• Clinical and Experimental Vaccine Research
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• v.13 no.3
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• pp.202-217
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• 2024

Structural vaccinology is pivotal in expediting vaccine design through high-throughput screening of immunogenic antigens. Leveraging the structural and functional characteristics of antigens and immune cell receptors, this approach employs protein structural comparison to identify conserved patterns in key pathogenic components. Molecular modeling techniques, including homology modeling and molecular docking, analyze specific three-dimensional (3D) structures and protein interactions and offer valuable insights into the 3D interactions and binding affinity between vaccine candidates and target proteins. In this review, we delve into the utilization of various immunoinformatics and molecular modeling tools to streamline the development of broad-protective vaccines against coronavirus disease 2019 variants. Structural vaccinology significantly enhances our understanding of molecular interactions between hosts and pathogens. By accelerating the pace of developing effective and targeted vaccines, particularly against the rapidly mutating severe acute respiratory syndrome coronavirus 2 and other prevalent infectious diseases, this approach stands at the forefront of advancing immunization strategies. The combination of computational techniques and structural insights not only facilitates the identification of potential vaccine candidates but also contributes to the rational design of vaccines, fostering a more efficient and targeted approach to combatting infectious diseases.

• ALGAE
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• v.19 no.3
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• pp.161-174
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• 2004

Phonological, morphological and molecular characteristics of Spatoglossum pacificum Yendo are examined. S. pacificum has an annual life cycle composed of saprophytes with apparent absence of male and female gametophytes in Korea. The seasonal growth of this species explains that the annual growth is closely related to the monthly variation of water temperature. S. pacificum has protruding reproductive structures above the outmost cortical layer. Although this observation is restricted to several species, reproductive structures on the thallus can make S. pacificurn distinguishable from S. crassum and S. lacturn. The morphogenesis of a midrib at the base of S. pacificum in this study is the same as those of Dictyopteris but different from those of S. crassum and S. lacturn, suggesting that S. pacificum is closely related to Dictyopteris. In the comparison of plastid gene sequences among species of Spatoglossum and Dictyopteris, S. pacificum is more similar to D. divaricata and D. undulate than those of S. crassum in rbcL, rbcS, psbA and psaA. This result is congruent with the anatomical characteristic of a midrib at the base of the thallus and the protrusion of reproductive organs on the thallus. The phylogenetic relationship based on these plastid genes also shows that S. pacifism is included in Dictyotpteris Glade and separated from S. crassum. We propose the new combination of Dictyopteris pacifica (Yendo) I.K. Hwang, H.S. Kim et W.J. Lee, comb. nov. based on the differences of anatomical characteristics of the midrib, the existence of reproductive organs on thallus and the molecular analyses.

• Molecules and Cells
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• v.39 no.11
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• pp.814-820
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• 2016

FtsZ, a tubulin homologue, is an essential protein of the Z-ring assembly in bacterial cell division. It consists of two domains, the N-terminal and C-terminal core domains, and has a conserved C-terminal tail region. Lateral interactions between FtsZ protofilaments and several Z-ring associated proteins (Zaps) are necessary for modulating Z-ring formation. ZapD, one of the positive regulators of Z-ring assembly, directly binds to the C-terminal tail of FtsZ and promotes stable Z-ring formation during cytokinesis. To gain structural and functional insights into how ZapD interacts with the C-terminal tail of FtsZ, we solved two crystal structures of ZapD proteins from Salmonella typhimurium (StZapD) and Escherichia coli (EcZapD) at a 2.6 and $3.1{\AA}$ resolution, respectively. Several conserved residues are clustered on the concave sides of the StZapD and EcZapD dimers, the suggested FtsZ binding site. Modeled structures of EcZapD-EcFtsZ and subsequent binding studies using bio-layer interferometry also identified the EcFtsZ binding site on EcZapD. The structural insights and the results of bio-layer interferometry assays suggest that the two FtsZ binding sites of ZapD dimer might be responsible for the binding of ZapD dimer to two protofilaments to hold them together.

• Journal of the Korean Association of Oral and Maxillofacial Surgeons
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• v.30 no.5
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• pp.438-443
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• 2004

Objectives : The proper development of the facial structures relies upon a sequence of tightly regulated signaling interactions between the ectoderm and mesoderm involving the participation of several families of signaling molecules. Among these, bone morphogenetic proteins (BMPs) have been suggested to be a key signal that regulates the development of the mandible and the initiation and morphogenesis of the teeth. The aim of this study was to examine the artificial development of the mandibular structures and to examine the role of BMPs on tooth morphogenesis and differentiation using an organ culture system. Materials and Methods : The tooth germs from Ed 11.5, 13.5 mice were dissected, and transplanted into the diastema of the mandible primordia. The mandibles containing the transplanted tooth germs were cultured in vitro. During this period, beads soaked with BMP4 were implanted around the transplanted tooth germs. In addition, a diastema block containing the transplanted tooth germ was dissected, then transferred to an adult mouse kidney. After the organ culture, the developing mandibular explant was removed from the kidney and prepared for the tissue specimens. Odontogeneis of the transplanted tooth germs was examined after Hematoxylin-eosin, Masson-trichrome staining. Results : Proliferation and differentiation of the tooth germs cultured in the diastema was observed. In the BMP4-treated tooth germs, the formation of the first and second molars was noted. The crown of the developing tooth showed the formation of a mature cusp with the deposition of enamel and dentin matrix. In conclusion, it was confirmed that BMP4 is involved in the formation of a dental crown and the differentiation of ameloblasts and odontoblasts of the molar tooth during the development of the transplanted tooth germs.

