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Journal of Molecular Recognition: JMR

Mousumi Sahu, Bibekanand Mallick
Recent studies have shown that long noncoding RNAs (lncRNAs) are crucial regulators of human embryonic stem cells (hESCs). However, modes of actions of lncRNAs in hESCs are not well illustrated. Here, we predicted a regulatory network in hESCs in which lncRNAs interact with TFs and thereby control the expressions of downstream targets of TFs. The predicted network is comprised of 2289 3-motif subgraphs which are characterized by 3 nodes: (i) a lncRNA which is predicted to interact with (ii) a TF and (iii) a gene which is a target of TF and coexpressing with lncRNA...
September 11, 2018: Journal of Molecular Recognition: JMR
Rajabrata Bhuyan, Alpana Seal
LytB or IspH is an indispensable enzyme and a suitable drug target of Plasmodium falciparum that participate in isoprenoid biosynthesis of nonmevalonate pathway (MEP). Recently, we have investigated the structural dynamics of Plasmodium LytB and proposed some novel diphosphate-based inhibitors using molecular modeling and docking studies. Here, we have tried to characterize those previously screened molecules by quantitative structure activity relationships and pharmacophore-based analyses, as well as validated the dynamics of their interactions with LytB protein...
September 7, 2018: Journal of Molecular Recognition: JMR
Jiajun Wang, Xueqing Xiang, Gesmi Milcovich, Jingru Chen, Chao Chen, Jiuju Feng, Sarah P Hudson, Xuexiang Weng, Yongming Ruan
A deep understanding of the molecular interactions of carbon nanodots with biomacromolecules is essential for wider applications of carbon nanodots both in vitro and in vivo. Herein, nitrogen and sulfur co-doped carbon dots (N,S-CDs) with a quantum yield of 16% were synthesized by a 1-step hydrothermal method. The N,S-CDs exhibited a good dispersion, with a graphite-like structure, along with the fluorescence lifetime of approximately 7.50 ns. Findings showed that the fluorescence of the N,S-CDs was effectively quenched by bovine hemoglobin as a result of the static fluorescence quenching...
August 22, 2018: Journal of Molecular Recognition: JMR
Xun Zhang, Rui Zhang, Wansong Zong, Rutao Liu
Bisphenol F (BPF), bisphenol S (BPS), and bisphenol B (BPB) have been extensively used in food packaging, plasticizer, and paper products, causing more concern about their biosafety. The mechanism of these bisphenols' toxicity was investigated by determining diverse effects of them on common protein bovine hemoglobin (BHb). The effects at the molecular level were determined by ultraviolet-visible, circular dichroism, resonance light scattering, fluorescence spectroscopy, and molecular docking. The irreversible cross-linking results of bisphenols and BHb demonstrate that hydrogen (H) bonding and hydrophobic forces play major roles in the interaction...
August 19, 2018: Journal of Molecular Recognition: JMR
Daria Parshukova, Liudmila P Smirnova, Evgeny A Ermakov, Nikolay A Bokhan, Arkadiy V Semke, Svetlana A Ivanova, Valentina N Buneva, Georgy A Nevinsky
Several different theories of schizophrenia (SCZ) were discussed; the causes of this disease are not yet clear. Using ELISA, it was shown that titers of autoantibodies against myelin basic protein (MBP) in SCZ patients are ~1.8-fold higher than in healthy individuals but 5.0-fold lower than in patients with multiple sclerosis. Several rigid criteria were checked to show that the MBP-hydrolyzing activity is an intrinsic property of SCZ IgGs. Approximately 82% electrophoretically homogeneous SCZ IgGs purified using several affinity sorbents including Sepharose with immobilized MBP hydrolyze specifically only MBP but not many other tested proteins...
August 15, 2018: Journal of Molecular Recognition: JMR
Svetlana E Soboleva, Evgeniya E Burkova, Pavel S Dmitrenok, Dmitrii V Bulgakov, Natalia I Menzorova, Valentina N Buneva, Georgy A Nevinsky
It was proposed that most biological processes are performed by different protein complexes. In contrast to individual proteins and enzymes, their complexes usually have other biological functions, and their formation may be important system process for the expansion of diversity and biological functions of different molecules. Identification and characterization of embryonic components including proteins and their multiprotein complexes seem to be very important for an understanding of embryo function. We have isolated and analyzed for the first time a very stable multiprotein complex (SPC; approximately 1100 kDa) from the soluble fraction of extracts of the sea urchin embryos...
August 14, 2018: Journal of Molecular Recognition: JMR
Guido Caluori, Jan Pribyl, Vratislav Cmiel, Martin Pesl, Tomas Potocnak, Ivo Provaznik, Petr Skladal, Vladimir Rotrekl
Calcium ions act like ubiquitous second messengers in a wide amount of cellular processes. In cardiac myocytes, Ca2+ handling regulates the mechanical contraction necessary to the heart pump function. The field of intracellular and intercellular Ca2+ handling, employing in vitro models of cardiomyocytes, has become a cornerstone to understand the role and adaptation of calcium signalling in healthy and diseased hearts. Comprehensive in vitro systems and cell-based biosensors are powerful tools to enrich and speed up cardiac phenotypic and drug response evaluation...
