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biomolecular interaction

Joshua A Rackers, Qiantao Wang, Chengwen Liu, Jean-Philip Piquemal, Pengyu Ren, Jay W Ponder
The principal challenge of using classical physics to model biomolecular interactions is capturing the nature of short-range interactions that drive biological processes from nucleic acid base stacking to protein-ligand binding. In particular most classical force fields suffer from an error in their electrostatic models that arises from an ability to account for the overlap between charge distributions occurring when molecules get close to each other, known as charge penetration. In this work we present a simple, physically motivated model for including charge penetration in the AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular Applications) force field...
November 30, 2016: Physical Chemistry Chemical Physics: PCCP
Jacob Anglister, Gautam Srivastava, Fred Naider
Intermolecular NOE interactions are invaluable for structure determination of biomolecular complexes by NMR and they represent the "gold-standard" amongst NMR measurements for characterizing interfaces. These NOEs constitute only a small fraction of the observed NOEs in a complex and are usually weaker than many of the intramolecular NOEs. A number of methods have been developed to remove the intramolecular NOEs that interfere with the identification of intermolecular NOEs. NMR experiments used to observe intermolecular NOE interactions in large protein complexes must cope with the short T2 relaxation time of the protons and heteronuclei in these complexes because they result in severe losses in sensitivity...
November 2016: Progress in Nuclear Magnetic Resonance Spectroscopy
Zeineb Farhane, Franck Bonnier, Hugh J Byrne
Raman microspectroscopy is a non-invasive, in vitro analytical tool which is being increasingly explored for its potential in clinical applications and monitoring the uptake, mechanism of action and cellular interaction at a molecular level of chemotherapeutic drugs, ultimately as a potential label-free preclinical screening and companion diagnostic tool. In this study, doxorubicin (DOX), a "gold standard" chemotherapeutic drug, is employed as a model in the in vitro lung cancer cell line A549 in order to demonstrate the potential of Raman microspectroscopy to screen and identify spectroscopic markers of its trafficking and mechanism of action...
November 25, 2016: Analytical and Bioanalytical Chemistry
Bo-Kai Liao, Andrew C Oates
Modular body organization is found widely across multicellular organisms, and some of them form repetitive modular structures via the process of segmentation. It's vastly interesting to understand how these regularly repeated structures are robustly generated from the underlying noise in biomolecular interactions. Recent studies from arthropods reveal similarities in segmentation mechanisms with vertebrates, and raise the possibility that the three phylogenetic clades, annelids, arthropods and chordates, might share homology in this process from a bilaterian ancestor...
November 22, 2016: Arthropod Structure & Development
Mílton Cordeiro, Fábio Ferreira Carlos, Pedro Pedrosa, António Lopez, Pedro Viana Baptista
The remarkable physicochemical properties of gold nanoparticles (AuNPs) have prompted developments in the exploration of biomolecular interactions with AuNP-containing systems, in particular for biomedical applications in diagnostics. These systems show great promise in improving sensitivity, ease of operation and portability. Despite this endeavor, most platforms have yet to reach maturity and make their way into clinics or points of care (POC). Here, we present an overview of emerging and available molecular diagnostics using AuNPs for biomedical sensing that are currently being translated to the clinical setting...
November 22, 2016: Diagnostics
Madhulika Gupta, Divya Nayar, Charusita Chakravarty, Sanjoy Bandyopadhyay
The secondary structure conformational properties and hydration shell metrics of the Trp-cage mini-protein are examined in the folded and unfolded ensembles in mTIP3P, TIP4P, and TIP4P-Ew water models with the CHARMM22 force-field using molecular dynamics simulations at 250 K. Upon changing the water model, the conformational order metrics of the peptide show significant differences in the unfolded rather than in the folded ensemble. The unfolding temperatures for Trp-cage are observed to be around 460, 470, and 430 K in mTIP3P, TIP4P, and TIP4P-Ew, respectively...
November 23, 2016: Physical Chemistry Chemical Physics: PCCP
Yung-Shin Sun
Microarrays of biological molecules such as DNAs, proteins, carbohydrates, and small molecules provide a high-throughput platform for screening tens of thousands of biomolecular interactions simultaneously, facilitating the functional characterization of these biomolecules in areas of genomics, proteomics, glycomics, and cytomics. Routinely, analysis of binding reactions between solution-phased probes and surface-immobilized targets involves some kinds of fluorescence-based detection methods. Even though these methods have advantages of high sensitivity and wide dynamic range, labeling probes and/or targets inevitably changes their innate properties and in turn affects probe-target interactions in often uncharacterized ways...
