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Journal of Biomolecular Structure & Dynamics

Sara Hadian Rasanani, Mahboube Eslami Moghadam, Esmaeil Soleimani, Adeleh Divsalar, Davood Ajloo, Aliakbar Tarlani, Majid Amiri
The aim of this study was synthesis of two new water-soluble fluorescent palladium and platinumcomplexes with formulas of [Pt(DACH)(FIP)](NO3)2 and [Pd(DACH)(FIP)](NO3)2, respectively, where FIP is 2-(furan-2-yl)-1H-imidazo[4,5-f][1,10] phenanthroline and DACH is 1R,2R-diaminocyclohexane. Fluorescence spectroscopy, circular dichroism (CD), thermal denaturation measurement, ionic strength, and kinetic study displayed groove binding of Pt complex on DNA, while due to binding of Pd complex,B form of DNA convert to Z form...
October 13, 2017: Journal of Biomolecular Structure & Dynamics
Teobaldo Cuya, Arlan da Silva Gonçalves, Jorge Alberto Valle da Silva, Teodorico C Ramalho, Kamil Kuca, Tanos C C França
Abstracts The oximes 4-carbamoyl-1-[({2-[(E)-(hydroxyimino) methyl] pyridinium-1-yl} methoxy) methyl] pyridinium (known as HI-6) and 3-carbamoyl-1-[({2-[(E)-(hydroxyimino) methyl] pyridinium-1-yl} methoxy) methyl] pyridinium (known as HS-6) are isomers differing from each other only by the position of the carbamoyl group on the pyridine ring. However this slight difference was verified to be responsible for big differences in the percentual of reactivation of acetylcholinesterase (AChE) inhibited by the nerve agents tabun, sarin, cyclosarin and VX...
October 11, 2017: Journal of Biomolecular Structure & Dynamics
Kazem Karami, Zohreh Mehri Lighvan, Hossein Farrokhpour, Maryam Dehdashti Jahromi, Amir Abbas Momtazi-Borojeni
[Pd{(C,N)-C6H4CH2NH(Et) (Qu)] (2) and [Pd{(C,N)-C6H4CH2NH(Et) (Nar)] (3) (Qu=Quercetin, Nar=Naringin) mononuclear palladium (II) complexes have been synthesized and characterized using elemental analysis, IR and electronic spectroscopy. The interaction of the prepared complexes with calf thymus DNA (CT DNA) and bovine serum albumin (BSA), monitored by UV-visible and fluorescence titrations, respectively, have been carried out to better understand the mode of their action under biological conditions. Intercalative binding mode between the complexes and DNA is suggested by the binding constant (Kb) values of 2...
October 11, 2017: Journal of Biomolecular Structure & Dynamics
P Chanphai, H A Tajmir-Riahi
Dietary polyphenols are abundant micronutrients in our diet and paly major role in prevention of degenerative diseases. The binding efficacy of antioxidant polyphenols resveratrol, genistein and curcumin with PAMAM-G3 and PAMAM-G4 nanoparticles was investigated in aqueous solution at physiological conditions, using multiple spectroscopic methods, TEM images and docking studies. The polyphenol bindings are via hydrophilic, hydrophobic and H-bonding contacts with resveratrol forming more stable conjugates. As PAMAM size increased the loading efficacy and the stability of polyphenol-polymer conjugates were increased...
October 11, 2017: Journal of Biomolecular Structure & Dynamics
Paromita Seal, Jyotirmoy Sikdar, Amartya Roy, Rajen Haldar
Ibuprofen, used for the treatment of acute and chronic pain, osteoarthritis, rheumatoid arthritis, and related conditions has ample affinity to globular proteins. Here we have explored this fundamental study pertaining to the interaction of ibuprofen with human hemoglobin (HHb), using multispectroscopic, calorimetric, and molecular modeling techniques to gain insights into molecular aspects of binding mechanism. Ibuprofen-induced graded decrease in absorption spectra indicates protein disruption along with sedimentation of HHb particle...
October 11, 2017: Journal of Biomolecular Structure & Dynamics
Swayansiddha Tripathy, Mohammed Afzal Azam, Srikanth Jupudi, Susanta Kumar Sahu
FtsZ is an appealing target for the design of antimicrobial agent that can be used to defeat the multidrug-resistant bacterial pathogens. Pharmacophore modelling, molecular docking and molecular dynamics (MD) simulation studies were performed on a series of three-substituted benzamide derivatives. In the present study a five-featured pharmacophore model with one hydrogen bond acceptors, one hydrogen bond donors, one hydrophobic and two aromatic rings was developed using 97 molecules having MIC values ranging from ...
