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Topic Review
Protein Ser/Thr Phosphatase Folding
Post-translational modification (PTM) is a key mechanism providing the functional diversity of proteins in cellular signaling and physiology and changing the functions or stability of proteins. 
  • 819
  • 25 Jul 2023
Topic Review
Tetraoctylammonium
Alkylammonium salts have been used extensively to study the structure and function of potassium channels. Here, we use the long-chain, hydrophobic tetraoctylammonium (TOA+) to shed light on the structure of the inactivated state of KcsA, a tetrameric prokaryotic potassium channel. By the combined use of a thermal denaturation assay and the analysis of homo-Förster resonance energy transfer in a mutant channel containing a single tryptophan (W67) per subunit, we found that TOA+ binds the channel cavity with high affinity, either with the inner gate open or closed. Moreover, bound TOA+ induces a decrease in the affinity for K+ in the two characteristic K+ binding events to the channel selectivity filter at pH 7.0, when the channel inner gate is in the closed conformation. This is similar to that observed in the absence of TOA+ upon acidic-pH-induced channel inactivation. Therefore, this suggests that TOA+ binding by itself causes inactivation at pH 7.0 when the inner gate is closed. Furthermore, in apparent agreement with such conclusion, the presence of bound TOA+ in the pH 4.0 samples has only modest effects on the affinity of the two binding events for K+, likely because the channel is already inactivated. Finally, we also observed that TOA+ bound at the cavity, allosterically modifies the conformation of the pore helices, leading to longer W67-W67 intersubunit distances at any K+ concentration and both at pH 7.0 and pH 4.0. The changes in the pore helix conformation, along with the decreased affinity for K+ at pH 7.0 caused by TOA+, seen in both homo-FRET and thermal denaturation experiments, are very similar to those effects caused by inactivation at pH 4.0.
  • 818
  • 30 Apr 2021
Topic Review
Pentameric Ligand-Gated Ion Channels
Pentameric ligand-gated ion channels (pLGICs) mediate or modulate fast synaptic communication in the central and peripheral nervous systems making them vital for neurological processes ranging from memory and learning to nicotine addiction. 
  • 811
  • 23 Jun 2022
Topic Review
Molecular Phase Separation in Chromosomes
Biomolecular phase separation denotes the demixing of a specific set of intracellular components without membrane encapsulation.
  • 798
  • 19 Oct 2021
Topic Review
Non-Targeted Effects of Australian and European Synchrotrons
The Australian Synchrotron (AS) and the European Synchrotron Radiation Facility (ESRF) are best configured for a wide range of biomedical research involving animals and future cancer patients. Due to ultra-high dose rates, treatment doses can be delivered within milliseconds, abiding by FLASH radiotherapy principles. In addition, a homogeneous radiation field can be spatially fractionated into a geometric pattern called microbeam radiotherapy (MRT); a coplanar array of thin beams of microscopic dimensions. Both are clinically promising radiotherapy modalities because they trigger a cascade of biological effects that improve tumor control, while increasing normal tissue tolerance compared to conventional radiation. Synchrotrons can deliver high doses to a very small volume with low beam divergence, thus facilitating the study of non-targeted effects of these novel radiation modalities in both in-vitro and in-vivo models. Non-targeted radiation effects studied at the AS and ESRF include monitoring cell–cell communication after partial irradiation of a cell population (radiation-induced bystander effect, RIBE), the response of tissues outside the irradiated field (radiation-induced abscopal effect, RIAE), and the influence of irradiated animals on non-irradiated ones in close proximity (inter-animal RIBE).
  • 792
  • 19 Apr 2022
Topic Review
AFM Investigation of Protein Crystals Morphology
Atomic force microscopy (AFM) enables the visualization of soft samples over a wide size range, from hundreds of micrometers up to the molecular level. The nonperturbative nature, the ability to scan in a liquid environment, and the lack of need for freezing, fixing, or staining make AFM a well-suited tool for studying fragile samples such as macromolecular crystals. The achievements of AFM underlined start from the study of crystal growth processes studying the surface morphology of protein crystals, passes through the in-depth analysis of the S-layer systems, and arrive at the introduction of the high-speed atomic force microscopy (HS-AFM) that allows the observation of molecular dynamics adsorption.
