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Journal of Biomolecular Structure & Dynamics

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https://read.qxmd.com/read/30856053/exploring-the-binding-mechanism-of-saccharin-and-sodium-saccharin-to-promoter-of-human-p53-gene-by-theoretical-and-experimental-methods
#1
Mahboubeh Mansourian, Karim Mahnam, Hamid Reza Rajabi, Mahmoud Roushani, Amir Hossein Doustimotlagh
In the past few decades, extensive discussions have been on the impact of artificial sweeteners on the risk of cancer. The present study aimed to evaluate the interaction of saccharin (SA) and sodium saccharin (SSA) with the promoter of the human p53 gene. The binding ability was assessed using the spectroscopic technique, molecular docking and molecular dynamics (MD) simulation methods. Free energy of binding has been calculated using Molecular Mechanics/Poisson-Boltzmann Surface Area (MM/PBSA) method. Fluorescence spectra of mentioned gene with concentration profiles of SA and SSA were obtained in a physiological condition...
March 11, 2019: Journal of Biomolecular Structure & Dynamics
https://read.qxmd.com/read/30843766/multispectral-and-molecular-docking-investigations-on-the-interaction-of-primethamine-trimethoprim-with-bsa-hsa
#2
Xiaoyue Sun, Shuyun Bi, Jun Wu, Rui Zhao, Di Shao, Zhe Song
Primethamine (PMA) and Trimethoprim (TMP) were investigated as traditional coccidiostats on the binding of bovine serum albumin (BSA) and human serum albumin (HSA) by multispectral and molecular docking techniques. The Stern-Volmer plots and time-resolved fluorescence measurement declared that PMA/TMP quenching the intrinsic fluorescence of BSA/HSA was static quenching process. The binding constants (Ka ) and binding sites (n) were calculated at different temperatures. Meanwhile, thermodynamic parameters showed electrostatic forces played a leading role in the interaction of PMA/TMP with BSA/HSA...
March 7, 2019: Journal of Biomolecular Structure & Dynamics
https://read.qxmd.com/read/30843765/molecular-dynamics-simulation-revealed-the-intrinsic-conformational-change-of-cellular-inhibitor-of-apoptosis-protein-1
#3
Heng Xu, Zhengkuan Tang, Yu Zuo, Fengmin Xiong, Kaixian Chen, Hualiang Jiang, Cheng Luo, Hao Zhang
Inhibitor of apoptosis proteins (IAPs) are important regulators of apoptosis, and protein targets for the development of anti-cancer drugs. Cellular inhibitor of apoptosis protein-1 (cIAP1) is an important member of IAPs. Peptides or small-molecular antagonists can induce the dimerization, auto-ubiquitination, and proteasomal degradation of the cellular inhibitor of apoptosis protein-1 (cIAP1). While in the absence of antagonists, several mutations of the cIAP1 protein also lead to its dimerization and auto-ubiquitination...
March 7, 2019: Journal of Biomolecular Structure & Dynamics
https://read.qxmd.com/read/30843759/decoding-molecular-mechanism-of-inhibitor-bindings-to-cdk2-using-molecular-dynamics-simulations-and-binding-free-energy-calculations
#4
Jianzhong Chen, Laixue Pang, Wei Wang, Lifei Wang, John Z H Zhang, Tong Zhu
ABSTARCT CDK2 can be used as an attractive target for development of efficient inhibitors curing multiple disease relating with CDK2. In this work, molecular dynamics (MD) simulations and binding free energy calculations were coupled to probe conformational changes of CDK2 due to inhibitor associations and binding mechanisms of inhibitors PM1, FMD and X64 to CDK2. The results suggest that the binding strength of FMD and X64 to CDK2 is stronger than that of PM1. Principal component (PC) analysis and cross-correlation map calculations based on the equilibrated MD trajectories demonstrate that the structural difference in inhibitors exert important impact on motion modes and dynamics behavior of CDK2...
March 7, 2019: Journal of Biomolecular Structure & Dynamics
https://read.qxmd.com/read/30836878/understanding-ligands-driven-mechanism-of-wild-and-mutant-aryl-hydrocarbon-receptor-in-presence-of-phytochemicals-combating-parkinson-s-disease-an-in-silico-and-in-vivo-study
#5
Surya Narayan Rath, Lingaraja Jena, Manorama Patri
Aryl Hydrocarbon Receptor (AhR) is a key player to regulate the expression of a group of enzymes known as cytochrome P450s (CYPs) super family (CYP1A1, CYP1B1, CYP2B6, and CYP2E1) which metabolites diverse endogenous as well as toxic compounds such as Benzo[a] Pyrene (B[a] P) and TCDD. B[a] P induces oxidative stress and causes degeneration of dopaminergic neurons in the midbrain, may leads to Parkinson's disease (PD). The metabolism of B[a] P through the expression of CYPs is mainly triggered after binding of B[a] P within ligand binding domain of AhR...
