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Molecular Discrimination of Barbital Enantiomer at the Propofol Binding Site of the Human β3 Homomeric GABAA Receptor 巴比妥对映体在人β3同源GABAA受体异丙酚结合位点的分子鉴别
IF 0.3
Chem-Bio Informatics Journal Pub Date : 2018-11-28 DOI: 10.1273/CBIJ.18.154
T. Seto, Minoru Katō, Kennichi Koyano
{"title":"Molecular Discrimination of Barbital Enantiomer at the Propofol Binding Site of the Human β3 Homomeric GABAA Receptor","authors":"T. Seto, Minoru Katō, Kennichi Koyano","doi":"10.1273/CBIJ.18.154","DOIUrl":"https://doi.org/10.1273/CBIJ.18.154","url":null,"abstract":"Intravenous anesthetic barbitals act on the GABAA receptor, and this receptor is the principal molecular target of loss of consciousness. Their action and side effects differ according to the enantiomer. Elucidation of their enantiomeric action is essential for a safe anesthetic agent. This study investigates molecular mechanisms of discrimination of enantiomeric barbital in the binding site of the GABAA receptor. Amobarbital, (R)-, (S)-pentobarbital, and (R)-, (S)-isobarbital bonded to the TM2-TM2’ transmembrane domain (TMD), i.e., the propofol binding site. There was a 2.9 kcal moldifference in enantiomeric pentobarbital bindings. Pentobarbital discrimination in the TM2-TM2’ TMD site was caused not only by the barbital ring’s hydrogen-bond, but also by steric fittings of the methyl-group adjacent to the chiral carbon atom.","PeriodicalId":40659,"journal":{"name":"Chem-Bio Informatics Journal","volume":null,"pages":null},"PeriodicalIF":0.3,"publicationDate":"2018-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83945693","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Random matrix theory for an inter-fragment interaction energy matrix in fragment molecular orbital method 碎片分子轨道法中碎片间相互作用能量矩阵的随机矩阵理论
IF 0.3
Chem-Bio Informatics Journal Pub Date : 2018-11-22 DOI: 10.1273/CBIJ.18.123
M. Yamanaka
{"title":"Random matrix theory for an inter-fragment interaction energy matrix in fragment molecular orbital method","authors":"M. Yamanaka","doi":"10.1273/CBIJ.18.123","DOIUrl":"https://doi.org/10.1273/CBIJ.18.123","url":null,"abstract":"The statistical properties of the inter-fragment interaction energy matrix of the fragment molecular orbital method are analyzed using the random matrix theory. The eigenvalue and eigenvector distributions, the inverse participation ratio, and the unfolded eigenvalue statistics are compared with the corresponding random matrix ensemble. Cluster analysis of the fragments with strong correlations is presented using the inverse participation ratio of the random matrix theory.","PeriodicalId":40659,"journal":{"name":"Chem-Bio Informatics Journal","volume":null,"pages":null},"PeriodicalIF":0.3,"publicationDate":"2018-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85270101","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
Accuracy of Dimer-ES Approximation on Fragment Molecular Orbital (FMO) Method 片段分子轨道(FMO)法二聚体- es近似的准确性
IF 0.3
Chem-Bio Informatics Journal Pub Date : 2018-10-05 DOI: 10.1273/CBIJ.18.119
T. Nakano, Kaori Fukuzawa, Yoshio Okiyama, C. Watanabe, Y. Komeiji, Y. Mochizuki
{"title":"Accuracy of Dimer-ES Approximation on Fragment Molecular Orbital (FMO) Method","authors":"T. Nakano, Kaori Fukuzawa, Yoshio Okiyama, C. Watanabe, Y. Komeiji, Y. Mochizuki","doi":"10.1273/CBIJ.18.119","DOIUrl":"https://doi.org/10.1273/CBIJ.18.119","url":null,"abstract":"The fragment molecular orbital (FMO) method is recently attracting attention as a method of calculating the electronic state of macromolecular systems. To enhance the speed of the FMO method, it is necessary to apply an approximation in which SCF calculations are neglected for distant fragment (monomer) pairs (dimers) and instead the electrostatic interactions between the two monomers are calculated. This approximation is called the dimer-es approximation. The accuracy and speed brought by the dimer-es approximation depend on the minimum threshold distance between two atoms to apply the approximation. This threshold distance given in unit of van der Waals radii is named “Ldimer-es”. In this communication, we examined dependence of HF and MP2 electron correlation energy errors on “Ldimer-es”, and it is preferable to calculate FMO4-HF and FMO4-MP2 for calculation of FMO-HF and FMO-MP2 of side chain-split peptides with Ldimer-es=2.0.","PeriodicalId":40659,"journal":{"name":"Chem-Bio Informatics Journal","volume":null,"pages":null},"PeriodicalIF":0.3,"publicationDate":"2018-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79176877","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
