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https://www.readbyqxmd.com/read/28726873/local-decomposition-of-imaginary-polarizabilities-and-dispersion-coefficients
#1
Ignat Harczuk, Balazs Nagy, Frank Jensen, Olav Vahtras, Hans Ågren
We present a new way to compute the two-body contribution to the dispersion energy using ab initio theory. By combining the complex polarization propagator method and the LoProp transformation, local contributions to the Casimir-Polder interaction is obtained. The full dispersion energy in dimer systems consisting of pairs of molecules including H2, N2, CO, CH4, pyridine, and benzene is investigated, where anisotropic as well as isotropic models of dispersion are obtained using a decomposition scheme for the dipole-dipole polarizability...
July 20, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28723204/crossed-surface-relief-gratings-as-nanoplasmonic-biosensors
#2
Srijit Nair, Carlos Escobedo, Ribal Georges Sabat
We present an original, low-cost nanoplasmonic (bio)sensor based on crossed surface relief gratings (CSRGs) generated from orthogonally superimposed surface relief gratings (SRGs) on gold-coated azo-glass substrate. This surface plasmon resonance (SPR)-based sensing approach is unique, since the light transmitted through a CSRG is zero except in the narrow bandwidth where the SPR conversion occurs, enabling quantitative monitoring of only the plasmonic signal from biomolecular interactions in real time. We validated the individual SRG plasmonic signature of CSRGs by observing their respective SPR excitation peaks, and tested them to detect both bulk and near-surface refractive index (RI) changes...
March 24, 2017: ACS Sensors
https://www.readbyqxmd.com/read/28721939/two-faces-of-competition-target-mediated-reverse-signalling-in-microrna-and-mitogen-activated-protein-kinase-regulatory-networks
#3
REVIEW
Yongjin Jang, Min A Kim, Yoosik Kim
Biomolecular regulatory networks are organised around hubs, which can interact with a large number of targets. These targets compete with each other for access to their common hubs, but whether the effect of this competition would be significant in magnitude and in function is not clear. In this review, the authors discuss recent in vivo studies that analysed the system level retroactive effects induced by target competition in microRNA and mitogen-activated protein kinase regulatory networks. The results of these studies suggest that downstream targets can regulate the overall state of their upstream regulators, and thus cannot be ignored in analysing biomolecular networks...
August 2017: IET Systems Biology
https://www.readbyqxmd.com/read/28716648/applications-of-high-speed-atomic-force-microscopy-to-real-time-visualization-of-dynamic-biomolecular-processes
#4
REVIEW
Takayuki Uchihashi, Simon Scheuring
BACKGROUND: Many biological processes in a living cell are consequences of sequential and hierarchical dynamic events of biological macromolecules such as molecular interactions and conformational changes. Hence, knowledge of structures, assembly and dynamics of proteins is the foundation for understanding how biological molecules work. Among several techniques to analyze dynamics of proteins, high-speed atomic force microscopy (HS-AFM) is unique to provide direct information about both structure and dynamics of single proteins at work...
July 14, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28710453/intrinsic-dynamics-study-identifies-two-amino-acids-of-timp-1-critical-for-its-lrp-1-mediated-endocytosis-in-neurons
#5
Laurie Verzeaux, Nicolas Belloy, Jessica Thevenard-Devy, Jérôme Devy, Géraldine Ferracci, Laurent Martiny, Stéphane Dedieu, Manuel Dauchez, Hervé Emonard, Nicolas Etique, Emmanuelle Devarenne-Charpentier
The tissue inhibitor of metalloproteinases-1 (TIMP-1) exerts inhibitory activity against matrix metalloproteinases and cytokine-like effects. We previously showed that TIMP-1 reduces neurite outgrowth in mouse cortical neurons and that this cytokine-like effect depends on TIMP-1 endocytosis mediated by the low-density lipoprotein receptor-related protein-1 (LRP-1). To gain insight into the interaction between TIMP-1 and LRP-1, we considered conformational changes that occur when a ligand binds to its receptor...
July 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28707518/interaction-of-copper-ii-complexes-by-bovine-serum-albumin-spectroscopic-and-calorimetric-insights
#6
Namrata Singh, Darshana Pagariya, Surbhi Jain, Sunil Naik, Nand Kishore
Serum albumins being the most abundant proteins in the blood and cerebrospinal fluid are significant carriers of essential transition metal ions in the human body. Studies of copper (II) complexes have gained attention because of their potential applications in synthetic, biological and industrial processes. Study of binding interactions of such bioinorganic complexes with serum albumins improves our understanding of biomolecular recognition process essential for rational drug desig. In the present investigation, we have applied quantitative approach to explore interactions of novel synthesized copper (II) complexes viz...
