Biomolecules Research Articles

The Transcriptomic Response of Cells of the Thermophilic Bacterium Geobacillus icigianus to Terahertz Irradiation

As areas of application of terahertz (THz) radiation expand in science and practice, evidence is accumulating that this type of radiation can affect not only biological molecules directly, but also cellular processes as a whole. In this study, the transcriptome in cells of the thermophilic bacterium Geobacillus icigianus was analyzed immediately after THz irradiation (0.23 W/cm2, 130 μm, 15 min) and at 10 min after its completion. THz irradiation does not affect the activity of heat shock protein genes and diminishes the activity of genes whose products are involved in peptidoglycan recycling, participate in redox reactions, and protect DNA and proteins from damage, including genes of chaperone protein ClpB and of DNA repair protein RadA, as well as genes of catalase and kinase McsB. Gene systems responsible for the homeostasis of transition metals (copper, iron, and zinc) proved to be the most sensitive to THz irradiation; downregulation of these systems increased significantly 10 min after the end of the irradiation. It was also hypothesized that some negative effects of THz radiation on metabolism in G. icigianus cells are related to disturbances in activities of gene systems controlled by metal-sensitive transcription factors.

Ultrafast Excitonic Transitions in Enantiopure and Racemic Squaraine Thin Films

ABSTRACTWhile chirality is a prevalent character of numerous biological and synthetic organic molecules, its selective absorption of circularly polarized light, known as circular dichroism (CD), is typically small due to intrinsically weak coupling between magnetic and electric dipoles. However, thin films of aggregated, enantiopure prolinol‐derived squaraine molecules (ProSQ‐C16) exhibit an unusually large excitonic CD signal, although the underlying mechanism is not yet known. In this study, we employ steady‐state and ultrafast transient absorption spectroscopy to investigate the nature and dynamics of excitons in aggregates of enantiopure and racemic ProSQ‐C16 thin films. Highly resembling transient responses of enantiopure thin films under excitations at different photon energies strongly indicate that a single type of aggregate dominates the linear optical response, that is, a strong red‐shifted (J‐like) and weak blue‐shifted (H‐like) absorption band. On the other hand, the transient properties of the racemic thin film deviate from this pattern and remain largely ambiguous. The short lifetime of excited states and coherent oscillations present in the dynamics of the transient absorption signal indicate that the early time dynamics are governed by a transition towards a dark intermediate state, which might arise from intermolecular charge transfer with potential contributions from the coupling of excitons to the vibrations. This non‐radiative relaxation pathway explains the unusually weak fluorescence of the predominately J‐like behaving aggregate. Our findings conclusively show that the chiral aggregate structure has a strong impact on the optical and dynamic response of the excitons and underline the significance of non‐Frenkel exciton states for the optical properties of anilino squaraine dyes.

Experimental Insights into the Formation, Reactivity, and Crosstalk of Thionitrite (SNO−) and Perthionitrite (SSNO−)

AbstractHydrogen sulfide (H2S) and nitric oxide (NO) are important gaseous biological signaling molecules that are involved in complex cellular pathways. A number of physiological processes require both H2S and NO, which has led to the proposal that different H2S/NO⋅ crosstalk species, including thionitrite (SNO−) and perthionitrite (SSNO−), are responsible for this observed codependence. Despite the importance of these S/N hybrid species, the reported properties and characterization, as well as the fundamental pathways of formation and subsequent reactivity, remain poorly understood. Herein we report new experimental insights into the fundamental reaction chemistry of pathways to form SNO− and SSNO−, including mechanisms for proton‐mediated interconversion. In addition, we demonstrate new modes of reactivity with other sulfur‐containing potential crosstalk species, including carbonyl sulfide (COS).