All-atom molecular dynamics of film supported flat-shaped DNA origami in water 薄膜支撑的平面DNA折纸在水中的全原子分子动力学
IF 0.3
Chem-Bio Informatics Journal Pub Date : 2018-09-19 DOI: 10.1273/CBIJ.18.96
R. Azuma, Sae Kishi, G. Gutmann, A. Konagaya
{"title":"All-atom molecular dynamics of film supported flat-shaped DNA origami in water","authors":"R. Azuma, Sae Kishi, G. Gutmann, A. Konagaya","doi":"10.1273/CBIJ.18.96","DOIUrl":"https://doi.org/10.1273/CBIJ.18.96","url":null,"abstract":"Here we present a novel technique that utilizes a supporting inorganic film for MD simulations of flat-shaped DNA origami structures in explicit solvent. The number of atoms is typically over 16 million including water molecules. By utilizing a GPU capable simulation engine, we have addressed conformational changes of a DNA origami structure under normal ionic strength and deionized water conditions up to the order of one nanosecond simulation time. Our results demonstrate that DNA origami configuration undergoes a continual growth in the absence of cations, while it is not the case for normal ionic strength. Statistical analysis of helix forms for these DNA origami structures reveals that not only cations but also water permittivity contributed to the maintenance of B-DNA helix form during the stretching motion. These results will provide key features in designing molecular robots as assembly of DNA origami structural components such as scaffolds, connectors and channels.","PeriodicalId":40659,"journal":{"name":"Chem-Bio Informatics Journal","volume":null,"pages":null},"PeriodicalIF":0.3,"publicationDate":"2018-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80667387","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
The Orbital-Effect-Myth 的Orbital-Effect-Myth
IF 0.3
Chem-Bio Informatics Journal Pub Date : 2018-07-20 DOI: 10.1273/CBIJ.18.86
M. Nishio, Yuji Kohno
{"title":"The Orbital-Effect-Myth","authors":"M. Nishio, Yuji Kohno","doi":"10.1273/CBIJ.18.86","DOIUrl":"https://doi.org/10.1273/CBIJ.18.86","url":null,"abstract":"In the cyclohexane derivatives, the equatorial conformer, having less steric repulsion of hydrogen atoms adjacent to substituent, is dominant over the axial conformer. This is a normal stereochemical requirement. In hexose, containing oxygen atoms in the ring, however, α-anomer (with axial substituent) is more stable than β-anomer (with equatorial substituent) and it is called the anomeric effect. Why does this phenomenon, which is not compatible with the stereochemical intuition (but still widely accepted), happen at all? It has been more than 60 years since Edward reported it, but the root cause has not yet become clear. At present, the most popular explanation for the anomeric effect is that it is due to the interaction between a lone pair of electrons on oxygen and the anti-bonding orbital (σ*) of C-R bond. Contrary to popular belief, we demonstrate that this explanation does not hold.","PeriodicalId":40659,"journal":{"name":"Chem-Bio Informatics Journal","volume":null,"pages":null},"PeriodicalIF":0.3,"publicationDate":"2018-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80494839","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Concerns regarding the deterioration of objectivity in molecular biology 对分子生物学客观性恶化的担忧
IF 0.3
Chem-Bio Informatics Journal Pub Date : 2018-07-10 DOI: 10.1273/CBIJ.18.173
T. Konishi
{"title":"Concerns regarding the deterioration of objectivity in molecular biology","authors":"T. Konishi","doi":"10.1273/CBIJ.18.173","DOIUrl":"https://doi.org/10.1273/CBIJ.18.173","url":null,"abstract":"Scientific objectivity was not a problem in the early days of molecular biology. However, relativism seems to have invaded some areas of the field, damaging the objectivity of its analyses. This review reports on the status of this issue by investigating a number of cases.","PeriodicalId":40659,"journal":{"name":"Chem-Bio Informatics Journal","volume":null,"pages":null},"PeriodicalIF":0.3,"publicationDate":"2018-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85355483","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