2017: Methods in Molecular Biology
Beatriz Roson-Burgo, Fermin Sanchez-Guijo, Consuelo Del Cañizo, Javier De Las Rivas
BACKGROUND: Mesenchymal Stromal/Stem Cells (MSCs), isolated under the criteria established by the ISCT, still have a poorly characterized phenotype that is difficult to distinguish from similar cell populations. Although the field of transcriptomics and functional genomics has quickly grown in the last decade, a deep comparative analysis of human MSCs expression profiles in a meaningful cellular context has not been yet performed. There is also a need to find a well-defined MSCs gene-signature because many recent biomedical studies show that key cellular interaction processes (i...
November 21, 2016: BMC Genomics
Marco Rusnati, Antonella Bugatti
Surface plasmon resonance (SPR) is an optical technique to evaluate biomolecular interactions. Briefly, SPR measures the capacity of two molecules to bind each other by detecting reflected light from a prism-gold film interface. One of the two putative interactants (called ligand) is chemically immobilized onto the gold film. When the sensor is exposed to a sample containing the second interactant (called analyte), its binding to the immobilized ligand causes a change of the refractive index of the material above the gold surface that is monitored as a real-time graph of the response units against time, producing a real-time graph called sensorgram...
2016: Methods in Molecular Biology
Maria Cristina Lo Giudice, Luciana M Herda, Ester Polo, Kenneth A Dawson
Nanoparticles interacting with, or derived from, living organisms are almost invariably coated in a variety of biomolecules presented in complex biological milieu, which produce a bio-interface or 'biomolecular corona' conferring a biological identity to the particle. Biomolecules at the surface of the nanoparticle-biomolecule complex present molecular fragments that may be recognized by receptors of cells or biological barriers, potentially engaging with different biological pathways. Here we demonstrate that using intense fluorescent reporter binders, in this case antibodies bound to quantum dots, we can map out the availability of such recognition fragments, allowing for a rapid and meaningful biological characterization...
November 15, 2016: Nature Communications
Iddo Heller, Niels Laurens, Daan Vorselen, Onno D Broekmans, Andreas S Biebricher, Graeme A King, Ineke Brouwer, Gijs J L Wuite, Erwin J G Peterman
Optical manipulation techniques provide researchers the powerful ability to directly move, probe and interrogate molecular complexes. Quadruple optical trapping is an emerging method for optical manipulation and force spectroscopy that has found its primary use in studying dual DNA interactions, but is certainly not limited to DNA investigations. The key benefit of quadruple optical trapping is that two molecular strands can be manipulated independently and simultaneously. The molecular geometries of the strands can thus be controlled and their interactions can be quantified by force measurements...
2017: Methods in Molecular Biology
Arnau Farré, Ferran Marsà, Mario Montes-Usategui
The ability to measure forces in the range of 0.1-100 pN is a key feature of optical tweezers used for biophysical and cell biological studies. Analysis of the interactions between biomolecules and the forces that biomolecular motors generate at the single-molecule level has provided valuable insights in the molecular mechanisms that govern key cellular functions such as gene expression and the long-distance transport of organelles. Methods for determining the minute forces that biomolecular motors generate exhibit notable constraints that limit their application for studies other than the well-controlled in vitro experiments (although recent advances have been made that permit more quantitative optical tweezers studies insight living cells)...
2017: Methods in Molecular Biology
M Pividori, C Dri, M E Orselli, F Berti, M Peressi, G Comelli
We report the observation of spontaneous chiral symmetry breaking within ordered, racemic monolayers of theophylline, manifesting itself as extended, nanoscale unichiral stripes at the interface between molecular domains. Theophylline is a xanthine derivative playing an important role in several biochemical processes. Molecular chirality is induced by adsorption on the Au(111) surface, resulting in extended domains with two different racemic, ordered structures, coexisting with a disordered phase. By combining low-temperature scanning tunneling microscopy (LT-STM) and ab initio density functional theory calculations, we first provide a detailed picture of the interactions within the ordered assemblies, and we uncover the origin of the distinct contrast features in STM images...
November 11, 2016: Nanoscale
Daniele Varsano, Stefano Caprasecca, Emanuele Coccia
Photoinitiated phenomena play a crucial role in many living organisms. Plants, algae, and bacteria absorb sunlight to perform photosynthesis, and convert water and carbon dioxide into molecular oxygen and carbohydrates, thus forming the basis for life on Earth. The vision of vertebrates is accomplished in the eye by a protein called rhodopsin, which upon photon absorption performs an ultrafast isomerisation of the retinal chromophore, triggering the signal cascade. Many other biological functions start with the photoexcitation of a protein-embedded pigment, followed by complex processes comprising, for example, electron or excitation energy transfer in photosynthetic complexes...
