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Journal of Molecular Recognition: JMR

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https://www.readbyqxmd.com/read/27933673/a-biophysical-and-computational-study-unraveling-the-molecular-interaction-mechanism-of-a-new-janus-kinase-inhibitor-tofacitinib-with-bovine-serum-albumin
#1
Ali Saber Abdelhameed, Saima Nusrat, Mohammad Rehan Ajmal, Syed Mohammad Zakariya, Masihuz Zaman, Rizwan Hasan Khan
The interaction of a recently certified kinase inhibitor Tofacitinib (TFB) with bovine serum albumin (BSA) has been studied, by spectroscopic and molecular docking studies. Spectrofluorimetric measurements at 3 different temperatures (288, 298, and 310 K) showed that TFB quench the intrinsic fluorescence of BSA upon forming a nonfluorescent complex. The intrinsic fluorescence data showed that TFB binds to BSA with binding constant (Kb ) of approximately 10(4) M(-1) , affirming a significant affinity of TFB with BSA...
December 9, 2016: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/27921334/synacton-and-individual-activity-of-synthetic-and-natural-corticotropins
#2
T V Vyunova, L A Andreeva, K V Shevchenko, N F Myasoedov
Short endogenous peptides represent one of the most important constituents of the mammalian body's general regulatory system. Some synthesized analogs and modified natural peptides (eg, corticotropins) also show high biological activity. Nevertheless, the mechanism of action of regulatory peptides remains unclear. To explain the effects of peptides of intermolecular processes, the hypothesis that a synactonal mechanism underlies the action of regulatory peptides, exemplified by the heptapeptide Semax, has been proposed...
December 6, 2016: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/27921323/the-application-of-strand-invasion-phenomenon-directed-by-peptide-nucleic-acid-pna-and-single-stranded-dna-binding-protein-ssb-for-the-recognition-of-specific-sequences-of-human-endogenous-retroviral-herv-w-family
#3
Grzegorz Machnik, Łukasz Bułdak, Jarosław Ruczyński, Tomasz Gąsior, Małgorzata Huzarska, Dariusz Belowski, Magdalena Alenowicz, Piotr Mucha, Piotr Rekowski, Bogusław Okopień
The HERV-W family of human endogenous retroviruses represents a group of numerous sequences that show close similarity in genetic composition. It has been documented that some members of HERV-W-derived expression products are supposed to play significant role in humans' pathology, such as multiple sclerosis or schizophrenia. Other members of the family are necessary to orchestrate physiological processes (eg, ERVWE1 coding syncytin-1 that is engaged in syncytiotrophoblast formation). Therefore, an assay that would allow the recognition of particular form of HERV-W members is highly desirable...
December 6, 2016: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/27917590/antichaperone-activity-and-heme-degradation-effect-of-methyl-tert-butyl-ether-mtbe-on-normal-and-diabetic-hemoglobins
#4
Ismaeil Hossein Najdegerami, Parvaneh Maghami, Vahid Sheikh-Hasani, Ghader Hosseinzadeh, Nader Sheibani, Ali A Moosavi-Movahedi
Because of the extensive use of methyl tert-butyl ether (MTBE) as an additive to increase the octane quality of gasoline, the environmental pollution by this compound has increased in recent decades. Environmental release of MTBE may lead to its entry to the blood stream through inhalation or drinking of contaminated water, and its interactions with biological molecules such as proteins. The present study was proposed to comparatively investigate the interactions of MTBE with hemoglobin (Hb) from diabetic and nondiabetic individuals using various spectroscopic methods including UV-visible, fluorescence, chemiluminescence, and circular dichroism...
December 5, 2016: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/27917540/interaction-of-procarbazine-with-calf-thymus-dna-a-biophysical-and-molecular-docking-study
#5
Razique Anwer, Nazia Ahmad, Khalid I Al Qumaizi, Osama A Al Khamees, Waleed Mohammed Al Shaqha, Tasneem Fatma
Interaction of procarbazine (PCZ) with calf thymus DNA was studied using biophysical and molecular docking studies. Procarbazine was to interact with DNA with a binding constant of 6.52 × 10(3)  M(-1) as calculated using ultraviolet-visible spectroscopy. To find out the binding mode, molecular docking was performed that predicted PCZ to interact with DNA through groove binding mode with binding affinity of -6.7 kcal/mole. To confirm the groove binding nature, different experiments were performed. Dye displacement assays confirmed the non-intercalative binding mode...
