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https://www.readbyqxmd.com/read/28530269/a-critical-comparison-of-coarse-grained-structure-based-approaches-and-atomic-models-of-protein-folding
#1
Jie Hu, Tao Chen, Moye Wang, Hue Sun Chan, Zhuqing Zhang
Structure-based coarse-grained Gō-like models have been used extensively in deciphering protein folding mechanisms because of their simplicity and tractability. Meanwhile, explicit-solvent molecular dynamics (MD) simulations with physics-based all-atom force fields have been applied successfully to simulate folding/unfolding transitions for several small, fast-folding proteins. To explore the degree to which coarse-grained Gō-like models and their extensions to incorporate nonnative interactions are capable of producing folding processes similar to those in all-atom MD simulations, here we systematically compare the computed unfolded states, transition states, and transition paths obtained using coarse-grained models and all-atom explicit-solvent MD simulations...
May 22, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28529409/an-experimental-check-of-backscattering-interferometry
#2
Michael M Baksh, M G Finn
Backscattering interferometry (BSI) was used to determine the association constants for four well-known biomolecular interactions: protein A + IgG, trypsin + antitrypsin, trypsin + p-aminobenzamidine, and antithrombin + heparin. Each gave well-defined binding curves and Kd values in close agreement with published findings obtained using other techniques. These results stand in direct contrast to the claims in a 2015 publication in this journal (Discussion of "Back Scattering Interferometry revisited-a theoretical and experimental investigation" Jørgensen, T...
May 2017: Sensors and Actuators. B, Chemical
https://www.readbyqxmd.com/read/28523911/cup-shaped-nanoantenna-arrays-for-zeptoliter-volume-biochemistry-and-plasmonic-sensing-in-the-visible-wavelengths-range
#3
Rokas Drevinskas, Tomas Rakickas, Algirdas Selskis, Lorenzo Rosa, Ramunas Valiokas
Although three-dimensional shaping of metallic nanostructures is an important strategy for control and manipulation of localized surface plasmon resonance (LSPR), its implementation in high-throughput, on-chip fabrication of plasmonic devices remains to be challenging. Here we demonstrate nanocontact-based large area fabrication of a novel, LSPR-active Au architecture consisting of periodic arrays of reduced symmetry nanoantennas having sub-50 nm, out-of-plane features. Namely, by combining nanosphere and molecular self-assembly processes we have patterned evaporated polycrystalline Au films for chemical etching of nanocups with controlled aspect ratios (an outer diameter d=100 nm, void volumes of 18 or 39 zeptoliters)...
May 19, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28521682/repurposing-of-copper-ii-chelating-drugs-for-the-treatment-of-neurodegenerative-diseases
#4
Valeria Lanza, Danilo Milardi, Giuseppe Di Natale, Giuseppe Pappalardo
BACKGROUND: There is mounting urgency to find new drugs for the treatment of neurodegenerative disorders. A large number of reviews has exhaustively described either the molecular or clinical aspects of neurodegenerative diseases as Alzheimer's (AD) and Parkinson's (PD). Conversely, reports outlining how known drugs in use for other diseases can be also effective as therapeutic agents in neurodegenerative diseases are less reported. This review focuses on the current uses of some copper(II) interacting molecules as potential drug candidates in neurodegeneration...
May 17, 2017: Current Medicinal Chemistry
https://www.readbyqxmd.com/read/28516911/electrostatic-melting-in-a-single-molecule-field-effect-transistor-with-applications-in-genomic-identification
#5
Sefi Vernick, Scott M Trocchia, Steven B Warren, Erik F Young, Delphine Bouilly, Ruben L Gonzalez, Colin Nuckolls, Kenneth L Shepard
The study of biomolecular interactions at the single-molecule level holds great potential for both basic science and biotechnology applications. Single-molecule studies often rely on fluorescence-based reporting, with signal levels limited by photon emission from single optical reporters. The point-functionalized carbon nanotube transistor, known as the single-molecule field-effect transistor, is a bioelectronics alternative based on intrinsic molecular charge that offers significantly higher signal levels for detection...
