Subject:
All Disciplines Arts & Humanities Biology & Life Sciences Business & Economics Chemistry & Materials Science Computer Science & Mathematics Engineering Environmental & Earth Sciences Medicine & Pharmacology Physical Sciences Public Health & Healthcare Social Sciences
Sort:
Most Viewed Latest Alphabetical (A-Z) Alphabetical (Z-A)
Filter:
All Topic Review Biography Peer Reviewed Entry Video Entry
Topic Review
Applications of Molecular Dynamics Simulation in Protein Study
Molecular Dynamics (MD) Simulations is increasingly used as a powerful tool to study protein structure-related questions. Starting from the early simulation study on the photoisomerization in rhodopsin in 1976, MD Simulations has been used to study protein function, protein stability, protein–protein interaction, enzymatic reactions and drug–protein interactions, and membrane proteins.
  • 959
  • 08 Sep 2022
Topic Review
The BIANCA Biophysical Model
Cancer ion therapy is constantly growing, thanks to its increased precision and, for heavy ions, its increased biological effectiveness (RBE) with respect to conventional photon therapy. The complex dependence of RBE on many factors demands for biophysical modelling. Up to now only the Local Effect Model (LEM), the Microdosimetric Kinetic Model (MKM) and the “mixed-beam” model are used in clinics. In this work the BIANCA biophysical model, after extensive benchmarking in vitro, was applied to develop a database predicting cell survival for different ions, energies and doses. Following interface with the FLUKA Monte Carlo transport code, for the first time BIANCA was benchmarked against in vivo data obtained by C-ion or proton irradiation of the rat spinal cord. The latter is a well-established model for CNS (Central Nervous System) late effects, which in turn are the main dose-limiting factor for head-and-neck tumors. Furthermore, these data have been considered to validate the LEM version applied in clinics. Although further benchmarking is desirable, the agreement between simulations and data suggests that BIANCA can predict RBE for C-ion or proton treatment of head-and-neck tumors. In particular, the agreement with proton data may be relevant if the current assumption of a constant proton RBE of 1.1 is revised. This work provides the bases for future benchmarking against patient data, as well as the development of other databases for specific tumor types and/or normal tissues.
  • 951
  • 02 Nov 2020
Topic Review
Molecular Simulations of RNA-Dependent RNA Polymerase of SARS-CoV-2
Molecular dynamics (MD) simulations are powerful theoretical methods that can reveal biomolecular properties, such as structure, fluctuations, and ligand binding, at the atomic level. All-atom MD simulations elucidated a difference in the dynamic properties of RNA-dependent RNA polymerases (RdRps) in severe acute respiratory syndrom coronavirus 2 (SARS-CoV-2) and SARS-CoV, which may cause activity differences of these RdRps. RdRp is also a drug target for Coronavirus disease 2019. Nucleotide analogs, such as remdesivir and favipiravir, are considered to be taken up by RdRp and inhibit RNA replication. The recognition mechanism of RdRp for these drug molecules and adenosine triphosphate (ATP) was revealed by MD simulations at the atomic detail. In addition, various simulation studies on the complexes of SARS-CoV-2 RdRp with several nucleotide analogs are also presented.
  • 938
  • 20 Feb 2023
Topic Review
Electrical Resistance Measurement
The blood–brain barrier (BBB) represents the tightest endothelial barrier within the cardiovascular system characterized by very low ionic permeability.
  • 934
  • 25 Jun 2021
Topic Review
Colorectal Cancer Treatment Based on Nanomaterials
Colorectal cancer (CRC) is a global health problem responsible for 10% of all cancer incidences and 9.4% of all cancer deaths worldwide. The number of new cases increases per annum, whereas the lack of effective therapies highlights the need for novel therapeutic approaches. Conventional treatment methods, such as surgery, chemotherapy and radiotherapy, are widely applied in oncology practice. Their therapeutic success is little, and therefore, the search for novel technologies is ongoing. Many efforts have focused recently on the development of safe and efficient cancer nanomedicines. Nanoparticles are among them. They are unique with their properties on a nanoscale and hold the potential to exploit intrinsic metabolic differences between cancer and healthy cells. This feature allows them to induce high levels of toxicity in cancer cells with little damage to the surrounding healthy tissues.