  • 785
  • 06 Sep 2023
Topic Review
Autofluorescent Biomolecules in Diptera
Light-based phenomena in insects have long attracted researchers’ attention. Surface color distribution patterns are commonly used for taxonomical purposes, while optically-active structures from Coleoptera cuticle or Lepidoptera wings have inspired technological applications, such as biosensors and energy accumulation devices. In Diptera, besides these optically-based phenomena, the ability of some biomolecules to fluoresce makes them to act as markers of bio-metabolic and structural features useful for vector control studies. Resilin or chitinous compounds, with their respective blue or green-to-red autofluorescence (AF), are commonly related to biomechanical and structural properties, helpful to clarify the mechanisms underlying substrate adhesion of ectoparasites’ leg appendages, or the antennal abilities in tuning sound detection. Metarhodopsin, a red fluorescing photoproduct of rhodopsin, allows to investigate visual mechanisms, whereas the AF of NAD(P)H and flavins, commonly correlated to energy metabolism, favor the investigation of sperm vitality. Lipofuscins are AF biomarkers of aging, as well as pteridines, which can be involved in the synthesis of pigments and, similarly to kynurenines, are also exploited in metabolic investigations. 
  • 783
  • 02 Aug 2022
Topic Review
Quantitative Super-Resolution Imaging and GPCR Oligomerization Analysis
G-protein coupled receptors (GPCRs) are the largest family of cell surface receptors in eukaryotic cells. These seven-transmembrane receptors have influence in physiological events such as cell to cell communication, immune responses, nerve transmission and even hunger and sleep regulation. The role of GPCRs in diseases such as rheumatoid arthritis, heart disease, cancer, obesity, and neurodegenerative disorders accentuates the need to investigate this family of receptors further. More than a third of all drugs approved by the FDA target GPCRs but often such drugs have a variety of poorly understood mechanisms, as a recent example surrounding opioid receptor agonists illustrates.
  • 779
  • 15 Nov 2021
Topic Review
Molecular Serum Albumin
Serum albumin is a popular macromolecule for studying the effect of proteins on the colloidal stability of nanoparticle (NP) dispersions, as well as the protein–nanoparticle interaction and protein corona formation.
  • 779
  • 05 Mar 2024
Topic Review Peer Reviewed
Biophysics and Quantum Limitation of Photoreceptive Processes
This entry paper is an attempt to explain how the discrete nature of light (energy discreteness in the form of photons) constrains the light detection process all along the evolutionary path, in the not-fully-understood photoreceptive systems of unicellular microorganisms (nonimaging systems) and in the complex and well-known visual system of higher organisms (imaging systems). All these systems are perfect examples of the interplay between physics and biology, i.e., they are the perfect topic of research for biophysicists. The paper describes how photoreceptive and visual systems achieve the goal of photon counting, which information is conveyed by a finite number of photons, and which noise factors limit light-detecting processes.
  • 761
  • 26 Dec 2023
Topic Review
Innovative Phosphorene Nanoplatform for Light Antimicrobial Therapy
Photodynamic therapy (PDT), largely employed as a clinical treatment for several malignant pathologies, has also gained importance as a promising antimicrobial approach. Antimicrobial PDT (aPDT) relies on the application of a photosensitizer able to produce singlet oxygen (1O2) or other cytotoxic reactive oxygen species (ROS) upon exposure to appropriate light, which leads to cell death after the induced photodamage. Among different types of 2D nanomaterials with antimicrobial properties, phosphorene, the exfoliated form of black phosphorus (bP), has the unique property intrinsic photoactivity exploitable for photothermal therapy (PTT) as well as for PDT against pathogenic bacteria.
  • 754
  • 18 Dec 2023
Topic Review
Advanced Microscopy Techniques for Molecular Biophysics
Though microscopy is most often intended as a technique for providing qualitative assessment of cellular and subcellular properties, when coupled with other instruments such as wavelength selectors, lasers, photoelectric devices and computers, it can perform a wide variety of quantitative measurements, which are demanding in establishing relationships between the properties and structures of biological material in all their spatial and temporal complexities. These combinations of instruments are a powerful approach to improve non-destructive investigations of cellular and subcellular properties (both physical and chemical) at a macromolecular scale resolution.