BioRxToolbox: A computational framework to streamline genetic circuit design in molecular data communications

ABSTRACT Developments in bioengineering and nanotechnology have ignited the research on biological and molecular communication systems. Despite potential benefits, engineering communication systems to carry data signals using biological messenger molecules and engineered cells is challenging. Diffusing molecules may fall behind their schedule to arrive at the receiver, interfering with symbols of subsequent time slots and distorting the signal. Existing theoretical molecular communication models often focus solely on the characteristics of a communication channel and fail to provide an end-to-end system response since they assume a simple thresholding process for a receiver cell and overlook how the receiver can detect the incoming distorted molecular signal. In this paper, we present a model-based and computational framework called BioRxToolbox for designing diffusion-based and end-to-end molecular communication systems coupled with synthetic genetic circuits. We describe a novel framework to encode information as a sequence of bits, each transmitted from the sender as a burst of molecules, control cellular behavior at the receiver, and minimize cellular signal interference by employing equalization techniques from communication theory. This approach allows the encoding and decoding of data bits efficiently using two different types of molecules that act as the data carrier and the antagonist to cancel out the heavy tail of the former. Here, BioRxToolbox is demonstrated using a biological design and computational simulations for various communication scenarios. This toolbox facilitates automating the choice of communication parameters and identifying the best communication scenarios that can produce efficient cellular signals.

Diatoms: harnessing nature’s microscopic marvels for biosensing and multifaceted applications

AbstractThis article discusses the use of diatom in biosensing and various applications. A thorough understanding of the biosensing properties of diatoms is essential for the advancement of life sciences technologies. This review elucidates the emerging significance of diatoms in biosensing applications by highlighting the high surface area-to-volume ratio, biocompatibility, and facile functionalization of them. We examined the possible application of diatoms as flexible biosensing systems for the detection of various analytes, such as biological molecules, heavy metals, and poisons, by considering the findings of earlier research. Additionally, to show how diatoms can be used to create precise and sensitive biosensors, by integrating with several transduction modalities, including optical, electrochemical, and piezoelectric methods. We also delve into the potential applications of diatom-based biosensing in the future as well as pertinent topics such as repeatability, stability, and scalability. This provides an in-depth analysis of the quickly evolving field of diatom-based biosensing, which could affect several industries, such as environmental monitoring, food security and medical diagnostics.

Rapid-response RNA-fluorescence in situ hybridization (FISH) assay platform for coronavirus antiviral high-throughput screening

Over the past 25 years, the global community has faced challenges posed by three distinct outbreaks of coronaviruses including severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The identification of a novel alphacoronavirus canine CoV (CCoV-HuPn2018) in human patients in Malaysia underscores the potential for crossover infections to humans. The threat of the ever-evolving nature of viral infections as well as the lingering health and socioeconomic effects of the recent SARS-CoV-2 pandemic emphasize the urgent need for advanced antiviral drug screening tools that can be quickly implemented to strengthen preparedness and preventive measures against future outbreaks. Here, we present the development and validation of a novel RNA-fluorescence in situ hybridization (FISH) imaging assay as a 384-well, high-throughput rapid response platform for antiviral drug discovery. RNA-FISH is a powerful tool to visualize specific mRNA in cultured cells using a high-content imaging platform. The flexibility of RNA-FISH probe sets allows for the rapid design of viral genome-specific probes, enabling in vitro assay development to test for inhibition of viral replication by either biologic or small molecule inhibitors. Screening of 170 antiviral compounds in concentration-response demonstrates a strong correlation between the RNA-FISH assay and an immunofluorescence assay (IFA) for both human coronaviruses HCoV-OC43 and HCoV-229E. Additionally, we successfully applied this methodology in the context of CCoV strain 1–71, proving rapid development and deployment, opening new avenues for the evaluation of antiviral drugs to potential future emerging threats.

Insight into the Natural Biomolecules (BMs): Promising Candidates as Zika Virus Inhibitors.

