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https://www.readbyqxmd.com/read/29151215/protein-structure-elucidation-from-nmr-data-with-the-program-xplor-nih
#1
Guillermo A Bermejo, Charles D Schwieters
Xplor-NIH is a popular software package for biomolecular structure determination from NMR (and other) experimental data. This chapter illustrates its use with the de novo structure determination of the B1 domain of streptococcal protein G (GB1), based on distances from nuclear Overhauser effects, torsion angles from scalar couplings, and bond-vector orientations from residual dipolar couplings. Including Xplor-NIH's latest developments, a complete structure calculation script is discussed in detail, and is intended to serve as a basis for other applications...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29151207/rapid-prediction-of-multi-dimensional-nmr-data-sets-using-fandas
#2
Siddarth Narasimhan, Deni Mance, Cecilia Pinto, Markus Weingarth, Alexandre M J J Bonvin, Marc Baldus
Solid-state NMR (ssNMR) can provide structural information at the most detailed level and, at the same time, is applicable in highly heterogeneous and complex molecular environments. In the last few years, ssNMR has made significant progress in uncovering structure and dynamics of proteins in their native cellular environments [1-4]. Additionally, ssNMR has proven to be useful in studying large biomolecular complexes as well as membrane proteins at the atomic level [5]. In such studies, innovative labeling schemes have become a powerful approach to tackle spectral crowding...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29151204/afterglow-solid-state-nmr-spectroscopy
#3
Gili Abramov, Nathaniel J Traaseth
Biomolecular solid-state NMR experiments have traditionally been collected through detection of (13)C or (15)N nuclei. Since these nuclei have relatively low sensitivity stemming from their smaller gyromagnetic ratios relative to (1)H, the time required to collect multi-dimensional datasets serves as a limitation to resonance assignment and structure determination. One improvement in the field has been to employ simultaneous or parallel acquisition techniques with the goal of acquiring more than one dataset at a time and therefore speeding up the overall data collection process...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29145826/gpu-based-detection-of-protein-cavities-using-gaussian-surfaces
#4
Sérgio E D Dias, Ana Mafalda Martins, Quoc T Nguyen, Abel J P Gomes
BACKGROUND: Protein cavities play a key role in biomolecular recognition and function, particularly in protein-ligand interactions, as usual in drug discovery and design. Grid-based cavity detection methods aim at finding cavities as aggregates of grid nodes outside the molecule, under the condition that such cavities are bracketed by nodes on the molecule surface along a set of directions (not necessarily aligned with coordinate axes). Therefore, these methods are sensitive to scanning directions, a problem that we call cavity ground-and-walls ambiguity, i...
November 16, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29140259/ramanomics-new-omics-disciplines-using-micro-raman-spectrometry-with-biomolecular-component-analysis-for-molecular-profiling-of-biological-structures
#5
REVIEW
Andrey N Kuzmin, Artem Pliss, Paras N Prasad
Modern instrumentation for Raman microspectroscopy and current techniques in analysis of spectral data provide new opportunities to study molecular interactions and dynamics at subcellular levels in biological systems. Implementation of biomolecular component analysis (BCA) to microRaman spectrometry provides basis for the emergence of Ramanomics, a new biosensing discipline with unprecedented capabilities to measure concentrations of distinct biomolecular groups in live cells and organelles. Here we review the combined use of microRaman-BCA techniques to probe absolute concentrations of proteins, DNA, RNA and lipids in single organelles of live cells...
