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Biophysical Chemistry

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Physical Chemistry".

Deadline for manuscript submissions: closed (30 June 2023) | Viewed by 25077

Special Issue Editor

Prof. Dr. Yanjun Hu

E-Mail Website
Guest Editor
Department of Chemistry, Hubei Normal University, Huangshi 435002, China
Interests: biomacromolecules; biothermodynamics; biophysical chemistry; photochemistry; chemical biology; molecular spectroscopy

Special Issue Information

Dear Colleagues,

The Biophysical Chemistry Special Issue of the journal Molecules publishes original, fundamental, and impactful research and timely review articles on biomacromolecules, bioactive molecules. Topics of interest include but are not limited to:

  • Theoretical and computational treatments of biomacromolecular systems;
  • Macromolecular interactions;
  • Biocatalysis (ribozymes and catalytic antibodies);
  • Membrane chemistry;
  • Protein and small biomolecules;
  • Protein–molecule interactions;
  • Molecular recognition of nucleic acids;
  • Molecular spectroscopy studies on biomolecules.

Prof. Dr. Yanjun Hu
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Molecules is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • macromolecular interactions
  • small biomolecules
  • molecular recognition
  • nucleic acids
  • protein

Published Papers (15 papers)

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Research

Jump to: Review, Other

12 pages, 6015 KiB  
Article
The Influence of pH Value on the Microstructure and Properties of Strontium Phosphate Chemical Conversion Coatings on Titanium
by Guochao Gu, Yibo Li, Kangqing Zuo and Guiyong Xiao
Molecules 2023, 28(18), 6651; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules28186651 - 16 Sep 2023
Viewed by 930
Abstract
Strontium (Sr) is a trace element in the human body that can promote bone formation and inhibit bone absorption. A conversion coating of strontium phosphate (Sr-P) on the surface of titanium (Ti) can improve its biological properties and has many potential applications in [...] Read more.
Strontium (Sr) is a trace element in the human body that can promote bone formation and inhibit bone absorption. A conversion coating of strontium phosphate (Sr-P) on the surface of titanium (Ti) can improve its biological properties and has many potential applications in the fields of dentistry and orthopedics. In the present study, Sr-P coatings with SrHPO4 and Sr3(PO4)2 crystals on Ti are prepared by a phosphate chemical conversion (PCC) treatment and the effect of pH values on the properties of the Sr-P coatings is researched. The results prove that the phase composition, morphology, and corrosion resistance of the coated Ti vary according to the pH values of the PCC solution. The morphology of the conversion deposition on Ti changes from plat-like to cluster-like and then to homogeneous microcrystals as the pH value changes from 2.50 to 3.25. Only discrete SrHPO4 crystals are generated on the substrate at lower pH values, while relatively stable Sr3(PO4)2 and SrHPO4 crystals grow and subsequently form an integrated coating on the Ti as the pH exceeds 2.50. The cross-sectional morphologies and bonding strength of different coatings are also researched. The corrosion resistance of coated Ti improves compared with that of bare Ti because of the Sr-P coatings with a Sr3(PO4)2 phase. In addition, it is indicated that the Sr-P coatings on Ti can improve the adhesion and differentiation of BMSCs. Full article
(This article belongs to the Special Issue Biophysical Chemistry)
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18 pages, 10824 KiB  
Article
Understanding of the Effect of the Adsorption of Atom and Cluster Silver on Chitosan: An In Silico Analysis
by Alejandro Rodríguez-Juárez, Veronica Carmona-Álvarez, Fernando Díaz-Monge, Ernesto Chigo-Anota and Orlando Zaca-Moran
Molecules 2023, 28(15), 5809; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules28155809 - 1 Aug 2023
Viewed by 906
Abstract
In this work, the structural, electronic, and optical stability properties of the chitosan monomer (M-Ch) and atomic silver complex are reported, as well as a unitary cell of a silver cluster in the gas phase and acetic acid. The generalized gradient approximation HSEh1PBE/def2-TZVPP50 [...] Read more.
In this work, the structural, electronic, and optical stability properties of the chitosan monomer (M-Ch) and atomic silver complex are reported, as well as a unitary cell of a silver cluster in the gas phase and acetic acid. The generalized gradient approximation HSEh1PBE/def2-TZVPP50 results established the structures’ anionic charge (Q = −1|e|) and the doublet state (M = 2). The high cohesive energy indicates structural stability, and the quantum-mechanical descriptors show a high polarity and low chemical reactivity. Also, the quantum-mechanical descriptors present a low work function that shows the structures are suitable for applications in light-emitting diodes. Finally, the electronic behavior observed by the |HOMO-LUMO| gap energy changes depending on the atomic silver incorporated into the complex. Full article