  • 753
  • 20 Jun 2023
Topic Review
Membrane Structure Obtained in an Experimental Evolution Process
The functionalized vesicle membrane is a product of the evolution process and is connected to several survival mechanisms. An octapeptide (KSPFPFAA) is identified which rapidly integrated into the vesicle membrane and is obviously connected to a particular advantage of the corresponding functionalized vesicle according to its significant accumulation.
  • 724
  • 09 Feb 2022
Topic Review
Exploring Biomolecular Self-Assembly with Far-Infrared Radiation
Physical engineering technology using far-infrared radiation has been gathering attention in chemical, biological, and material research fields. In particular, the high-power radiation at the terahertz region can give remarkable effects on biological materials distinct from a simple thermal treatment. Self-assembly of biological molecules such as amyloid proteins and cellulose fiber plays various roles in medical and biomaterials fields. A common characteristic of those biomolecular aggregates is a sheet-like fibrous structure that is rigid and insoluble in water, and it is often hard to manipulate the stacking conformation without heating, organic solvents, or chemical reagents.
  • 718
  • 21 Oct 2022
Topic Review
Arabidopsis thaliana Plant Natriuretic Peptide Active Domain
Plant natriuretic peptides (PNPs) are hormones that have been extracted from many different species, with the Arabidopsis thaliana PNP (AtPNP-A) being the most studied among them. AtPNP-A is a signaling molecule that consists of 130 residues and is secreted into the apoplast, under conditions of biotic or abiotic stress. AtPNP-A has distant sequence homology with human ANP, a protein that forms amyloid fibrils in vivo.
  • 715
  • 23 Dec 2021
Topic Review
Patient-Derived Xenotransplant of CNS Neoplasms in Zebrafish
Glioblastoma and neuroblastoma are the most common central nervous system malignant tumors in adult and pediatric populations. Both are associated with poor survival. These tumors are highly heterogeneous, having complex interactions among different cells within the tumor and with the tumor microenvironment. One of the main challenges in the neuro-oncology field is achieving optimal conditions to evaluate a tumor’s molecular genotype and phenotype. In this respect, the zebrafish biological model is becoming an excellent alternative for studying carcinogenic processes and discovering new treatments. It is possible to maintain glioblastoma and neuroblastoma primary cell cultures and transplant the cells into zebrafish embryos. The zebrafish is a suitable biological model for understanding tumor progression and the effects of different treatments. This model offers new perspectives in providing personalized care and improving outcomes for patients living with central nervous system tumors.
  • 711
  • 30 Jun 2022
Topic Review
Terahertz Radiation Modulates Neuronal Morphology and Dynamics Properties
Terahertz radiation falls within the spectrum of hydrogen bonding, molecular rotation, and vibration, as well as van der Waals forces, indicating that many biological macromolecules exhibit a strong absorption and resonance in this frequency band. Research has shown that the terahertz radiation of specific frequencies and energies can mediate changes in cellular morphology and function by exciting nonlinear resonance effects in proteins. However, current studies have mainly focused on the cellular level and lack systematic studies on multiple levels. Moreover, the mechanism and law of interaction between terahertz radiation and neurons are still unclear. 
  • 707
  • 21 Mar 2024
Topic Review
Site-Search Process for Synaptic Protein-DNA Complexes
The assembly of synaptic protein-DNA complexes by specialized proteins is critical for bringing together two distant sites within a DNA molecule or bridging two DNA molecules. The assembly of such synaptosomes is needed in numerous genetic processes requiring the interactions of two or more sites. The molecular mechanisms by which proteins bring the sites together, enabling the assembly of synaptosomes, remain unknown. Such proteins can utilize sliding, jumping, and segmental transfer pathways for the single-site search process, but none of these pathways explains how the synaptosome assembles. Here we used restriction enzyme SfiI, that requires the assembly of synaptosome for DNA cleavage, as our experimental system and applied time-lapse high-speed AFM (HS-AFM) to directly visualize the site search process accomplished by the SfiI enzyme.
  • 706
  • 17 Jan 2022
Topic Review
Optical Sensors in Mechanobiology
Optical sensors play a central role in the study of mechanobiology by enabling the accurate detection and measurement of mechanical forces and their effects on biological systems. Mechanobiology explores how mechanical forces influence cellular processes, tissue development, and overall physiological functions.
  • 706
  • 03 Nov 2023
Topic Review
RNA X-ray Crystallography
Approaches for crystallization of RNA and how they are used in practice.
  • 702
  • 07 Mar 2023
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