  • 930
  • 21 Jul 2022
Topic Review
Remodeler Catalyzed Nucleosome Repositioning
The packaging of the eukaryotic genome into chromatin regulates the storage of genetic information, including the access of the cell's DNA metabolism machinery.  Indeed, since the processes of DNA replication, translation, and repair require access to the underlying DNA, several mechanisms, both active and passive, have evolved by which chromatin structure can be regulated and modified.  One mechanism relies upon the function of chromatin remodeling enzymes which couple the free energy obtained from the binding and hydrolysis of ATP to the mechanical work of repositioning and rearranging nucleosomes.  Here we review recent work on the nucleosome mobilization activity of this essential family of molecular machines.
  • 929
  • 08 Jan 2021
Topic Review
Probe for Single-Molecule Fluorescence Microscopy
Probe choice in single-molecule microscopy requires deeper evaluations than those adopted for less sensitive fluorescence microscopy studies. Fluorophore characteristics can alter or hide subtle phenomena observable at the single-molecule level, wasting the potential of the sophisticated instrumentation and algorithms developed for this kind of advanced applications. The three typical groups of fluorophores are fluorescent proteins, organic dyes and quantum dots; here their advantages, drawbacks and use in single-molecule microscopy are discussed. Some requirements are common to all applications, such as high brightness and photostability, specific and efficient labeling, controlled stoichiometry, no perturbation on the system. Other requirements depend on the specific type of single-molecule technique; some of them are here described with their specific requirements for probe choice.
  • 911
  • 13 Feb 2023
Topic Review
Single-Molecule Labeling and Imaging Strategies
Single-molecule imaging is emerging as a revolutionary approach to studying fundamental questions in plants. However, compared with its use in animals, the application of single-molecule imaging in plants is still underexplored. 
  • 905
  • 31 May 2021
Topic Review
Factors Affecting Protein Cysteine Reactivity
Protein cysteines are involved in many critical structural and functional roles that can be performed thanks to the peculiar properties of their sulfhydryl group, which, in its deprotonated form, becomes an active nucleophile. Due to the physiological importance of this residue, it represents an attractive and emerging target for the development and design of covalent ligands, which are able to modulate the function of specific proteins and enzymes.
  • 904
  • 01 Oct 2020
Topic Review
Autonomous Molecular Design: Machine Intelligence
The workflow for computational autonomous molecular design (CAMD) must be an integrated and closed-loop system with (i) efficient data generation and extraction tools, (ii) robust data representation techniques, (iii) physics-informed predictive machine learning (ML) models, and (iv) tools to generate new molecules using the knowledge learned from steps i–iii.
  • 902
  • 29 Mar 2022
Topic Review
Intrinsically Disordered Proteins in Diseases
Many proteins and protein segments cannot attain a single stable three-dimensional structure under physiological conditions; instead, they adopt multiple interconverting conformational states. Such intrinsically disordered proteins or protein segments are highly abundant across proteomes, and are involved in various effector functions.
  • 899
  • 02 Dec 2022
Topic Review
Candida albicans Cells
In the absence of proper immunity, such as in the case of acquired immune deficiency syndrome (AIDS) patients, Candida albicans, the most common human fungal pathogen, may cause mucosal and even life-threatening systemic infections. P-113 (AKRHHGYKRKFH), an antimicrobial peptide (AMP) derived from the human salivary protein histatin 5, shows good safety and efficacy profiles in gingivitis and human immunodeficiency virus (HIV) patients with oral candidiasis. However, little is known about how P-113 interacts with Candida albicans or its degradation by Candida-secreted proteases that contribute to the fungi’s resistance. Here, we use solution nuclear magnetic resonance (NMR) methods to elucidate the molecular mechanism of interactions between P-113 and living Candida albicans cells. Furthermore, we found that proteolytic cleavage of the C-terminus prevents the entry of P-113 into cells and that increasing the hydrophobicity of the peptide can significantly increase its antifungal activity.
