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Journal of Biomolecular Structure & Dynamics

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https://www.readbyqxmd.com/read/28345378/probing-the-behavior-of-bovine-serum-albumin-upon-binding-to-atenolol-insights-from-spectroscopic-and-molecular-docking-approaches
#1
Tuo-Ying Jiang, Kai-Li Zhou, Yan-Yue Lou, Dong-Qi Pan, Jie-Hua Shi
Molecular interaction of atenolol, a selective β1 receptor antagonist with the major carrier protein, bovine serum albumin (BSA), was investigated under imitated physiological conditions (pH 7.4) by means of fluorescence spectroscopy, UV absorption spectroscopy, Fourier transform infrared spectroscopy (FT-IR), and molecular modeling studies. The steady-state fluorescence spectra manifested that static type, due to formation of the atenolol-BSA complex, was the dominant mechanism for fluorescence quenching...
March 27, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28335682/effect-of-lipophilicity-of-amylamine-and-amylglycine-ligands-on-biological-activity-of-new-anticancer-cisplatin-analog
#2
Fatemeh Safa Shams Abyaneh, Mahboube Eslami Moghadam, Moayyed Hoseini Sadr, Adeleh Divsalar
Investigation of side effects and solubility of anticancer drugs is a major challenge in chemotherapy science. Thus, design and synthesis of cisplatin analogs with higher lipophilicity as novel water-soluble anticancer drugs is valuable. In this work, two new Pt (II) complexes were synthesized with formula cis-[Pt (NH3)2(amylgly)] NO3 and cis-[Pt (amylamine)2(amylgly)]NO3; where gly is penthyl glycine as an amino acid. The new compounds were synthesized and extensively characterized using analytical techniques; spectroscopic methods and conductivity measurement...
March 23, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28330421/the-proteinopathy-of-d169g-and-k263e-mutants-at-the-rna-recognition-motif-rrm-domain-of-tar-dna-binding-protein-tdp43-causing-neurological-disorders-a-computational-study
#3
Vishwambhar Vishnu Bhandare, Amutha Ramaswamy
One of the multitasking proteins, transactive response DNA-binding protein 43 (tdp43) plays a key role in RNA regulation and the two pathogenic mutations such as D169G and K263E, located at the RNA Recognition Motif (RRM) of tdp43, are reported to cause neurological disorders such as Amyotrophic Lateral Sclerosis (ALS) and Fronto Temporal Lobar Degeneration (FTLD). As the exploration of the proteinopathy demands both structural and functional characterization of mutants, a comparative analysis on the wild type and mutant tdp43 (D169G and K263E) and their complexes with RNA have been performed using computational approaches...
March 22, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28330413/molecular-dynamic-simulation-and-dft-study-on-the-drug-dna-interaction-crocetin-as-an-anticancer-and-dna-nanostructure-model
#4
Ebrahim Azarhazin, Mohammad Izadyar, Mohammad Reza Housaindokht
In this research, the interaction of Crocetin as an anticancer drug and a Dickerson DNA has been investigated. 25 ns molecular dynamic simulations of Crocetin and DNA composed of twelve base pairs and a sequence of d(CGCGAATTCGCG)2 were done in water. Three definite parts of the B-DNA were considered in analyzing the best interactive site from the thermodynamic point of view. Binding energy analysis showed that van der Waals interaction is the most important part related to the reciprocal O and H atoms of the Crocetin and DNA...
March 22, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28325114/complexes-of-dna-bases-and-watson-crick-base-pairs-interaction-with-neutral-silver-agn-n-8-10-12-clusters-a-dft-and-tddft-study
#5
Ruby Srivastava
We study the binding of the neutral Agn (n = 8, 10, 12) to the DNA base- adenine (A), guanine (G) and Watson-Crick -adenine-thymine (AT), guanine-cytosine (GC) pairs. Geometries of complexes were optimized at the DFT level using the hybrid B3LYP functional. LANL2DZ effective core potential (ECP) was used for silver and 6-31+G(**) was used for all other atoms. NBO charges were analyzed using the Natural population analysis. The absorption properties of Agn-A,G/WC complexes were also studied using time-dependent density functional theory (TDDFT)...
