• Title, Summary, Keyword: Pocket proteins

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Conformational Dynamics of Heme Pocket in Myoglobin and Hemoglobin

  • Kim, Seong-Heun;Heo, Jeong-Hee;Lim, Man-Ho
    • Bulletin of the Korean Chemical Society
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    • v.26 no.1
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    • pp.151-156
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    • 2005
  • The conformational dynamics of heme pocket, a small vacant site near the binding site of heme proteins -myoglobin (Mb) and hemoglobin (Hb), was investigated after photolysis of carbon monoxide from MbCO and HbCO in D$_2$O solution at 283 K by probing time-resolved vibrational spectra of photolyzed CO. Two absorption bands, arising from CO in the heme pocket, evolve nonexponentially in time. The band at higher energy side blue shifts and broadens with time and the one at lower energy side narrows significantly with a negligible shift. These spectral evolutions are induced by protein conformational changes following photolysis that modify structure and electric field of heme pocket, and ligand dynamics in it. The conformational changes affecting the spectrum of photolyzed CO in heme pocket likely modulates ligand-binding activity.

Effects of Solvent Viscosity on Conformational Dynamics of Heme-pocket in Myoglobin and Hemoglobin

  • Kim, Seong-Heun;Lim, Man-Ho
    • Bulletin of the Korean Chemical Society
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    • v.27 no.11
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    • pp.1825-1831
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    • 2006
  • The influence of solvent viscosity on conformational dynamics of the heme-pocket, a small vacant site near the binding site of myoglobin (Mb) and hemoglobin (Hb), and playing a functionally important role by serving as a station in ligand binding and escape, was studied by probing time-resolved vibrational spectra of CO photodissociated from MbCO and HbCO in $D_2O$, 75 wt% glycerol/$D_2O$, and trehalose at 283 K. Two absorption bands ($B_1$ and $B_2$) of the sample in viscous solvents, arising from CO in the heme pocket, are very similar to those in $D_2O$. Two bands in Mb and Hb under all three solvents exhibit very similar nonexponential spectral evolution ($B_1$ band; blue shifting and broadening, $B_2$ band; narrowing with a negligible shifting), suggesting that in the present experimental time window of 100 ps, the extents of the spectral shift and narrowing is much influenced neither by the viscosity of solvent nor by the quaternary contact of Hb. Spectral evolution can be described by a biexponential function with a fast universal time constant of 0.52 ps and a slow time constant ranging from 13 to 32 ps. For both proteins in all three solvents majority of spectral evolution occurs with the fast universal time constant. The magnitude of the slow rate in the spectral shift of B1 band decreases with increasing solvent viscosity, indicating that it is influenced by global conformational change which is retarded in viscous solvent, thereby serve as a reporter of global conformational change of heme proteins after deligation.

Structural Bioinformatics Analysis of Disease-related Mutations

  • Park, Seong-Jin;Oh, Sang-Ho;Park, Dae-Ui;Bhak, Jong
    • Genomics & Informatics
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    • v.6 no.3
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    • pp.142-146
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    • 2008
  • In order to understand the protein functions that are related to disease, it is important to detect the correlation between amino acid mutations and disease. Many mutation studies about disease-related proteins have been carried out through molecular biology techniques, such as vector design, protein engineering, and protein crystallization. However, experimental protein mutation studies are time-consuming, be it in vivo or in vitro. We therefore performed a bioinformatic analysis of known disease-related mutations and their protein structure changes in order to analyze the correlation between mutation and disease. For this study, we selected 111 diseases that were related to 175 proteins from the PDB database and 710 mutations that were found in the protein structures. The mutations were acquired from the Human Gene Mutation Database (HGMD). We selected point mutations, excluding only insertions or deletions, for detecting structural changes. To detect a structural change by mutation, we analyzed not only the structural properties (distance of pocket and mutation, pocket size, surface size, and stability), but also the physico-chemical properties (weight, instability, isoelectric point (IEP), and GRAVY score) for the 710 mutations. We detected that the distance between the pocket and disease-related mutation lay within $20\;{\AA}$ (98.5%, 700 proteins). We found that there was no significant correlation between structural stability and disease-causing mutations or between hydrophobicity changes and critical mutations. For large-scale mutational analysis of disease-causing mutations, our bioinformatics approach, using 710 structural mutations, called "Structural Mutatomics," can help researchers to detect disease-specific mutations and to understand the biological functions of disease-related proteins.