March 5, 2019: Journal of Biomolecular Structure & Dynamics
https://read.qxmd.com/read/30836858/synthesis-anticholinesterase-activity-and-molecular-modeling-studies-of-novel-carvacrol-substituted-amide-derivatives
#6
Belma Zengin Kurt, Serdar Durdagi, Gulsen Celebi, Ramin Ekhteiari Salmas, Fatih Sonmez
In the present study, 23 novel carvacrol derivatives involving the amide moiety as a linker between the alkyl chains and/or the heterocycle nucleus were synthesized and tested in vitro as acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE) inhibitors. 2-(5-isopropyl-2-methylphenoxy)-N-(quinolin-8-yl)acetamide (5v) revealed the highest inhibition properties against AChE and BuChE with the IC50 values of 1.93 µM and 0.05 µM, respectively. The blood-brain barrier (BBB) permeability of the potent inhibitor (5v) was also assessed by the widely used parallel artificial membrane permeability assay (PAMPA-BBB)...
March 5, 2019: Journal of Biomolecular Structure & Dynamics
https://read.qxmd.com/read/30836854/molecular-mechanism-of-acetoacetyl-coa-enhanced-kinetics-for-increased-bioplastic-production-from-cupriavidus-necator-428
#7
Aditi Singh, Mriganko Das, Abhinav Grover
Polyhydroxyalkanoates are gaining importance due to their biodegradable nature and close analogy to plastics. Polyhydroxybutyrate (PHB) is the most widely used bioplastic from polyalkanoate family, which is produced by a legion of bacterial species via phbCAB operon encoding β-ketothiolase (PhaA), NADPH-dependent acetoacetyl-coenzyme A (acetoacetyl-CoA) reductase (PhaB) and polyhydroxyalkanoate synthase (PhaC). Augmentation in the activity of these enzymes is promising for increased PHB production which is achieved by enzyme engineering strategies including non-structural and structural approaches...
March 5, 2019: Journal of Biomolecular Structure & Dynamics
https://read.qxmd.com/read/30831056/experimental-and-theoretical-investigations-of-novel-oxidovanadium-iv-juglone-complex-dna-hsa-interaction-and-cytotoxic-activity
#8
Fatemeh Abyar, Leila Tabrizi
A new oxidovanadium(IV) complex VO(L)(Jug) (HL = 5-methoxy-1,3-bis (1-methyl-1H-benzo[d]imidazol-2-yl)benzene, Jug = juglone) was synthesized and characterized. Interactions of the V(IV) complex with calf thymus DNA (CT DNA) and human serum albumin were studied using different techniques such as UV-vis and fluorescence emission spectroscopy. The experimental results were confirmed by the molecular docking study. The oxidovanadium(IV) complex can efficiently cleave pUC19 DNA in the presence of Hydrogen peroxide...
March 4, 2019: Journal of Biomolecular Structure & Dynamics
https://read.qxmd.com/read/30831055/delineating-the-interaction-of-combretastatin-a-4-with-%C3%AE-%C3%AE-tubulin-isotypes-present-in-drug-resistant-human-lung-carcinoma-using-a-molecular-modeling-approach
#9
Bajarang Vasant Kumbhar, Vishwambhar Vishnu Bhandare, Dulal Panda, Ambarish Kunwar
Tubulin isotypes are known to regulate microtubule dynamic instability and contribute to the development of drug resistance in certain types of cancers. Combretastatin-A4 (CA-4) has a potent anti-mitotic, vascular disrupting and anti-angiogenic activity. It binds at the interface of αβ tubulin heterodimers and inhibits microtubules assembly. Interestingly, the CA-4 resistant human lung carcinoma shows alteration of βI and βIII isotype levels, a higher expression of βI tubulin isotype and a decreased expression of βIII tubulin isotypes has been reported in drug resistant cell lines...
