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Journal of Molecular Recognition: JMR

Shize Zhang, Yan Zhao
Molecular recognition in water is an important challenge in supramolecular chemistry. Surface-core double cross-linking of template-containing surfactant micelles by the click reaction and free radical polymerization yields molecularly imprinted nanoparticles (MINPs) with guest-complementary binding sites. An important property of MINP-based receptors is the surface-cross-linking between the propargyl groups of the surfactants and a diazide cross-linker. Decreasing the number of carbons in between the two azides enhanced the binding affinity of the MINPs, possibly by keeping the imprinted binding site more open prior to the guest binding...
November 12, 2018: Journal of Molecular Recognition: JMR
Lionel Chièze, Anthony Le Cigne, Marie Meunier, Alexandre Berquand, Stéphane Dedieu, Jérôme Devy, Michael Molinari
A method was developed to characterize the adhesion properties of single cells by using protein-functionalized atomic force microscopy (AFM) probes. The quantification by force spectroscopy of the mean detachment force between cells and a gelatin-functionalized colloidal tip reveals differences in cell adhesion properties that are not within reach of a traditional bulk technique, the washing assay. In this latter method, experiments yield semiquantitative and average adhesion properties of a large population of cells...
November 7, 2018: Journal of Molecular Recognition: JMR
Konda Mani Saravanan, Karthe Ponnuraj
The location of certain amino acid sequences like repeats along the polypeptide chain is very important in the context of forming the overall shape of the protein molecule which in fact determines its function. In gram-positive bacteria, fibronectin-binding protein (FnBP) is one such repeat containing protein, and it is a cell wall-attached protein responsible for various acute infections in human. Several studies on sequence, structure, and function of fibronectin-binding regions of FnBPs were reported; however, no detailed study was carried out on the full-length protein sequence...
November 5, 2018: Journal of Molecular Recognition: JMR
Dixit Sharma, Ankita Sharma, Shailender Kumar Verma, Birbal Singh
Orientia tsutsugamushi (Ott) is a causative agent of chigger-borne zoonosis, scrub typhus which is life threatening and highly pervasive illness in humans. In this report, we have mined and classified the proteins involved in pathways unique to Ott by using high-throughput computational techniques. The 12 metabolic pathways were found to be unique to the pathogen. Forty-six proteins were reported to be essential for the pathogen's survival and non-homologous to the humans. The proteins were categorized into different classes, ie, enzymes, transporters, DNA-binding, secretory, and outer membrane proteins...
October 21, 2018: Journal of Molecular Recognition: JMR
Daniel J Mermelstein, J Andrew McCammon, Ross C Walker
Beta-secretase 1 (BACE-1) is an aspartyl protease implicated in the overproduction of β-amyloid fibrils responsible for Alzheimer disease. The process of β-amyloid genesis is known to be pH dependent, with an activity peak between solution pH of 3.5 and 5.5. We have studied the pH-dependent dynamics of BACE-1 to better understand the pH dependent mechanism. We have implemented support for graphics processor unit (GPU) accelerated constant pH molecular dynamics within the AMBER molecular dynamics software package and employed this to determine the relative population of different aspartyl dyad protonation states in the pH range of greatest β-amyloid production, followed by conventional molecular dynamics to explore the differences among the various aspartyl dyad protonation states...
September 27, 2018: Journal of Molecular Recognition: JMR
A-Ru Kim, Na-Reum Ha, In-Pil Jung, Sang-Heon Kim, Moon-Young Yoon
Endocrine-disrupting chemicals are a major public health problem throughout the world. In the human body, these compounds functionalize the same as sexual hormones, inducing precocious puberty, gynecomastia, etc. To help prevent this occurrence, a simple detection system is needed. In this study, a nonylphenol ethoxylate (NPE)-specific aptamer was selected by reduced graphene oxide-systematic evolution of ligands by exponential enrichment. A random ssDNA library was incubated with rGO for adsorption, followed by elution with the target molecule...
September 24, 2018: 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
Samrat Dutta, Claudio Rivetti, Natalie R Gassman, Carl G Young, Bradley T Jones, Karin Scarpinato, Martin Guthold
Bent DNA, or DNA that is locally more flexible, is a recognition motif for many DNA binding proteins. These DNA conformational properties can thus influence many cellular processes, such as replication, transcription, and DNA repair. The importance of these DNA conformational properties is juxtaposed to the experimental difficulty to accurately determine small bends, locally more flexible DNA, or a combination of both (bends with increased flexibility). In essence, many current bulk methods use average quantities, such as the average end-to-end distance, to extract DNA conformational properties; they cannot access the additional information that is contained in the end-to-end distance distributions...