December 5, 2016: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/27891685/the-dna-aptamer-binds-stemness-enriched-cancer-cells-in-pancreatic-cancer
#6
Yoon-Jin Kim, Hee Seung Lee, Dawoon E Jung, Jeong Mi Kim, Si Young Song
Pancreatic cancer remains one of the most common and lethal cancers. Most patients (80%) present with inoperable advanced pancreatic cancer at initial diagnosis, and their early diagnosis is a significant unmet challenge. Recent studies indicate that cancer, including pancreatic cancer, is initiated and propagated by cancer stem cells (CSCs). CSCs are responsible not only for the pathogenesis of cancer but also for the heterogeneity, malignant degree, anticancer therapy resistance, and recurrence of tumors...
November 28, 2016: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/27891677/staurosporine-scaffold-based-rational-discovery-of-the-wild-type-sparing-reversible-inhibitors-of-egfr-t790m-gatekeeper-mutant-in-lung-cancer-with-analog-sensitive-kinase-technology
#7
Xiaoyun Song, Xingcai Liu, Xi Ding
The human epidermal growth factor receptor (EGFR) has been established as an attractive target for lung cancer therapy. However, an acquired EGFR T790M gatekeeper mutation is frequently observed in patients treated with first-line anticancer agents such as gefitinib and erlotinib to cause drug resistance, largely limiting the application of small-molecule kinase inhibitors in EGFR-targeted chemotherapy. Previously, the reversible pan-kinase inhibitor staurosporine and its several analogs such as Gö6976 and K252a have been reported to selectively inhibit the EGFR T790M mutant (EGFR(T790M) ) over wild-type kinase (EGFR(WT) ), suggesting that the staurosporine scaffold is potentially to develop the wild-type sparing reversible inhibitors of EGFR(T790M) ...
November 28, 2016: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/27885734/simultaneous-determination-of-thermodynamic-and-kinetic-parameters-of-aminopolycarbonate-complexes-of-cobalt-ii-and-nickel-ii-based-on-isothermal-titration-calorimetry-data
#8
Aleksandra Tesmar, Dariusz Wyrzykowski, Eva Muñoz, Bogusław Pilarski, Joanna Pranczk, Dagmara Jacewicz, Lech Chmurzyński
The influence of the different side chain residues on the thermodynamic and kinetic parameters for complexation reactions of the Co(2)(+) and Ni(2)(+) ions has been investigated by using the isothermal titration calorimetry (ITC) technique supported by potentiometric titration data. The study was concerned with the 2 common tripodal aminocarboxylate ligands, namely, nitrilotriacetic acid and N-(2-hydroxyethyl) iminodiacetic acid. Calorimetric measurements (ITC) were run in the 2-(N-morpholino)ethanesulfonic acid hydrate (2-(N-morpholino) ethanesulfonic acid), piperazine-N,N'-bis(2-ethanesulfonic acid), and dimethylarsenic acid buffers (0...
November 25, 2016: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/27885729/new-biosourced-chiral-molecularly-imprinted-polymer-synthesis-characterization-and-evaluation-of-the-recognition-capacity-of-methyltestosterone
#9
Asma Saadaoui, Corinne Sanglar, Raouf Medimagh, Anne Bonhomme, Robert Baudot, Saber Chatti, Sylvain Marque, Damien Prim, Mongia Saïd Zina, Herve Casabianca
New biosourced chiral cross-linkers were reported for the first time in the synthesis of methyltestosterone (MT) chiral molecularly imprinted polymers (cMIPs). Isosorbide and isomannide, known as 1,4:3,6-dianhydrohexitols, were selected as starting diols. The cMIPs were synthesized following a noncovalent approach via thermal radical polymerization and monitored by Raman spectroscopy. These cross-linkers were fully characterized by (1) H and (13) C nuclear magnetic resonance (NMR) spectroscopy and high-resolution mass spectrometry...