  • 886
  • 29 Oct 2020
Topic Review
COVID 19 MATHEMATICS AND STATISTICS
In this approach we will summarise the the last three publications highlighting the key mathematical approach like Exponential F ( x ) to further exponential –Gaussian F ( x ) and finally the Linear Combination of Atomic Orbital ( LCAO ) ie a hybridised SP orbital overlapping to Remdesivir ( Drug ) –Covid19 approach. .Sigmoid Statistics or Logistics regression is a method to applied to Infection fatality rate ( IFR ) the most important epidemological parameters is also under consideration .
  • 885
  • 29 Oct 2020
Topic Review
Structure of Blood–Brain Barrier and Substance Transportation
The complex structure of the blood–brain barrier (BBB), which blocks nearly all large biomolecules, hinders drug delivery to the brain and drug assessment, thus decelerating drug development. Conventional in vitro models of BBB cannot mimic some crucial features of BBB in vivo including a shear stress environment and the interaction between different types of cells. There is a great demand for a new in vitro platform of BBB that can be used for drug delivery studies.
  • 885
  • 01 Mar 2023
Topic Review
The Coupling in Biological Membranes
Cell membrane structure is proposed as a lipid matrix with embedded proteins, and thus, their emerging mechanical and electrostatic properties are commanded by lipid behavior and their interconnection with the included and absorbed proteins, cytoskeleton, extracellular matrix and ionic media. Structures formed by lipids are soft, dynamic and viscoelastic, and their properties depend on the lipid composition and on the general conditions, such as temperature, pH, ionic strength and electrostatic potentials. The dielectric constant of the apolar region of the lipid bilayer contrasts with that of the polar region, which also differs from the aqueous milieu, and these changes happen in the nanometer scale. Besides, an important percentage of the lipids are anionic, and the rest are dipoles or higher multipoles, and the polar regions are highly hydrated, with these water molecules forming an active part of the membrane. Therefore, electric fields (both, internal and external) affects membrane thickness, density, tension and curvature, and conversely, mechanical deformations modify membrane electrostatics. As a consequence, interfacial electrostatics appears as a highly important parameter, affecting the membrane properties in general and mechanical features in particular.
  • 878
  • 12 Jul 2021
Topic Review
G Protein-Coupled Receptor (GPCR) Dimers
G protein-coupled receptor (GPCR) oligomerization, while contentious, continues to attract the attention of researchers. Numerous experimental investigations have validated the presence of GPCR dimers, and the relevance of dimerization in the effectuation of physiological functions intensifies the attractiveness of this concept as a potential therapeutic target. GPCRs, as a single entity, have been the main source of scrutiny for drug design objectives for multiple diseases such as cancer, inflammation, cardiac, and respiratory diseases. The existence of dimers broadens the research scope of GPCR functions, revealing new signaling pathways that can be targeted for disease pathogenesis that have not previously been reported when GPCRs were only viewed in their monomeric form. This review will highlight several aspects of GPCR dimerization, which include a summary of the structural elucidation of the allosteric modulation of class C GPCR activation offered through recent solutions to the three-dimensional, full-length structures of metabotropic glutamate receptor and γ-aminobutyric acid B receptor as well as the role of dimerization in the modification of GPCR function and allostery. 
