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Journal of Molecular Recognition: JMR

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https://read.qxmd.com/read/30779238/beyond-esterase-like-activity-of-serum-albumin-histidine-nitro-phenol-radical-formation-in-conversion-cascade-of-p-nitrophenyl-acetate-and-the-role-of-infrared-light
#1
Magdalena Kowacz, Piotr Warszyński
Serum albumin, recognized mainly for its capacity to act as a carrier protein for many compounds, can also actively transform some organic molecules. As a starting point in this study, we consider esterase-like activity of bovine serum albumin (BSA) toward p-nitrophenyl acetate (p-NPA). Our results reveal that the reaction goes beyond ester hydrolysis step. In fact, the transformation product, p-nitrophenol (p-NP), becomes a substrate for further reaction with BSA in which its nitro group in subtracted and released in the form of HNO2 ...
February 18, 2019: Journal of Molecular Recognition: JMR
https://read.qxmd.com/read/30761651/structural-prediction-of-antibody-april-complexes-by-computational-docking-constrained-by-antigen-saturation-mutagenesis-library-data
#2
Andrew M Wollacott, Luke N Robinson, Boopathy Ramakrishnan, Hamid Tissire, Karthik Viswanathan, Zachary Shriver, Gregory J Babcock
IgA nephropathy (IgAN) is the most prevalent cause of primary glomerular disease worldwide, and the cytokine A PRoliferation-Inducing Ligand (APRIL) is emerging as a key player in IgAN pathogenesis and disease progression. For a panel of anti-human APRIL antibodies with known antagonistic activity, we sought to define their structural mode of engagement to understand molecular mechanisms of action and aid rational antibody engineering. Reliable computational prediction of antibody-antigen complexes remains challenging, and experimental methods such as X-ray co-crystallography and cryoEM have considerable technical, resource, and throughput barriers...
February 13, 2019: Journal of Molecular Recognition: JMR
https://read.qxmd.com/read/30761635/dnase-and-rnase-activities-of-fresh-cow-milk-lactoferrin
#3
Svetlana E Soboleva, Ol'ga D Zakharova, Sergey E Sedykh, Nikita V Ivanisenko, Valentina N Buneva, Georgy A Nevinsky
Lactoferrin (LF) is an Fe3+ -binding glycoprotein first recognized in milk and then in other epithelial secretions and barrier body fluids to which many different functions have been attributed to LF, including protection from iron-induced lipid peroxidation, immunomodulation, cell growth regulation, DNA and RNA binding, as well as transcriptional activation, еtс. The polyfunctional physiological role of LF is still unclear, but it has been suggested to be responsible for primary defense against microbial and viral infections...
February 13, 2019: Journal of Molecular Recognition: JMR
https://read.qxmd.com/read/30701606/multispectroscopic-exploration-and-molecular-docking-analysis-on-interaction-of-eriocitrin-with-bovine-serum-albumin
#4
Xiangyu Cao, Zhijun Yang, Yonglin He, Ying Xia, Yin He, Jianli Liu
Eriocitrin is a flavanone glycoside, which exists in lemon or lime citrus fruits. It possesses antioxidant, anticancer, and anti-allergy activities. In order to investigate the pharmacokinetics and pharmacological mechanisms of eriocitrin in vivo, the interaction between eriocitrin and bovine serum albumin (BSA) was studied under the simulated physiological conditions by multispectroscopic and molecular docking methods. The results well indicated that eriocitrin and BSA formed a new eriocitrin-BSA complex because of intermolecular interactions, which was demonstrated by the results of ultraviolet-visible (UV-vis) absorption spectra...
