Interactions Of Biomolecules Research Articles

Conformational detection of heat shock protein through bio-interactions with microstructures

The molecular mechanical interaction between the heat shock protein 90 (HSP90) and the adenosine triphosphate (ATP) molecules is detected by employing a polyvinyl-di-chlorofluoride (PVDF) aluminum-coated microcantilever beams, considered as a mechanical transducer. Here the chaperone protein called HSP90 performs the interaction. The microcantilever beam will sense the molecular mechanical interaction between the HSP90 and ATP molecules. This protein forms a complex molecule with ATP, and because of this molecular interaction, the beam will deflect which is measured using the optical lever method. This optical technique is able to detect the biomechanical interaction of ATP and HSP90 at various concentrations. The response time and sensitivity of this technique are found to be superior to similar methods such as piezoresistive technology known to be used for studying biomolecules interaction. This work will enable the reader to understand the behavior of micro-electro-mechanical systems (MEMS) based microcantilever structure under the influence of different concentrations of HSP90. The work provides a methodological approach to develop point-of-care devices for the detection of biomolecules.

Interactions of nitrogen-donor biomolecules with copper(II) complexes in Tris buffer

Comprehensive mole-ratio, kinetic, EPR and X-ray studies were performed to investigate substitution reactions between square-planar [CuCl2(en)] (en = ethylenediamine) and square-pyramidal [CuCl2(terpy)] (terpy = 2,2’:6’,2”-terpyridine) complexes with bio-relevant nucleophiles at 295 K in 0.010 M Tris-HCl buffer (pH = 7.4) in the presence of 0.010 M NaCl. According to mole-ratio and EPR studies, Tris buffer reacts with [CuCl2(en)], and likely the complex geometry remains square-planar. Kinetic results have shown that the order of reactivity of nucleophiles towards [CuCl2(en)] in solution for both reaction steps is 1,2,4-triazole > imidazole > pyrazine. The order of reactivity of the azole and diazine ligands toward [CuCl2(terpy)] for the first reaction step is imidazole > 1,2,4-triazole > pyrazine, while for the second one is pyrazine > 1,2,4-triazole > imidazole. X-ray studies indicate great affinity of ethylenediamine toward Cu(II), which results in crystal structures of [Cu(en)2]Cl2·H2O and [Cu(en)2][ZnCl4], instead of dinuclear or heteronuclear complexes with a bridging pyrazine ligand. The recorded EPR spectra demonstrate that all ligands interact with Cu(II) complexes, except in the case of the [CuCl2(en)] complex, where the competition between ligand and Tris molecules might be observed.

Electron and positron scattering from pyridine

SynopsisAdvancement in medical technology is a much needed demand in the present scenario. To stem a robust technology, one should be aware of the knowledge behind such sciences. In view of this, we investigate here the interaction of biomolecules with the most elementary particle, electron along with its anti-particle positron. The cross sections computed here using SCOP formalism for pyridine molecule will be useful for simulations of bio molecular systems. We further compare the cross sections for e− and e+ scattering extracting some rudimentary information about these basic interactions.

Establishing the accuracy of density functional approaches for the description of noncovalent interactions in biomolecules.

Biomolecules have complex structures, and noncovalent interactions are crucial to determine their conformations and functionalities. It is therefore critical to be able to describe them in an accurate but efficient manner in these systems. In this context density functional theory (DFT) could provide a powerful tool to simulate biological matter either directly for relatively simple systems or coupled with classical simulations like the QM/MM (quantum mechanics/molecular mechanics) approach. Additionally, DFT could play a fundamental role to fit the parameters of classical force fields or to train machine learning potentials to perform large scale molecular dynamics simulations of biological systems. Yet, local or semi-local approximations used in DFT cannot describe van der Waals (vdW) interactions, one of the essential noncovalent interactions in biomolecules, since they lack a proper description of long range correlation effects. However, many efficient and reasonably accurate methods are now available for the description of van der Waals interactions within DFT. In this work, we establish the accuracy of several state-of-the-art vdW-aware functionals by considering 275 biomolecules including interacting DNA and RNA bases, peptides and biological inhibitors and compare our results for the energy with highly accurate wavefunction based calculations. Most methods considered here can achieve close to predictive accuracy. In particular, the non-local vdW-DF2 functional is revealed to be the best performer for biomolecules, while among the vdW-corrected DFT methods, uMBD is also recommended as a less accurate but faster alternative.