  • 866
  • 30 Apr 2021
Topic Review
Single-Stranded DNA Binding Protein in DNA Metabolism
Single-stranded DNA-binding proteins (SSBs) play vital roles in DNA metabolism. Proteins of the SSB family exclusively and transiently bind to ssDNA, preventing the DNA double helix from re-annealing and maintaining genome integrity. In the meantime, they interact and coordinate with various proteins vital for DNA replication, recombination, and repair. Although SSB is essential for DNA metabolism, proteins of the SSB family have been long described as accessory players, primarily due to their unclear dynamics and mechanistic interaction with DNA and its partners. Recently-developed single-molecule tools, together with biochemical ensemble techniques and structural methods, have enhanced our understanding of the different coordination roles that SSB plays during DNA metabolism. 
  • 849
  • 15 Feb 2023
Topic Review
3D Live Cell Imaging Challenges
Relevant samples are described and various problems and challenges—including 3D Challenges of 3D imaging by optical sectioning, light scattering and phototoxicity—are addressed. Furthermore, enhanced methods of wide-field or laser scanning microscopy together with some relevant examples and applications are summarized. In the future one may profit from a continuous increase in microscopic resolution, but also from molecular sensing techniques in the nanometer range using e.g., non-radiative energy transfer (FRET).
  • 846
  • 23 Aug 2021
Topic Review
Francisella FupA and FupB Proteins
Responsible for tularemia, Francisella tularensis bacteria are highly infectious Gram-negative, category A bioterrorism agents. The molecular mechanisms for their virulence and resistance to antibiotics remain largely unknown. FupA (Fer Utilization Protein), a protein mediating high-affinity transport of ferrous iron across the outer membrane, is associated with both. Recent studies demonstrated that fupA deletion contributed to lower F. tularensis susceptibility towards fluoroquinolones, by increasing the production of outer membrane vesicles. Although the paralogous FupB protein lacks such activity, iron transport capacity and a role in membrane stability were reported for the FupA/B chimera, a protein found in some F. tularensis strains, including the live vaccine strain (LVS). To investigate the mode of action of these proteins, we purified recombinant FupA, FupB and FupA/B proteins expressed in Escherichia coli and incorporated them into mixed lipid bilayers. We examined the porin-forming activity of the FupA/B proteoliposomes using a fluorescent 8-aminonaphthalene-1,3,6-trisulfonic acid, disodium salt (ANTS) probe. Using electrophysiology on tethered bilayer lipid membranes, we confirmed that the FupA/B fusion protein exhibits pore-forming activity with large ionic conductance, a property shared with both FupA and FupB. This demonstration opens up new avenues for identifying functional genes, and novel therapeutic strategies against F. tularensis infections.
  • 842
  • 27 Oct 2020
Topic Review
DNA Manipulation and Single-Molecule Imaging
DNA replication, repair, and recombination in the cell play a significant role in the regulation of the inheritance, maintenance, and transfer of genetic information. To elucidate the biomolecular mechanism in the cell, some molecular models of DNA replication, repair, and recombination have been proposed. These biological studies have been conducted using bulk assays, such as gel electrophoresis. Because in bulk assays, several millions of biomolecules are subjected to analysis, the results of the biological analysis only reveal the average behavior of a large number of biomolecules. Therefore, revealing the elementary biological processes of a protein acting on DNA (e.g., the binding of protein to DNA, DNA synthesis, the pause of DNA synthesis, and the release of protein from DNA) is difficult. Single-molecule imaging allows the analysis of the dynamic behaviors of individual biomolecules that are hidden during bulk experiments. Thus, the methods for single-molecule imaging have provided new insights into almost all of the aspects of the elementary processes of DNA replication, repair, and recombination. However, in an aqueous solution, DNA molecules are in a randomly coiled state. Thus, the manipulation of the physical form of the single DNA molecules is important. 
  • 834
  • 01 Apr 2021
  • Page
  • of
  • 10
Featured Entry Collections
>>

Featured Books

>>
Encyclopedia of Social Sciences
Encyclopedia of COVID-19
Encyclopedia of Fungi
Encyclopedia of Digital Society, Industry 5.0 and Smart City
ScholarVision Creations
Feedback