Theoretical approaches for dynamical ordering of biomolecular systems

BACKGROUND

Living systems are characterized by the dynamic assembly and disassembly of biomolecules. The dynamical ordering mechanism of these biomolecules has been investigated both experimentally and theoretically. The main theoretical approaches include quantum mechanical (QM) calculation, all-atom (AA) modeling, and coarse-grained (CG) modeling. The selected approach depends on the size of the target system (which differs among electrons, atoms, molecules, and molecular assemblies). These hierarchal approaches can be combined with molecular dynamics (MD) simulation and/or integral equation theories for liquids, which cover all size hierarchies.

SCOPE OF REVIEW

We review the framework of quantum mechanical/molecular mechanical (QM/MM) calculations, AA MD simulations, CG modeling, and integral equation theories. Applications of these methods to the dynamical ordering of biomolecular systems are also exemplified.

MAJOR CONCLUSIONS

The QM/MM calculation enables the study of chemical reactions. The AA MD simulation, which omits the QM calculation, can follow longer time-scale phenomena. By reducing the number of degrees of freedom and the computational cost, CG modeling can follow much longer time-scale phenomena than AA modeling. Integral equation theories for liquids elucidate the liquid structure, for example, whether the liquid follows a radial distribution function.

GENERAL SIGNIFICANCE

These theoretical approaches can analyze the dynamic behaviors of biomolecular systems. They also provide useful tools for exploring the dynamic ordering systems of biomolecules, such as self-assembly. This article is part of a Special Issue entitled "Biophysical Exploration of Dynamical Ordering of Biomolecular Systems" edited by Dr. Koichi Kato.

Four Aromatic Sulfates with an Inhibitory Effect against HCV NS3 Helicase from the Crinoid Alloeocomatella polycladia

Bioassay-guided separation of a lipophilic extract of the crinoid Alloeocomatella polycladia, inhibiting the activity of HCV NS3 helicase, yielded two groups of molecules: cholesterol sulfate and four new aromatic sulfates 1–4. The structures of the aromatics were elucidated by spectroscopic analysis in addition to theoretical studies. The aromatic sulfates 1–4 showed moderate inhibition against NS3 helicase with IC₅₀ values of 71, 95, 7, and 5 μM, respectively.

Extrauterine Choriocarcinoma in the Fallopian Tube Following Infertility Treatment: Implications for the Management of Early-Detected Ectopic Pregnancies

Extrauterine choriocarcinoma in the fallopian tube is very rare and is often diagnosed and treated as an ectopic tubal pregnancy. A 34-year-old woman who initially became pregnant after infertility treatment using ovulation induction with clomiphene citrate and intrauterine insemination was later diagnosed with an extrauterine choriocarcinoma in the left fallopian tube. Because of suspected left ectopic tubal pregnancy based on ultrasonography findings and a high level of β-human chorionic gonadotropin (β-hCG; 7054.3 mIU/mL), the patient underwent diagnostic laparoscopy at a gestational age of 6 weeks. Left salpingectomy was performed based on the operative diagnosis of an ectopic tubal pregnancy. No signs of tubal rupture or leakage of contents from the fallopian tube were observed during the operation. Her serum β-hCG dropped to 10.3 mIU/mL at 15 days postoperatively. Histopathology demonstrated an extrauterine choriocarcinoma in the removed fallopian tube, and the patient was referred to a regional oncologic hospital to receive additional adjuvant chemotherapy. This case indicates that conservative treatment for ectopic pregnancy should be chosen carefully, and that histopathology diagnosis and appropriate β-hCG monitoring following treatment are important not only to diagnose persistent ectopic pregnancy, but also to rule out the possibility of a tubal choriocarcinoma.

Radiologic-Pathologic Correlation of Primary and Secondary Cardiomyopathies: MR Imaging and Histopathologic Findings in Hearts from Autopsy and Transplantation

RSNA, 2017.

