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https://www.readbyqxmd.com/read/29145826/gpu-based-detection-of-protein-cavities-using-gaussian-surfaces
#1
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
#2
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
#3
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/29135256/improved-solution-state-properties-of-monoclonal-antibodies-by-targeted-mutations
#4
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/29131585/antibody-templated-assembly-of-an-rna-mimic-of-green-fluorescent-protein
#5
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
#6
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
#7
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/29129810/discerning-molecular-interactions-a-comprehensive-review-on-biomolecular-interaction-databases-and-network-analysis-tools
#8
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/29125973/creation-of-antifouling-microarrays-by-photopolymerization-of-zwitterionic-compounds-for-protein-assay-and-cell-patterning
#9
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
https://www.readbyqxmd.com/read/29123668/nanoehs-beyond-toxicity-focusing-on-biocorona
#10
Sijie Lin, Monika Mortimer, Ran Chen, Aleksandr Kakinen, Jim E Riviere, Thomas P Davis, Feng Ding, Pu Chun Ke
The first phase of environmental health and safety of nanomaterials (nanoEHS) studies has been mainly focused on evidence-based investigations that probe the impact of nanoparticles, nanomaterials and nano-enabled products on biological and ecological systems. The integration of multiple disciplines, including colloidal science, nanomaterial science, chemistry, toxicology/immunology and environmental science, is necessary to understand the implications of nanotechnology for both human health and the environment...
July 1, 2017: Environmental Science. Nano
https://www.readbyqxmd.com/read/29121073/diffslc-a-graph-centrality-method-to-detect-essential-proteins-of-a-protein-protein-interaction-network
#11
Divya Mistry, Roger P Wise, Julie A Dickerson
Identification of central genes and proteins in biomolecular networks provides credible candidates for pathway analysis, functional analysis, and essentiality prediction. The DiffSLC centrality measure predicts central and essential genes and proteins using a protein-protein interaction network. Network centrality measures prioritize nodes and edges based on their importance to the network topology. These measures helped identify critical genes and proteins in biomolecular networks. The proposed centrality measure, DiffSLC, combines the number of interactions of a protein and the gene coexpression values of genes from which those proteins were translated, as a weighting factor to bias the identification of essential proteins in a protein interaction network...
2017: PloS One
https://www.readbyqxmd.com/read/29119782/intracellular-protein-labeling-probes-for-multicolor-single-molecule-imaging-of-immune-receptor-adaptor-molecular-dynamics
#12
Ryota Sato, Jun Kozuka, Masahiro Ueda, Reiko Mishima, Yutaro Kumagai, Akimasa Yoshimura, Masafumi Minoshima, Shin Mizukami, Kazuya Kikuchi
Single-molecule imaging (SMI) has been widely utilized to investigate biomolecular dynamics and protein-protein interactions in living cells. However, multicolor SMI of intracellular proteins is challenging because of high background signals and other limitations of current fluorescence labeling approaches. To achieve reproducible intracellular SMI, a labeling probe ensuring both efficient membrane permeability and minimal non-specific binding to cell components is essential. We developed near-infrared (NIR) fluorescent probes for protein-labeling, which specifically binds to a mutant β-lactamase tag...
November 9, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29117675/many-body-coarse-grained-interactions-using-gaussian-approximation-potentials
#13
Sebastian T John, Gábor Csányi
We introduce a computational framework that is able to describe general many-body coarse-grained (CG) interactions of molecules and use it to model the free energy surface of molecular liquids as a cluster expansion in terms of monomer, dimer, and trimer terms. The contributions to the free energy due to these terms are inferred from all-atom molecular dynamics (MD) data using Gaussian Approximation Potentials, a type of machine-learning model that employs Gaussian process regression. The resulting CG model is much more accurate than those possible using pair potentials...
November 8, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29117511/the-role-of-mucus-as-an-invisible-cloak-to-transepithelial-drug-delivery-by-nanoparticles
#14
María García-Díaz, Ditlev Birch, Feng Wan, Hanne Mørck Nielsen
Mucosal administration of drugs and drug delivery systems has gained increasing interest. However, nanoparticles intended to protect and deliver drugs to epithelial surfaces require transport through the surface-lining mucus. Translation from bench to bedside is particularly challenging for mucosal administration since a variety of parameters will influence the specific barrier properties of the mucus including the luminal fluids, the microbiota, the mucus composition and clearance rate, and the condition of the underlying epithelia...
November 5, 2017: Advanced Drug Delivery Reviews
https://www.readbyqxmd.com/read/29115333/an-apolipoprotein-enriched-biomolecular-corona-switches-the-cellular-uptake-mechanism-and-trafficking-pathway-of-lipid-nanoparticles
#15
L Digiacomo, F Cardarelli, D Pozzi, S Palchetti, M A Digman, E Gratton, A L Capriotti, M Mahmoudi, G Caracciolo
Following exposure to biological milieus (e.g. after systemic administration), nanoparticles (NPs) get covered by an outer biomolecular corona (BC) that defines many of their biological outcomes, such as the elicited immune response, biodistribution, and targeting abilities. In spite of this, the role of BC in regulating the cellular uptake and the subcellular trafficking properties of NPs has remained elusive. Here, we tackle this issue by employing multicomponent (MC) lipid NPs, human plasma (HP) and HeLa cells as models for nanoformulations, biological fluids, and target cells, respectively...