• Journal of Microbiology and Biotechnology
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• v.26 no.12
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• pp.2019-2029
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• 2016

Zinc finger proteins are among the most extensively applied metalloproteins in the field of biotechnology owing to their unique structural and functional aspects as transcriptional and translational regulators. The classical zinc fingers are the largest family of zinc proteins and they provide critical roles in physiological systems from prokaryotes to eukaryotes. Two cysteine and two histidine residues ($Cys_2His_2$) coordinate to the zinc ion for the structural functions to generate a ${\beta}{\beta}{\alpha}$ fold, and this secondary structure supports specific interactions with their binding partners, including DNA, RNA, lipids, proteins, and small molecules. In this account, the structural similarity and differences of well-known $Cys_2His_2$-type zinc fingers such as zinc interaction factor 268 (ZIF268), transcription factor IIIA (TFIIIA), GAGA, and Ros will be explained. These proteins perform their specific roles in species from archaea to eukaryotes and they show significant structural similarity; however, their aligned amino acids present low sequence homology. These zinc finger proteins have different numbers of domains for their structural roles to maintain biological progress through transcriptional regulations from exogenous stresses. The superimposed structures of these finger domains provide interesting details when these fingers are applied to specific gene binding and editing. The structural information in this study will aid in the selection of unique types of zinc finger applications in vivo and in vitro approaches, because biophysical backgrounds including complex structures and binding affinities aid in the protein design area.

• Polymer(Korea)
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• v.30 no.6
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• pp.453-463
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• 2006

Molecular simulation is an exceptionally useful method for predicting self-assembled structures in various macromolecular systems, enlightening the origins of many interesting molecular events such as protein folding, polymer micellization, and ordering of molten block copolymer. The length scales of those events ranges widely from sub-nanometer scale to micron-scale or to even larger, which is the main obstacle to simulate all the events in an ab initio principle. In order to detour this major obstacle in the molecular simulation approach, a molecular model can be rebuilt by sacrificing some unimportant molecular details, based on two different perspectives with respect to the resolution of model. These two perspectives are generally referred to as 'atomistic' and 'mesoscopit'. This paper reviews various simulation methods for macromolecular self-assembly in both atomistic and mesoscopic perspectives.

• Journal of Life Science
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• v.10 no.1
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• pp.22-36
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• 2000

The mammary gland contains a subpopulation of epithelial cells with large proliferative potentials which are the likely targets for carcinogens. These clonogenic cells can proliferate and differentiate into functional glandular structures. Multicellular secretory alveolar units (AU) develop from these clonogens in grafts of monodispersed rat mammary epithelial cells (RMEC) in gland-free mammary fat pads in intact recipient F344 rats co-grafted with mammotropic hormone-secreting pituitary tumors (MtT F4). Multicellular nonsecretory ductal units (DU) develop in grafts of monodispersed RMEC in gland-free fat pads in adrenalectomized recipient WF rats co-grafted with MtT W10. However, this effect were reversed by hydrocortisone replacement therapy. RMEC were isolated from appropriate donor rats as monodispersed mixed cells or, alternatively, RNA＋ cells were sorted by flow cytometry of mixed RMEC stained with FITC-RNA and PE-anti-Thy-1.1 monoclonal antibody. We grafted mixed or sorted PNA+ cells in gland-free mammary fat pads in recipient rats that were endocrinologically manipulated to induce AU or DU. Cells were also isolated from these AU or DU as mixed or sorted RNA＋ cells and sub-transplanted in recipient rats treated appropriately to induce AU or DU, respectively. Cells obtained from AU in grafts gave rise to clonal AU and from DU in grafts to DU on sub-transplantation in appropriate recipients. When adrenalectomized recipient WF rats co-grafted with MtT W10 received daily subcutaneous injections of hydrocortisone for periods of 21 days following the PHA＋ cell transplantation, AU, instead of DU, were developed. The histologies of these secondary AU and DU were not different from those of the primary AU and DU. Casein and laminin proteins were demonstrated by immunocytochemical staining of primary and secondary AU. Electron micrographs also demonstrated that AU were composed of secretory cells with milk protein in the cytoplasm. DU were composed of little or non-secretory ductal epithelial cells. These AU and DU also secreted large amounts of lipids. Clonogenic cells were more common in DU than in AU. Thus, AU and DU contain persistent subpopulations of clonogenic stem-like cells.

