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biomolecular interaction

Jejoong Yoo, Aleksei Aksimentiev
In contrast to ordinary polymers, the vast majority of biological macromolecules adopt highly ordered three-dimensional structures that define their functions. The key to folding of a biopolymer into a unique 3D structure or to an assembly of several biopolymers into a functional unit is a delicate balance between the attractive and repulsive forces that also makes such self-assembly reversible under physiological conditions. The all-atom molecular dynamics (MD) method has emerged as a powerful tool for studies of individual biomolecules and their functional assemblies, encompassing systems of ever increasing complexity...
March 16, 2018: Physical Chemistry Chemical Physics: PCCP
Nicole M Cordina, Nima Sayyadi, Lindsay M Parker, Arun Everest-Dass, Louise J Brown, Nicolle H Packer
Bio-imaging is a key technique in tracking and monitoring important biological processes and fundamental biomolecular interactions, however the interference of background autofluorescence with targeted fluorophores is problematic for many bio-imaging applications. This study reports on two novel methods for reducing interference with cellular autofluorescence for bio-imaging. The first method uses fluorescent nanodiamonds (FNDs), containing nitrogen vacancy centers. FNDs emit at near-infrared wavelengths typically higher than most cellular autofluorescence; and when appropriately functionalized, can be used for background-free imaging of targeted biomolecules...
March 14, 2018: Scientific Reports
H A E Hub Zwart
This paper addresses the cultural impact of genomics and the Human Genome Project (HGP) on human self-understanding. Notably, it addresses the claim made by Francis Collins (director of the HGP) that the genome is the language of God and the claim made by Max Delbrück (founding father of molecular life sciences research) that Aristotle must be credited with having predicted DNA as the soul that organises bio-matter. From a continental philosophical perspective I will argue that human existence results from a dialectical interaction between two types of texts: the language of molecular biology and the language of civilisation; the language of the genome and the language of our socio-cultural, symbolic ambiance...
April 2018: New Bioethics: a Multidisciplinary Journal of Biotechnology and the Body
M Gianneli, E Polo, H Lopez, V Castagnola, T Aastrup, K A Dawson
Nanomedicine, nanotargeting and nanotherapeutics have in the last few years faced several difficulties in translating the promising results obtained in vitro to an in vivo scenario. The origin of this discrepancy might be found in the lack of a detailed and realistic characterization of the biological surface of nanoparticles. Despite the capability to engineer nanomaterials with a great variety and a precise control of the surface functionalization, the targeting capability is lost when the nanoparticles are embedded in complex biological media, due to the formation of a biological layer (biomolecular corona)...
March 7, 2018: Nanoscale
Yi-Hsuan Lin, Julie D Forman-Kay, Hue Sun Chan
Liquid-liquid phase separation and related condensation processes of intrinsically disordered proteins (IDPs), proteins with intrinsically disordered regions and nucleic acids underpin various condensed-liquid droplets or gel-like assemblies in the cellular environment. Collectively referred to as condensates, these bodies provide spatial/temporal compartmentalization, often serving as hubs for regulated biomolecular interactions. Examples include certain extracellular materials, transcription complexes, and membraneless organelles such as germ and stress granules and the nucleolus...
March 6, 2018: Biochemistry
Anastasia Ioanna Skilitsi, Damianos Agathangelou, Ievgen Shulov, Jamie Conyard, Stefan Haacke, Yves Mély, Andrey Klymchenko, Jérémie Léonard
The excited state intramolecular proton transfer (ESIPT) of 3-hydroxyflavone derivatives results in a fluorescence spectrum composed of two emission bands, the relative intensity of which is strongly influenced by the interaction with the local environment. We use time-resolved fluorescence and ultrafast transient absorption spectroscopies to investigate the photophysics of 4'-methoxy-3-hydroxyflavone in different solvents characterized by various polarities and hydrogen (H) bonding capabilities. We evidence that in this compound, the ESIPT reaction rate varies by more than 3 orders of magnitude, depending on the H-bonding capability of its local environment...
March 6, 2018: Physical Chemistry Chemical Physics: PCCP
Tirayut Vilaivan
Fluorogenic oligonucleotide probes that can produce a change in fluorescence signal upon binding to specific biomolecular targets, including nucleic acids as well as non-nucleic acid targets, such as proteins and small molecules, have applications in various important areas. These include diagnostics, drug development and as tools for studying biomolecular interactions in situ and in real time. The probes usually consist of a labeled oligonucleotide strand as a recognition element together with a mechanism for signal transduction that can translate the binding event into a measurable signal...