Zika virus (ZIKV) is among the relatively new infectious disease threats that include SARS-CoV-2, coronavirus, monkeypox (Mpox) virus, etc. ZIKV has been reported to cause severe health risks to the fetus. To date, satisfactory treatment is still not available for the treatment of ZIKV infection. This review examines the last five years of work using natural biomolecules (BMs) to counteract the ZIKV through virtual screening and in vitro investigations. Virtual screening has identified doramectin, pinocembrin, hesperidins, epigallocatechin gallate, pedalitin, and quercetin as potentially active versus ZIKV infection. In vitro, testing has shown that nordihydroguaiaretic acid, mefloquine, isoquercitrin, glycyrrhetinic acid, patentiflorin-A, rottlerin, and harringtonine can reduce ZIKV infections in cell lines. However, in vivo, testing is limited, fortunately, emetine, rottlerin, patentiflorin-A, and lycorine have shown in vivo anti- ZIKV potential. This review focuses on natural biomolecules that show a particularly high selective index (>10). There is limited in vivo and clinical trial data for natural BMs, which needs to be an active area of investigation. This review aims to compile the known reference data and discuss the barriers associated with discovering and using natural BM agents to control ZIKV infection.

Limitations and Principles of Safety in the 3D Bioprinting Process

The importance of biological printing is in tissue structures that imitate the micro and real environment of human tissues and organs. This is very important in medicinal tests and clinical tests. In biological printing, cells or molecules are printed directly on a substrate in a particular pattern so that the cells can be kept together and formed the required 3D structure. This technology is widely used in medical science, including tissue regeneration, diagnosis of drugs, tissue transplantation, cosmetic surgery, and more. In this study, we have tried to point out existing damage and safety tips in this technology. Studies show the challenges facing this technology, such as high clarity in cell construction, lack of mechanical resistance and adequate integration of bio -printing structures made with soft hydrogel, material printing speed, recurreability and cell preservation. Also, work safety instructions with bio -printers including personal hygiene, printer cleaning, work room cleaning, ventilation system, periodic medical tests for operators are provided. Bioprinting technology is developing and requires further research to remove restrictions and reduce risk management

Tsa1 is the dominant peroxide scavenger and a source of H2O2-dependent GSSG production in yeast

Hydrogen peroxide (H2O2) is an important biological molecule, functioning both as a second messenger in cell signaling and, especially at higher concentrations, as a cause of cell damage. Cells harbor multiple enzymes that have peroxide reducing activity in vitro. However, the contribution of each of these enzymes towards peroxide scavenging in vivo is less clear. Therefore, to directly investigate in vivo peroxide scavenging, we used the genetically encoded peroxide sensors, roGFP2-Tsa2ΔCR and HyPer7, to systematically screen the peroxide scavenging capacity of baker’s yeast thiol and heme peroxidase mutants. We show that the 2-Cys peroxiredoxin Tsa1 alone is responsible for almost all exogenous H2O2 and tert-butyl hydroperoxide scavenging. Furthermore, Tsa1 can become an important source of H2O2-dependent cytosolic glutathione disulfide production. The two catalases and cytochrome c peroxidase only produce observable scavenging defects at higher H2O2 concentrations when these three heme peroxidases are deleted in combination. We also analyzed the reduction of Tsa1 in vitro, revealing that the enzyme is efficiently reduced by thioredoxin-1 with a rate constant of 2.8×106 M–1s–1 but not by glutaredoxin-2. Tsa1 reduction by reduced glutathione occurs nonenzymatically with a rate constant of 2.9 M–1s–1. Hence, the observed Tsa1-dependent glutathione disulfide production in yeast probably requires the oxidation of thioredoxins. Our findings clarify the importance of the various thiol and heme peroxidases for peroxide removal and suggest that most thiol peroxidases have alternative or specialized functions in specific subcellular compartments.

Early Days in the Hunt Laboratory at UVA, 1969-1980

Arriving at the University of Virginia in the autumn of 1969, Donald Hunt began his 50+ year career in academics with the study of organometallic chemistry, on which he had done his PhD thesis, and mass spectrometry, to which he was introduced while a postdoc in Klaus Biemann’s laboratory at the Massachusetts Institute of Technology. In the 1970s, Hunt’s lab pioneered the use of negative chemical ionization (CI) to enhance sensitivity for studying organic molecules, developed a system for simultaneously obtaining positive and negative CI spectra to augment structure elucidation, and built a prototype triple quadrupole instrument so effective at collisional dissociation that its commercial counterpart became the analytical instrument of choice for mixture analysis for the next decade and beyond. Foreseeing that the future lay in the analysis of biological molecules, by the end of the decade Hunt shifted his focus to peptides. The analysis of protein fragments had suddenly become more accessible thanks to the advent of the triple quadrupole and Barber’s invention of fast atom bombardment. As the ‘80s began and Hunt and his team sought to pursue larger and larger pieces of proteins, his attention turned to the development of mass spectrometers with greater mass range. While recounting their memories of these events, several of Hunt’s students and colleagues pay tribute to his support for them as individuals, as well as to his infectious enthusiasm for scientific endeavors that he so generously shared.