March 4, 2019: Journal of Biomolecular Structure & Dynamics
https://read.qxmd.com/read/30829560/identification-of-human-tau-tubulin-kinase-1inhibitors-an-integrated-e-pharmacophore-based-virtual-screening-and-molecular-dynamics-simulation
#10
Srabanti Jana, Sushil Kumar Singh
Tau-tubulin kinase 1 inhibitors inhibit tau protein phosphorylation on Ser198, Ser199, Ser202, Ser422, and also in paired helical filaments. We developed receptor-based pharmacophore models by exploiting three TTBK1 protein structures, i.e., 4NFN, 4BTM, and 4BTK. The integrated e-pharmacophore based virtual screening and molecular dynamics simulation recognized four hits viz. ZINC14644839, ZINC00012956, ZINC91332506, and ZINC69775110 as TTBK1 inhibitors. The Glide XP docking energies (-8.48 to -10.71 kcal...
March 4, 2019: Journal of Biomolecular Structure & Dynamics
https://read.qxmd.com/read/30821653/symmetrization-of-the-backbone-of-nucleic-acids-a-molecular-dynamics-study
#11
Pradeep Pant, Amita Pathak, B Jayaram
DNA displays directional asymmetry (5'→3'), a fundamental property associated with each strand of the nucleic acids and is crucial to several biological processes such as transcription and replication. We observe that this asymmetry can be altered by a number of ways leading to directionally symmetric nucleic acids. We report six such approaches for the creation of symmetric backbones, their insertion in a regular B-DNA structure followed by their characterization using molecular dynamics (MD) simulations on a microsecond timescale in explicit solvent...
March 1, 2019: Journal of Biomolecular Structure & Dynamics
https://read.qxmd.com/read/30821650/characterization-of-interactions-between-cromolyn-sodium-and-bovine-serum-albumin-by-spectroscopic-calorimetric-and-computational-methods
#12
Shama Yasmeen, Riyazuddeen, Samima Khatun, Faizan Abul Qais
Cromolyn sodium, an anti-inflammatory drug is used in the treatment of allergic disorders. Bovine serum albumin (BSA) a blood plasma protein is used as a model protein for studying protein folding and ligand binding mechanism as it is the main transporter protein which decides the disposition and pharmacodynamics of numerous drugs. In this study, interaction of cromolyn sodium with bovine serum albumin was investigated using isothermal titration calorimetry, UV-vis, fluorescence, circular dichroism spectroscopy and molecular docking tecniques...
March 1, 2019: Journal of Biomolecular Structure & Dynamics
https://read.qxmd.com/read/30821624/impact-of-k16a-and-k28a-mutation-on-the-structure-and-dynamics-of-amyloid-%C3%AE-42-peptide-in-alzheimer-s-disease-key-insights-from-molecular-dynamics-simulations-%C3%A2
#13
Suniba Shuaib, Rajneet Kaur Saini, Deepti Goyal, Bhupesh Goyal
The aggregation of amyloid-β42 (Aβ42 ) peptide into toxic oligomers and fibrils is a key step in the Alzheimer disease pathogenesis. The recent studies highlighted that lysine residues (K16 and K28) play a critical role in the Aβ42 self-assembly and are the target of entities like molecular tweezer, CLR01. The studies reveal that lysine to alanine mutation significantly affect Aβ oligomerization, toxicity and aggregation process. However, the molecular mechanism behind reduced Aβ toxicity on K16A and K28A mutation remain elusive...
March 1, 2019: Journal of Biomolecular Structure & Dynamics
https://read.qxmd.com/read/30810494/spermine-as-a-porcine-pancreatic-elastase-activator-spectroscopic-and-molecular-simulation-studies
#14
Sakineh Sadeghi-Kaji, Behzad Shareghi, Ali Akbar Saboury, Sadegh Farhadian
The aim of this study was to investigate the spermine effect on the thermal denaturation, conformation and activity of elastase at three temperatures of 303, 313 and 323 K in the Tris buffer, at pH 8.5, using UV-vis spectrophotometry, spectrofluorometry and circular dichroism as well as molecular docking and molecular simulation. The increased absorption of elastase in the presence of spermine suggested a change in the environment of tryptophan. It was found that under the influence of spermine, the emission intensity of elastase extremely was reduced, and the use of the Stern-Volmer equation showed that some static quenching had occurred...
February 27, 2019: Journal of Biomolecular Structure & Dynamics
https://read.qxmd.com/read/30806581/an-oxidodiperoxido-vanadium-based-artificial-nuclease-dna-binding-and-cleavage-studies
#15
Haimanti Adhikari, Rina Ghosh, Kalyan K Mukherjea
Ammoniumdiaqua oxidodiperoxidophenanthrolinevanadate(V) complex has been synthesized and structurally characterized to develop DNA nuclease. The investigation of the interaction of DNA with this oxidodiperoxido vanadium complex has been carried out by various physicochemical tools like UV-vis, fluorescence, viscosity and circular dichroism (CD). The high order of intrinsic binding constant, the quenching constant of the complex with DNA and the viscosity measurements support the intercalative mode of binding with calf thymus DNA (CT-DNA)...
