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https://www.readbyqxmd.com/read/28283570/stabilization-of-a-soluble-native-like-trimeric-form-of-an-efficiently-cleaved-indian-hiv-1-clade-c-envelope-glycoprotein
#1
Shubbir Ahmed, Tripti Shrivastava, Naresh Kumar, Gabriel Ozorowski, Andrew B Ward, Bimal K Chakrabarti
Designing an effective HIV-1 envelope glycoprotein (Env) immunogen for elicitation of broadly neutralizing antibodies (bNAbs) is a challenging task owing to the high sequence diversity, heavy glycosylation and inherent meta-stability of Env. Based on the antigenic profile of recently isolated bNAbs, the rational approach to immunogen design is to make a stable version of the Env trimer, which mimics the native trimeric Env present on the viral surface. The SOSIP.664 form of a clade A Env, BG505, yields a homogeneous and well-ordered pre-fusion trimeric form, which maintains structural integrity and desired antigenicity...
March 10, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28276018/reconstitution-of-mitochondrial-membrane-proteins-into-nanodiscs-by-cell-free-expression
#2
Ketan Malhotra, Nathan N Alder
The isolation and characterization of mitochondrial membrane proteins is technically challenging because they natively reside within the specialized environment of the lipid bilayer, an environment that must be recapitulated to some degree during reconstitution to ensure proper folding, stability, and function. Here we describe protocols for the assembly of a membrane protein into lipid bilayer nanodiscs in a series of cell-free reactions. Cell-free expression of membrane proteins circumvents problems attendant with in vivo expression such as cytotoxicity, low expression levels, and the formation of inclusion bodies...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28262589/mechanistic-roles-of-protein-disorder-within-transcription
#3
REVIEW
Sarah L Shammas
Understanding the interactions of proteins involved in transcriptional regulation is critical to describing biological systems because they control the expression profile of the cell. Yet sadly they belong to a less well biophysically characterized subset of proteins; they frequently contain long disordered regions that are highly dynamic. A key question therefore is, why? What functional roles does protein disorder play in transcriptional regulation? Experimental data exemplifying these roles are starting to emerge, with common themes being enabling complexity within networks and quick responses...
March 2, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28256223/orientation-and-location-of-the-cyclotide-kalata-b1-in-lipid-bilayers-revealed-by-solid-state-nmr
#4
Stephan L Grage, Marc-Antoine Sani, Olivier Cheneval, Sónia Troeira Henriques, Constantin Schalck, Ralf Heinzmann, Joshua S Mylne, Pavel K Mykhailiuk, Sergii Afonin, Igor V Komarov, Frances Separovic, David J Craik, Anne S Ulrich
Cyclotides are ultra-stable cyclic disulfide-rich peptides from plants. Their biophysical effects and medically interesting activities are related to their membrane-binding properties, with particularly high affinity for phosphatidylethanolamine lipids. In this study we were interested in understanding the molecular details of cyclotide-membrane interactions, specifically with regard to the spatial orientation of the cyclotide kalata B1 from Oldenlandia affinis when embedded in a lipid bilayer. Our experimental approach was based on the use of solid-state (19)F-NMR of oriented bilayers in conjunction with the conformationally restricted amino acid L-3-(trifluoromethyl)bicyclopent-[1...
February 28, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28246639/biophysical-properties-of-human-%C3%AE-cardiac-myosin-with-converter-mutations-that-cause-hypertrophic-cardiomyopathy
#5
Masataka Kawana, Saswata S Sarkar, Shirley Sutton, Kathleen M Ruppel, James A Spudich
Hypertrophic cardiomyopathy (HCM) affects 1 in 500 individuals and is an important cause of arrhythmias and heart failure. Clinically, HCM is characterized as causing hypercontractility, and therapies are aimed toward controlling the hyperactive physiology. Mutations in the β-cardiac myosin comprise ~40% of genetic mutations associated with HCM, and the converter domain of myosin is a hotspot for HCM-causing mutations; however, the underlying primary effects of these mutations on myosin's biomechanical function remain elusive...