March 21, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28317461/hydroxy-methoxy-benzaldehyde-from-sesbania-grandilfora-inhibits-the-advanced-glycation-end-products-ages-mediated-fibrillation-in-hemoglobin
#6
G Prasanna, N Hari, N T Saraswathi
The present study was aimed to identify the active anti-glycation constituent from the leaves of Sesbania grandiflora. Characterization of the active constituent resulted in the identification of hydroxy methoxy benzaldehyde (HMB). The potential of HMB as anti-glycation lead was analyzed by fluorescence spectroscopy, fluorescence microscopy, scanning electron microscopy (SEM) and molecular interaction studies. Our results suggested that HMB inhibited formation of early (HbA1c) and advanced glycation end products (AGEs)...
March 20, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28317434/dynamics-of-the-active-site-loops-in-catalyzing-aminoacylation-reaction-in-seryl-and-histidyl-trna-synthetases
#7
Saheb Dutta, Soumya Kundu, Amrita Saha, Nilashis Nandi
Aminoacylation reaction is the first step of protein biosynthesis. The catalytic reorganization at the active site of aminoacyl tRNA synthetases (aaRSs) is driven by the loop motions. There remain lacunae of understanding concerning the catalytic loop dynamics in aaRSs. We analyzed the functional loop dynamics in seryl tRNA synthetase from Methanopyrus kandleri ((mk)SerRS) and histidyl tRNA synthetases from Thermus thermophilus ((tt)HisRS), respectively, using molecular dynamics. Results confirm that the motif 2 loop and other active site loops are flexible spots within the catalytic domain...
March 20, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28298157/conserved-charged-amino-acids-are-key-determinants-for-fatty-acid-binding-proteins-fabps-membrane-interactions-a-multi-methodological-computational-approach
#8
Fernando Zamarreño, Alejandro Giorgetti, María Julia Amundarain, Juan Francisco Viso, Betina Córsico, Marcelo D Costabel
Based on the analysis of the mechanism of ligand transfer to membranes employing in vitro methods, Fatty Acid Binding Protein (FABP) family has been divided in two subgroups: collisional and diffusional FABPs. Although the collisional mechanism has been well characterized employing in vitro methods, the structural features responsible for the difference between collisional and diffusional mechanisms remain uncertain. In this work, we have identified the amino acids putatively responsible for the interaction with membranes of both, collisional and diffusional, subgroups of FABPs...
March 16, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28298161/a-simulation-investigation-on-interaction-mechanism-between-ebola-nucleoprotein-and-vp35-peptide
#9
Jing-Na Ding, Yan-Jun Zhang, Hui Zhong, Cheng-Cheng Ao, Ju-Guang Han
Ebola viruses (EBOV) will induce acute hemorrhagic fever fatally to humans and nonhuman primates. The combination of EBOV VP35 peptide with nucleoprotein N-terminal (NPNTD) is proposed based on static crystal structures in recent studies, but VP35 binding mechanism and conformational dynamics are still unclear. This investigation, using Molecular Dynamic (MD) simulation and Molecular Mechanics Generalized Born Surface Area (MM-GB/SA) energy calculation, more convincingly proves the greater roles of the protein binding mechanisms than do hints from the static crystal structure observations...
March 15, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28278027/in-silico-investigation-on-the-inhibition-of-a%C3%AE-42-aggregation-by-a%C3%AE-40-peptide-by-potential-of-mean-force-study
#10
Mary Dutta, Venkata Satish Kumar Mattaparthi
Recent experimental data revealed that small, soluble Amyloid beta (Aβ42) oligomers, especially dimers impair synaptic plasticity and memory leading to Alzheimer's disease. Here, we have studied dimerization of Aβ42/Aβ42 homo-dimer and Aβ40/Aβ42 hetero-dimer in terms of free energy profile by all-atom simulations using the ff99SB force field. We have found that in the presence of Aβ40 peptide, there exists a strong tendency to form a hetero-dimer with Aβ42 peptide, suggesting that a possible co-oligomerization...