2018: Beilstein Journal of Organic Chemistry
Jerome M Fox, Mengxia Zhao, Michael J Fink, Kyungtae Kang, George M Whitesides
Biomolecular recognition can be stubborn; changes in the structures of associating molecules, or the environments in which they associate, often yield compensating changes in enthalpies and entropies of binding and no net change in affinities. This phenomenon-termed enthalpy/entropy (H/S) compensation-hinders efforts in biomolecular design, and its incidence-often a surprise to experimentalists-makes interactions between biomolecules difficult to predict. Although characterizing H/S compensation requires experimental care, it is unquestionably a real phenomenon that has, from an engineering perspective, useful physical origins...
March 5, 2018: Annual Review of Biophysics
Marketa Paloncyova, Michal Langer, Michal Otyepka
Carbon dots (CDs), one of the youngest members of the carbon nanostructure family, are now widely experimentally studied for their tunable fluorescence properties, bleaching resistance and biocompatibility. Their interaction with biomolecular systems has also been explored experimentally. However, many atomistic details still remain unresolved. Molecular dynamics (MD) simulations enabling atomistic and femtosecond resolutions simultaneously are a well-established tool of computational chemistry which can provide useful insights into investigated systems...
March 2, 2018: Journal of Chemical Theory and Computation
Jodi Kraus, Rupal Gupta, Manman Lu, Jenna B Yehl, David A Case, Angela M Gronenborn, Mikael Akke, Tatyana Polenova
Magic angle spinning NMR spectroscopy is uniquely suited to probe the structure and dynamics of insoluble proteins and protein assemblies at atomic resolution, with NMR chemical shifts containing rich information about biomolecular structure. Access to this information, however, is problematic since accurate quantum mechanical calculation of chemical shifts in proteins remains challenging, particularly for15 NH . Here we report on isotropic chemical shift predictions for the carbohydrate recognition domain of microcrystalline galectin-3, obtained from using hybrid quantum mechanics/molecular mechanics (QM/MM) calculations, implemented using an automated fragmentation approach, and using very high resolution (0...
March 2, 2018: Journal of Physical Chemistry. B
Zhao Wang, Ting Luo, Amin Cao, Jingjing Sun, Lin Jia, Ruilong Sheng
In this study, a series of diblock glycopolymers, poly(6- O -methacryloyl-d-galactopyranose)- b -poly(6-cholesteryloxyhexyl methacrylate) (PMAgala- b -PMAChols), with cholesterol/galactose grafts were prepared through a sequential reversible addition-fragmentation chain transfer (RAFT) polymerization and deprotection process. The glycopolymers could self-assemble into aggregates with various morphologies depending on cholesterol/galactose-containing block weight ratios, as determined by transmission electronic microscopy (TEM) and dynamic laser light scattering (DLS)...
February 28, 2018: Nanomaterials
Valeria Vetri, Federica Piccirilli, Johannes Krausser, Gianpiero Buscarino, Urszula Łapińska, Bente Vestergaard, Alessio Zaccone, Vito Foderà
Protein self-assembly into amyloid fibrils or highly hierarchical superstructures is closely linked to neurodegenerative pathologies as Alzheimer's and Parkinson´s diseases. Moreover, protein assemblies also emerged as building blocks for bio-inspired nanostructured materials. In both the above mentioned fields the main challenge is to control the growth and properties of the final protein structure. This relies on a more fundamental understanding of how interactions between proteins can determine structures and functions of biomolecular aggregates...
February 28, 2018: Journal of Physical Chemistry. B
Ankit Sabharwal, Disha Sharma, Shamsudheen Karuthedath Vellarikkal, Rijith Jayarajan, Ankit Verma, Vigneshwar Senthivel, Vinod Scaria, Sridhar Sivasubbu
Mitochondria are organelles involved in a variety of biological functions in the cell, apart from their principal role in generation of ATP, the cellular currency of energy. The mitochondria, in spite of being compact organelles, are capable of performing complex biological functions largely because of the ability to exchange proteins, RNA, chemical metabolites and other biomolecules between cellular compartments. A close network of biomolecular interactions are known to modulate the crosstalk between the mitochondria and the nuclear genome...