The ion dependence of carbohydrate binding of CBM36: an MD and 3D-RISM study

The molecular recognition process of the carbohydrate-binding module family 36 (CBM36) was examined theoretically. The mechanism of xylan binding by CBM36 and the role of Ca(2+) were investigated by the combined use of molecular dynamics simulations and the 3D reference interaction site model method. The CBM36 showed affinity for xylan after Ca(2+) binding, but not after Mg(2+) binding. Free-energy component analysis of the xylan-binding process revealed that the major factor for xylan-binding affinity is the electrostatic interaction between the Ca(2+) and the hydroxyl oxygens of xylan. The van der Waals interaction between the hydrophobic side chain of CBM36 and the glucopyranose ring of xylan also contributes to the stabilization of the xylan-binding state. Dehydration on the formation of the complex has the opposite effect on these interactions. The affinity of CBM36 for xylan results from a balance of the interactions between the binding ion and solvents, hydrophilic residues around xylan, and the hydroxyl oxygens of xylan. When CBM binds Ca(2+), these interactions are well balanced; in contrast, when CBM binds Mg(2+), the dehydration penalty is excessively large.

Abstract WP210: Urgent Detection of Acute Type A Aortic Dissection in Ischemic Stroke or TIA

Background and purpose: Urgent diagnosis of acute Stanford type A aortic dissection (AAD) in patients with acute ischemic stroke (AIS) or transient ischemic attack (TIA) is sometimes challenging. Several markers such as systolic blood pressure (SBP) laterality, initial D-dimer level, mediastinal-width to chest-width (M/C) ratio on X-ray, common carotid artery (CCA) dissection on carotid ultrasonography and pericardial effusion on echocardiography are reported to be useful to identify AAD in AIS or TIA. We validated these findings using our prospective stroke registry (ClinicalTrials.gov: NCT02251665).

Methods: Consecutive AIS or TIA patients with AAD who were admitted to our institute within 4.5 h of onset from Jan 2007 to Dec 2014 were reviewed. They were compared with AIS or TIA patients without AAD who admitted within 4.5 h of onset from Jan 2014 to Dec 2014.

Results: We found 24 AIS/TIA patients with AAD (15 women, 75±12 y.o.), and 245 patients without AAD (86 women, 74±12 y.o.). As compared to patients without AAD, AAD patients had higher SBP laterality (30±20 mmHg vs. 10±9 mmHg, p<0.001), higher initial D-dimer level (median 1.0μg/ml, IQR 0.5-2.4μg/ml vs. median 38.1μg/ml, IQR 8.1-155.1μg/ml; p<0.001), and higher M/C ratio in the recumbent position (0.35±0.05 vs. 0.29±0.05, p<0.001), and more frequently had occlusion or the intimal flap of the proximal CCA (85% vs. 1%, p<0.001) and pericardial effusion (43% vs. 1%, p<0.001). Using receiver operating characteristic curve analysis, the cutoff of SBP laterality, D-dimer level and M/C ratio was 17 mmHg, 4.1μg and 0.32, respectively, with c-statistic of 0.84, 0.96 and 0.82, respectively. Sensitivity, specificity, positive predictive value and negative predictive value to identify AAD were as follows.

Conclusions: High D-dimer level can be the most reliable screening test of AAD in AIS or TIA patients. Proximal CCA occlusion or flap appears to be the most disease specific finding with acceptable sensitivity.

Combined Electrostatically Embedded Multiconfiguration Molecular Mechanics and Molecular Mechanical Method: Application to Molecular Dynamics Simulation of a Chemical Reaction in Aqueous Solution with Hybrid Density Functional Theory

We here combine the electrostatically embedded multiconfiguration molecular mechanics (EE-MCMM) method for generating global potential energy surfaces in the presence of an electrostatic potential with molecular mechanics (MM). The resulting EE-MCMM/MM method is illustrated by applying it to carry out a molecular dynamics simulation for the symmetric bimolecular reaction Cl(-) + CH3Cl' → ClCH3 + Cl'(-) in aqueous solution with hybrid density functional theory as the quantum mechanical level. The potential of mean force is calculated, and the free energy barrier is found to be 25.3 kcal/mol, which is in good agreement with previous work. The advantage of the combined EE-MCMM and MM method is that the number of quantum mechanical calculations required for the active subsystem is very small compared to straight direct dynamics.

A New Trinor-guaiane Sesquiterpene from an Indonesian Soft Coral Anthelia sp

A new trinor-guaiane sesquiterpene has been isolated from an Indonesian soft coral Anthelia sp. The planar structure, possessing an octahydroazulene skeleton, and relative stereochemistry were established by analyzing 1D and 2D NMR data, including NOE experiments. Its absolute stereochemistry was elucidated to be 1S, 4S, 7R, and 10R by comparing observed and calculated optical rotation values. The new compound showed weak cytotoxicity against NBT-T2 cells.