November 15, 2017: Biosensors
https://www.readbyqxmd.com/read/29139285/subradiant-dipolar-interactions-in-plasmonic-nanoring-resonator-array-for-integrated-label-free-biosensing
#6
Yuzhang Liang, Hui Zhang, Wenqi Zhu, Amit Agrawal, Henri J Lezec, Lixia Li, Wei Peng, Yi Zou, Yan-Qing Lu, Ting Xu
With the development of advanced nanofabrication technologies over the last decade, plasmonic nanostructures have attracted wide attention for their potential in label-free biosensing applications. However, the sensing performance of nanostructured plasmonic sensors is primarily limited by the broad-linewidth features with low peak-to-dip signal ratio in the extinction spectra that result from strong radiative damping. Here, we propose and systematically investigate the in-plane and out-of-plane dipolar interactions in an array of plasmonic nanoring resonators that are from the spatial combination of classic nanohole and nanodisk structures...
November 15, 2017: ACS Sensors
https://www.readbyqxmd.com/read/29137811/improving-the-safety-of-metal-based-drugs-by-tuning-their-metabolism-with-chemoprotective-agents
#7
Jürgen Gailer
Metal-based drugs remain a tiny minority of all drugs that are on the market. The success story of the quintessential metal-based drug cisplatin (CP), which is intravenously administered to 70% of all cancer patients, however, demonstrates the inherent potential of metal-based drugs. A distinct disadvantage of CP is the dose-limiting severe toxic-side effects that it exerts in patients. To better understand the biomolecular basis for its toxicity, we employed a metallomics method to observe all platinum metabolites that are formed in blood plasma...
November 8, 2017: Journal of Inorganic Biochemistry
https://www.readbyqxmd.com/read/29136138/calcific-aortic-valve-stenosis-hard-disease-in-the-heart-a-biomolecular-approach-towards-diagnosis-and-treatment
#8
Frederique E C M Peeters, Steven J R Meex, Marc R Dweck, Elena Aikawa, Harry J G M Crijns, Leon J Schurgers, Bas L J H Kietselaer
Calcific aortic valve stenosis (CAVS) is common in the ageing population and set to become an increasing economic and health burden. Once present, it inevitably progresses and has a poor prognosis in symptomatic patients. No medical therapies are proven to be effective in holding or reducing disease progression. Therefore, aortic valve replacement remains the only available treatment option. Improved knowledge of the mechanisms underlying disease progression has provided us with insights that CAVS is not a passive disease...
November 10, 2017: European Heart Journal
https://www.readbyqxmd.com/read/29135256/improved-solution-state-properties-of-monoclonal-antibodies-by-targeted-mutations
#9
Alexander B Kuhn, Sebastian Kube, Anne R Karow-Zwick, Daniel Seeliger, Patrick Garidel, Michaela Blech, Lars V Schäfer
Monoclonal antibody (mAb) based therapeutics often require high concentration formulations. Unfortunately, highly concentrated antibody solutions often have biophysical properties that are disadvantageous for therapeutic development, such as high viscosity, solubility limitations, precipitation issues, or liquid-liquid phase separation. In this work, we present a computational rational design principle for improving the thermodynamic stability of mAb solutions through targeted point mutations. Two publicly available IgG1 monoclonal antibodies that exhibit high viscosity at high concentrations were used as model systems...
November 14, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29135007/nanoscale-imaging-and-force-probing-of-biomolecular-systems-using-atomic-force-microscopy-from-single-molecules-to-living-cells
#10
REVIEW
Mi Li, Dan Dang, Ning Xi, Yuechao Wang, Lianqing Liu
Due to the lack of adequate tools for observation, native molecular behaviors at the nanoscale have been poorly understood. The advent of atomic force microscopy (AFM) provides an exciting instrument for investigating physiological processes on individual living cells with molecular resolution, which attracts the attention of worldwide researchers. In the past few decades, AFM has been widely utilized to investigate molecular activities on diverse biological interfaces, and the performances and functions of AFM have also been continuously improved, greatly improving our understanding of the behaviors of single molecules in action and demonstrating the important role of AFM in addressing biological issues with unprecedented spatiotemporal resolution...