Acetylation of Retinoblastoma Like Protein2 (Rb2/p130) in Tumor Tissues

  • Khan, Z.N.;Sabir, M.;Kayani, M.A.;Saeed, M.
    • Asian Pacific Journal of Cancer Prevention
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    • v.14 no.4
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    • pp.2255-2258
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    • 2013
  • The activity of Rb proteins is controlled by post-translational modifications, especially through phosphorylation. Acetylation of Rb2/p130 was reported recently in NIH3T3 cells but its physiological relevance in cell cycle control and tumorigenesis is still unknown. Efforts are underway to investigate possible interplay between Rb2/p130 phosphorylation and acetylation. Here we hypothesized that Rb2/p130 acetylation, like p53 acetylation, may play a role in development of the tumor phenotype. The proposed hypothesis regarding acetylation of Rb2/p130 in tumor VS normal cells was found to be true in our case study of 36 tumor samples. Statistical analysis of results suggest strong correlation among Rb2/p130 acetylation and cancer phenotype.

Crystal Structure of GRIP1 PDZ6-peptide complex reveals the structural basis for class II PDZ target recognition and PDZ domain-mediated multimerization

  • Im, Young-Jun;Park, Seong-Ho;Park, Seong-Hwan;Lee, Jun-Hyuck;Kang, Gil-Bu;Morgan Sheng;Kim, Eunjoon;Eom, Soo-Hyun
    • Proceedings of the Korea Crystallographic Association Conference
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    • pp.4-4
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    • 2002
  • PDZ domains bind to short segments within target proteins in a sequence-specific fashion. GRIP/ABP family proteins contain six to seven PDZ domains and interact via its sixth PDZ domain (class Ⅱ) with the C-termini of various proteins, including liprin-α. In addition the PDZ456 domain mediates the formation of homo- and heteromultimers of GRIP proteins. To better understand the structural basis of peptide recognition by a class Ⅱ PDZ domain and DZ-mediated multimerization, we determined the crystal structures of the GRIPI PDZ6 domain, alone and in complex with a synthetic C-terminal octapeptide of human liprin-α, at resolutions of 1.5 Å and 1.8 Å, respectively. Remarkably, unlike other class Ⅱ PDZ domains, Ile736 at αB5 rather than conserved Leu732 at αB1 makes a direct hydrophobic contact with the side chain of the Tyr at the -2 position of the ligand. Moreover, the peptide-bound structure of PDZ6 shows a slight reorientation of helix αB, indicating that the second hydrophobic pocket undergoes a conformational adaptation to accommodate the bulkiness of the Tyr's side chain, and forms an antiparallel dimer through an interface located at a site distal to the peptide-binding groove. This configuration may enable formation of GRIP multimers and efficient clustering of GRIP-binding proteins.

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Biochemical and NMR Characterization of MTH1880 Mutant Proteins for Folding-Unfolding Studies

  • Kim, Hee-Youn;Ryu, Soo-Young;Yun, Ji-Hye;Kim, Suhk-Mann;Chang, Ik-Soo;Lee, Weon-Tae
    • Bulletin of the Korean Chemical Society
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    • v.31 no.12
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    • pp.3521-3524
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    • 2010
  • MTH1880 is a hypothetical protein derived from Methanobacterium thermoautotrophicum, thermophilic methanogen. The solution structure determined by NMR spectroscopy showed that it has a novel $\alpha+\beta$-fold with a highly acidic ligand binding pocket. Since MTH1880 maintains its ultra-stable structural characteristics at both high temperature and pressure, it has been considered as an excellent model for studying protein folding. To initiate the structural and folding study of MTH1880 in proving its unusual stability, we performed the site directed mutagenesis and biochemical analysis of MTH1880 mutants. Data from circular dichroism and NMR spectroscopy suggest that the point mutations perturbed the structural stability of protein even though the secondary structure is retained. This study will provide the useful information in understanding the role of participating residues during folding-unfolding process and our result will be used in designing further folding experiments for hyper-thermopile proteins like MTH1880.

Rescuing p53 from mdm2 by a pre-structured motif in intrinsically unfolded SUMO specific protease 4

  • Kim, Do-Hyoung;Lee, Chewook;Kim, Bom;Lee, Si-Hyung;Han, Kyou-Hoon
    • BMB Reports
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    • v.50 no.10
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    • pp.485-486
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    • 2017
  • Many intrinsically unstructured/unfolded proteins (IUPs) contain transient local secondary structures even though they are "unstructured" in a tertiary sense. These local secondary structures are named "pre-structured motifs (PreSMos)" and in fact are the specificity determinants for IUP-target binding, i.e., the active sites in IUPs. Using high-resolution NMR we have delineated a PreSMo active site in the intrinsically unfolded mid-domain (residues 201-300) of SUMO-specific protease 4 (SUSP4). This 29-residue motif which we termed a p53 rescue motif can protect p53 from mdm2 quenching by binding to the p53-helix binding pocket in mdm2(3-109). Our work demonstrates that the PreSMo approach is quite effective in providing a structural rationale for interactions of p53-mdm2-SUSP4 and opens a novel avenue for designing mdm2-inhibiting anticancer compounds.