A New Trinor-guaiane Sesquiterpene from an Indonesian Soft Coral Anthelia sp

A new trinor-guaiane sesquiterpene has been isolated from an Indonesian soft coral Anthelia sp. The planar structure, possessing an octahydroazulene skeleton, and relative stereochemistry were established by analyzing 1D and 2D NMR data, including NOE experiments. Its absolute stereochemistry was elucidated to be 1 S, 4 S, 7 R, and 10 R by comparing observed and calculated optical rotation values. The new compound showed weak cytotoxicity against NBT-T2 cells.

Impact of Elevated D-Dimer on Diagnosis of Acute Aortic Dissection With Isolated Neurological Symptoms in Ischemic Stroke

BACKGROUND

Plasma D-dimer is known to be a useful clinical marker of thrombogenic status, and D-dimer is used as a diagnostic marker for acute aortic dissection (AAD). Little is known, however, regarding the clinical value of D-dimer for diagnosis of asymptomatic AAD in patients with ischemic stroke. We investigated whether D-dimer could be used for early diagnosis of AAD with isolated neurological symptoms in ischemic stroke patients.

METHODS AND RESULTS

We evaluated a total of 1,236 consecutive patients with symptomatic ischemic stroke without chest or back pain who underwent either head computed tomography or magnetic resonance imaging. D-dimer was measured within 24 h after onset. There were 9 patients with Stanford type A AAD and they had significantly higher D-dimer than the patients without AAD (mean, 46.47±54.48 μg/ml; range, 6.9-167.1 μg/ml vs. 2.33±3.58 μg/ml, 0.3-57.9 μg/ml, P<0.001). When a cut-off of 6.9 μg/ml was adopted for d-dimer on the basis of receiver operating characteristics analysis, the sensitivity and specificity for AAD were 100% and 94.8%, respectively, while the positive and negative predictive values were 14.7% and 100%, respectively.

CONCLUSIONS

D-dimer might be a useful marker for the early diagnosis of AAD with isolated neurological symptoms in ischemic stroke patients. Whole-body contrast-enhanced computed tomography should be performed in ischemic stroke patients who have high D-dimer.

Endocytoscopic observation of various esophageal lesions at ×600: can nuclear abnormality be recognized?

Endocytoscopy (ECS) is a novel endoscopic technique that allows detailed diagnostic examination of the gastrointestinal tract at the cellular level. We previously reported that use of ECS at ×380 magnification (GIF-Y0002) allowed a pathologist to diagnose esophageal squamous cell carcinoma (ESCC) with high sensitivity (94.9%) but considerably low specificity (46.7%) because this low magnification did not reveal information about nuclear abnormality. In the present study, we used the same magnifying endoscope to observe various esophageal lesions, but employed digital 1.6-fold magnification to achieve an effective magnification of ×600, and evaluated whether this improved the diagnostic accuracy in distinguishing neoplastic from non-neoplastic lesions.We examined the morphology of surface cells using vital staining with toluidine blue and compared the histological features of 40 cases, including 19 case of ESCC and 21 non-neoplastic esophageal lesions (18 cases of esophagitis, 1 case of glycogenic acanthosis, 1 case of leiomyoma, and 1 case of normal squamous epithelium). One endoscopist classified the lesions using the type classification, and we consulted one pathologist for judgment of the ECS images as 'neoplastic', 'borderline', or 'non-neoplastic'. At ×600 magnification, the pathologist confirmed that nuclear abnormality became evident, in addition to the information about nuclear density provided by observation at ×380. The overall sensitivity and specificity with which the endoscopist was able to predict neoplastic lesions using the type classification was 100% (19/19) and 90.5% (19/21), respectively, in comparison with values of 94.7% (18/19 cases) and 76.2% (16/21), respectively, for the pathologist using a magnification of ×600. The pathologist diagnosed two non-neoplastic lesions and one case of ESCC showing an apparent increase of nuclear density with weak nuclear abnormality as 'borderline'. Among the 21 non-cancerous lesions, two cases of esophagitis that were misdiagnosed by the endoscopist were also misinterpreted as 'neoplastic' by the pathologist. We have shown, by consultation with a pathologist, that an ECS magnification of ×600 (on a 19-inch monitor) is adequate for recognition of nuclear abnormality. We consider that it is feasible to diagnose esophageal neoplasms on the basis of ECS images, and that biopsy histology can be omitted if a combination of increased nuclear density and nuclear abnormality is observed.