October 11, 2017: Journal of Biomolecular Structure & Dynamics
Nayyar Rabbani, Shams Tabrez, Badar Ul Islam, Md Tabish Rehman, Abdulrahman M Alsenaidy, Mohamed F Alajmi, Rais Ahmad Khan, Mohammad A Alsenaidy, Mohd Shahnawaz Khan
The transport of more than 90% of the drugs viz. anticoagulants, analgesics and general anesthetics in the blood takes place by albumin. Hence, albumin is the prime protein needs to be investigated to find out the nature of drug binding. Serum albumin molecules are prone to glycation at elevated blood glucose levels as observed in diabetics. In this piece of work, glycation of bovine serum albumin (BSA) was carried out glyceraldehyde and characterized by molecular docking and fluorometry techniques. Glycation of BSA showed 25% loss of free amino groups and decreased protein fluorescence (60%) with blue shift of 6 nm...
October 9, 2017: Journal of Biomolecular Structure & Dynamics
Peter V Dubovskii, Maxim A Dubinnyi, Pavel E Volynsky, Yulia E Pustovalova, Anastasia G Konshina, Yuri N Utkin, Alexander S Arseniev, Roman G Efremov
Cobra cytotoxins (CTs) belong to the three-fingered protein family. They are classified into S- and P-types, the latter exhibiting higher membrane-perturbing capacity. In this work we investigated the interaction of CTs with phospholipid bilayers, using coarse-grained (CG) and full-atom (FA) molecular dynamics (MD). The object of this work is a CT of an S-type, cytotoxin I (CT1) from N.oxiana venom. Its spatial structure in aqueous solution and in the micelles of dodecylphosphocholine (DPC) were determined by (1)H-NMR spectroscopy...
October 9, 2017: Journal of Biomolecular Structure & Dynamics
Babban Jee, Sanjay Kumar, Renu Yadav, Yogesh Singh, Anuj Kumar, Naveen Sharma
Small heat shock protein16.3 (sHSP16.3) is a crucial protein for survival of Mycobacterium tuberculosis (MTB) in its host. Besides, this protein acts as a molecular chaperone during stress and is indispensable for MTB's growth, virulence and cell wall thickening. sHSP16.3 is also a promising candidate for vaccine, serodiagnosis and drug design as well. In the present study, we have targeted sHSP16.3 with two phytochemicals namely ursolic acid and carvacrol using in silico approach. Molecular docking analysis showed that both phytochemicals (ursolic acid and carvacrol) has docked with sHSP16...
October 6, 2017: Journal of Biomolecular Structure & Dynamics
Su-Chun How, Wei-Tse Hsu, Chia-Ping Tseng, Chun-Hsien Lo, Wei-Lung Chou, Steven S-S Wang
Amyloid fibril formationis associated with an array of degenerative diseases. While no real cure is currently available, evidence suggests that suppression of amyloidfibrillogenesis is an effective strategy toward combating these diseases. Brilliant blue R (BBR), a disulfonatedtriphenylmethane compound, has been shown to interact with fibril-forming proteins but exert different effects on amyloid fibrillogenesis. These inconsistent findings prompted us to further evaluate BBR's effect on the inhibition/suppresion of protein fibrillogenesis...
October 6, 2017: Journal of Biomolecular Structure & Dynamics
K V Dileep, K Nithiyanandan, C Remya
No abstract text is available yet for this article.
October 6, 2017: Journal of Biomolecular Structure & Dynamics
Sameeksha Tiwari, Manika Awasthi, Swati Singh, Veda P Pandey, Upendra N Dwivedi
Protein-protein interactions (PPI) are a new emerging class of novel therapeutic targets. In order to probe these interactions, computational tools provide a convenient and quick method towards the development of therapeutics. Keeping this in view the present study was initiated to analyze interaction of tumour suppressor protein p53 (TP53) and breast cancer associated protein (BRCA1) as promising target against breast cancer. Using computational approaches such as protein-protein docking, hot spot analyses, molecular docking and molecular dynamics simulation (MDS), stepwise analyses of the interactions of the wild type and mutant TP53 with that of wild type BRCA1 and their modulation by alkaloids were done...
October 5, 2017: Journal of Biomolecular Structure & Dynamics
Zechun Wang, Ning Wang, Xinxin Han, Ruiyong Wang, Junbiao Chang
The binding of two flavonols with fat mass and obesity associated protein (FTO) was studied using fluorescence spectroscopy, Stern-Volmer kinetics, UV-vis absorption and molecular docking. The quenching of FTO fluorescence was determined to be static with binding constants on the order of 10(4) M(-1). The interaction was studied over three temperatures, and the binding was found to be exothermic with a positive change in entropy. Thermodynamic analysis and molecular modeling suggest that hydrophobic interaction and hydrogen bonding interaction are the mainly binding force in stabilizing the flavonol-FTO complex...