August 6, 2018: Journal of Molecular Recognition: JMR
Farideh Badalkhani-Khamseh, Azadeh Ebrahim-Habibi, Nasser L Hadipour
Poly(amidoamine) (PAMAM) dendrimers are promising nanocarriers that can enhance the solubility of hydrophobic drugs. The surface chemistry of dendrimers is of great relevance as end groups of these nanocarriers can be easily modified to improve the bioavailability and sustained release of the cargo. Therefore, a molecular-level understanding of the host-guest interactions that can give both qualitative and quantitative information is particularly desirable. In this work, fully atomistic molecular dynamics simulations were used to study the association of a bioactive natural product, ie, chalcone, with amine-, acetyl-, and carboxyl-terminated PAMAM dendrimers at physiological and acidic pH environments...
July 25, 2018: Journal of Molecular Recognition: JMR
Eliel Ruiz-May, Aldo Segura-Cabrera, Jose M Elizalde-Contreras, Laura M Shannon, Víctor M Loyola-Vargas
Plants, as sessile organisms, have acquired through evolution sophisticated regulatory signal pathways to overcome external variable factors during each stage of the life cycle. Among these regulatory signals, two pathways in particular, reactive oxygen species and reactive nitrogen species, have become of significant interest in several aspects of plant biology, underpinning these molecules as critical regulators during development, cellular differentiation, and plant-pathogen interaction. Recently, redox posttranslational modifications (PTM), such as S-nitrosylation on cysteine residues and tyrosine nitration, have shed light on multiple protein targets, as they are associated with signal networks/downstream metabolic pathways, capable of transducing the imbalance of redox hemostasis and consequently redirecting the biochemical status under stress conditions...
July 23, 2018: Journal of Molecular Recognition: JMR
Chaoqun Li, Xiaojia Zhao, Pengtao Xie, Junping Hu, Huimin Bi
Riboswitches are RNA molecules that regulate gene expression using conformation change, affected by binding of small molecule ligands. Although a number of ligand-bound aptamer complex structures have been solved, it is important to know ligand-free conformations of the aptamers in order to understand the mechanism of specific binding by ligands. In this paper, we use dynamics simulations on a series of models to characterize the ligand-free and ligand-bound aptamer domain of the c-di-GMP class I (GEMM-I) riboswitch...
July 23, 2018: Journal of Molecular Recognition: JMR
Sofia Tabares-da Rosa, Linda A Wogulis, Mark D Wogulis, Gualberto González-Sapienza, David K Wilson
The variable VHH domains of camelid single chain antibodies have been useful in numerous biotechnology applications due to their simplicity, biophysical properties, and abilities to bind to their cognate antigens with high affinities and specificity. Their interactions with proteins have been well-studied, but considerably less work has been done to characterize their ability to bind haptens. A high-resolution structural study of three nanobodies (T4, T9, and T10) which have been shown to bind triclocarban (TCC, 3-(4-chlorophenyl)-1-(3,4-dichlorophenyl)urea) with near-nanomolar affinity shows that binding occurs in a tunnel largely formed by CDR1 rather than a surface or lateral binding mode seen in other nanobody-hapten interactions...
July 23, 2018: Journal of Molecular Recognition: JMR
Joanna Zemła, Tomasz Stachura, Iwona Gross-Sondej, Karolina Górka, Krzysztof Okoń, Grażyna Pyka-Fościak, Jerzy Soja, Krzysztof Sładek, Małgorzata Lekka
Asthma is not a single disease, but recently, it is considered as a syndrome characterized through various clinical presentations and different etiopathologies. Large degree of the disease heterogeneity manifests in distinct characteristics that translate into variability of properties at single cell and molecular levels. Here, we conducted measurements of mechanical properties of bronchial tissue samples collected from patients suffering from asthma. The results obtained from different applied protocols for sample preparation may indicate that deep freezing and storage in liquid nitrogen, followed by consecutive unfreezing of tissue samples, preserve tissue mechanical properties as indicated by a parameter referred here as a tissue relative stiffness index...
July 18, 2018: Journal of Molecular Recognition: JMR
Nilkanta Chowdhury, Angshuman Bagchi
RhlR protein from opportunistic pathogen Pseudomonas aeruginosa is involved in the transcription of virulence genes of the organism. The RhlR protein functions as a dimer and binds to the cognate promoter DNA with the help of an autoinducer ligand BHL to initiate the transcription of the virulence genes. Till date, there are no reports that detail the mechanism of virulence gene expression by RhlR protein in P. aeruginosa. In this work, we tried to analyse the molecular aspects of the various binding interactions of the RhlR protein while formimg the dimmer as well as with the promoter DNA...