May 18, 2017: Nature Communications
https://www.readbyqxmd.com/read/28511021/the-selectivity-challenge-in-organic-solvent-nanofiltration-membrane-and-process-solutions
#6
Patrizia Marchetti, Ludmila Peeva, Andrew Livingston
Recent development of organic solvent nanofiltration (OSN) materials has been overwhelmingly directed toward tight membranes with ultrahigh permeance. However, emerging research into OSN applications is suggesting that improved separation selectivity is at least as important as further increases in membrane permeance. Membrane solutions are being proposed to improve selectivity, mostly by exploiting solute/solvent/membrane interactions and by fabricating tailored membranes. Because achieving a perfect separation with a single membrane stage is difficult, process engineering solutions, such as membrane cascades, are also being advocated...
May 16, 2017: Annual Review of Chemical and Biomolecular Engineering
https://www.readbyqxmd.com/read/28510311/rapid-microfluidic-dilution-for-single-molecule-spectroscopy-of-low-affinity-biomolecular-complexes
#7
Niels Zijlstra, Fabian Dingfelder, Bengt Wunderlich, Franziska Zosel, Stephan Benke, Daniel Nettels, Benjamin Schuler
To enable the investigation of low-affinity biomolecular complexes with confocal single-molecule spectroscopy, we have developed a microfluidic device that allows a concentrated sample to be diluted by up to five orders of magnitude within milliseconds, at the physical limit dictated by diffusion. We demonstrate the capabilities of the device by studying the dissociation kinetics and structural properties of low-affinity protein complexes using single-molecule two-color and three-color Förster resonance energy transfer (FRET)...
May 16, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28508363/glycoproteins-enrichment-and-lc-ms-ms-glycoproteomics-in-central-nervous-system-applications
#8
Rui Zhu, Ehwang Song, Ahmed Hussein, Firas H Kobeissy, Yehia Mechref
Proteins and glycoproteins play important biological roles in central nervous systems (CNS). Qualitative and quantitative evaluation of proteins and glycoproteins expression in CNS is critical to reveal the inherent biomolecular mechanism of CNS diseases. This chapter describes proteomic and glycoproteomic approaches based on liquid chromatography/tandem mass spectrometry (LC-MS or LC-MS/MS) for the qualitative and quantitative assessment of proteins and glycoproteins expressed in CNS. Proteins and glycoproteins, extracted by a mass spectrometry friendly surfactant from CNS samples, were subjected to enzymatic (tryptic) digestion and three down-stream analyses: (1) a nano LC system coupled with a high-resolution MS instrument to achieve qualitative proteomic profile, (2) a nano LC system combined with a triple quadrupole MS to quantify identified proteins, and (3) glycoprotein enrichment prior to LC-MS/MS analysis...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28501583/combining-nmr-and-small-angle-x-ray-scattering-for-the-study-of-biomolecular-structure-and-dynamics
#9
Haydyn D T Mertens, Dmitri I Svergun
Small-angle X-rays scattering (SAXS) and Nuclear Magnetic Resonance (NMR) are established methods to analyze the structure and structural transitions of biological macromolecules in solution. Both methods are directly applicable to near-native macromolecular solutions and allow one to study structural responses to physical and chemical changes or ligand additions. Whereas SAXS is applied to elucidate overall structure, interactions and flexibility over a wide range of particle sizes, NMR yields atomic resolution detail for moderately sized macromolecules...