Protective Role of Sphingosine-1-Phosphate During Radiation-Induced Testicular Injury

The impact of ionizing radiation on the male reproductive system is gaining increasing attention, particularly when it comes to testicular damage, which may result in decreased sperm quality and hormonal imbalances. Finding effective protective measures to mitigate testicular damage caused by radiation has become a focal point in the biomedical field. S1P, an essential biological signaling molecule, has garnered significant interest due to its multiple roles in regulating cellular functions and its protective effects against radiation-induced testicular injury. S1P not only effectively reduces the generation of ROS induced by radiation but also alleviates oxidative stress by enhancing the activity of antioxidant enzymes. Furthermore, S1P inhibits radiation-induced cell apoptosis by regulating the expression of anti-apoptotic and pro-apoptotic proteins. Additionally, S1P alleviates radiation-induced inflammation by inhibiting the production of inflammatory factors, thereby further protecting testicular tissue. In summary, S1P effectively reduces radiation-induced testicular damage through multiple mechanisms, offering a promising therapeutic approach to safeguard male reproductive health. Future research should explore the specific mechanisms of action and clinical application potential of S1P, aiming to contribute significantly to the prevention and treatment of radiation damage.

Late-Stage Fluorination of Tyrosine Residues in Antiviral Protein Cyanovirin-N.

The applications of fluorinated molecules in chemical biology are rapidly expanding driven by the unique properties of C-F bonds, leading to increased interest in methodologies for controlled introduction of this atom. In this study, we present the first method for late-stage fluorination of tyrosine residues in proteins. Our results demonstrate that electrophilic fluorination using Selectfluor, a stable and non-toxic reagent, offers a straightforward and cost-effective method for labeling Cyanovirin-N (CVN), a 101-amino-acid lectin with effective antiviral activity. Uni- and bidimensional 1H, 13C and 19F NMR analyses, along with mass spectrometry, revealed chemoselective fluorination of the three tyrosine residues in CVN without affecting its overall structure or mannose-binding affinity. Additionally, we observed that other aromatic amino acids, such as tryptophan, phenylalanine, and histidine, are not fluorinated using this method. These findings advance our understanding of protein fluorination and its applications in studying structure, dynamics, and interactions, as well as other biological utilities.

3D Printed Metallic Pillar Nanomechanical Resonators Decorated with TiO2 Nanotubes for Highly Sensitive Environmental Applications

AbstractMicro and nanomechanical devices offer enhanced sensing capabilities for detecting biological and chemical small molecules. However, miniaturization necessitates advanced fabrication processes and complex measurement systems, hindering routine sensor analysis. While alternative methods like 3D printing show promise, challenges such as low device resolution persist due to intrinsic damping of polymer inks. In this study, an array of micrometric pillar resonators is fabricated in Ti6Al4 V alloy using additive manufacturing based on laser powder bed fusion technology. These metallic nanomechanical resonators exhibit a very high quality factor with minimal difference between air and vacuum measurements due to low intrinsic damping. Furthermore, titania nanotubes grown on the pillars via anodic oxidation heighten sensitivity for molecular dye degradation evaluation. Leveraging the weak coupling phenomenon among the pillars in the array, these devices facilitate large‐scale parallelized measurements, here demonstrated with real‐time analysis of dye degradation process. This approach to creating mass sensing devices via metallic additive manufacturing can usher in a new generation of highly performing resonating sensor arrays, offering a cost‐effective and efficient alternative to traditional silicon microfabrication methods.

Perspective: on the importance of extensive, high-quality and reliable deposition of biomolecular NMR data in the age of artificial intelligence.

