• Archives of Pharmacal Research
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• 제25권1호
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• pp.11-24
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• 2002

The antitumor antibiotic (+)-CC-1065 can alkylate N3 of guanine in certain sequences. A previous high-field $^1H$ NMR study on the$(+)-CC-1065d[GCGCAATTG*CGC]_2$ adduct ($^*$ indicates the drug alkylation site) showed that drag modification on N3 of guanine results in protonation of the cross-strand cytosine [Park, H-J.; Hurley, L. H. J. Am. Chem. Soc.1997, 119,629]. In this contribution we describe a further analysis of the NMR data sets together with restrained molecular dynamics. This study provides not only a solution structure of the (+)-CC-1065(N3- guanine) DNA duplex adduct but also new insight into the molecular basis for the sequence- specific interaction between (+)-CC-1065 and N3-guanine in the DNA duplex. On the basis of NOESY data, we propose that the narrow minor groove at the 7T8T step and conformational kinks at the junctions of 16C17A and 18A19T are both related to DNA bending in the drugDNA adduct. Analysis of the one-dimensional $^1H$ NMR (in $H_2O$) data and rMD trajectories strongly suggests that hydrogen bonding linkages between the 8-OH group of the (+)-CC-1065 A-sub-unit and the 9G10C phosphate via a water molecule are present. All the phenomena observed here in the (+)-CC-1065(N3-guanine) adduct at 5'$-AATTG^*$are reminiscent of those obtained from the studies on the (+)-CC-1065(N3-adenine) adduct at $5'-AGTTA^*$, suggesting that (+)-CC-1065 takes advantage of the conformational flexibility of the 5'-TPu step to entrap the bent structure required for the covalent bonding reaction. This study reveals a common molecular basis for (+)-CC-1065 alkylation at both $5'-TTG^*$ and $5'-TTA^*$, which involves a trapping out of sequence-dependent DNA conformational flexibility as well as sequence-dependent general acid and general base catalysis by duplex DNA.

• 한국광물학회지
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• 제19권4호
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• pp.347-353
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• 2006

자연계에 존재하는 다양한 지구물질의 조성은 여러 성분들로 구성된 다성분계이므로 자연계의 현상을 이해하기 위해서는 이러한 다성분계 지구물질의 구조를 규명하는 것이 필수적이다. 이러한 중요성에도 불구하고 다성분계 비정질의 자세한 원자-나노 구조는 비정질 자체가 갖고 있는 여러 가지고유의 무질서도 등으로 인하여 최근까지도 정확히 알려지지 않았다. 본 연구에서는 일차원 O-17 MAS와 이차원 3QMAS NMR을 이용하여, 다성분계 비정질인 Ca-Na 알루미노규산염 $[(CaO)_x(Na_2O)_{1-x}]\;(A1_2O_3)_{0.5}(SiO_2)_6.\;CNAS)$의 자세한 원자단위의 조성에 따른 변화를 보고한다. 비정질 CNAS의 비연결 산소 (non-bridging oxygen, NBO) 중 Ca-NBO는 Na/Ca 비율이 증가함에 따라서 (Ca, Na)-NBO를 형성한다. 이는 비정질 CNAS 내에서 비연결산소와 Ca와 Na 간에 강한 상호작용이 있음을 지시한다. 연결산소인 경우(bridging oxygen, BO, Si-O-Si나 Si-O-Al)의 경우에도 Na/Ca 비율에 따라, 감소의 폭이 비연결 산소보다는 상대적으로 작지만 화학차폐(NMR chemical shift)가 선형적으로 감소한다. 비정질 규산염의 연결산소의 결합각과 결합길이의 분포에 의해 결정되는 위상무질서도(topological disorder)는 Ca 함량이 증가할수록 비선형적으로 증가한다. 이러한 결과들은 비정질 CNAS의 구조가 기존에 알려진 데로 비연결산소만이 Na와 Ca 같은 구조교란양이온(network modifying cation)에 의해 많은 영향을 받는 것이 아니라 연결산소도 이들 양이온에 의하여 영향을 받음을 지시한다 이에 따라 다양한 양이온세기가 비정질의 무질서도에 미치는 영향을 정리하였다.