October 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
Rasha M Bashatwah, Mohammad A Khanfar, Sanaa K Bardaweel
Inorganic polyphosphate (polyP) is present in all living forms of life. Studied mainly in prokaryotes, polyP and its associated enzymes are vital in diverse metabolic activities, in some structural functions, and most importantly in stress responses. Bacterial species, including many pathogens, encode a homolog of a major polyP synthesis enzyme, Poly Phosphate Kinase (PPK) with 2 different genes coding for PPK1 and PPK2. Genetic deletion of the ppk1 gene leads to reduced polyP levels and the consequent loss of virulence and stress adaptation responses...
October 2018: Journal of Molecular Recognition: JMR
E Kozlova, A Chernysh, V Sergunova, O Gudkova, E Manchenko, A Kozlov
The morphology and functional state of red blood cells (RBCs) mainly depends on the configuration of the spectrin network, which can be broken under the influence of intoxication because of oxidation processes in the cells. Measurement of these processes is a complex problem. The most suitable and prospective method that resolves this problem is atomic force microscopy (AFM). We used AFM to study the changes in the spectrin matrix and RBC morphology during oxidation processes caused by ultraviolet (UV) irradiation in RBC suspension...
October 2018: Journal of Molecular Recognition: JMR
Pascale Milani, Julien Chlasta, Rawad Abdayem, Sanja Kezic, Marek Haftek
During formation of the stratum corneum (SC) barrier, terminally differentiated keratinocytes continue their maturation process within the dead superficial epidermal layer. Morphological studies of isolated human corneocytes have revealed differences between cornified envelopes purified from the deep and superficial SC. We used atomic force microscopy to measure the mechanical properties of native human corneocytes harvested by tape-stripping from different SC depths. Various conditions of data acquisition have been tested and optimized, in order to obtain exploitable and reproducible results...
September 2018: Journal of Molecular Recognition: JMR
Van-Chien Bui, Thi-Huong Nguyen
Cations-induced DNA aggregation can modify the local structure of oligonucleotides and has potential applications in medicine and biotechnology. Here, we used atomic force microscopy to investigate λ-DNA aggregation on Mg2+ -treated glass (Mg2+ /glass) and in Mg2+ solution. Atomic force microscopy topography images showed that some DNA fragments were slightly stacked together on 10 mM Mg2+ /glass and stacked stronger on ≥50 mM Mg2+ /glass. They also showed that DNA aggregated stronger in Mg2+ solution than on Mg2+ /glass, ie, DNAs are strongly stacked and twisted at 10 mM Mg2+ , rolled together at 50 mM Mg2+ , and slightly aggregated to form small particles at 100 mM Mg2+ ...
September 2018: Journal of Molecular Recognition: JMR
Agnieszka Kolodziejczyk, Aleksandra Jakubowska, Magdalena Kucinska, Tomasz Wasiak, Piotr Komorowski, Krzysztof Makowski, Bogdan Walkowiak
Endothelial cells, due to their location, are interesting objects for atomic force spectroscopy study. They constitute a barrier between blood and vessel tissues located deeper, and therefore they are the first line of contact with various substances present in blood, eg, drugs or nanoparticles. This work intends to verify whether the mechanical response of immortalized human umbilical vein endothelial cells (EA.hy926), when exposed to silver nanoparticles, as measured using force spectroscopy, could be effectively used as a bio-indicator of the physiological state of the cells...
September 2018: Journal of Molecular Recognition: JMR
Prem Kumar Viji Babu, Carmela Rianna, Gazanfer Belge, Ursula Mirastschijski, Manfred Radmacher
Mechanical properties of myofibroblasts play a key role in Dupuytren's disease. Here, we used atomic force microscopy to measure the viscoelastic properties of 3 different types of human primary fibroblasts derived from a same patient: normal and scar dermal fibroblasts and palmar fascial fibroblasts from Dupuytren's nodules. Different stiffness hydrogels (soft ~1 kPa and stiff ~ 50 kPa) were used as cell culture matrix to mimic the mechanical properties of the natural tissues, and atomic force microscopy step response force curves were used to discriminate between elastic and viscous properties of cells...
September 2018: Journal of Molecular Recognition: JMR
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