November 25, 2016: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/27859846/molecularly-imprinted-core-shell-magnetic-nanoparticles-for-selective-extraction-of-triazines-in-soils
#10
María José Patiño-Ropero, Myriam Díaz-Álvarez, Antonio Martín-Esteban
In this work, a propazine-imprinted polymer was synthesized on the surface of modified magnetic nanoparticles to be used in the solid-phase extraction of triazines in soil samples. The effect of different solvents on the selective extraction of target analytes was assessed to establish the optimum rebinding conditions. The obtained magnetic molecularly imprinted particles exhibited high selectivity for triazines and were easily collected and separated by an external magnetic field without additional centrifugation or filtration steps...
November 18, 2016: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/27862476/analysis-of-the-binding-loops-configuration-and-surface-adaptation-of-different-crystallized-single-domain-antibodies-in-response-to-various-antigens
#11
Mohammed M Al Qaraghuli, Valerie A Ferro
Monoclonal antibodies have revolutionized the biomedical field through their ubiquitous utilization in different diagnostics and therapeutic applications. Despite this widespread use, their large size and structural complexity have limited their versatility in specific applications. The antibody variable region that is responsible for binding antigen is embodied within domains that can be rescued individually as single-domain antibody (sdAb) fragments. Because of the unique characteristics of sdAbs, such as low molecular weight, high physicochemical stability, and the ability to bind antigens inaccessible to conventional antibodies, they represent a viable alternative to full-length antibodies...
November 16, 2016: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/27859766/structural-and-molecular-analysis-of-a-protective-epitope-of-lyme-disease-antigen-ospa-and-antibody-interactions
#12
Shivender Shandilya, Nese Kurt Yilmaz, Andrew Sadowski, Ejemel Monir, Zachary A Schiller, William D Thomas, Mark S Klempner, Celia A Schiffer, Yang Wang
The murine monoclonal antibody LA-2 recognizes a clinically protective epitope on outer surface protein (OspA) of Borrelia burgdorferi, the causative agent of Lyme disease in North America. Human antibody equivalence to LA-2 is the best serologic correlate of protective antibody responses following OspA vaccination. Understanding the structural and functional basis of the LA-2 protective epitope is important for developing OspA-based vaccines and discovering prophylactic antibodies against Lyme disease. Here, we present a detailed structure-based analysis of the LA-2/OspA interaction interface and identification of residues mediating antibody recognition...
November 16, 2016: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/27862500/antibodies-to-h1-histone-from-the-sera-of-hiv-infected-patients-recognize-and-catalyze-site-specific-degradation-of-this-histone
#13
Svetlana V Baranova, Pavel S Dmitrienok, Nikita V Ivanisenko, Valentina N Buneva, Georgy A Nevinsky
Histones and their posttranslational modifications have key roles in chromatin remodeling and gene transcription. Besides intranuclear functions, histones act as damage-associated molecules when they are released into the extracellular space. Administration of histones to animals leads to systemic inflammatory and toxic responses. Autoantibodies with enzymatic activities (abzymes) are distinctive feature of some autoimmune and viral diseases. Electrophoretically and immunologically homogeneous IgGs containing no canonical enzymes were isolated from sera of human immunodeficiency virus-infected patients by chromatography on several affinity sorbents...
November 10, 2016: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/27808434/force-spectroscopy-reveals-the-presence-of-structurally-modified-dimers-in-transthyretin-amyloid-annular-oligomers
#14
Ricardo H Pires, Maria J Saraiva, Ana M Damas, Miklós S Z Kellermayer
Toxicity in amyloidogenic protein misfolding disorders is thought to involve intermediate states of aggregation associated with the formation of amyloid fibrils. Despite their relevance, the heterogeneity and transience of these oligomers have placed great barriers in our understanding of their structural properties. Among amyloid intermediates, annular oligomers or annular protofibrils have raised considerable interest because they may contribute to a mechanism of cellular toxicity via membrane permeation...
November 3, 2016: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/27790778/poly-ethylene-glycol-acrylate-functionalized-hydrogels-for-heparan-sulfate-oligosaccharide-recognition
#15
Mouna Mothéré, Dominique Singabraya, Pierre-Alexandre Driguez, Fernando Siñeriz, Dulce Papy-Garcia
Heparan sulfates are complex polysaccharides belonging to the family of glycosaminoglycans that participate to the regulation of cell behavior and tissue homeostasis. The biological activities conferred to heparan sulfates are largely dependent on the content and positioning of the sulfate groups along their saccharidic units. At present, identification of particular sulfation patterns in biologically relevant heparan sulfate sequences remains challenging. Although several approaches for structure analysis exist, the complexity of heparan sulfates makes new and original approaches still required...