March 13, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28279127/in-silico-prediction-of-drug-resistance-due-to-s247r-mutation-of-influenza-h1n1-neuraminidase-protein
#11
Rahul Shubhra Mandal, Samiran Panda, Santasabuj Das
We present here in silico studies on antiviral drug resistance due to a novel mutation of influenza A/H1N1 neuraminidase (NA) protein. Influenza A/H1N1 virus was responsible for a recent pandemic and is currently circulating among the seasonal influenza strains. M2 and NA are the two major viral proteins related to pathogenesis in humans and have been targeted for drug designing. Among them, NA is preferred because the ligand-binding site of NA is highly conserved between different strains of influenza virus...
March 9, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28279122/biochemical-changes-induced-by-grapeseed-extract-and-low-level-laser-therapy-administration-during-intraoral-wound-healing-in-rat-liver-an-experimental-and-in-silico-study
#12
Mehmet Erman Erdemli, Ramin Ekhteiari Salmas, Serdar Durdagi, Hasan Akgul, Mehmet Demirkol, Zeynep Aksungur, Zeliha Selamoglu
In the present study, the changes that occur in rat liver tissue as a result of the use of grapeseed extract (GSE) and low level laser therapy (LLLT) in intraoral wound healing are analyzed using biochemical parameters. Diode laser application groups received 8 J/cm(2) dose LLLT once a day for 4 days (810 nm wavelength, continuous mode, 0.25 W, 9 sec.). As a result of the biological parameter analysis, it was determined that the oxidative damage caused by the intraoral wounds and recovery period on 7(th) and 14(th) days could be substantially removed with GSE applications that have antioxidant capacity especially in rat liver tissue...
March 9, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28279118/insight-into-binding-mechanisms-of-inhibitors-mkp56-mkp73-mkp86-and-mkp97-to-hiv-1-protease-by-using-molecular-dynamics-simulation
#13
Shuhua Shi, Shaolong Zhang, Qinggang Zhang
HIV-1 protease (PR) has been a significant target for design of potent inhibitors curing acquired immunodeficiency syndrome (AIDS). Molecular dynamics (MD) simulations coupled with molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method were performed to study interaction modes of four inhibitors MKP56, MKP73, MKP86 and MKP97 with PR. The results suggest that the main force controlling interactions of inhibitors with PR should be contributed by van der Waals interactions between inhibitors and PR...
March 9, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28276274/multi-spectroscopic-and-molecular-modelling-approach-to-investigate-the-interaction-of-riboflavin-with-human-serum-albumin
#14
Md Maroof Alam, Faizan Abul Qais, Iqbal Ahmad, Parvez Alam, Rizwan Hasan Khan, Imrana Naseem
Riboflavin (RF) plays an important role in various metabolic redox reactions in the form of flavin adenine dinucleotide and flavin mononucleotide. Human serum albumin (HSA) is an important protein involved in the transportation of drugs, hormones, fatty acid and other molecules which determine the biodistribution and physiological fate of these molecules. In this study, we have investigated the interaction of riboflavin RF with HSA under simulative physiological conditions using various biophysical, calorimetric and molecular docking techniques...
March 9, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28274181/structure-of-the-carboxypeptidase-b-complex-with-n-sulfamoyl-l-phenylalanine-a-transition-state-analog-of-non-specific-substrate
#15
Valery Akparov, Vladimir Timofeev, Ilyas Khaliullin, Vytas Švedas, Inna Kuranova
Carboxypeptidase B (EC 3.4.17.2) (CPB) is commonly used in the industrial insulin production and as a template for drug design. However its ability to discriminate substrates with hydrophobic, hydrophilic and charged side chains is not well understood. We report structure of CPB complex with a transition-state analogue N-sulfamoyl-L-phenylalanine solved at 1.74Å. The study provided an insight into structural basis of CPB substrate specificity. Ligand binding is affected by structure-depended conformational changes of Asp255 in S1'-subsite, interactions with Asn144 and Arg145 in C-terminal binding subsite, and Glu270 in the catalytic center...