February 2017: Science Advances
https://www.readbyqxmd.com/read/28245984/conformational-and-thermal-characterization-of-left-ventricle-remodeling-post-myocardial-infarction
#6
V Samouillan, E Revuelta-López, C Soler-Botija, J Dandurand, Aleyda Benitez-Amaro, L Nasarre, D de Gonzalo-Calvo, A Bayes-Genis, C Lacabanne, V Llorente-Cortés
Adverse cardiac remodeling after myocardial infarction (MI) causes impaired ventricular function and heart failure. Histopathological characterization is commonly used to detect the location, size and shape of MI sites. However, the information about chemical composition, physical structure and molecular mobility of peri- and infarct zones post-MI is rather limited. The main objective of this work was to explore the spatiotemporal biochemical and biophysical alterations of key cardiac components post-MI. The FTIR spectra of healthy and remote myocardial tissue shows amides A, I, II and III associated with proteins in freeze-died tissue as major absorptions bands...
February 25, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28243767/practical-considerations-for-investigation-of-protein-conformational-dynamics-by-15-n-r-1%C3%AF-relaxation-dispersion
#7
Erik Walinda, Daichi Morimoto, Masahiro Shirakawa, Kenji Sugase
It is becoming increasingly apparent that proteins are not static entities and that their function often critically depends on accurate sampling of multiple conformational states in aqueous solution. Accordingly, the development of methods to study conformational states in proteins beyond their ground-state structure ("excited states") has crucial biophysical importance. Here we investigate experimental schemes for optimally probing chemical exchange processes in proteins on the micro- to millisecond timescale by (15)N R 1ρ relaxation dispersion...
February 28, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28240702/utility-of-genetic-testing-in-elite-volleyball-players-with-aortic-root-dilation
#8
Nicole Herrick, Christopher Davis, Lisa Vargas, Hal Dietz, Paul Grossfeld
Basketball and volleyball attract individuals with a characteristic biophysical profile, mimicking features of Marfan Syndrome (MFS). Consequently, identification of these abnormalities can be lifesaving. PURPOSE: To determine how physical examination, echocardiography, and genetic screening can identify elite volleyball players with a previously undiagnosed aortopathy. METHODS: We have performed cardiac screening on 90 US Volleyball National Team members and identified four individuals with dilated sinuses of Valsalva...
February 25, 2017: Medicine and Science in Sports and Exercise
https://www.readbyqxmd.com/read/28211084/endothelial-cells-biophysical-biochemical-and-chromosomal-aberrancies-in-high-glucose-condition-within-the-diabetic-range
#9
Aysa Rezabakhsh, Elahe Nabat, Mina Yousefi, Soheila Montazersaheb, Omid Cheraghi, Amir Mehdizadeh, Farzaneh Fathi, Ali Akbar Movassaghpour, Nasrin Maleki-Dizaji, Reza Rahbarghazi, Alireza Garjani
To date, many studies have been conducted to find out the underlying mechanisms of hyperglycemia-induced complications in diabetes mellitus, attributed to the cellular pathologies of different cells-especially endothelial cells. However, there are still many ambiguities and unresolved issues to be clarified. Here, we investigated the alteration in biophysical and biochemical properties in human umbilical vein endothelial cells exposed to a high-glucose concentration (30mM), comparable to glucose content in type 2 diabetes mellitus, over a course of 120 hours...
March 2017: Cell Biochemistry and Function
https://www.readbyqxmd.com/read/28195578/specific-membrane-capacitance-cytoplasm-conductivity-and-instantaneous-young-s-modulus-of-single-tumour-cells
#10
Ke Wang, Yang Zhao, Deyong Chen, Beiyuan Fan, Yulan Lu, Lianhong Chen, Rong Long, Junbo Wang, Jian Chen
As label-free biomarkers, biophysical properties of cells are widely used for cell type classification. However, intrinsic biophysical markers, e.g., specific membrane capacitance (Cspecific membrane), cytoplasm conductivity (σconductivity) and instantaneous Young's modulus (Einstantaneous) measured for hundreds of single cells were not yet reported. In this study, single cells in suspension (adherent cells treated with trypsin) were aspirated through a microfluidic constriction channel at 25 °C, and the entry processes and impedance profiles were recorded and translated to Cspecific membrane, σconductivity and Einstantaneous...