• 한국자기공명학회논문지
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• 제4권1호
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• pp.29-40
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• 2000

Coupled carbon-13 relaxation study of 1,1,1-trichloroethane dissolved in DMSO has been performed to gain some crucial insight into the dynamics of methyl group in this compound. For this purpose the relaxation behaviors of several observable magnetization modes for CH3 spin system generated by various perturbing pulse sequences have been carefully investigated and various dipolar spectral densities were estimated by nonlinear numerical fittings of the observed data with the relaxation curves, which were then employed to determine the three principal values for the diffusion tensor for end-over-end molecular rotation as well as internal rotational parameters of methyl group. In this process we could uniquely determine two correlation times $\tau$int(1) and $\tau$int(2) which give valuable information on internal rotor dynamics and thus obtained data were interpreted on the basis of various proposed models for internal rotation. compound undergoes three-fold jumps at 25$^{\circ}$. The fact that the ratio $\tau$int(1) / $\tau$int(2) is close to 1.0 may be interpreted as indicating that methyl group in this C.

• 한국자기공명학회논문지
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• 제5권2호
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• pp.130-137
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• 2001

Backbone dynamics of the catalytic residues in free and steroid-bound $\Delta$$^{5}$ -3- ketosteroid isomerase from Pseudomonas testosteroni has been examined by $^{15}$ N relaxation measurements. The relaxation data were analyzed using the model-free formalism to extract the model-free parameters (S$^2$, $\tau$$_{e}$, and R$_{ex}$). Tyr-34 and Asp-99 exhibit enhanced high-frequency (pico- to nanosecond) internal motions in the free enzyme, which are restricted upon ligand binding, while Asp-38 experiences severe restriction of the internal motions in the fee enzyme, suggesting that Tyr-14 and Asp-99 are more actively involved in the ligand binding than Asp-38. The results also indicate that the H-bond network in the catalytic cavity might be slightly strengthened upon ligand binding, which may have some implications on the enzyme mechanism.he enzyme mechanism.m.

• Bulletin of the Korean Chemical Society
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• 제30권10호
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• pp.2449-2452
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• 2009

• Bulletin of the Korean Chemical Society
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• 제19권12호
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• pp.1326-1333
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• 1998

The study of coupled relaxation for methyl spin system in 2,6-dichlorotoluene was performed on the basis of the magnetization mode formalism. Using five initial perturbing pulse sequences, eight experimntal data sets were obtained, which were fitted with theoretical expressions with nine spectral density parameters. The same experiment was carried out at both 50.3 MHz and 125.6 MHz in carbon frequency. The measured spectral densities at both fields are similar in the exception of that related with carbon random field term. Furthermore, from the dipolar spectral density, the physical values may be extracted depending on the model of molecular reorientation. For example, it was assumed that the molecular framework undergoes asymmetric diffusive rotational process and methyl group reorients by either diffusive rotation about its symmetry axis or jump among internal rotational potential minima.

• BMB Reports
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• 제51권12호
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• pp.609-610
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• 2018

Glycosylation is one form of protein modification and plays a key role in protein stability, function, signaling regulation and even cancer. NleB and SseK are bacterial effector proteins and possess glycosyltransferase activity, even though they have different substrate preferences. NleB/SseKs transfer the GlcNAc sugar to an arginine residue of host proteins, leading to reduced $NF-{\kappa}B-dependent$ responses. By combining X-ray crystallography, NMR, molecular dynamics, enzyme kinetic assays and in vivo experiments, we demonstrated that a conserved HEN (His-Glu-Asn) motif in the active site plays a key role in enzyme catalysis and virulence. The lid-domain regulates the opening and closing of the active site and the HLH domain determines the substrate specificity. Our findings provide evidence for the enzymatic mechanism by which arginine can be glycosylated by SseK/NleB enzymes.