6th International conference “Nanobiophysics: fundamental and applied aspects”

6th International conference “NANOBIOPHYSICS: Fundamental and Applied Aspects” (NBP-2019) took place on October 1-4, 2019 at the Institute of Physics of the National Academy of Sciences of Ukraine (Kyiv, Ukraine). Previous five conferences, starting from 2009, were organized due to joint efforts of B. Verkin Institute for Low Temperature Physics and Engineering of the NAS of Ukraine and Institute of Physics of the NAS of Ukraine on biennial basis in Kyiv and Kharkiv alternatively.63 leading scientists from 14 countries took part in the conference, Ukraine, Belarus, Italy, France, Latvia, Lithuania, Estonia, Germany, Poland, Check Republics, Canada, Denmark, USA and ARE were represented. 36 scientific lectures, including 17 invited, and 27 poster presentations were made. The goal of the conference was in exchange of information concerning recent achievements in the field of nanobiophysics, aimed at the inspiration of further advancement of basic investigations as well as innovations in the related areas of nanotechnology. Friendly format of the scientific meeting provided the exchange of ideas in such urgent topics as physical properties of biomolecular nanosystems, interactions of biomolecules with nanoparticles and nanostructured surfaces, enhancement of optical processes in biomolecules by nanostructured metal surfaces, formation of nanohybrids of biomolecules with carbon nanostructures, theory and computer modeling of nanoscopic biological systems, applications of bionanomaterials and bionanocomposites. In the framework of the conference special sessions for communications between the participants of the current international projects HORIZON 2020 and NATO Workshop were organized. Book of abstract based on NBP-2019 materials was published.

Chemically triggered crosslinking with bioorthogonal cyclopropenones.

We report a proximity-driven crosslinking strategy featuring bioorthogonal cyclopropenones. These motifs react with phosphines to form electrophilic ketene-ylides. Such intermediates can be trapped by neighboring proteins to form covalent adducts. Successful crosslinking was achieved using a model split reporter, and the rate of crosslinking could be tuned using different phosphine triggers. We further demonstrated that the reaction can be performed in cell lysate. Based on these features, we anticipate that cyclopropenones will enable unique studies of protein-protein and other biomolecule interactions.

Nanocalorimeters for biomolecular analysis and cell metabolism monitoring.

Nanocalorimeters, or microfabricated calorimeters, provide a promising way to characterize the thermal process of biological processes, such as biomolecule interactions and cellular metabolic activities. They enabled miniaturized heat measurement onto a chip device with potential benefits including low sample consumption, low cost, portability, and high throughput. Over the past few decades, researchers have tried to improve nanocalorimeters' performance, in terms of sensitivity, accuracy, and detection resolution, by exploring different sensing methods, thermal insulation techniques, and liquid handling methods. The enhanced devices resulted in new applications in recent years, and here we have summarized the performance parameters and applications based on categories. Finally, we have listed the current technical difficulties in nanocalorimeter research and hope for future solutions to overcome them.

Application of Quantitative Cell Imaging Using Label-free Optical Diffraction Tomography

The cell is three-dimensionally and dynamically organized into cellular compartments, including the endoplasmic reticulum, mitochondria, vesicles, and nucleus, which have high relative molecular density. The structure and functions of these compartments and organelles may be deduced from the diffusion and interaction of related biomolecules. Among these cellular components, various protein molecules can freely access the nucleolus or mitotic chromosome through Brownian diffusion, even though they have a densely packed structure. However, physicochemical properties of the nucleolus and chromosomes, such as molecular density and volume, are not yet fully understood under changing cellular conditions. Many studies have been conducted based on high-resolution imaging and analysis techniques using fluorescence. However, there are limitations in imaging only fluorescently labeled molecules, and cytotoxicity occurs during three-dimensional imaging. Alternatively, the recently developed label-free three-dimensional optical diffraction tomography (ODT) imaging technique can divide various organelles in cells into volumes and analyze them by refractive index, although specific molecules cannot be observed. A previous study established an analytical method that provides comprehensive insights into the physical properties of the nucleolus and mitotic chromosome by utilizing the advantages of ODT and fluorescence techniques, such as fluorescence correlation spectroscopy and confocal laser scanning microscopy. This review article summarizes a recent study and discusses the future aspects of the ODT for cellular compartments.