Treatment of Palatogingival Groove using Glass-Ionomer cement and Emdogain$^{(R)}$ (Original Article 2 - 글라스-아이오노머 시멘트와 Emdogain$^{(R)}$을 이용한 구개치은발육구의 치료)

  • Jin, Myoung-Uk
    • The journal of the Korean dental association
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    • v.48 no.1
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    • pp.56-62
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    • 2010
  • In recent years, a number of special treatment procedures have been introduced to reestablish new tooth supporting tissues with varying degrees of success including guided tissue regeneration(GTR), bone grafting(BG) and the use of enamel matrix derivative(EMD). EMD is an extract of enamel matrix and contains amelogenins of various molecular weights. Emdogain(EMD) might have some advantages over other methods of regenerating the tissue supporting teeth lost by gum disease, such as less postoperative complications. Emdogain contains proteins(derived from developing pig teeth) believed to regenerate tooth attachment. The decrease in probing depth after EMD treatment is achieved primarily by clinical attachment gain and bone regeneration and only to a minor extent by gingival recession. In conclsion, EMD seems to be safe, was able to regenerate lost periodontal tissues in previously diseased sites based on clinical parameters.

A Conserved Mechanism for Binding of p53 DNA-Binding Domain and Anti-Apoptotic Bcl-2 Family Proteins

  • Lee, Dong-Hwa;Ha, Ji-Hyang;Kim, Yul;Jang, Mi;Park, Sung Jean;Yoon, Ho Sup;Kim, Eun-Hee;Bae, Kwang-Hee;Park, Byoung Chul;Park, Sung Goo;Yi, Gwan-Su;Chi, Seung-Wook
    • Molecules and Cells
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    • v.37 no.3
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    • pp.264-269
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    • 2014
  • The molecular interaction between tumor suppressor p53 and the anti-apoptotic Bcl-2 family proteins plays an essential role in the transcription-independent apoptotic pathway of p53. In this study, we investigated the binding of p53 DNA-binding domain (p53DBD) with the anti-apoptotic Bcl-2 family proteins, Bcl-w, Mcl-1, and Bcl-2, using GST pull-down assay and NMR spectroscopy. The GST pull-down assays and NMR experiments demonstrated the direct binding of the p53DBD with Bcl-w, Mcl-1, and Bcl-2. Further, NMR chemical shift perturbation data showed that Bcl-w and Mcl-1 bind to the positively charged DNA-binding surface of p53DBD. Noticeably, the refined structural models of the complexes between p53DBD and Bcl-w, Mcl-1, and Bcl-2 showed that the binding mode of p53DBD is highly conserved among the anti-apoptotic Bcl-2 family proteins. Furthermore, the chemical shift perturbations on Bcl-w, Mcl-1, and Bcl-2 induced by p53DBD binding occurred not only at the p53DBD-binding acidic region but also at the BH3 peptide-binding pocket, which suggests an allosteric conformational change similar to that observed in Bcl-$X_L$. Taken altogether, our results revealed a structural basis for a conserved binding mechanism between p53DBD and the anti-apoptotic Bcl-2 family proteins, which shed light on to the molecular understanding of the transcription-independent apoptosis pathway of p53.

Elucidation of the Inhibitory Effect of Phytochemicals with Kir6.2 Wild-Type and Mutant Models Associated in Type-1 Diabetes through Molecular Docking Approach

  • Jagadeb, Manaswini;Konkimalla, V. Badireenath;Rath, Surya Narayan;Das, Rohit Pritam
    • Genomics & Informatics
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    • v.12 no.4
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    • pp.283-288
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    • 2014
  • Among all serious diseases globally, diabetes (type 1 and type 2) still poses a major challenge to the world population. Several target proteins have been identified, and the etiology causing diabetes has been reasonably well studied. But, there is still a gap in deciding on the choice of a drug, especially when the target is mutated. Mutations in the KCNJ11 gene, encoding the kir6.2 channel, are reported to be associated with congenital hyperinsulinism, having a major impact in causing type 1 diabetes, and due to the lack of its 3D structure, an attempt has been made to predict the structure of kir6.2, applying fold recognition methods. The current work is intended to investigate the affinity of four phytochemicals namely, curcumin (Curcuma longa), genistein (Genista tinctoria), piperine (Piper nigrum), and pterostilbene (Vitis vinifera) in a normal as well as in a mutant kir6.2 model by adopting a molecular docking methodology. The phytochemicals were docked in both wild and mutated kir6.2 models in two rounds: blind docking followed by ATP-binding pocket-specific docking. From the binding pockets, the common interacting amino acid residues participating strongly within the binding pocket were identified and compared. From the study, we conclude that these phytochemicals have strong affinity in both the normal and mutant kir6.2 model. This work would be helpful for further study of the phytochemicals above for the treatment of type 1 diabetes by targeting the kir6.2 channel.