Binding properties between curcumin and malarial tubulin: molecular-docking and ab initio fragment molecular orbital calculations 姜黄素与疟疾微管蛋白的结合特性:分子对接和从头算片段分子轨道计算
IF 0.3
Chem-Bio Informatics Journal Pub Date : 2018-03-25 DOI: 10.1273/CBIJ.18.44
Shintaro Ota, Shougo Tomioka, Haruki Sogawa, Riku Satou, Mitsuki Fujimori, P. A. Karpov, S. V. Shul'ga, Y. Blume, N. Kurita
{"title":"Binding properties between curcumin and malarial tubulin: molecular-docking and ab initio fragment molecular orbital calculations","authors":"Shintaro Ota, Shougo Tomioka, Haruki Sogawa, Riku Satou, Mitsuki Fujimori, P. A. Karpov, S. V. Shul'ga, Y. Blume, N. Kurita","doi":"10.1273/CBIJ.18.44","DOIUrl":"https://doi.org/10.1273/CBIJ.18.44","url":null,"abstract":"Curcumin can bind to tubulin and inhibit the formation of tubulin polymer, which contributes to the formation of microtubule. Binding sites of curcumin on the αand β-tubulin heterodimer were predicted by a molecular docking study to ascertain probable causes for the observed anti-microtubule effects of curcumin. However, the specific interactions between curcumin and the tubulins have yet to be elucidated at an electronic level. We here investigated the binding properties between curcumin and αor β-tubulin of Plasmodium falciparum, using ab initio fragment molecular orbital (FMO) calculations, in order to reveal the preferable binding sites of curcumin on these tubulins. The results were compared with those for some microtubule destabilizing drugs evaluated by the same method to confirm the efficiency of curcumin as an inhibitor to the tubulins. Our ab initio FMO calculations might provide useful information for proposing novel therapeutic agents with significant binding affinity to both the αand β-tubulins.","PeriodicalId":40659,"journal":{"name":"Chem-Bio Informatics Journal","volume":null,"pages":null},"PeriodicalIF":0.3,"publicationDate":"2018-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87779221","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 3
Specific interactions between vitamin D receptor and ligand depending on its chirality: ab initio fragment molecular orbital calculations 维生素D受体和配体之间的特定相互作用取决于其手性:从头开始片段分子轨道计算
IF 0.3
Chem-Bio Informatics Journal Pub Date : 2018-03-21 DOI: 10.1273/CBIJ.18.32
Ryosuke Takeda, Rie Suzuki, Ittetsu Kobayashi, Kentaro Kawai, A. Kittaka, M. Takimoto-Kamimura, N. Kurita
{"title":"Specific interactions between vitamin D receptor and ligand depending on its chirality: ab initio fragment molecular orbital calculations","authors":"Ryosuke Takeda, Rie Suzuki, Ittetsu Kobayashi, Kentaro Kawai, A. Kittaka, M. Takimoto-Kamimura, N. Kurita","doi":"10.1273/CBIJ.18.32","DOIUrl":"https://doi.org/10.1273/CBIJ.18.32","url":null,"abstract":"The chirality of a compound affects its biochemical and pharmaceutical properties. It was found that the binding affinity between vitamin D receptor (VDR) and its ligand depends significantly on the chirality of the ligand. To elucidate the reason for this dependence, we here investigated the specific interactions between VDR and two types of ligands with different chirality, using ab initio fragment molecular orbital (FMO) calculations. The FMO results reveal that the part of ligand with different chirality interacts strongly with the imidazole ring of histidine side-chain in VDR, and that the binding affinity between VDR and the ligands depends on the protonation state of the histidine. This finding indicates the possibility that ligands with different chirality can assign the protonation state of VDR histidine residues existing near the ligand.","PeriodicalId":40659,"journal":{"name":"Chem-Bio Informatics Journal","volume":null,"pages":null},"PeriodicalIF":0.3,"publicationDate":"2018-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72869641","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 5
Biomolecular Chemical Simulations toward Elucidation of the Enantioselectivity and Reactivity of Lipases in Organic Synthesis 有机合成中脂肪酶对映体选择性和反应性的生物分子化学模拟