January 31, 2019: Journal of Molecular Recognition: JMR
https://read.qxmd.com/read/30663161/application-of-quantitative-structure-activity-relationship-analysis-on-an-antibody-and-alternariol-like-compounds-interaction-study
#5
Jianyi Wang, Tao Peng, Xiya Zhang, Sanlei Xie, Pimiao Zheng, Kai Yao, Yuebin Ke, Zhanhui Wang, Haiyang Jiang
The antigen-antibody interaction determines the sensitivity and specificity of competitive immunoassay for hapten detection. In this paper, the specificity of a monoclonal antibody against alternariol-like compounds was evaluated through indirect competitive ELISA. The results showed that the antibody had cross-reactivity with 33 compounds with the binding affinity (expressed by IC50 ) ranging from 9.4 ng/mL to 12.0 μg/mL. All the 33 compounds contained a common moiety and similar substituents. To understand how this common moiety and substituents affected the recognition ability of the antibody, a three-dimensional quantitative structure-activity relationship (3D-QSAR) between the antibody and the 33 alternariol-like compounds was constructed using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) methods...
January 20, 2019: Journal of Molecular Recognition: JMR
https://read.qxmd.com/read/30592338/modification-of-nanocrystalline-tio-2-coatings-with-molecularly-imprinted-tio-2-for-uric-acid-recognition
#6
Chunlei Zhang, Zhiguo Xiao, Tongtong Qin, Zhengpeng Yang
Combining the surface modification and molecular imprinting technique, a novel piezoelectric sensing platform with excellent molecular recognition capability was established for the detection of uric acid (UA) based on the immobilization of TiO2 nanoparticles onto quartz crystal microbalance (QCM) electrode and modification of molecularly imprinted TiO2 (MIT) layer on TiO2 nanoparticles. The performance of the fabricated biosensor was evaluated, and the results indicated that the biosensor exhibited high sensitivity in UA detection, with a linear range from 0...
December 28, 2018: Journal of Molecular Recognition: JMR
https://read.qxmd.com/read/30575149/the-role-of-chlorine-atom-on-the-binding-between-2-phenyl-1h-benzimidazole-analogues-and-fat-mass-and-obesity-associated-protein
#7
Junya Li, Ying Wang, Xinxin Han, Ning Wang, Wenquan Yu, Ruiyong Wang, Junbiao Chang
In this work, nine 2-phenyl-1H-benzimidazole structural analogues were screened for potential inhibitor of the fat mass and obesity-associated protein (FTO) by isothermal titration calorimetry (ITC). The results show that the binding between 6-chloro-2-phenyl-1H-benzimidazole (1d) and FTO was dominated by entropy. Results of enzymatic activity assays provided an IC50 value of 24.65 μM for 1d. Our previous results and comparison of nine structural analogues indicated that the chlorine atom was crucial for the binding of small molecules with FTO...
December 21, 2018: Journal of Molecular Recognition: JMR
https://read.qxmd.com/read/30565321/fifteen-years-of-servitude-et-grandeur-to-the-application-of-a-biophysical-technique-in-medicine-the-tale-of-afmbiomed
#8
EDITORIAL
Jean-Luc Pellequer, Pierre Parot, Daniel Navajas, Sanjay Kumar, Vesna Svetličić, Simon Scheuring, Jun Hu, Bin Li, Adam Engler, Susana Sousa, Małgorzata Lekka, Marek Szymoński, Hermann Schillers, Michael Odorico, Frank Lafont, Sebastien Janel, Felix Rico
AFMBioMed is the founding name under which international conferences and summer schools are organized around the application of atomic force microscopy in life sciences and nanomedicine. From its inception at the Atomic Energy Commission in Marcoule near 2004 to its creation in 2007 and to its 10th anniversary conference in Krakow, a brief narrative history of its birth and rise will demonstrate how and what such an organization brings to laboratories and the AFM community. With the current planning of the next AFMBioMed conference in Münster in 2019, it will be 15 years of commitment to these events...
December 18, 2018: Journal of Molecular Recognition: JMR
https://read.qxmd.com/read/30520537/assembly-of-a-mirna-modified-qcm-sensor-for-mirna-recognition-through-response-patterns
#9
Xue Li, Ding Ma, Sheng-Run Zheng, Jun Fan, Tai Wang, Zong Dai, Xiao-Yong Zou, Shao-Hua Teng, Wei-Guang Zhang
In this paper, a miRNA-based quartz crystal microbalance (QCM) biosensor was fabricated and used to the rapid and effective sensing of miRNA. The specific hybridization between probe miRNA and different selected miRNAs (miR-27a, miR-27b, and Let-7a) cause a different interaction mode, thus display different frequency change and response patterns in the QCM sensor, which were used to detect miR-27a and miR-27b. The selective sensing of miR-27a in mixed miRNA solution was also achieved. This miRNA-based QCM biosensor has the advantages of real-time, label-free, and short cycle detection...
