelial cell lines promotes anchorageindependent growth and cell invasion (3,20).How EZH2 promotes cell proliferation and tumor progression is still largely unknown. It is believed that EZH2 functions by forming polycomb repressive complex (PRC) with other PcG proteins (29, 35). These protein complexes are characterized by an intrinsic histone lysine methyltransferase (HMTase) activity that is mediated by the SET domain of EZH2 (25) and that targets different lysine residues on histones H1 or H3 in vitro (5, 23). Core histone methylation facilitates the establishment of a stable, repressive chromatin structure to prevent transcription initiation by prebound factors (7). In addition, several PcG proteins interact or colocalize with various nonPcG proteins, including the transcription modulators CtBP (41), E2F6 (2, 51), RYBP (12), AF9 (13), SSX (49), and the mitogen-activated protein/kinase-activated protein kinase 3...

Although SIRT7 is a member of sirtuin family proteins that are described as NAD+-dependent class III histone deacetylases, the intrinsic enzymatic activity of this sirtuin protein remains to be investigated and the cellular function of SIRT7 remains to be explored. Here we report that SIRT7 is an NAD+-dependent histone desuccinylase. We show that SIRT7 is recruited to DNA double-strand breaks (DSBs) in a PARP1-dependent manner and catalyses desuccinylation of H3K122 therein, thereby promoting chromatin condensation and DSB repair. We demonstrate that depletion of SIRT7 impairs chromatin compaction during DNA-damage response and sensitizes cells to genotoxic stresses. Our study indicates SIRT7 is a histone desuccinylase, providing a molecular basis for the understanding of epigenetic regulation by this sirtuin protein. Our experiments reveal that SIRT7-catalysed H3K122 desuccinylation is critically implemented in DNA-damage response and cell survival, providing a mechanistic insight into the cellular function of SIRT7.

It is well-documented that the methylation of histone H3 lysine 4 (H3K4) and of H3K9 are mutually exclusive, an epigenetic phenomenon conserved from yeast to humans. How this opposed methylation modification is accomplished and coordinated in mammalian cells is poorly understood. Here we report that the H3K9 trimethyl demethylase JMJD2B is an integral component of the H3K4-specific methyltransferase, the mixed-lineage leukemia (MLL) 2 complex. We show that the JMJD2B/MLL2 complex is copurified with estrogen receptor α (ERα) and is required for ERα-regulated transcription. We demonstrate that H3K9 demethylation and H3K4 methylation are coordinated in ERα-activated transcription such that H3K9 demethylation is a prerequisite for H3K4 methylation. Significantly, depletion of JMJD2B impairs the estrogen-induced G 1 /S transition of the cell cycle in vitro and inhibits breast tumorigenesis in vivo. Interestingly, JMJD2B itself is an ERα target gene, and forms a feed-forward regulatory loop in regulation of the hormone response. Our results provide a molecular basis for the coordinated H3K4 methylation/H3K9 demethylation in transcription activation, link the trimethyl demethylase JMJD2B to euchromatin functions, and provide a mechanism for JMJD2B in breast carcinogenesis.histone methylation | breast cancer R ecent studies indicate that, analogous to other covalent histone modifications such as acetylation, histone methylation is reversible. However, in contrast to histone acetylation, which is generally associated with active transcription, histone methylation can be associated with either activation or repression of transcription, depending on what effector protein is recruited (1). Even within the same lysine residue, the biological consequences of methylation seem to be variable. For example, methylation of histone H3 lysine 9 (H3K9), long considered a hallmark of heterochromatin (2-8), was recently found to also be present at the transcribed regions of active mammalian genes (9, 10), suggesting that certain methyl marks can have multiple functions in the cell.Given the complexity of histone methylation modification, the integration and/or coordination of methylation/demethylation in a particular biological process becomes an issue of great importance in further understanding the role of histone methylation in nucleosome functioning. Specifically, actively transcribed genes, including the ones that are regulated by estrogen receptor (ER) (11-13), are marked by methylation at histone H3K4, but at the same time by demethylation at H3K9; H3K4 and H3K9 methylation levels are mutually exclusive, and this relationship is conserved from fission yeast to humans. How opposed H3K4 methylation and H3K9 demethylation are achieved and coordinated in transcription activation in mammalian cells is not fully understood.H3K4 methylation is deposited by a family of histone methyltransferases (HMT) that share a conserved SET (Su(var), E(z), and Trithorax) domain. In mammalian cells, multiple HMTs have been characterized: SET1A and SE...

Estrogen exhibits a broad spectrum of physiological functions ranging from regulation of the menstrual cycle and reproduction to modulation of bone density, brain function, and cholesterol mobilization. Despite the beneficial actions of endogenous estrogen, sustained exposure to exogenous estrogen is a well-established risk factor for various cancers. We summarize our current understanding of the molecular mechanisms of estrogen signaling in normal and cancer cells and discuss the major challenges to existing antiestrogen therapies.

Cancer is associated with a profound perturbation in myelopoiesis that results in the accumulation of myeloid-derived suppressor cells (MDSCs) to promote disease progression. Recent studies in mice suggest that tumor-derived factors could regulate the differentiation of hematopoietic stem and progenitor cells (HSPCs) in the bone marrow and subsequently contribute to dysregulation of hematopoiesis. However, the nature and role of HPSCs in patients with cancer remain unknown. Here we show, in detailed studies of the peripheral blood from 133 untreated patients with seven different types of tumors, that the composition of circulating HSPCs was significantly altered in patients with solid tumors. The frequencies of circulating granulocyte-monocyte progenitors (GMPs) were increased four to seven fold in all types of tumors examined, and the circulating hematopoietic precursors exhibited myeloid bias with a skew toward granulocytic differentiation in patients with solid tumors. These myeloid precursors are selectively enriched in tumor tissues, and the high levels of circulating GMPs were positively correlated with disease progression. By using cord blood-derived CD34 + cells, we developed an in vitro short-term culture model to effectively induce the rapid generation of MDSCs. We found that, among the factors produced by various tumors, GM-CSF, granulocyte colony-stimulating factor, and IL-6 could not only promote the myeloidbiased differentiation, but also induce the differentiation of myeloid precursors into functional MDSCs. These findings suggest that the altered circulating HSPCs may serve as an important link between dysregulated bone marrow hematopoiesis and accumulated MDSCs in patients with cancer.