October 28, 2016: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/27790761/single-molecule-force-spectroscopy-applied-to-heparin-induced-thrombocytopenia
#16
REVIEW
Thi-Huong Nguyen
Heparin-induced thrombocytopenia (HIT), occurring up to approximately 1% to 5% of patients receiving the antithrombotic drug heparins, has a complex pathogenesis involving multiple partners ranging from small molecules to cells/platelets. Recently, insights into the mechanism of HIT have been achieved by using single-molecule force spectroscopy (SMFS), a methodology that allows direct measurements of interactions among HIT partners. Here, the potential of SMFS in unraveling the mechanism of the initial steps in the pathogenesis of HIT at single-molecule resolution is highlighted...
October 28, 2016: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/27785842/interaction-of-almond-cystatin-with-pesticides-structural-and-functional-analysis
#17
Azad Alam Siddiqui, Peerzada Shariq Shaheen Khaki, Bilqees Bano
Pesticides are chemical substances that eliminate or control a variety of agricultural pests that damage crops and livestock. They not only affect the targeted pests but also affect the nontargeted systems, raising more concerns for their effect on both plant and animal systems. Cystatins (cysteine protease inhibitor) are ubiquitously present in all living cells and show a variety of important physiological functions. The present study shows the effect of different pesticides (pendimethalin, methoxyfenozide, and Cu(II) hydroxide) on purified almond cystatin...
October 27, 2016: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/27774692/isolation-and-partial-characterization-of-3-nontoxic-d-galactose-specific-isolectins-from-seeds-of-momordica-balsamina
#18
Amna K E Awadallah, Makarim Elfadil M Osman, Mariam A Ibrahim, Emerson S Bernardes, Marcelo Dias-Baruffi, Emadeldin Hassan E Konozy
Three isolectins denoted hereforth MBaL-30, MBaL-60, and MBaL-80 were isolated from seeds extract of Momordica balsamina by 30%, 60%, and 80% ammonium sulfate saturations, respectively. The native molecular weights of these lectins, as judged by gel filtration, were 108, 56, and 160 kDa, respectively. On SDS-PAGE, under reduced condition, 27 kDa band was obtained for all isolectins. The lectins hemagglutinating activities were variably inhibited by d-galactose (minimum inhibitory concentrations = 12.5mM, 50mM, and 0...
October 24, 2016: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/27714883/characteristics-of-c-terminal-%C3%AE-amyloid-peptide-binding-fragment-of-neuroprotective-protease-inhibitor-cystatin-c
#19
Marta Spodzieja, Katarzyna Kalejta, Aleksandra S Kołodziejczyk, Martyna Maszota-Zieleniak, Sylwia Rodziewicz-Motowidło, Wioletta Żmudzińska, Paulina Czaplewska
Cystatin C originally identified as a cysteine proteases inhibitor has a broad spectrum of biological roles ranging from inhibition of extracellular cysteine protease activities, bone resorption, and modulation of inflammatory responses to stimulation of fibroblasts proliferation. There is an increasing number of evidence to suggest that human cystatin C (hCC) might play a protective role in the pathophysiology of sporadic Alzheimer's disease. In vivo and in vitro results well documented the association of hCC with Aβ and the hCC-induced inhibition of Aβ fibril formation...
October 7, 2016: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/27696554/evaluation-of-staphylococcus-aureus-dna-aptamer-by-enzyme-linked-aptamer-assay-and-isothermal-titration-calorimetry
#20
Ceren Bayraç, Hüseyin Avni Öktem
To monitor the specificity of Staphylococcus aureus aptamer (SA-31) against its target cell, we used enzyme-linked aptamer assay. In the presence of target cell, horseradish peroxidase-conjugated streptavidin bound to biotin-labeled SA-31 showed specific binding to S  aureus among 3 different bacteria with limit of detection of 10(3) colony-forming unit per milliliter. The apparent Ka was 1.39 μM(-1)  ± 0.3 μM(-1) . The binding of SA-31 to membrane proteins extracted from cell surface was characterized using isothermal titration calorimetry, and the effect of changes in binding temperature and salt concentrations of binding buffer was evaluated based on thermodynamic parameters (Ka , ΔH, and ΔG)...
October 3, 2016: Journal of Molecular Recognition: JMR
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