Analysis of specific interactions of biomolecules by atomic force microscopy

Analysis of specific interactions of biomolecules by atomic force microscopy

Quantitative determination of H2O2 for detection of alanine aminotransferase using thin film electrodes

The abnormal concentrations or absence of biomolecules (e.g., proteins) in blood can further be used in diagnosis of a particular pathology at an early stage. Current studies are intensely focusing on the analysis of interaction and detection of biomolecules via point-of-care systems (POCs), allowing miniaturized and parallelized reactions, simultaneously. Recent developments have shown that the collaboration of electrochemical sensing techniques and POCs to overcome challenging problems in health-care settings provides new approaches in diagnosis and treatment of diseases. The aim of this study was to adapt the alanine aminotransferase (ALT) enzyme to the platinum (Pt) thin film electrode system and quantitatively determine the enzyme levels via enzymatically generated H2O2 with differential pulse voltammetry (DPV). A simple potentiostat architecture with expanded sweep range utilizing dual LMP91000 devices was developed and adapted to the needs of the biosensor. In order to calibrate the system, known concentrations of H2O2 were also tested. Moreover, signals associated with the other electroactive species coming from the ALT reaction were eliminated. Resulted potential range has been achieved between +500 mV and +900 mV and the linear range was found to be 0.05 M–0.5 M for H2O2, whereas 5 UL−1 to 120 UL−1 for ALT enzyme.

Nanomaterials in the Environment Acquire an "Eco-Corona" Impacting their Toxicity to Daphnia Magna-a Call for Updating Toxicity Testing Policies.

Nanomaterials (NMs) are particles with at least one dimension between 1 and 100nm and a large surface area to volume ratio, providing them with exceptional qualities that are exploited in a variety of industrial fields. Deposition of NMs into environmental waters during or after use leads to the adsorption of an ecological (eco-) corona, whereby a layer of natural biomolecules coats the NM changing its stability, identity and ultimately toxicity. The eco-corona is not currently incorporated into ecotoxicity tests, although it has been shown to alter the interactions of NMs with organisms such as Daphnia magna (D. magna). Here, the literature on environmental biomolecule interactions with NMs is synthesized and a framework for understanding the eco-corona composition and its role in modulating NMs ecotoxicity is presented, utilizing D. magna as a model. The importance of including biomolecules as part of the current international efforts to update the standard testing protocols for NMs, is highlighted. Facilitating the formation of an eco-corona prior to NMs ecotoxicity testing will ensure that signaling pathways perturbed by the NMs are real rather than being associated with the damage arising from reactive NM surfaces "acquiring" a corona by pulling biomolecules from the organism's surface.

Inverted Hydration Layers on Bio-Magnesium Surfaces in the Initial Degradation Stage and their Influence on Adsorption of Amino Acid Analogues: The Metadynamics Simulations.

Deeply exploring the interaction of biomolecules with magnesium in solution is essential to understand the formation of complex bio-magnesium interfaces accompanied with corrosion products. Using the accelerated metadynamics simulations, we have investigated the interactions of amino acid analogues on clean and hydroxylated Mg(0001) surfaces by identifying their free energy barriers and adsorption sites. We find that there are two hydration layers stacked on the clean Mg(0001) surfaces and the hydroxylated Mg(0001) surfaces, which mainly determine the free energy barriers and adsorbed configurations. Further studies reveal that the water molecules in double hydration layers present two opposite orientations, depending on the charge distribution of the substrate. Specifically, oxygen atoms of water concentrate in the center of double hydration layers for a clean Mg surface but transfer to the outside surface once the Mg substrate is degraded. The reversed hydration layers greatly reduce the binding affinities of positively charged and electroneutral analogues. Overall, our simulation findings provide new insights into the interaction mechanism of biomolecules on a bio-magnesium device in the implantation initial stage, which is noteworthy for revealing the magnesium degradation mechanism in vivo.