• Archives of Pharmacal Research
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• 제24권5호
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• pp.455-465
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• 2001

The highly potent cytotoxic DNA-DNA cross-linker consists of two cyclopropa[c]pyrrolo[3,4-3]indol-4(5H)-ones insoles [(+)-CPI-I] joined by a bisamido pyrrole (abbreviated to "Pyrrole"). The Pyrrole is a synthetic analog of Bizelesin, which is currently in phase II clinical trials due to its excellent in vivo antitumor activity. The Pyrrole has 10 times more potent cytotoxicity than Bizelesin and mostly form DNA-DNA interstrand cross-links through the N3 of adenines spaced 7 bp apart. The Pyrrole requires a centrally positioned GC base pair for high cross-linking reactivity (i.e., $5^1$-T$AT_2$A*-$3^1$), while Bizelesin prefers purely AT-rich sequences (i.e., $5^1$-T$AT_4$A*-$3^1$, where /(equation omitted) represents the cross-strand adenine alkylation and A* represents an adenine alkylation) (Park et al., 1996). In this study, the high-field $^1$H-NMR and rMD studies are conducted on the 1 1-mer DNA duplex adduct of the Pyrrole where the 5′(equation omitted)TAGTTA*-3′sequence is cross-linked by the drug. A severe structural perturbation is observed in the intervening sequences of cross-linking site, while a normal B-DNA structure is maintained in the region next to the drug-modified adenines. Based upon these observations, we propose that the interplay between the bisamido pyrrole unit of the drug and central C/C base pair (hydrogen-bonding interactions) is involved in the process of cross-linking reaction, and sequence specificity is the outcome of those interactions. This study suggests a mechanism for the sequence specific cross-linking reaction of the Pyrrole, and provides a further insight to develop new DNA sequence selective and distortive cross-linking agents.

• Bulletin of the Korean Chemical Society
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• 제14권1호
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• pp.137-143
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• 1993

The tetranuclear heterometallic complex CpMo$Os_3(CO)_{10}({\mu]-H)2[{\mu}3-{\eta}^2-C(O)CH_2Tol]\;(1,\;Cp={\eta}^5-C_5H_5,\;Tol=p-C_6H_4Me)$ has been examined by variable-temperature $^{13}$C-NMR spectroscopy and by a full three-dimensional X-ray structual analysis. Complex 1 crystallizes in the orthorhombic space group Pna2$_1$ with a = 12.960(1) ${\AA}$, b = 11.255(l) ${\AA}$, c = 38.569(10)${\AA}$, V = 5626(2) ${\AA}^3$ and ${\rho}$(calcd) = 2.71 gcm$^{-3}$ for Z = 8 and molecular weight 1146.9. Diffraction data were collectedon a CAD4 diffractometer, and the structure was refined to $R_F$ = 9.7% and $R_{W^F}$ = 9.9% for 2530 data (MoK${\alpha}$ radiation). There are two essentially equivalent molecules in the crystallographic asymmetric unit. The tetranuclear molecule contains a triangulated rhomboidal arrangement of metal atoms with Os(2) and Mo at the two bridgehead positions. The metal framework is planar; the dihedral angle between Os(l)-Os(2)-Mo and Os(3)-Os(2)-Mo planes is 180$^{\circ}$. A triply bridging (${\mu}_3,\;{\eta}^2$) acyl ligand lies above the Os(l)-Os(2)-Mo plane; the oxygen atom spans the two bridgehead positions, while the carbon atom spans one bridgehead position and an acute apical position. The molecular architecture is completed by an ${\eta}^5$-cyclopentadienyl ligand and a semi-triply bridging carbonyl ligand on the molybdenum atom, and nine terminal carbonyl ligands-four on Os(3), three on Os(l), and two on Os(2). The two hydride ligands are inferred to occupy the Os(l)-Os(2) and Mo-Os(3) edges from structural and NMR data.

• 한국자기공명학회논문지
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• 제11권1호
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• pp.30-41
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• 2007

The backbone molecular dynamics of the C-terminal part of the mouse Cdt1 protein (tCdt1, residues 420-557) was studied by high field NMR spectroscopy. The Secondary structure of this protein was suggested by analyzing of chemical shift of backbone atoms with programs TALOS and PECAN, together with NOE connectivities from 3D $^{15}N-HSQC-NOESY$ data. Measurement of dynamic parameters $T_1,\;T_2$ and NOE and limited proteolysis experiment provided information for domain organization of tCdt1(420-557). Analysis of the experimental data showed that the C-terminal part of the tCdt1 has well folded domain for residues 455-553. The residues 420-453 including ${\alpha}-helix$ (432-441) are flexible and probably belong to other functional domain in intact full length Cdt1 protein.