October 5, 2017: Journal of Biomolecular Structure & Dynamics
Lakshmi Maganti, Mahua Ghosh, J Chakrabarti
Molecular understanding of bio-macromolecular binding is a challenging task due to large sizes of the molecules and presence of variety of interactions. Here we study the molecular mechanism of calmodulin (CaM) binding to Orai1 that regulates Ca(2+)-dependent inactivation process in eukaryotic cells. Although experimental observations indicate that Orai1 binds to the C-terminal of Ca(2+) loaded CaM, it is not decisive if N-domain of CaM interacts with Orai1. We address the issue of interaction of different domains of CaM with Orai1 using conformational thermodynamic changes, computed from histograms of dihedral angles over simulated trajectories of CaM, CaM binding domain of Orai1 and complexes of CaM with Orai1...
October 5, 2017: Journal of Biomolecular Structure & Dynamics
Arthur F V F Reis, Igor L P Gonçalves, Abel F G Neto, Alberdan S Santos, Kamil Kuca, Eugenie Nepovimova, Antonio M J C Neto
In this work we carried out a theoretical investigation regarding amphetamine-type stimulants, which can cause central nervous system degeneration, interacting with human DNA. Theseinclude amphetamine, methamphetamine,3,4-Methylenedioxymethamphetamine (also known as ecstasy), as well as their main metabolites. The studies were performed through molecular docking and molecular dynamics simulations, where molecular interactions of the receptor-ligand systems, along with their physical-chemical energies, were reported...
October 5, 2017: Journal of Biomolecular Structure & Dynamics
Sameer Shakeel Ansari, Rizwan Hasan Khan, Saeeda Naqvi
Intermolecular interaction study of human serum albumin (HSA) with two anthraquinones i.e., danthron and quinizarin has been performed through fluorescence, UV-Vis and CD spectroscopy along with docking analysis. The titration of drugs into HSA solution brought about the quenching of fluorescence emission by way of complex formation. The binding constants were found to be 1.51 × 10(4) L mol(-1) and 1.70 × 10(4) L mol(-1) at λexc = 280 nm while at λexc = 295 nm, the values of binding constants were 1.81 × 10(4) L mol(-1) and 1...
October 4, 2017: Journal of Biomolecular Structure & Dynamics
Vivek Kumar, Sarbjit Singh Jhamb, M Elizabeth Sobhia
The arising cases of isoniazid-resistance have motivated research interests towards new class of molecules known as direct InhA inhibitors. Here, a combine approach of shape-based pharmacophore and descriptor based-2D QSAR was used to identify the potential direct InhA inhibitors. The approach is duly assisted with in vitro testing and molecular dynamics simulations. A combination of empirical parameters was derived to use as a filter for cell wall permeability while 2D QSAR was used another filter to predict the biological activity...
October 4, 2017: Journal of Biomolecular Structure & Dynamics
Sushmita Pradhan, Venkata Satish Kumar Mattaparthi
Nucleotide Excision Repair (NER) in higher organisms repair massive DNA abrasions caused by ultra-violet (UV) rays, and various mutagens, where Xeroderma Pigmentosum group A (XPA) protein is known to be involved in damage recognition step. Any mutations in XPA cause classical Xeroderma Pigmentosum (XP) disease. The extent to which XPA is required in the NER is still unclear. Here, we present the comparative study on the structural and conformational changes in globular DNA binding domain of XPA98-210 in DNA bound and DNA free state...
October 4, 2017: Journal of Biomolecular Structure & Dynamics
Brett Janis, Vladimir N Uversky, Michael A Menze
Late embryogenesis abundant (LEA) proteins are a large group of anhydrobiosis-associated intrinsically disordered proteins (IDP), which are commonly found in plants and some animals. The brine shrimp Artemiafranciscana is the only known animal that expresses LEA proteins from three, and not only one, different groups in its anhydrobiotic life stage. The reason for the higher complexity in the A. franciscana LEA proteome (LEAome), compared with other anhydrobiotic animals, remains mostly unknown. To address this issue, we have employed a suite of bioinformatics tools to evaluate the disorder status of the ArtemiaLEAome and to analyze the roles of intrinsic disorder in functioning of brine shrimp LEA proteins...
October 3, 2017: Journal of Biomolecular Structure & Dynamics
Samima Khatun, Riyazuddeen
No abstract text is available yet for this article.
September 27, 2017: Journal of Biomolecular Structure & Dynamics
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