November 14, 2017: Nanoscale
https://www.readbyqxmd.com/read/29134599/phage-genome-annotation-using-the-rast-pipeline
#11
Katelyn McNair, Ramy Karam Aziz, Gordon D Pusch, Ross Overbeek, Bas E Dutilh, Robert Edwards
Phages are complex biomolecular machineries that have to survive in a bacterial world. Phage genomes show many adaptations to their lifestyle such as shorter genes, reduced capacity for redundant DNA sequences, and the inclusion of tRNAs in their genomes. In addition, phages are not free-living, they require a host for replication and survival. These unique adaptations provide challenges for the bioinformatics analysis of phage genomes. In particular, ORF calling, genome annotation, noncoding RNA (ncRNA) identification, and the identification of transposons and insertions are all complicated in phage genome analysis...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29134095/the-york-gospels-a-1000-year-biological-palimpsest
#12
Matthew D Teasdale, Sarah Fiddyment, Jiří Vnouček, Valeria Mattiangeli, Camilla Speller, Annelise Binois, Martin Carver, Catherine Dand, Timothy P Newfield, Christopher C Webb, Daniel G Bradley, Matthew J Collins
Medieval manuscripts, carefully curated and conserved, represent not only an irreplaceable documentary record but also a remarkable reservoir of biological information. Palaeographic and codicological investigation can often locate and date these documents with remarkable precision. The York Gospels (York Minster Ms. Add. 1) is one such codex, one of only a small collection of pre-conquest Gospel books to have survived the Reformation. By extending the non-invasive triboelectric (eraser-based) sampling technique eZooMS, to include the analysis of DNA, we report a cost-effective and simple-to-use biomolecular sampling technique for parchment...
October 2017: Royal Society Open Science
https://www.readbyqxmd.com/read/29133421/early-neolithic-wine-of-georgia-in-the-south-caucasus
#13
Patrick McGovern, Mindia Jalabadze, Stephen Batiuk, Michael P Callahan, Karen E Smith, Gretchen R Hall, Eliso Kvavadze, David Maghradze, Nana Rusishvili, Laurent Bouby, Osvaldo Failla, Gabriele Cola, Luigi Mariani, Elisabetta Boaretto, Roberto Bacilieri, Patrice This, Nathan Wales, David Lordkipanidze
Chemical analyses of ancient organic compounds absorbed into the pottery fabrics from sites in Georgia in the South Caucasus region, dating to the early Neolithic period (ca. 6,000-5,000 BC), provide the earliest biomolecular archaeological evidence for grape wine and viniculture from the Near East, at ca. 6,000-5,800 BC. The chemical findings are corroborated by climatic and environmental reconstruction, together with archaeobotanical evidence, including grape pollen, starch, and epidermal remains associated with a jar of similar type and date...
November 13, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29131585/antibody-templated-assembly-of-an-rna-mimic-of-green-fluorescent-protein
#14
Alessandro Bertucci, Alessandro Porchetta, Francesco Ricci
One of the most intriguing ways through which Nature achieves regulation of biological pathways encompasses the coordination of non-covalent interactions that bring biomolecules to be co-localized in a designated restricted space. This nano-confinement leads to a drastic increase in the effective local concentration of the species involved, which ultimately triggers reactions that would otherwise not occur at the low concentrations found in cells. Inspired by this mechanism, we have explored the possibility of using antibodies as bivalent biomolecular substrates for the templated assembly of a functional RNA structure...
November 13, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29131580/modular-self-assembly-of-protein-cage-lattices-for-multistep-catalysis
#15
Masaki Uchida, Kimberly McCoy, Masafumi Fukuto, Lin Yang, Hideyuki Yoshimura, Heini M Miettinen, Ben LaFrance, Dustin P Patterson, Benjamin Schwarz, Jonathan A Karty, Peter E Prevelige, Byeongdu Lee, Trevor Douglas
The assembly of individual molecules into hierarchical structures is a promising strategy for developing three-dimensional materials with properties arising from interaction between the individual building blocks. Virus capsids are elegant examples of biomolecular nanostructures, which are themselves hierarchically assembled from a limited number of protein subunits. Here we demonstrate the bio-inspired modular construction of materials with two levels of hierarchy; the formation of catalytically active individual virus-like particles (VLPs) through directed self-assembly of capsid subunits with enzyme encapsulation, and the assembly of these VLP building blocks into three-dimensional arrays...