November 10, 2016: Journal of Physics. Condensed Matter: An Institute of Physics Journal
Christian Cuba Samaniego, Giulia Giordano, Franco Blanchini, Elisa Franco
Oscillators are essential to fuel autonomous behaviours in molecular systems. Artificial oscillators built with programmable biological molecules such as DNA and RNA are generally easy to build and tune, and can serve as timers for biological computation and regulation. We describe a new artificial nucleic acid biochemical reaction network, and we demonstrate its capacity to exhibit oscillatory solutions. This network can be built in vitro using nucleic acids and three bacteriophage enzymes, and has the potential to be implemented in cells...
December 2017: Journal of Biological Dynamics
Myung-Sic Chae, Jinsik Kim, Dahye Jeong, YoungSoo Kim, Jee Hoon Roh, Sung Min Lee, Youhee Heo, Ji Yoon Kang, Jeong Hoon Lee, Dae Sung Yoon, Tae Geun Kim, Suk Tai Chang, Kyo Seon Hwang
We performed oxygen plasma treatment on reduced graphene oxide (rGO) to improve its surface reactivity with respect to biomolecular interactions. Oxygen-plasma-treated rGO surfaces were employed as reactive interfaces for the detection of amyloid-beta (Aβ) peptides, the pathological hallmarks of Alzheimer's disease (AD), as the target analytes. By measuring the changes in electrical characteristics and confirmation through topographic analysis, the oxygen-plasma-treated rGO sensors had enhanced surface functionality for better antibody immobilization and sensing performance, with a 3...
October 21, 2016: Biosensors & Bioelectronics
Takuya Koriyama, Yosuke Takayama, Chiho Hisatsune, Taka-Aki Asoh, Akihiko Kikuchi
To confirm the modification of a dense thermoresponsive polymer brush on a silica surface by surface-initiated (SI) atom transfer radical polymerization (ATRP), poly(N-isopropylacrylamide) (PNIPAAm) was polymerized from a free ATRP initiator and an ATRP initiator immobilized silica particle (SiP) via ATRP under various initiator concentrations. The obtained PNIPAAm exhibited a well-controlled molecular weight and modification of the concentrated PNIPAAm brush on the SiP surface was confirmed. Based on the optimal ATRP conditions, the PNIPAAm- and poly(NIPAAm-co-butyl methacrylate [BMA]) (PIB)-grafted capillary lumen were prepared by SI-ATRP and used as capillary columns for micro high-performance liquid chromatography for the modulation of biomolecular interactions...
November 21, 2016: Journal of Biomaterials Science. Polymer Edition
Yijun Li, Cheng Wang, Yibo Zhu, Xiaohong Zhou, Yu Xiang, Miao He, Siyu Zeng
This work presents a fully integrated graphene field-effect transistor (GFET) biosensor for the label-free detection of lead ions (Pb(2+)) in aqueous-media, which first implements the G-quadruplex structure-switching biosensing principle in graphene nanoelectronics. We experimentally illustrate the biomolecular interplay that G-rich DNA single-strands with one-end confined on graphene surface can specifically interact with Pb(2+) ions and switch into G-quadruplex structures. Since the structure-switching of electrically charged DNA strands can disrupt the charge distribution in the vicinity of graphene surface, the carrier equilibrium in graphene sheet might be altered, and manifested by the conductivity variation of GFET...
October 25, 2016: Biosensors & Bioelectronics
Yuxin Lin, Xuye Yuan, Bairong Shen
Complex diseases are caused by disorders of both internal and external factors, and they account for a large proportion of human diseases. They are multigenetic and rarely a consequence of the dysfunction of single molecules. Systems biology views the living organism as an organic network. Compared with reductionism-based viewpoints, systems biology pays more attention to the interactions among molecules located at different omics levels. Based on this theory, the concepts of network biomarkers and network medicine have been proposed sequentially, which integrate clinical data with knowledge of network sciences, thereby promoting the investigation of disease pathogenesis in the era of biomedical informatics...
2016: Advances in Experimental Medicine and Biology
Michael Senske, Diana Constantinescu-Aruxandei, Martina Havenith, Christian Herrmann, Hermann Weingärtner, Simon Ebbinghaus
The Hofmeister series is a universal homologous series to rank ion-specific effects on biomolecular properties such as protein stability or aggregation propensity. Although this ranking is widely used, outliers and exceptions are discussed controversially and a molecular level understanding is still lacking. Studying the thermal unfolding equilibrium of RNase A, we here show that this ambiguity arises from the oversimplified approach to determine the ion rankings. Instead of measuring salt effects on a single point of the protein folding stability curve (e...
November 2, 2016: Physical Chemistry Chemical Physics: PCCP
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