July 14, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28703788/preparation-of-a-trp-bodipy-fluorogenic-amino-acid-to-label-peptides-for-enhanced-live-cell-fluorescence-imaging
#7
Lorena Mendive-Tapia, Ramon Subiros-Funosas, Can Zhao, Fernando Albericio, Nick D Read, Rodolfo Lavilla, Marc Vendrell
Fluorescent peptides are valuable tools for live-cell imaging because of the high specificity of peptide sequences for their biomolecular targets. When preparing fluorescent versions of peptides, labels must be introduced at appropriate positions in the sequences to provide suitable reporters while avoiding any impairment of the molecular recognition properties of the peptides. This protocol describes the preparation of the tryptophan (Trp)-based fluorogenic amino acid Fmoc-Trp(C2-BODIPY)-OH and its incorporation into peptides for live-cell fluorescence imaging-an approach that is applicable to most peptide sequences...
August 2017: Nature Protocols
https://www.readbyqxmd.com/read/28699919/towards-sensitive-high-throughput-biomolecular-assays-based-on-fluorescence-lifetime
#8
Anastasia Ioanna Skilitsi, Timothé Turko, Damien Cianfarani, Sophie Barre, Wilfried Uhring, Ulrich Hassiepen, Jérémie Léonard
Time-resolved fluorescence detection for robust sensing of biomolecular interactions is developed by implementing Time Correlated Single Photon Counting in high-throughput conditions. Droplet microfluidics is used as a promising platform for the very fast handling of low-volume samples. We illustrate the potential of this very sensitive and cost-effective technology in the context of an enzymatic activity assay based on fluorescently-labeled biomolecules. Fluorescence lifetime detection by Time Correlated Single Photon Counting is shown to enable reliable discrimination between positive and negative control samples at a throughput as high as several hundred samples per second...
July 12, 2017: Methods and Applications in Fluorescence
https://www.readbyqxmd.com/read/28696692/evaluating-force-field-performance-in-thermodynamic-calculations-of-cyclodextrin-host-guest-binding-water-models-partial-charges-and-host-force-field-parameters
#9
Niel M Henriksen, Michael K Gilson
Computational prediction of noncovalent binding free energies with methods based on molecular mechanical force fields has become increasingly routine in drug discovery projects, where they promise to speed the discovery of small molecule ligands to bind targeted proteins with high affinity. Because the reliability of free energy methods still has significant room for improvement, new force fields, or modifications of existing ones, are regularly introduced with the aim of improving the accuracy of molecular simulations...
July 11, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28695160/recent-advances-in-nonbiofouling-pdms-surface-modification-strategies-applicable-to-microfluidic-technology
#10
Aslihan Gokaltun, Martin L Yarmush, Ayse Asatekin, O Berk Usta
In the last decade microfabrication processes including rapid prototyping techniques have advanced rapidly and achieved a fairly mature stage. These advances have encouraged and enabled the use of microfluidic devices by a wider range of users with applications in biological separations and cell and organoid cultures. Accordingly, a significant current challenge in the field is controlling biomolecular interactions at interfaces and the development of novel biomaterials to satisfy the unique needs of the biomedical applications...
March 2017: Technology
https://www.readbyqxmd.com/read/28676869/impact-of-the-biomolecular-corona-on-the-structure-of-pegylated-liposomes
#11
Luca Digiacomo, Daniela Pozzi, Heinz Amenitsch, Giulio Caracciolo
Driven by the promises of gene therapy, PEGylated cationic liposomes (CLs) have been investigated for decades, but their use in the clinical setting is far from established. Such a dichotomy is due to several factors that have been ignored over the last two decades. The hardest challenge seems to occur when PEGylated CLs come into contact with a physiological environment (e.g. the blood). Recent evidence has demonstrated that PEGylation does not completely prevent protein binding (as believed so far), but a biomolecular shell, termed "biomolecular corona" (BC), covers the liposome surface...
July 5, 2017: Biomaterials Science
https://www.readbyqxmd.com/read/28666087/crowding-in-cellular-environments-at-an-atomistic-level-from-computer-simulations
#12
Michael Feig, Isseki Yu, Po-Hung Wang, Grzegorz Nawrocki, Yuji Sugita
The effects of crowding in biological environments on biomolecular structure, dynamics, and function remain not well understood. Computer simulations of atomistic models of concentrated peptide and protein systems at different levels of complexity are beginning to provide new insights. Crowding, weak interactions with other macromolecules and metabolites, and altered solvent properties within cellular environments appear to remodel the energy landscape of peptides and proteins in significant ways including the possibility of native state destabilization...
July 12, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28664877/birefringence-of-flow-assembled-chitosan-membranes-in-microfluidics
#13
K Li, S O Correa, P Pham, C B Raub, X Luo
Biopolymer membrane assembly in microfluidics offers precise spatial and temporal resolution for biomolecular and cellular interactions during and after assembly. Control over molecular transport across the biofabricated membranes requires microstructural characterization. This study investigates, for the first time, the birefringence of chitosan membranes assembled with flow in a microfluidic environment, and the effects of pH and flow rate on the membrane's micro-alignment. The optical anisotropy of the formed membranes was quantified using a de Sénarmont compensator for transmitted quantitative polarized light microscopy...