February 26, 2019: Journal of Biomolecular Structure & Dynamics
https://read.qxmd.com/read/30806580/identification-of-novel-nad-p-h-dehydrogenase-quinone-1-antagonist-using-computational-approaches
#16
Rajendran Selvakumar, Dhanabalan Anantha Krishnan, Chandrasekaran Ramakrishnan, Devadasan Velmurugan, Krishnasamy Gunasekaran
NAD(P)H: quinone oxidoreductase 1 (NQO1) inhibitors are proved as promising therapeutic agents against cancer. This study is to determine potent NAD(P)H dependent NQO1 inhibitors with new scaffold. Pharmacophore-based 3D QSAR model has been built based on 45 NQO1 inhibitors reported in the literature. The structure-function correlation coefficient graph represents the relationship between phase activity and phase predicted activity for training and test sets. A QSAR model statistics shows the excellent correlation of the generated model...
February 26, 2019: Journal of Biomolecular Structure & Dynamics
https://read.qxmd.com/read/30806579/structural-debilitation-of-mutation-g322d-associated-with-msh2-and-their-role-in-triple-negative-breast-cancer
#17
Sriroopreddy Ramireddy, P Raghuraman, C Sudandiradoss
The missense mutation in the mismatch repair gene MSH2 underlies in several hereditary cancers. In this study, we have detailed the disruptive mutation of G322D that overtly pathogenic and clinically relevant to the triple negative breast cancer (TNBC) on the basis of structural aspect to untangle the unknown factors. We systematically evaluated the conformational changes that undergo upon mutation from the annotation of intra-residual contacts, secondary structural arrangements and fold recognition through molecular dynamics simulation...
February 26, 2019: Journal of Biomolecular Structure & Dynamics
https://read.qxmd.com/read/30806578/assessment-on-the-binding-affinity-between-ritonavir-with-model-transport-protein-a-combined-multi-spectroscopic-approaches-with-computer-simulation
#18
Bao-Li Wang, Kai-Li Zhou, Yan-Yue Lou, Dong-Qi Pan, Song-Bo Kou, Zhen-Yi Li, Jie-Hua Shi
The binding affinity between ritonavir (RTV) and model transport protein, BSA was assessed through multi-spectroscopic approaches and computer simulation. The findings revealed RTV statically quenched the fluorescence of BSA and formed the 1:1 RTV-BSA complex with the binding constant (Kb ) of 1.06 × 103 ∼ 5.08 × 103 M-1 under the studied temperatures (298 ∼ 310 K). During the interaction of RTV with BSA, the hydrogen bonds and van der Waals forces acted as predominant function while the hydrophobicity played an assistant function...
February 26, 2019: Journal of Biomolecular Structure & Dynamics
https://read.qxmd.com/read/30806572/syntheses-characterization-dna-hsa-binding-ability-and-antitumor-activities-of-a-family-of-isostructural-binuclear-lanthanide-complexes-containing-hydrazine-schiff-base
#19
Xue-Qing Song, Zhi-Gang Wang, Yang Wang, Yu-Ying Huang, Yu-Xuan Sun, Yan Ouyang, Cheng-Zhi Xie, Jing-Yuan Xu
Three dinuclear lanthanide complexes, [Ln2 (L)2 (μ3 -OAc)4 (H2 O)2 ]⋅2H2 O (Ln = La (1), Eu (2) and Dy (3), HL = N'-(2-hydroxybenzylidene) nicotinohydrazide), have been synthesized and characterized by IR, elemental analysis, and X-ray single-crystal diffraction. Crystallographic study revealed the representative complex 1 display a discrete dinuclear structure with a distorted tricapped trigonal prismatic geometry around La(III) ion. The interaction of complexes 1-3 with CT-DNA was investigated by absorption spectra, fluorescence quenching and viscosity, which reveals the complexes binds to CT-DNA with a moderate intercalative mode...
February 26, 2019: Journal of Biomolecular Structure & Dynamics
https://read.qxmd.com/read/30806177/elucidating-the-tight-binding-mechanism-of-two-oral-anticoagulants-to-factor-xa-by-using-induced-fit-docking-and-molecular-dynamics-simulation
#20
Qingqing Du, Yan Qian, Xiaojun Yao, Weiwei Xue
No abstract text is available yet for this article.
February 26, 2019: Journal of Biomolecular Structure & Dynamics
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