• Molecules and Cells
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• v.39 no.4
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• pp.286-291
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• 2016

Epstein-Barr virus (EBV) is the prototypical ${\gamma}$-herpesvirus and an obligate human pathogen that infects mainly epithelial cells and B cells, which can result in malignancies. EBV infects these target cells by fusing with the viral and cellular lipid bilayer membranes using multiple viral factors and host receptor(s) thus exhibiting a unique complexity in its entry machinery. To enter epithelial cells, EBV requires minimally the conserved core fusion machinery comprised of the glycoproteins gH/gL acting as the receptor-binding complex and gB as the fusogen. EBV can enter B cells using gp42, which binds tightly to gH/gL and interacts with host HLA class II, activating fusion. Previously, we published the individual crystal structures of EBV entry factors, such as gH/gL and gp42, the EBV/host receptor complex, gp42/HLA-DR1, and the fusion protein EBV gB in a postfusion conformation, which allowed us to identify structural determinants and regions critical for receptor-binding and membrane fusion. Recently, we reported different low resolution models of the EBV B cell entry triggering complex (gHgL/gp42/HLA class II) in "open" and "closed" states based on negative-stain single particle electron microscopy, which provide further mechanistic insights. This review summarizes the current knowledge of these key players in EBV entry and how their structures impact receptor-binding and the triggering of gB-mediated fusion.

• Molecules and Cells
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• v.41 no.6
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• pp.545-552
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• 2018

Spleen tyrosine kinase (SYK) is a cytosolic non-receptor protein tyrosine kinase. Because SYK mediates key receptor signaling pathways involving the B cell receptor and Fc receptors, SYK is an attractive target for autoimmune disease and cancer treatments. To date, representative oral SYK inhibitors, including fostamatinib (R406 or R788), entospletinib (GS-9973), cerdulatinib (PRT062070), and TAK-659, have been assessed in clinical trials. Here, we report the crystal structures of SYK in complex with two newly developed inhibitors possessing 4-aminopyrido[4,3-D]pyrimidine moieties (SKI-G-618 and SKI-O-85). One SYK inhibitor (SKI-G-618) exhibited moderate inhibitory activity against SYK, whereas the other inhibitor (SKI-O-85) exhibited a low inhibitory profile against SYK. Binding mode analysis indicates that a highly potent SYK inhibitor might be developed by modifying and optimizing the functional groups that interact with Leu377, Gly378, and Val385 in the G-loop and the nearby region in SYK. In agreement with our structural analysis, one of our SYK inhibitor (SKI-G-618) shows strong inhibitory activities on the ${\beta}$-hexosaminidase release and phosphorylation of SYK/Vav in RBL-2H3 cells. Taken together, our findings have important implications for the design of high affinity SYK inhibitors.

• Journal of the Korean Chemical Society
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• v.67 no.2
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• pp.81-88
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• 2023

The contribution of hydrophobic residues to the protein folding reaction was studied by using HubWA variant proteins with I and L to V mutation. Folding kinetics of all V variant proteins was observed to be satisfied by a three-state on-pathway mechanism, U ⇌ I ⇌ N, where U, I, and N represent unfolded, intermediate, and native state, respectively. Three-state folding reaction was quantitatively analyzed and the free energy of folding of each elementary reactions and overall folding reaction, ΔG^o_UI, ΔG^o_IN, and ΔG^o_UN, were obtained. From the ratio of free energy difference between the variant protein and HubWA, ΔΔG^o_UI/ΔΔG^o_UN (ΔΔG^o_UI = ΔG^o_UI (variant protein) - ΔG^o_UI (HubWA) and ΔΔG^o_UN = ΔG^o_UN (variant protein) - ΔG^o_UN(HubWA)), the contribution of hydrophobic residues to HubWA folding was analyzed. The residues which are located in the hydrophobic core between α-helix and β-sheet, I3, I13, L15, I30, L43, I61 and L67, showed ΔΔG^o_UI/ΔΔG^o_UN value of ~0.5 when each of these residues was mutated to V, indicating that these residues form relatively solid hydrophobic core in the intermediate state. Residues located at the end of secondary structures and loop, I23, L69 and I36 showed ΔΔG^o_UI/ΔΔG^o_UN value below 0.4 when each of these residues was mutated to V, indicating that the region containing these residues are loosely formed in the intermediate state. V17A, L50V and L56V showed fairly high ΔΔG^o_UI/ΔΔG^o_UN value of ~0.8. Since L50 and L56 are located in the region containing long loop (residue 46 to 62), it is suggested that the high ΔΔG^o_UI/ΔΔG^o_UN value of these residues prevents the formation of aggregate at the early stage of folding reaction.