February 24, 2018: Mitochondrion
Paul S Nerenberg, Teresa Head-Gordon
Biomolecular force field development has been instrumental in improving the predictive power of molecular simulations over the past four decades. More recently, the era of large quantitative experimental datasets and ubiquitous high performance computing power has enabled rapid progress in the field. In this review we summarize recent developments in all-atom protein, nucleic acid, and small molecule force fields, paying specific attention to developments in parameterization methods and improvements in the representations of nonbonded interactions that are critical for solving the challenging biophysical problems of the present...
February 21, 2018: Current Opinion in Structural Biology
Graeme A King, Andreas S Biebricher, Iddo Heller, Erwin Peterman, Gijs Wuite
The ability to measure mechanics and forces in biological nanostructures, such as DNA, proteins and cells, is of great importance as a means to analyze biomolecular systems. However, current force detection methods often require specialized instrumentation. Here, we present a novel and versatile method to quantify tension in molecular systems locally and in real time using intercalated DNA fluorescence. This approach can report forces over a range of ~1-65 pN with a resolution of 1-3 pN, using commercially available intercalating dyes and a general-purpose fluorescence microscope...
February 23, 2018: Nano Letters
Jongrae Kim, Mathias Foo, Declan G Bates
Measurement techniques in biology are now able to provide data on the trajectories of multiple individual molecules simultaneously, motivating the development of techniques for the stochastic spatio-temporal modelling of biomolecular networks. However, standard approaches based on solving stochastic reaction-diffusion equations are computationally intractable for large-scale networks. We present a novel method for modeling stochastic and spatial dynamics in biomolecular networks using a simple form of the Langevin equation with noisy kinetic constants...
February 22, 2018: Scientific Reports
Javier De Las Rivas, Diego Alonso-López, Mónica M Arroyo
Unraveling the protein interaction wiring that occurs in human cells as a scaffold of biological processes requires the identification of all elements that constitute such molecular interaction networks. Proteome-wide experimental studies and bioinformatic comprehensive efforts have provided reliable and updated compendiums of the human protein interactome. In this work, we present a current view of available databases of human protein-protein interactions (PPIs) that allow building protein interaction networks...
2018: Advances in Protein Chemistry and Structural Biology
Idris Yazgan, Jing Zhang, Victor Murithi Kariuki, Ayfer Akgul, Lauren Cronmiller, Ali Akgul, Francis Osonga, Abbey McMahon, Yang Gao, Gaddi Eshun, Seokheun Choi, Omowunmi A Sadik
The blue-green mold Penicillium italicum is among the most problematic post-harvest plant infections limiting the integrity of citrus and many other crops during storage and transportation, but there is no sensor for its on-site or field detection. We hereby, for the first time, report the development of novel biomolecular sensor for assessing the presence of Penicillium italicum spores and hyphae using carbohydrate-lectin recognitions. Two approaches were developed: (i) lateral tests using stand-alone poly (amic) acid (PAA) membranes and glass surfaces and (ii) quantitative tests on 96-well polystyrene plates and paper electrodes...
February 20, 2018: ACS Sensors
Boyang Hua, Yanbo Wang, Seongjin Park, Kyu Young Han, Digvijay Singh, Jin Hyun Kim, Wei Cheng, Taekjip Ha
Here, we demonstrate that the use of single-molecule centroid localization algorithm can improve the accuracy of fluorescence binding assays. Two major artifacts in this type of assays, i.e., non-specific binding events and optically overlapping receptors, can be detected and corrected during analysis. The effectiveness of our method was confirmed by measuring two weak biomolecular interactions, the interaction between the B1 domain of streptococcal protein G (pGB1) and immunoglobulin G (IgG), and the one between double-stranded DNA (dsDNA) and the Cas9-RNA complex with limited sequence matches...
February 19, 2018: Biochemistry
Wen-Jing Bao, Jian Li, Jin Li, Qian-Wen Zhang, Yang Liu, Cai-Feng Shi, Xing-Hua Xia
A versatile and sensitive platform for label-free bioanalysis has been proposed based on attenuated total reflection-surface enhanced infrared absorption spectroscopy (ATR-SEIRAS) using Au/ZnSe as the enhancement substrate that allows wide spectral range down to 700 cm-1. Au nanoparticles are stably deposited on the surface of ZnSe prism due to the formation of Au-Se bond via electroless deposition, and the enhancement factor of the resultant Au/ZnSe substrate is about two times larger than that of the commonly used Au/Si substrate...
February 19, 2018: Analytical Chemistry
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