July 2, 2018: Journal of Molecular Recognition: JMR
Muntazir S Khan, Sourav Pal
We present a benchmark study of binding energies for dioxin-imprinted polymer complexes. A density functional theory approach was used for screening the polymerization precursors in the rational design of molecularly imprinted polymers (MIPs). Tetrachlorodibenzo-p-dioxin (TCDD) was taken as an imprinted molecule. The geometry optimization, natural bond orbital charge, and molecular electrostatic potential of TCDD and acrylamide (AM) were studied at the M062X level and 6-31G(d,p) belonging to one of the hybrid density functional theories...
July 1, 2018: Journal of Molecular Recognition: JMR
Mohammad Hasanzadeh, Elnaz Javidi, Abolghasem Jouyban, Ahad Mokhtarzadeh, Nasrin Shadjou, Soltanali Mahboob
The rapid and accurate determination of the level of taurine biomarker in various tissues and body fluids can be of great interest in the early diagnosis of several important pathologies and diseases. In the present study, an innovative electrochemical interface for quantitation of taurine based on ternary signal amplification strategy was fabricated. In this work, silver nanoparticles were electrodeposited onto green and biocompatible nanocomposite containing α-cyclodextrin as conductive matrix. Therefore, a double layer film based on α-cyclodextrin and silver nanoparticles was exploited to develop a highly sensitive electrochemical sensor for detection of taurine...
June 28, 2018: Journal of Molecular Recognition: JMR
Bushra Taj Muhammad, Azeem Ullah, Munira Taj Muhammad, Tanzila Arshad
Role of heterocyclic compounds with nitrogen substitution in therapeutic frontiers is well established. The efforts made in this study are directed to dissect the biological significance of benzimidazole-substituted zinc phthalocyanine derivative. Its capacity to act as an anticancer agent against the 2 B-lymphoma cell lines (low-grade and high-grade malignancy) was found out by recording florescence using Alamar blue dye. Further cytotoxic effect at the DNA level was analyzed by performing agarose gel electrophoresis...
June 27, 2018: Journal of Molecular Recognition: JMR
Dong-Ru Sun, Zhi-Jun Wang, Qing-Chuan Zheng, Hong-Xing Zhang
Targeting transcription factors HIF-2 is currently considered to be the most direct way for the therapy of clear cell renal cell carcinoma. The preclinical inhibitor PT2399 and artificial inhibitor 0X3 have been identified as promising on-target inhibitors to inhibit the heterodimerization of HIF-2. However, the inhibition mechanism of PT2399 and 0X3 on HIF-2 remains unclear. To this end, molecular dynamics (MD) simulations and molecular docking were applied to investigate the effects of 2 inhibitors on structural motifs and heterodimerization of HIF-2...
October 2018: Journal of Molecular Recognition: JMR
Birgit J Waldner, Johannes Kraml, Ursula Kahler, Alexander Spinn, Michael Schauperl, Maren Podewitz, Julian E Fuchs, Gabriele Cruciani, Klaus R Liedl
Serine proteases of the Chymotrypsin family are structurally very similar but have very different substrate preferences. This study investigates a set of 9 different proteases of this family comprising proteases that prefer substrates containing positively charged amino acids, negatively charged amino acids, and uncharged amino acids with varying degree of specificity. Here, we show that differences in electrostatic substrate preferences can be predicted reliably by electrostatic molecular interaction fields employing customized GRID probes...
October 2018: Journal of Molecular Recognition: JMR
Anas Shamsi, Azaj Ahmed, Mohd Shahnawaz Khan, Fohad Mabood Husain, Samreen Amani, Bilqees Bano
In our present study, binding between an important anti renal cancer drug temsirolimus and human transferrin (hTF) was investigated employing spectroscopic and molecular docking approach. In the presence of temsirolimus, hyper chromaticity is observed in hTF in UV spectroscopy suggestive of complex formation between hTF and temsirolimus. Fluorescence spectroscopy revealed the occurrence of quenching in hTF in the presence of temsirolimus implying complex formation taking place between hTF and temsirolimus. Further, the mode of interaction between hTF and temsirolimus was revealed to be static by fluorescence quenching analysis at 3 different temperatures...
October 2018: Journal of Molecular Recognition: JMR
S Dinarelli, M Girasole, P Spitalieri, R V Talarico, M Murdocca, A Botta, G Novelli, R Mango, F Sangiuolo, G Longo
Myotonic Dystrophy type 1 (DM1) is the most common form of muscular dystrophy in adults, characterized by a variety of multisystemic features and associated with cardiac anomalies. Among cardiac phenomena, conduction defects, ventricular arrhythmias, and dilated cardiomyopathy represent the main cause of sudden death in DM1 patients. Patient-specific induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) represent a powerful in vitro model for molecular, biochemical, and physiological studies of disease in the target cells...
October 2018: Journal of Molecular Recognition: JMR
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