November 16, 2017: Nanoscale
https://www.readbyqxmd.com/read/29096505/the-biofragment-database-bfdb-an-open-data-platform-for-computational-chemistry-analysis-of-noncovalent-interactions
#16
Lori A Burns, John C Faver, Zheng Zheng, Michael S Marshall, Daniel G A Smith, Kenno Vanommeslaeghe, Alexander D MacKerell, Kenneth M Merz, C David Sherrill
Accurate potential energy models are necessary for reliable atomistic simulations of chemical phenomena. In the realm of biomolecular modeling, large systems like proteins comprise very many noncovalent interactions (NCIs) that can contribute to the protein's stability and structure. This work presents two high-quality chemical databases of common fragment interactions in biomolecular systems as extracted from high-resolution Protein DataBank crystal structures: 3380 sidechain-sidechain interactions and 100 backbone-backbone interactions that inaugurate the BioFragment Database (BFDb)...
October 28, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29093508/vp2-of-chicken-anaemia-virus-interacts-with-apoptin-for-down-regulation-of-apoptosis-through-de-phosphorylated-threonine-108-on-apoptin
#17
Guan-Hua Lai, Yi-Yang Lien, Ming-Kuem Lin, Jai-Hong Cheng, Jason Tc Tzen, Fang-Chun Sun, Meng-Shiunn Lee, Hsi-Jien Chen, Meng-Shiou Lee
Chicken anaemia virus (CAV) is an important contagious agent that causes immunosuppressive disease in chickens. CAV Apoptin is a nucleoplasmic shuffling protein that induces apoptosis in chicken lymphoblastoid cells. In the present study, confocal microscopy revealed co-localisation of expressed CAV non-structural protein VP2 with Apoptin in the nucleus of MDCC-MSB1 cells and the nucleoplasmic compartment of CHO-K1 cells. In vitro pull-down and ex vivo biomolecular fluorescent complementation (BiFC) assays further showed that the VP2 protein directly interacts with Apoptin...
November 1, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29093465/modulation-of-the-vault-protein-protein-interaction-for-tuning-of-molecular-release
#18
Kang Yu, Yin Hoe Yau, Ameya Sinha, Tabitha Tan, Valerie A Kickhoefer, Leonard H Rome, Hwankyu Lee, Susana G Shochat, Sierin Lim
Vaults are naturally occurring ovoid nanoparticles constructed from a protein shell that is composed of multiple copies of major vault protein (MVP). The vault-interacting domain of vault poly(ADP-ribose)-polymerase (INT) has been used as a shuttle to pack biomolecular cargo in the vault lumen. However, the interaction between INT and MVP is poorly understood. It is hypothesized that the release rate of biomolecular cargo from the vault lumen is related to the interaction between MVP and INT. To tune the release of molecular cargos from the vault nanoparticles, we determined the interactions between the isolated INT-interacting MVP domains (iMVP) and wild-type INT and compared them to two structurally modified INT: 15-amino acid deletion at the C terminus (INTΔC15) and histidine substituted at the interaction surface (INT/DSA/3 H) to impart a pH-sensitive response...
November 1, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29092176/dual-kretschmann-and-otto-configuration-fiber-surface-plasmon-resonance-biosensor
#19
Lixia Li, Yuzhang Liang, Jianye Guang, Wenli Cui, Xinpu Zhang, Jean-Francois Masson, Wei Peng
We present a dual-resonance fiber surface plasmon resonance (SPR) sensor for biological analysis. The sensing element was fabricated by sequentially sputtering layers of indium tin oxide (ITO) (100 nm thickness) and Au (35 nm thickness) on the surface of an optical fiber. The refractive index dispersion effect of ITO material led to resonances in the near infrared and visible wavelength regions. The refractive index of ITO is larger than the optical fiber in visible spectral area (400 to 733nm), such that the structure is a typical Kretschmann configuration surface plasmon resonance sensor...
October 30, 2017: Optics Express
https://www.readbyqxmd.com/read/29091442/spatially-heterogeneous-surface-water-diffusivity-around-structured-protein-surfaces-at-equilibrium
#20
Ryan Barnes, Sheng Sun, Yann Fichou, Frederick W Dahlquist, Matthias Heyden, Songi Han
Hydration water on the surface of a protein is thought to mediate the thermodynamics of protein-ligand interaction. For hydration water to play a role beyond modulating global protein solubility or stability, the thermodynamic properties of hydration water must reflect on the properties of the heterogeneous protein surface, and thus spatially vary over the protein surface. A potent read-out of local variations in thermodynamic properties of hydration water is its equilibrium dynamics spanning picosecond to nanosecond timescales...
November 1, 2017: Journal of the American Chemical Society
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