December 6, 2018: Journal of Molecular Recognition: JMR
https://read.qxmd.com/read/30515937/exploring-aggregation-induced-emission-through-tuning-of-ligand-structure-for-picomolar-detection-of-pyrene
#10
Milan Ghosh, Sabyasachi Ta, Sisir Lohar, Sudipta Das, Paula Brando, Vitor Felix, Debasis Das
Tuning of ligand structures through controlled variation of ring number in fused-ring aromatic moiety appended to antipyrine allows detection of 7.8 × 10-12  M pyrene via aggregation-induced emission (AIE) associated with 101-fold fluorescence enhancement. In one case, antipyrine unit is replaced by pyridine to derive bis-methylanthracenyl picolyl amine. The structures of four molecules have been confirmed by single crystal X-ray diffraction analysis. Among them, pyrene-antipyrine conjugate (L) undergoes pyrene triggered inhibition of photo-induced electron transfer (PET) leading to water-assisted AIE...
December 4, 2018: Journal of Molecular Recognition: JMR
https://read.qxmd.com/read/30458580/analysis-of-the-nucleotide-content-of-escherichia-coli-promoter-sequences-related-to-the-alternative-sigma-factors
#11
Gabriel Dall'Alba, Pedro Lenz Casa, Daniel Luis Notari, Andre Gustavo Adami, Sergio Echeverrigaray, Scheila de Avila E Silva
Promoters are DNA sequences located upstream of the transcription start site of genes. In bacteria, the RNA polymerase enzyme requires additional subunits, called sigma factors (σ) to begin specific gene transcription in distinct environmental conditions. Currently, promoter prediction still poses many challenges due to the characteristics of these sequences. In this paper, the nucleotide content of Escherichia coli promoter sequences, related to five alternative σ factors, was analyzed by a machine learning technique in order to provide profiles according to the σ factor which recognizes them...
November 20, 2018: Journal of Molecular Recognition: JMR
https://read.qxmd.com/read/30419606/tuning-surface-cross-linking-of-molecularly-imprinted-cross-linked-micelles-for-molecular-recognition-in-water
#12
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
https://read.qxmd.com/read/30403313/quantitative-characterization-of-single-cell-adhesion-properties-by-atomic-force-microscopy-using-protein-functionalized-microbeads
#13
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
https://read.qxmd.com/read/30397967/sequence-and-structural-analysis-of-fibronectin-binding-protein-reveals-importance-of-multiple-intrinsic-disordered-tandem-repeats
#14
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
https://read.qxmd.com/read/30343521/targeting-metabolic-pathways-proteins-of-orientia-tsutsugamushi-using-combined-hierarchical-approach-to-combat-scrub-typhus
#15
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
https://read.qxmd.com/read/29862590/analysis-of-single-cisplatin-induced-dna-bends-by-atomic-force-microscopy-and-simulations
#16
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
https://read.qxmd.com/read/29797434/exploring-the-inhibition-mechanism-on-hif-2-by-inhibitor-pt2399-and-0x3-using-molecular-dynamics-simulations
#17
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
https://read.qxmd.com/read/29785722/electrostatic-recognition-in-substrate-binding-to-serine-proteases
#18
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
https://read.qxmd.com/read/29770561/investigating-the-interaction-of-anticancer-drug-temsirolimus-with-human-transferrin-molecular-docking-and-spectroscopic-approach
#19
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
https://read.qxmd.com/read/29748973/afm-nano-mechanical-study-of-the-beating-profile-of-hipsc-derived-cardiomyocytes-beating-bodies-wt-and-dm1
#20
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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