May 10, 2017: Archives of Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28499197/biomolecular-stiffness-detection-based-on-positive-frequency-shift-of-cmos-compatible-gigahertz-solidly-mounted-resonators
#10
Qingrui Yang, Shuting Pan, Yuan Zhao, Hao Zhang, Wei Pang, Xuexin Duan
In this work, gigahertz solidly mounted resonators (SMRs) (2.5GHz) were designed and fabricated to construct a novel particle-resonator system to achieve the biomolecular stiffness sensing in real time. The positive frequency shift of the system was used to estimate the stiffness of biomolecules connecting between the SMR and attached particles. The working principle was revealed by the mathematical analysis of the general block-spring model of the system. Further interpretations about the mechanism of such elastic interaction from the perspective of acoustic resonant modes of SMRs were given by finite element method...
May 4, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28497135/unscrambling-micro-solvation-of-cooh-and-nh-groups-in-neat-dimethyl-sulfoxide-insights-from-1-h-nmr-spectroscopy-and-computational-studies
#11
Panteleimon G Takis, Konstantinos D Papavasileiou, Loukas D Peristeras, Georgios C Boulougouris, Vasilios S Melissas, Anastassios N Troganis
Dimethyl sulfoxide (DMSO) has a significant, multi-faceted role in medicine, pharmacy, and biology as well as in biophysical chemistry and catalysis. Its physical properties and impact on biomolecular structures still attract major scientific interest, especially the interactions of DMSO with biomolecular functional groups. In the present study, we shed light on the "isolated" carboxylic (-COOH) and amide (-NH) interactions in neat DMSO via(1)H NMR studies along with extensive theoretical approaches, i.e. molecular dynamics (MD) simulations, density functional theory (DFT), and ab initio calculations, applied on model compounds (i...
May 12, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28489952/revisiting-hydrogen-bond-thermodynamics-in-molecular-simulations
#12
Liel Sapir, Daniel Harries
In processes involving aqueous solutions and in almost every biomolecular interaction, hydrogen bonds play important roles. Though weak compared to the covalent bond, hydrogen bonds modify the stability and conformation of numerous small and large molecules and modulate their intermolecular interactions. We propose a simple methodology for extracting hydrogen bond strength from atomistic level simulations. The free energy associated with hydrogen bond formation is conveniently calculated as the reversible work required to reshape a completely random pair probability distribution reference state into the one found in simulations where hydrogen bonds are formed...
May 10, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28484455/real-time-characterization-of-antibody-binding-to-receptors-on-living-immune-cells
#13
Sina Bondza, Eleanor Foy, Jonathan Brooks, Karl Andersson, James Robinson, Pascale Richalet, Jos Buijs
Understanding molecular interactions on immune cells is crucial for drug development to treat cancer and autoimmune diseases. When characterizing molecular interactions, the use of a relevant living model system is important, as processes such as receptor oligomerization and clustering can influence binding patterns. We developed a protocol to enable time-resolved analysis of ligand binding to receptors on living suspension cells. Different suspension cell lines and weakly adhering cells were tethered to Petri dishes with the help of a biomolecular anchor molecule, and antibody binding was analyzed using LigandTracer...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28482223/biological-effects-of-%C3%AE-adrenergic-phentolamine-on-erythrocyte-hemeprotein-molecular-insights-from-biorecognition-behavior-protein-dynamics-and-flexibility
#14
Wei Peng, Fei Ding, Yu-Kui Peng, Yong Xie
Phentolamine is one of the most representative nonselective α-adrenoreceptor blocking agents, which have been proved to be owned various pharmacological actions. Unfortunately, whether erythrocytes in the veins intervene in biological behaviors of such drug are largely obscured. With the aid of multiple biophysical techniques, this scenario was to detailed explore the potential biorecognition between phentolamine and the hemeprotein in the cytosol of erythrocytes, and the influences of dynamic characters of protein during the bioreaction...