Artificial intelligence (AI) models are revolutionising scientific data analysis but are reliant on large training data sets. While artificial training data can be used in the context of NMR processing and data analysis methods, relating NMR parameters back to protein sequence and structure requires experimental data. In this perspective we examine what the biological NMR community needs to do, in order to store and share its data better so that we can make effective use of AI methods to further our understanding of biological molecules. We argue, first, that the community should be depositing much more of its experimental data. In particular, we should be depositing more spectra and dynamics data. Second, the NMR data deposited needs to capture the full information content required to be able to use and validate it adequately. The NMR Exchange Format (NEF) was designed several years ago to do this. The widespread adoption of NEF combined with a new proposal for dynamics data specifications come at the right time for the community to expand its deposition of data. Third, we highlight the importance of expanding and safeguarding our experimental data repository, the Biological Magnetic Resonance Data Bank (BMRB), not only in the interests of NMR spectroscopists, but biological scientists more widely. With this article we invite others in the biological NMR community to champion increased (possibly mandatory) data deposition, to get involved in designing new NEF specifications, and to advocate on behalf of the BMRB within the wider scientific community.

The Influence of Cholesterol on Membrane Targeted Bioactive Peptides: Modulating Peptide Activity Through Changes in Bilayer Biophysical Properties.

Cholesterol is a biological molecule that is essential for cellular life. It has unique features in terms of molecular structure and function, and plays an important role in determining the structure and properties of cell membranes. One of the most recognized functions of cholesterol is its ability to increase the level of lipid packing and rigidity of biological membranes while maintaining high levels of lateral mobility of the bulk lipids, which is necessary to sustain biochemical signaling events. There is increased interest in designing bioactive peptides that can act as effective antimicrobial agents without causing harm to human cells. For this reason, it becomes relevant to understand how cholesterol can affect the interaction between bioactive peptides and lipid membranes, in particular by modulating the peptides' ability to penetrate and disrupt the membranes through these changes in membrane rigidity. Here we discuss cholesterol and its role in modulating lipid bilayer properties and discuss recent evidence showing how cholesterol modulates bioactive peptides to different degrees.

Corticosteroid Use in Randomized Clinical Trials of Biologics and Small Molecules in Inflammatory Bowel Disease: A Systematic Review.

This systematic review aims to elucidate the use of corticosteroids in randomized clinical trials (RCTs) evaluating biologics and small molecules for inflammatory bowel disease (IBD). We analyzed corticosteroid use during both the induction and maintenance phases, highlighting areas needing standardization and improvement in clinical research. We selected placebo-controlled phase 3 RCTs involving adults with moderate to severe IBD. These studies included detailed reports on corticosteroid use during induction and maintenance phases, with clinical remission and/or corticosteroid-free clinical remission (CSF-CR) as primary endpoints. Initially, 324 studies were identified and refined to 26 RCTs after screening. Analysis revealed variability in corticosteroid administration. Over time, corticosteroid use showed a decreasing trend (Spearman ρ = -0.42, P = .045). Studies allowing higher corticosteroid doses (up to 40mg/day of prednisone or equivalent) reported a higher proportion of corticosteroid users (51.8%, range: 42.9%-61%) compared to those excluding patients on doses >20mg/day (37.5%, range: 31.6%-51.8%; P = .007) or >30mg/day (41.1%, range: 29.6%-53.7%; P=.023). Trials with mandatory tapering protocols showed a narrower gap between overall clinical remission and CSF-CR rates, with an average difference of 6% in the group without mandatory tapering and 1.2% in the group with forced tapering (T-test P=.038; Cohen's d ≈ 1.1). This review highlights the variability in corticosteroid use across RCTs and its impact on evaluating new IBD therapies. Standardizing tapering protocols and defining CSF-CR are essential for accurate outcomes.

Conformational Characterization of Peptides and Proteins by 193 nm Ultraviolet Photodissociation in the Collision Cell of a Trapped Ion Mobility Spectrometry-Time-of-Flight Mass Spectrometer.