Valine adsorption on pristine and N-doped graphenes: DFT, AIM, and IGM study

Deep insight into interactions of various biomolecules with nanomaterials is very important to design novel materials for different applications. The present work studies physical adsorption of valine, an amino acid, on the surfaces of graphene and N-doped graphenes using density functional theory (DFT). Atoms-in-molecules (AIM) and independent gradient model (IGM) analyses have been implemented to reveal the features of interactions in studied complexes. The SAPT0 method has been used to decompose total interaction energy into constituents, which allows one to carry out the complete analysis of the valine/adsorbent interactions. Dispersion forces have been found to play major roles in attractive interactions for the considered complexes. They are followed by electrostatic components. Studies of N-doping effects reveal that valine binds more strongly to the N-doped graphene surfaces in comparison with pristine graphene. The total interaction energy reaches—0.82 eV, which is ∼65% larger than that for pristine graphene. Our results demonstrate that N-doped graphenes with the large interaction energy would be of importance for technical realization of the targeted delivery of valine.

Supported Solid Lipid Bilayers as a Platform for Single-Molecule Force Measurements.

Biocompatible surfaces are important for basic and applied research in life science with experiments ranging from the organismal to the single-molecule level. For the latter, examples include the translocation of kinesin motor proteins along microtubule cytoskeletal filaments or the study of DNA-protein interactions. Such experiments often employ single-molecule fluorescence or force microscopy. In particular for force measurements, a key requirement is to prevent nonspecific interactions of biomolecules and force probes with the surface, while providing specific attachments that can sustain loads. Common approaches to reduce nonspecific interactions include supported lipid bilayers or PEGylated surfaces. However, fluid lipid bilayers do not support loads and PEGylation may require harsh chemical surface treatments and have limited reproducibility. Here, we developed and applied a supported solid lipid bilayer (SSLB) as a platform for specific, load bearing attachments with minimal nonspecific interactions. Apart from single-molecule fluorescence measurements, anchoring molecules to lipids in the solid phase enabled us to perform force measurements of molecular motors and overstretch DNA. Furthermore, using a heating laser, we could switch the SSLB to its fluid state allowing for manipulation of anchoring points. The assay had little nonspecific interactions, was robust, reproducible, and time-efficient, and required less hazardous and toxic chemicals for preparation. In the long term, we expect that SSLBs can be widely employed for single-molecule fluorescence microscopy, force spectroscopy, and cellular assays in mechanobiology.

Fluorescent Protein-Based Indicators for Functional Super-Resolution Imaging of Biomolecular Activities in Living Cells.

Super-resolution light microscopy (SRM) offers a unique opportunity for diffraction-unlimited imaging of biomolecular activities in living cells. To realize such potential, genetically encoded indicators were developed recently from fluorescent proteins (FPs) that exhibit phototransformation behaviors including photoactivation, photoconversion, and photoswitching, etc. Super-resolution observations of biomolecule interactions and biochemical activities have been demonstrated by exploiting the principles of bimolecular fluorescence complementation (BiFC), points accumulation for imaging nanoscale topography (PAINT), and fluorescence fluctuation increase by contact (FLINC), etc. To improve functional nanoscopy with the technology of genetically encoded indicators, it is essential to fully decipher the photo-induced chemistry of FPs and opt for innovative indicator designs that utilize not only fluorescence intensity but also multi-parametric readouts such as phototransformation kinetics. In parallel, technical improvements to both the microscopy optics and image analysis pipeline are promising avenues to increase the sensitivity and versatility of functional SRM.

Computed terahertz near-field mapping of molecular resonances of lactose stereo-isomer impurities with sub-attomole sensitivity

Terahertz near-field microscopy (THz-NFM) could locally probe low-energy molecular vibration dynamics below diffraction limits, showing promise to decipher intermolecular interactions of biomolecules and quantum matters with unique THz vibrational fingerprints. However, its realization has been impeded by low spatial and spectral resolutions and lack of theoretical models to quantitatively analyze near-field imaging. Here, we show that THz scattering-type scanning near-field optical microscopy (THz s-SNOM) with a theoretical model can quantitatively measure and image such low-energy molecular interactions, permitting computed spectroscopic near-field mapping of THz molecular resonance spectra. Using crystalline-lactose stereo-isomer (anomer) mixtures (i.e., α-lactose (≥95%, w/w) and β-lactose (≤4%, w/w)), THz s-SNOM resolved local intermolecular vibrations of both anomers with enhanced spatial and spectral resolutions, yielding strong resonances to decipher conformational fingerprint of the trace β-anomer impurity. Its estimated sensitivity was ~0.147 attomoles in ~8 × 10−4 μm3 interaction volume. Our THz s-SNOM platform offers a new path for ultrasensitive molecular fingerprinting of complex mixtures of biomolecules or organic crystals with markedly enhanced spatio-spectral resolutions. This could open up significant possibilities of THz technology in many fields, including biology, chemistry and condensed matter physics as well as semiconductor industries where accurate quantitative mappings of trace isomer impurities are critical but still challenging.