February 14, 2017: Scientific Data
https://www.readbyqxmd.com/read/28182292/metastatic-neuroblastoma-diagnosed-on-prenatal-sonographic-examination-performed-for-decreased-fetal-movement
#11
Hector O Chapa, Steven Gywnn Geddie, Rebecca Flores
We report a case of fetal neuroblastoma presenting with massive liver metastasis diagnosed during the biophysical profile sonographic examination performed for decreased fetal movement. The patient presented at 37 weeks' gestation with limited fetal movement over 24 hours. Biophysical profile showed marked polyhydramnios and an enlarged abdomen filled with a homogeneous mass lesion suspicious for liver metastasis. Primary urgent cesarean section was performed revealing a cachectic neonate with a rigid and grossly distended abdomen...
February 9, 2017: Journal of Clinical Ultrasound: JCU
https://www.readbyqxmd.com/read/28163113/the-estimation-of-the-traditionally-used-yarrow-achillea-millefolium-l-asteraceae-oil-extracts-with-anti-inflamatory-potential-in-topical-application
#12
Vanja Tadić, Ivana Arsić, Jelena Zvezdanović, Ana Zugić, Dragan Cvetković, Sava Pavkov
ETHNOPHARMACOLOGICAL RELEVANCE: Olive or sunflower oil yarrow extracts have been extensively used against inflammatory disorders and skin wound healing in traditional medicine. AIM OF THE STUDY: To evaluate oil yarrow extracts traditional use in treatment of topical/dermatological skin impairments, sodium lauryl sulfate test was applied, and in vivo measuring of the biophysical parameters (erythema index, skin capacitance and the pH of the skin) in the artificially irritated skin was performed...
February 2, 2017: Journal of Ethnopharmacology
https://www.readbyqxmd.com/read/28163018/multiplexed-fc-array-for-evaluation-of-antigen-specific-antibody-effector-profiles
#13
Eric P Brown, Karen G Dowell, Austin W Boesch, Erica Normandin, Alison E Mahan, Thach Chu, Dan H Barouch, Chris Bailey-Kellogg, Galit Alter, Margaret E Ackerman
Antibodies are widely considered to be a frequent primary and often mechanistic correlate of protection of approved vaccines; thus evaluating the antibody response is of critical importance in attempting to understand and predict the efficacy of novel vaccine candidates. Historically, antibody responses have been analyzed by determining the titer of the humoral response using measurements such as an ELISA, neutralization, or agglutination assays. In the simplest case, sufficiently high titers of antibody against vaccine antigen(s) are sufficient to predict protection...
April 2017: Journal of Immunological Methods
https://www.readbyqxmd.com/read/28158217/3-4-dihydroxyphenylacetate-2-3-dioxygenase-from-pseudomonas-aeruginosa-an-fe-ii-containing-enzyme-with-fast-turnover
#14
Soraya Pornsuwan, Somchart Maenpuen, Philaiwarong Kamutira, Pratchaya Watthaisong, Kittisak Thotsaporn, Chanakan Tongsook, Maneerat Juttulapa, Sarayut Nijvipakul, Pimchai Chaiyen
3,4-dihydroxyphenylacetate (DHPA) dioxygenase (DHPAO) from Pseudomonas aeruginosa (PaDHPAO) was overexpressed in Escherichia coli and purified to homogeneity. As the enzyme lost activity over time, a protocol to reactivate and conserve PaDHPAO activity has been developed. Addition of Fe(II), DTT and ascorbic acid or ROS scavenging enzymes (catalase or superoxide dismutase) was required to preserve enzyme stability. Metal content and activity analyses indicated that PaDHPAO uses Fe(II) as a metal cofactor. NMR analysis of the reaction product indicated that PaDHPAO catalyzes the 2,3-extradiol ring-cleavage of DHPA to form 5-carboxymethyl-2-hydroxymuconate semialdehyde (CHMS) which has a molar absorptivity of 32...
2017: PloS One
https://www.readbyqxmd.com/read/28139759/the-intervening-domain-from-mecp2-enhances-the-dna-affinity-of-the-methyl-binding-domain-and-provides-an-independent-dna-interaction-site
#15
Rafael Claveria-Gimeno, Pilar M Lanuza, Ignacio Morales-Chueca, Olga C Jorge-Torres, Sonia Vega, Olga Abian, Manel Esteller, Adrian Velazquez-Campoy
Methyl-CpG binding protein 2 (MeCP2) preferentially interacts with methylated DNA and it is involved in epigenetic regulation and chromatin remodelling. Mutations in MeCP2 are linked to Rett syndrome, the leading cause of intellectual retardation in girls and causing mental, motor and growth impairment. Unstructured regions in MeCP2 provide the plasticity for establishing interactions with multiple binding partners. We present a biophysical characterization of the methyl binding domain (MBD) from MeCP2 reporting the contribution of flanking domains to its structural stability and dsDNA interaction...
