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B-cell lymphoma (Bcl-2) protein is an anti-apoptotic member of the Bcl-2 family. It is functionally demarcated into four Bcl-2 homology (BH) domains: BH1, BH2, BH3, BH4, one flexible loop domain (FLD), a transmembrane domain (TM), and an X domain. Bcl-2's BH domains have clearly been elucidated from a structural perspective, whereas the conformation of FLD has not yet been predicted, despite its important role in regulating apoptosis through its interactions with JNK-1, PKC, PP2A phosphatase, caspase 3, MAP kinase, ubiquitin, PS1, and FKBP38. Many important residues that regulate Bcl-2 anti-apoptotic activity are present in this domain, for example Asp34, Thr56, Thr69, Ser70, Thr74, and Ser87. The structural elucidation of the FLD would likely help in attempts to accurately predict the effect of mutating these residues on the overall structure of the protein and the interactions of other proteins in this domain. Therefore, we have generated an increased quality model of the Bcl-2 protein including the FLD through modeling. Further, molecular dynamics (MD) simulations were used for FLD optimization, to predict the flexibility, and to determine the stability of the folded FLD. In addition, essential dynamics (ED) was used to predict the collective motions and the essential subspace relevant to Bcl-2 protein function. The predicted average structure and ensemble of MD-simulated structures were submitted to the Protein Model Database (PMDB), and the Bcl-2 structures obtained exhibited enhanced quality. This study should help to elucidate the structural basis for Bcl-2 anti-apoptotic activity regulation through its binding to other proteins via the FLD.

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Hematopoietic Stem Cells (HSCs) gained popularity in the area of medicine because of its remarkable potential to cure an enormous range of human diseases. These stem cells are used for therapeutic purposes for its regenerative capacity and possessed hematopoiesis. This process reflects characteristic properties, proliferation, and differentiation. These behaviors are a result of protein-mediated molecular interactions. However, these molecular interactions underlying are yet to be explored. Thus, the present review focuses on the molecular basis of hematopoiesis wherein, significant molecular interactions which regulate differentiation and proliferation has been discussed. Primarily, we have addressed the role of cytokines, transcription factors, proliferation, and pathways involved in hematopoiesis. Also, relationship with multiple cytokines, small molecules, nutrients, cell-cell contacts and the extracellular matrix which impel a cascade of signals that controls stem cell behavior and fate has been summarized in this review. A large number of datasets of hematopoiesis is publicly available to researchers around the world. This review also provides databases on hematopoiesis which will be very beneficial in facilitating common analysis, basic research and clinical diagnosis for the treatment of blood-related disorders.

BackgroundInducing apoptosis in cancer cells is an important step for the successful treatment of cancer patients. Bcl‐2 is an antiapoptotic protein which determines apoptosis by interacting with proapoptotic members of the Bcl‐2 family. Exome sequencing has identified Bcl‐2 and Bax missense mutations in more than 40 cancer types. However, a little information is available about the functional impact of each Bcl‐2 and Bax mutation on the pathogenesis of cancer.MethodsThe mutational data from cancer tissues and cell lines were retrieved from the cBioPortal web resource. The 13 mutated Bcl‐2 and wild‐type Bax complexes with experimentally verified binding were identified from previous studies wherein, binding for all complexes was reportedly disrupted except one. Several protein–protein docking methods such as ClusPro, HDOCK, PatchDock, FireDock, InterEVDock2 and several mutation prediction methods such as PolyPhen‐2, SIFT, and OncoKB have been used to predict the effect of mutation to disrupt the binding between Bcl‐2 and Bax. The result obtained was compared with the known experimental data.ResultsThe protein–protein docking method, ClusPro, employed in the present study confirmed that the binding affinity of 11 out of 13 complexes decreases. Similarly, binding affinity computed for all the 10 wild‐type Bcl‐2 and mutated Bax complexes agreed with experimentally verified results.ConclusionSeveral methods like PolyPhen‐2, SIFT, and OncoKB have been developed to predict cancer‐associated or deleterious mutations, but no method is available to predict apoptosis‐inducing mutations. Thus, in this study, we have examined the mutations in Bcl‐2 and Bax proteins that disrupt their binding, which is crucial for inducing apoptosis to eradicate cancer. This study suggests that protein–protein docking methods can play a significant role in the identification of hotspot mutations in Bcl‐2 or Bax that can disrupt their binding with wild‐type partner to induce apoptosis in cancer cells.

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Enhancement of hematopoietic stem cells (HSCs) proliferation is a central aim in bone marrow transplantation (BMT). A stem cell factor (SCF) and c-Kit mediated extracellular signaling trigger proliferation of HSCs. This signaling is negatively regulated by protein tyrosine phosphatases (PTPs), SHP-1 and SHP-2. Although NSC87877 (N) is known to inhibit SHP-1/SHP-2, c-Kit-mediated HSCs proliferation by inhibiting SHP-1/SHP-2 has not been reported. This study investigated the combined effect of SCF (S) and N in c-Kit mediated proliferation and underlying mechanisms. The growth of human megakaryoblastic cell line, MO7e and HSCs, upon treatment with S and N alone, and in combination was assessed by PrestoBlue staining. The expression of c-Kit, phosphorylated c-Kit, SHP-1/SHP-2 and HePTP inhibition using S and N treatment were evaluated in the MO7e cells. Megakaryoblast cell proliferation was determined by quantification of Ki-67+, S-phase, BrdU+ and CFDA-SE+ cells using flow cytometry. The combination of S and N leads to enhanced cell growth compared with either S or N alone. Collectively, the results reveal a novel mechanism by which S in combination with N significantly enhances proliferation of human megakaryoblast cells. The pretreatment of N before S enhances proliferation of cells than S alone. This promising combination would likely play an essential role in enhancing the proliferation of cells.

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