April 28, 2017: Journal of Photochemistry and Photobiology. B, Biology
https://www.readbyqxmd.com/read/28474302/f-1-f-2-selective-nmr-spectroscopy
#15
Erik Walinda, Daichi Morimoto, Masahiro Shirakawa, Kenji Sugase
Fourier transform NMR spectroscopy has provided unprecedented insight into the structure, interaction and dynamic motion of proteins and nucleic acids. Conventional biomolecular NMR relies on the acquisition of three-dimensional and four-dimensional (4D) data matrices to establish correlations between chemical shifts in the frequency domains F 1, F 2, F 3 and F 1, F 2, F 3, F 4 respectively. While rich in information, these datasets require a substantial amount of acquisition time, are visually highly unintuitive, require expert knowledge to process, and sample dark and bright regions of the frequency domains equally...
May 4, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28469995/computational-analysis-of-host-pathogen-protein-interactions-between-humans-and-different-strains-of-enterohemorrhagic-escherichia-coli
#16
Tungadri Bose, K V Venkatesh, Sharmila S Mande
Serotype O157:H7, an enterohemorrhagic Escherichia coli (EHEC), is known to cause gastrointestinal and systemic illnesses ranging from diarrhea and hemorrhagic colitis to potentially fatal hemolytic uremic syndrome. Specific genetic factors like ompA, nsrR, and LEE genes are known to play roles in EHEC pathogenesis. However, these factors are not specific to EHEC and their presence in several non-pathogenic strains indicates that additional factors are involved in pathogenicity. We propose a comprehensive effort to screen for such potential genetic elements, through investigation of biomolecular interactions between E...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28466873/corrigendum-insights-into-cancer-severity-from-biomolecular-interaction-mechanisms
#17
Francesco Raimondi, Gurdeep Singh, Matthew J Betts, Gordana Apic, Ranka Vukotic, Pietro Andreone, Lincoln Stein, Robert B Russell
No abstract text is available yet for this article.
May 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28460184/nanoscale-aggregation-in-acid-and-ion-containing-polymers
#18
L Robert Middleton, Karen I Winey
In this review we summarize recent efforts in understanding nanoaggregation in acid- and ion-containing polymer systems. The acid and ionic groups have specific interactions that drive aggregation and alter polymer behavior at the nano-, micro-, and bulk length scales. Advancements in synthetic methods, characterization techniques, and computer simulations have enabled researchers to better understand the morphologies and dynamics, particularly at the nanoscale. This overview of recent advancements in nano-aggregated polymer systems highlights the current understanding of the field and presents promising directions for future investigations and new applications...
April 26, 2017: Annual Review of Chemical and Biomolecular Engineering
https://www.readbyqxmd.com/read/28453667/linearity-of-network-proximity-measures-implications-for-set-based-queries-and-significance-testing
#19
Sean Maxwell, Mark R Chance, Mehmet Koyutürk
Motivation: In recent years, various network proximity measures have been proposed to facilitate the use of biomolecular interaction data in a broad range of applications. These applications include functional annotation, disease gene prioritization, comparative analysis of biological systems and prediction of new interactions. In such applications, a major task is the scoring or ranking of the nodes in the network in terms of their proximity to a given set of 'seed' nodes (e.g. a group of proteins that are identified to be associated with a disease, or are deferentially expressed in a certain condition)...
May 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28453019/site-accessibility-tailors-dna-cleavage-by-restriction-enzymes-in-dna-confined-monolayers
#20
Chiara Rotella, Giovanni Doni, Alessandro Bosco, Matteo Castronovo, Alessandro De Vita, Loredana Casalis, Giovanni M Pavan, Pietro Parisse
Density-tunable nanografted monolayers (NAMs) of short oligonucleotide sequences on gold surfaces show novel properties that make them suitable for advanced biosensing applications, and in particular to study the effects of crowding and confinement on biomolecular interactions. Here, combining atomic force microscopy nanolithography, topography measurements and coarse-grained molecular dynamics simulations, we investigated restriction enzyme reaction mechanisms within confined DNA brushes highlighting the role played by the DNA sequence conformation and restriction site position along the chain, respectively, in determining the accessibility of the enzyme, and its consequent cleavage efficiency...
May 18, 2017: Nanoscale
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