January 31, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28119456/nectin-like-4-complexes-with-choline-transporter-like-protein-1-and-regulates-schwann-cell-choline-homeostasis-and-lipid-biogenesis-in-vitro
#16
Corey Heffernan, Mohit R Jain, Tong Liu, Hyosung Kim, Kevin Barretto, Hong Li, Patrice Maurel
Nectin-like 4 (NECL4, CADM4) is a Schwann cell-specific cell adhesion molecule that promotes axo-glial interactions. In vitro and in vivo studies have shown that NECL4 is necessary for proper peripheral nerve myelination. However, the molecular mechanisms that are regulated by NECL4 and affect peripheral myelination currently remain unclear. We used an in vitro approach to begin identifying some of the mechanisms that could explain NECL4 function. Using mass spectrometry and Western blotting techniques, we have identified choline transporter-like 1 (CTL1) as a putative complexing partner with NECL4...
March 17, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28117825/mapping-the-binding-site-of-an-aptamer-on-atp-using-microscale-thermophoresis
#17
Clemens Entzian, Thomas Schubert
Characterization of molecular interactions in terms of basic binding parameters such as binding affinity, stoichiometry, and thermodynamics is an essential step in basic and applied science. MicroScale Thermophoresis (MST) is a sensitive biophysical method to obtain this important information. Relying on a physical effect called thermophoresis, which describes the movement of molecules through temperature gradients, this technology allows for the fast and precise determination of binding parameters in solution and allows the free choice of buffer conditions (from buffer to lysates/sera)...
January 7, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28109791/identification-of-a-selective-inhibitor-of-transforming-growth-factor-%C3%AE-activated-kinase-1-by-biosensor-based-screening-of-focused-libraries
#18
Takaaki Miura, Atsushi Matsuo, Terushige Muraoka, Mitsuaki Ide, Kenji Morikami, Takayuki Kamikawa, Masamichi Nishihara, Hirotaka Kashiwagi
Transforming growth factor-β activated kinase 1 (TAK1), a member of the mitogen-activated protein kinase kinase kinase family, plays an essential role in mediating signals from various pro-inflammatory cytokines and therefore may be a good target for developing anti-inflammation agents. Herein, we report our efforts to identify TAK1 inhibitors with a good selectivity profile with which to initiate medicinal chemistry. Instead of resorting to a high-throughput screening campaign, we performed biosensor-based biophysical screening for a limited number of compounds by taking advantage of existing knowledge on kinase inhibitors...
December 29, 2016: Bioorganic & Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/28099727/association-of-biochemical-markers-with-the-severity-of-pre-eclampsia
#19
Ahmed M Maged, Gamal Aid, Nehal Bassiouny, Doaa S Eldin, Sherif Dahab, Nevein K Ghamry
OBJECTIVE: To assess the association between pre-eclampsia severity and biochemical and ultrasonography markers. METHODS: A retrospective study was undertaken of women with severe pre-eclampsia (group 1, n=90), mild pre-eclampsia (group 2, n=90), or a normal pregnancy (group 3, n=90) who attended a hospital in Egypt in October 2013-April 2015. Associations between pre-eclampsia and biochemical, cardiotocography, and ultrasonography markers were investigated. RESULTS: There were significant differences between the groups in C-reactive protein (331...
February 2017: International Journal of Gynaecology and Obstetrics
https://www.readbyqxmd.com/read/28088651/limitations-in-biexponential-fitting-of-nmr-inversion-recovery-curves
#20
Mohammed Salman Shazeeb, Christopher H Sotak
NMR relaxation agents have long been employed as contrast agents in MRI. In many cases, the contrast agent is confined to either (i) the vascular and/or extracellular compartment (EC), as is the case with gadolinium(III)-based agents, or (ii) the intracellular compartment (IC), as is the case with manganese(II) ions. The compartmentalization of contrast agents often results in tissue-water (1)H relaxation profiles that are well modeled as biexponential. It has long been recognized that water exchange between compartments modifies the biexponential relaxation parameters (amplitudes and rate constants) from those that would be found in the absence of exchange...
January 6, 2017: Journal of Magnetic Resonance
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