Supramolecular interaction of modificated nanodiamonds, biomolecules and drugs: molecular modeling

Using molecular modeling by the density functional theory B3LYP method with 6-31 G(d) basic set, we analyse the hydrogen bonds formation and their influence on IR-spectra and structure of molecular complexes which is formed due to interaction between nanodiamonds with COOH- surface functionalization and highly toxic drugs on example of doxorubicin and mitoxantrone. Molecular modeling of modificated nanodiamonds and drugs interaction is based on nanodiamond representation by a diamond-like nanoparticle with simpler structure. As a result of calculations the combined IR spectrum is obtained as imposing of IR spectra for molecular complexes of drugs and nanodiamonds in various interaction positions. Combined IR spectra demonstrate a good agreement with experimental data. Received results demonstrate that there can be strong supramolecular interaction between drugs and modificated detonation nanodiamonds. Formed hydrogen bonds can be considered as one of the main mechanisms for targeted drug delivery and for drug retention in cells and, thus, for enhancement of anti-cancer therapeutic efficacy.

Nucleic acid detection strategy using gold nanoprobe of two diverse origin.

In recent years, nanoparticles especially with gold and silver nanoparticles based point of care diagnostic methods is being developed for the lethal diseases like dengue. This study focused to work on the dengue virus detection in a simplest method using gold nanoparticles probe (AuNPs) with thiol tagged single strand DNA (ss-DNA). A sensitive, fluorescence-based detection strategy was designed to examine and quantified the hybridisation process and also elucidated the behaviour of AuNPs before and after interaction of biomolecule. The detection process was focused on aggregation of gold nanoprobe in the presence of complementary strand (target region). Hence the percentage of aggregation was measured and as a result, the limit of detection was found to be 10-6 dilutions. Current detection method was highly sensitive, easy to perform and the reaction timing is rapid between 5 and 10 min, and it can be observed through naked eye.

The Biomolecular Corona in 2D and Reverse: Patterning Metal–Phenolic Networks on Proteins, Lipids, Nucleic Acids, Polysaccharides, and Fingerprints

AbstractThe adsorption of biomolecules onto nanomaterials can alter the performance of the nanomaterials in vitro and in vivo. Recent studies have primarily focused on the protein “corona”, formed upon adsorption of proteins onto nanoparticles in biological fluids, which can change the biological fate of the nanoparticles. Conversely, interactions between nanomaterials and other classes of biomolecules namely, lipids, nucleic acids, and polysaccharides have received less attention despite their important roles in biology. A possible reason is the challenge associated with investigating biomolecule interactions with nanomaterials using current technologies. Herein, a protocol is developed for studying bio–nano interactions by depositing four classes of biomolecules (proteins, lipids, nucleic acids, and polysaccharides) and complex biological media (blood) onto planar substrates, followed by exposure to metal–phenolic network (MPN) complexes. The MPNs preferentially interact with the biomolecule over the inorganic substrate (glass), highlighting that patterned biomolecules can be used to engineer patterned MPNs. Subsequent formation of silver nanoparticles on the MPN films maintains the patterns and endows the films with unique reflectance and fluorescence properties, enabling visualization of latent fingerprints (i.e., invisible residual biomolecule patterns). This study demonstrates the potential complexity of the biomolecule corona as all classes of biomolecules can adsorb onto MPN‐based nanomaterials.

Modeling Crowded Environment in Molecular Simulations.

Biomolecules perform their various functions in living cells, namely in an environment that is crowded by many macromolecules. Thus, simulating the dynamics and interactions of biomolecules should take into account not only water and ions but also other binding partners, metabolites, lipids and macromolecules found in cells. In the last decade, research on how to model macromolecular crowders around proteins in order to simulate their dynamics in models of cellular environments has gained a lot of attention. In this mini-review we focus on the models of crowding agents that have been used in computer modeling studies of proteins and peptides, especially via molecular dynamics simulations.