June 30, 2017: Biofabrication
https://www.readbyqxmd.com/read/28651056/significantly-improved-protein-folding-thermodynamics-using-a-dispersion-corrected-water-model-and-a-new-residue-specific-force-field
#14
Hao-Nan Wu, Fan Jiang, Yun-Dong Wu
An accurate potential energy model is crucial for biomolecular simulations. Despite many recent improvements of classical protein force fields, there are remaining key issues: much weaker temperature dependence of folding/unfolding equilibrium and overly collapsed unfolded or disordered states. For the latter problem, a new water model (TIP4P-D) has been proposed to correct the significantly underestimated water dispersion interactions. Here, using TIP4P-D, we reveal problems in current force fields through failures in folding model systems (a polyalanine peptide, Trp-cage, and the GB1 hairpin)...
June 30, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28648524/molecular-modelling-of-biomolecules-by-paramagnetic-nmr-and-computational-hybrid-methods
#15
REVIEW
Kala Bharath Pilla, Kari Gaalswyk, Justin L MacCallum
The 3D atomic structures of biomolecules and their complexes are key to our understanding of biomolecular function, recognition, and mechanism. However, it is often difficult to obtain structures, particularly for systems that are complex, dynamic, disordered, or exist in environments like cell membranes. In such cases sparse data from a variety of paramagnetic NMR experiments offers one possible source of structural information. These restraints can be incorporated in computer modelling algorithms that can accurately translate the sparse experimental data into full 3D atomic structures...
June 22, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28639674/transition-from-disordered-aggregates-to-ordered-lattices-kinetic-control-of-the-assembly-of-a-computationally-designed-peptide
#16
Yu Tian, Huixi Violet Zhang, Kristi L Kiick, Jeffery G Saven, Darrin J Pochan
Natural biomolecular self-assembly typically occurs under a narrow range of solution conditions, and the design of sequences that can form prescribed structures under a range of such conditions would be valuable in the bottom-up assembly of predetermined nanostructures. We present a computationally designed peptide that robustly self-assembles into regular arrays under a wide range of solution pH and temperature conditions. Controling the solution conditions provides the opportunity to exploit a simple and reproducible approach for altering the pathway of peptide solution self-assembly...
June 22, 2017: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/28636761/molecular-tools-for-facilitative-carbohydrate-transporters
#17
Marina Tanasova, Joseph R Fedie
Facilitative carbohydrate transporters - Gluts - have received a wide attention over decades due to their essential role in the nutrient uptake and links with various metabolic disorders, including diabetes, obesity, and cancer. Endeavors into understanding mechanisms of Glut-mediated nutrient uptake have resulted in the multidisciplinary research field, branching protein chemistry, chemical biology, organic synthesis, crystallography, and biomolecular modeling. Gluts became attractive targets for cancer research and medicinal chemistry, leading to the development of new approaches to cancer diagnostics and providing avenues for cancer-targeting therapeutics...
June 21, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28632260/visualization-of-the-protein-corona-towards-a-biomolecular-understanding-of-nanoparticle-cell-interactions
#18
Maria Kokkinopoulou, Johanna Simon, Katharina Landfester, Volker Mailänder, Ingo Lieberwirth
The use of nanocarriers in biology and medicine is complicated by the current need to understand how nanoparticles interact in complex biological surroundings. When nanocarriers come into contact with serum, proteins immediately adsorb onto their surface, forming a protein corona which defines their biological identity. Although the composition of the protein corona has been widely determined by proteomics, its morphology still remains unclear. In this study we show for the first time the morphology of the protein corona using transmission electron microscopy...
June 29, 2017: Nanoscale
https://www.readbyqxmd.com/read/28632153/fabrication-and-characterization-of-plasmonic-nanopores-with-cavities-in-the-solid-support
#19
Bita Malekian, Kunli Xiong, Gustav Emilsson, Jenny Andersson, Cecilia Fager, Eva Olsson, Elin M Larsson-Langhammer, Andreas B Dahlin
Plasmonic nanostructures are widely used for various sensing applications by monitoring changes in refractive index through optical spectroscopy or as substrates for surface enhanced Raman spectroscopy. However, in most practical situations conventional surface plasmon resonance is preferred for biomolecular interaction analysis because of its high resolution in surface coverage and the simple single-material planar interface. Still, plasmonic nanostructures may find unique sensing applications, for instance when the nanoscale geometry itself is of interest...
June 20, 2017: Sensors
https://www.readbyqxmd.com/read/28616954/surface-charge-and-particle-size-determine-the-metabolic-fate-of-dendritic-polyglycerols
#20
Kritee Pant, Johanna Pufe, Kristof Zarschler, Ralf Bergmann, Jörg Steinbach, Sabine Reimann, Rainer Haag, Jens Pietzsch, Holger Stephan
Dendritic polyglycerols (dPG) are water soluble, polyether-based nanomaterials which hold great potential in diagnostic as well as therapeutic applications. In order to translate them for in vivo applications, a systematic assessment regarding their cell and tissue interactions as well as their metabolic fate in vivo is a crucial step. Herein, we explore the structure-activity relationship of three different sizes (ca. 3, 5, and 10 nm) of neutral dendritic polyglycerol (dPG) and their corresponding negatively charged sulfate analogs (dPGS) on their in vitro and in vivo characteristics...
June 29, 2017: Nanoscale
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