IF 0.3
Chem-Bio Informatics Journal Pub Date : 2018-02-28 DOI: 10.1273/CBIJ.18.21
Y. Yagi, Takatomo Kimura, M. Kamezawa, Y. Naoshima
{"title":"Biomolecular Chemical Simulations toward Elucidation of the Enantioselectivity and Reactivity of Lipases in Organic Synthesis","authors":"Y. Yagi, Takatomo Kimura, M. Kamezawa, Y. Naoshima","doi":"10.1273/CBIJ.18.21","DOIUrl":"https://doi.org/10.1273/CBIJ.18.21","url":null,"abstract":"We are presently continuing to perform biomolecular chemical simulations for Burkholderia cepacia lipase (BCL) and Candida antarctica lipase typeB (CALB) to predict their enantioselectivity and reactivity toward various organic compounds. Here, we describe molecular dynamics (MD) and fragment molecular orbital (FMO) calculations on the complexes of CALB with primary and secondary alcohol esters. For esters with high enantioselectivity, the fast-reacting enantiomer of esters is located near the active site of CALB, whereas the slow-reacting enantiomer of esters moves away from the active site of CALB. On the other hand, for the esters with low enantioselectivity, we found that both (R)and (S)-enantiomers of esters remain the active site of CALB. The FMO computations indicate that for the esters with high enantioselectivity, each fast-reacting enantiomer shows strong interactions with some particular amino acid residues, including Thr40, whereas for the esters with low enantioselectivity, both (R)and (S)-enantiomers interact with identical amino acid residues including Thr40. It is predictable that Thr40 in CALB plays an important role in the chiral recognition of enantiomers through lipase-catalyzed biotransformations.","PeriodicalId":40659,"journal":{"name":"Chem-Bio Informatics Journal","volume":null,"pages":null},"PeriodicalIF":0.3,"publicationDate":"2018-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82825440","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
Analysis of physicochemical properties of drugs included in anticholinergic rating scales 抗胆碱能评定量表所含药物理化性质分析
IF 0.3
Chem-Bio Informatics Journal Pub Date : 2018-01-11 DOI: 10.1273/CBIJ.18.1
Junko Nagai, H. Kagaya, Y. Uesawa
{"title":"Analysis of physicochemical properties of drugs included in anticholinergic rating scales","authors":"Junko Nagai, H. Kagaya, Y. Uesawa","doi":"10.1273/CBIJ.18.1","DOIUrl":"https://doi.org/10.1273/CBIJ.18.1","url":null,"abstract":"Adverse effects induced by the duplication of drugs with anticholinergic effects are a problem among elderly people who take many drugs. Various anticholinergic rating scales have been published and are applied clinically to evaluate a patient’s anticholinergic burden; however, there are some problems with these scales, such as drugs that are assessed differently between scales. We aimed to construct a method to more correctly distinguish between drugs with and without anticholinergic effects and to understand the properties of drugs that have anticholinergic effects. We constructed a model for identifying anticholinergic effects via a decision tree, using descriptors indicating the physicochemical properties of the drugs. The best split yielded a decision tree with 46 branches (area under the receiver operating characteristic curve = 0.99). However, only seven branches, defined by six descriptors: ASA_P, GCUT_PEOE_0, opr_brigid, PEOE_VSA+1, GCUT_SLOGP_0, vsa_pol (related to van der Waals surface areas, partial charges, and molecule structures), were required to identify drugs with anticholinergic effects. This result suggests a relationship between the hydrophobic interactions of drugs and the muscarinic receptor. In this study, we constructed a model to predict whether drugs have anticholinergic effects, and obtained essential physicochemical information on the drugs to distinguish their anticholinergic effects. It is our hope that these findings provide useful information for predicting anticholinergic effects of drugs in clinical","PeriodicalId":40659,"journal":{"name":"Chem-Bio Informatics Journal","volume":null,"pages":null},"PeriodicalIF":0.3,"publicationDate":"2018-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82997246","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
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