March 8, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28271963/biospectroscopic-analysis-of-human-breast-cancer-tissue-probing-infrared-signatures-to-comprehend-biochemical-alterations
#16
Ranjana Mehrotra, Gunjan Tyagi, Sonika Charak, Bhumika Ray, Geeta Kadayaprath, Harit Chaturvedi, Urmi Mukherjee, Andleeb Abrari
No abstract text is available yet for this article.
March 8, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28271957/cobalt-ii-complex-with-novel-unsymmetrical-tetradentate-schiff-base-on-ligand-in-vitro-cytotoxicity-studies-of-complex-interaction-with-dna-protein-molecular-docking-studies-and-antibacterial-activity
#17
Zahra Shokohi-Pour, Hossein Chiniforoshan, Mohammad R Sabzalian, Seyed-Alireza Esmaeili, Amir Abbas Momtazi-Borojeni
[C20H17N3O2] and cobalt (II) complex [Co(L(2))(MeOH)2].ClO4, (L(2) = 4-((E)-1-((2-(((E)-pyridin-2-ylmethylene) amino) phenyl) imino) ethyl) benzene-1, 3-diol) novel Schiff base has been synthesiszed and chracterized by Fourier transform infrared, UV-vis, (1)H-NMR spectroscopy, and elemental analysis techniques. The interaction of Co(II) complex with DNA and BSA was investigated by electronic absorption spectroscopy, fluorescence spectroscopy, circular dichroism, and thermal denaturation studies. Our experiments indicate that this complex could strongly bind to CT-DNA via minor groove mechanism...
March 8, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28271955/probing-the-interaction-mechanism-of-menthol-with-blood-plasma-proteins-and-its-cytotoxicity-activities
#18
Daniel Pushparaju Yeggoni, Aparna Rachamallu, Shreya Dubey, Argha Mitra, Rajagopal Subramanyam
No abstract text is available yet for this article.
March 8, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28271723/interaction-of-iron-nanoparticles-with-nervous-system-an-invitro-study
#19
Gelare Hajsalimi, Saba Taheri, Farshad Shahi, Leila Pishkar, Farnoosh Attar, Hosein Ahmadi, Mojtaba Falahati
Nanoparticles (NPs) are one of interesting and widely studying issues mainly because of their particular physico-chemical features and broad applications in the field of biomedical sciences, such as diagnosis and drug delivery. In this study, the interaction of iron nanoparticles (Fe-NPs) with Tau protein and PC12 cell, as potential nervous system models, was investigated with a range of techniques including dynamic light scattering (DLS), intrinsic fluorescence spectroscopy, circular dichroism (CD), [(3-(4, 5-dimethylthiazol-2-yl)-2, 5-diphenyl-tetrazolium-bromid] (MTT) assay, and acridine orange/ethidium bromide (AO/EB) dual staining method...
March 8, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28270032/development-of-oxidovanadium-and-oxido-peroxido-vanadium-based-artificial-dna-nucleases-via-multi-spectroscopic-investigations-and-theoretical-simulation-of-dna-binding
#20
Eshita Palmajumder, Nayim Sepay, Kalyan K Mukherjea
Benzimidazole is a neutral ligand which is often used to synthesize bioactive compounds. Two transition metal benzimidazole based complexes, namely, vanadium (IV) dioxido complex (complex 1) and vanadium (V) oxido-peroxido complex (complex 2) with tridentate benzimidazole ligand, 2, 6-di (1H-benzo[d]imidazol-2-yl) pyridine (Byim) have been designed with the intention of developing potential DNA nuclease. Different studies involving biochemical and biophysical techniques along with molecular docking suggest that both the complexes interact with DNA, while the mode of binding is intercalation...
March 7, 2017: Journal of Biomolecular Structure & Dynamics
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