Ultraviolet photodissociation (UVPD) has been shown to be a versatile ion activation strategy for the characterization of peptides and intact proteins among other classes of biological molecules. Combining the high-performance mass spectrometry (MS/MS) capabilities of UVPD with the high-resolution separation of trapped ion mobility spectrometry (TIMS) presents an opportunity for enhanced structural elucidation of biological molecules. In the present work, we integrate a 193 nm excimer laser in a TIMS-time-of-flight (TIMS-TOF) mass spectrometer for UVPD in the collision cell and use it for the analysis of several mass-mobility-selected species of ubiquitin and myoglobin. The resultant data displayed differences in fragmentation that could be correlated with changes in protein conformation. Additionally, this mobility-resolved UVPD strategy was applied to collision-induced unfolded ions of ubiquitin to follow changes in fragmentation patterns relating to the extent of protein unfolding. This platform and methodology offer new opportunities for exploring how conformational variations are manifested in the fragmentation patterns of gas-phase ions.

Leveraging Transfer Learning for Predicting Protein-Small Molecule Interactions.

A complex web of intermolecular interactions defines and regulates biological processes. Understanding this web has been particularly challenging because of the sheer number of actors in biological systems: ∼10 4 proteins in a typical human cell offer a plausible 10 8 interactions. This number grows rapidly if we consider metabolites, drugs, nutrients, and other biological molecules. The relative strength of interactions also critically affects these biological processes. However, the small and often incomplete datasets (10 3 -10 4 protein-ligand interactions) traditionally used for binding affinity predictions limit the ability to capture the full complexity of these interactions. To overcome this challenge, we developed Yuel 2, a novel neural network-based approach that leverages transfer learning to address the limitations of small datasets. Yuel 2 is pre-trained on a large-scale dataset to learn intricate structural features and then fine-tuned on specialized datasets like PDBbind to enhance the predictive accuracy and robustness. We show that Yuel 2 predicts multiple binding affinity metrics - Kd, Ki, and IC50 - between proteins and small molecules, offering a comprehensive representation of molecular interactions crucial for drug design and development.

Photoredox Catalyzed Tandem Denitrogenative [4 + 2] Annulation of 1,2,3-Benzotriazin-4(3H)-ones with Terminal Olefins.

The dihydroisoquinolones skeleton is ubiquitous in natural products and biological molecules. Reported strategies for constructing dihydroisoquinolones usually require noble metal catalysts or stoichiometric oxidants, which limit their wide applications. Herein, we developed a photoredox catalyzed tandem denitrogenative [4 + 2] annulation reaction of 1,2,3-benzotriazin-4(3H)-ones with terminal olefins. A variety of dihydroisoquinolones can be accessed in moderate to excellent yield. This protocol features high atom-economy, mild reaction conditions, and is external oxidant-free, enabling the synthesis of various substituted dihydroisoquinolones.

Self‐Calibrating Copper‐Based Metal Organic Frameworks for Ratiometric Electrochemical Sensing of Creatinine

AbstractNanostructures that can undergo redox reactions have significant potential for electrochemical analysis. They can act as signal amplifiers to determine concentrations of targets in biological samples. In this work, a rational combination of electroactive copper‐based metal‐organic frameworks (Cu‐MOFs) and ferrocene carboxylic acid (Fc) was designed for ratiometric electrochemical detection of creatinine. The synthesized Fc@Cu‐MOFs exhibited two redox signals from the Cu2+/Cu+ and Fe3+/Fe2+ systems in the skeleton of Cu‐MOFs and Fc, respectively. In the presence of chloride (Cl−), the oxidation current of Cu+ increased due to formation of solid‐state cuprous chloride (CuCl). Adding strong Cu+ chelators, e. g. creatinine, coordinated with Cu+ and caused the current output of solid‐state CuCl to decrease significantly. The anodic current of Fc did not appreciably change, serving as an internal reference signal. The ratiometric responses (ICu(I)/IFc) changed with increasing concentrations of creatinine from 0.017–130 μM with a detection limit (S/N=3) of 0.005 μM. The main advantages of Fc@Cu‐MOFs are the low LOD, high selectivity, and reliability, making it a suitable platform for determining creatinine in human serum and urine samples. The as‐fabricated sensor is a reliable approach for determining (bio) molecules that can form stable complexes with Cu+ ions.