November 13, 2017: ACS Nano
https://www.readbyqxmd.com/read/29130305/tuning-the-sensing-performance-of-multilayer-plasmonic-core-satellite-assemblies-for-rapid-detection-of-targets-from-lysed-cells
#16
Nguyen Hoang Le, Bach Kim Nguyen, Gang Ye, Chun Peng, Jennifer I L Chen
Optical sensors based on discrete plasmonic nanostructures are invaluable for probing biomolecular interactions when applied as plasmonic rulers or reconfigurable multi-nanoparticle assemblies. However, their adaptation as a versatile sensing platform is limited by the research-grade instrumentation required for single-nanostructure imaging and/or spectroscopy and complex data fitting and analysis. Additionally, the dynamic range is often too narrow for the quantitative analysis of targets of interest in biodiagnostics, food safety or environmental monitoring...
November 13, 2017: ACS Sensors
https://www.readbyqxmd.com/read/29129855/-biomolecular-mass-spectrometry
#17
(no author information available yet)
No abstract text is available yet for this article.
2017: Analytical Sciences: the International Journal of the Japan Society for Analytical Chemistry
https://www.readbyqxmd.com/read/29129810/discerning-molecular-interactions-a-comprehensive-review-on-biomolecular-interaction-databases-and-network-analysis-tools
#18
REVIEW
Sravan Kumar Miryala, Anand Anbarasu, Sudha Ramaiah
Computational analysis of biomolecular interaction networks is now gaining a lot of importance to understand the functions of novel genes/proteins. Gene interaction (GI) network analysis and protein-protein interaction (PPI) network analysis play a major role in predicting the functionality of interacting genes or proteins and gives an insight into the functional relationships and evolutionary conservation of interactions among the genes. An interaction network is a graphical representation of gene/protein interactome, where each gene/protein is a node, and interaction between gene/protein is an edge...
November 9, 2017: Gene
https://www.readbyqxmd.com/read/29129642/approach-to-biomolecular-science-by-cyborg-supramolecular-chemistry
#19
REVIEW
Kensuke Kurihara, Muneyuki Matsuo, Takumi Yamaguchi, Sota Sato
BACKGROUND: To imitate the essence of living systems via synthetic chemistry approaches has been attempted. With the progress in supramolecular chemistry, it has become possible to synthesize molecules of a size and complexity close to those of biomacromolecules. Recently, the combination of precisely designed supramolecules with biomolecules has generated structural platforms for designing and creating unique molecular systems. Bridging between synthetic chemistry and biomolecular science is also developing methodologies for the creation of artificial cellular systems...
November 9, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29125973/creation-of-antifouling-microarrays-by-photopolymerization-of-zwitterionic-compounds-for-protein-assay-and-cell-patterning
#20
Xiuhua Sun, Huaixin Wang, Yuanyuan Wang, Taijiang Gui, Ke Wang, Changlu Gao
Nonspecific binding or adsorption of biomolecules presents as a major obstacle to higher sensitivity, specificity and reproducibility in microarray technology. We report herein a method to fabricate antifouling microarray via photopolymerization of biomimetic betaine compounds. In brief, carboxybetaine methacrylate was polymerized as arrays for protein sensing, while sulfobetaine methacrylate was polymerized as background. With the abundant carboxyl groups on array surfaces and zwitterionic polymers on the entire surfaces, this microarray allows biomolecular immobilization and recognition with low nonspecific interactions due to its antifouling property...
November 7, 2017: Biosensors & Bioelectronics
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