(This article belongs to the Special Issue Biophysical Chemistry)
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12 pages, 2886 KiB  
Article
Effect of Amphotericin B on the Thermodynamic Properties and Surface Morphology of the Pulmonary Surfactant Model Monolayer during Respiration
by Juan Wang, Jia Wang, Xinzhong Wang and Zhen Wang
Molecules 2023, 28(12), 4840; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules28124840 - 18 Jun 2023
Cited by 3 | Viewed by 1212
Abstract
During the COVID-19 pandemic, the treatment of pulmonary fungal infection faced noteworthy challenges. Amphotericin B has shown promising therapeutic effects as an inhalation treatment for pulmonary fungal infections, especially those associated with the COVID-19 virus, due to its rare resistance. However, because the [...] Read more.
During the COVID-19 pandemic, the treatment of pulmonary fungal infection faced noteworthy challenges. Amphotericin B has shown promising therapeutic effects as an inhalation treatment for pulmonary fungal infections, especially those associated with the COVID-19 virus, due to its rare resistance. However, because the drug frequently produces renal toxicity, its effective dose is limited in clinical use. In this work, the DPPC/DPPG mixed monolayer was used as the pulmonary surfactant monolayer to study the interaction between amphotericin B and the pulmonary surfactant monolayer during inhalation therapy using the Langmuir technique and atomic force microscopy. The effects of different molar ratios of AmB on the thermodynamic properties and surface morphology of the pulmonary surfactant monolayer at different surface pressures was evaluated. The results showed that when the molar ratio of AmB to lipids in the pulmonary surfactant was less than 1:1, the main intermolecular force was attractive at a surface pressure greater than 10 mN/m. This drug had little effect on the phase transition point of the DPPC/DPPG monolayer, but decreased the height of the monolayer at 15 mN/m and 25 mN/m. When the molar ratio of AmB to lipids was greater than 1:1, the intermolecular force was mainly repulsive at a surface pressure greater than 15 mN/m, and AmB increased the height of the DPPC/DPPG monolayer at both 15 mN/m and 25 mN/m. These results are helpful in understanding the interaction between the pulmonary surfactant model monolayer and different doses of drugs at various surface tensions during respiration. Full article
(This article belongs to the Special Issue Biophysical Chemistry)
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11 pages, 1766 KiB  
Article
A Novel Peptide Reagent for Investigating Disulfide-Coupled Folding Intermediates of Mid-Size Proteins
by Nana Sakata, Yuri Murakami, Mitsuhiro Miyazawa, Shigeru Shimamoto and Yuji Hidaka
Molecules 2023, 28(8), 3494; https://doi.org/10.3390/molecules28083494 - 15 Apr 2023
Cited by 1 | Viewed by 1629
Abstract
Investigations of protein folding have largely involved the use of disulfide-containing proteins, since the disulfide-coupled folding of proteins allows folding intermediates to be trapped and their conformations determined. However, studies of the folding mechanisms of mid-size proteins face several problems, one of which [...] Read more.
Investigations of protein folding have largely involved the use of disulfide-containing proteins, since the disulfide-coupled folding of proteins allows folding intermediates to be trapped and their conformations determined. However, studies of the folding mechanisms of mid-size proteins face several problems, one of which is that detecting folding intermediates is difficult. Therefore, to solve this issue, a novel peptide reagent, maleimidohexanoyl-Arg5-Tyr-NH2, was designed and applied to the detection of folding intermediates of model proteins. BPTI was chosen as a model small protein to estimate the ability of the novel reagent to detect folding intermediates. In addition, a precursor protein (prococoonase) of Bombyx mori cocoonase was used as a model mid-size protein. Cocoonase is classified as a serine protease and has a high homology with trypsin. We recently found that the propeptide sequence of prococoonase (proCCN) is important for the folding of cocoonase. However, it was difficult to study the folding pathway of proCCN since the folding intermediates could not be separated on a reversed-phase HPLC (RP-HPLC). Therefore, to separate the folding intermediates by RP-HPLC, the novel labeling reagent was used to accomplish this for proCCN. The results indicated that the peptide reagent allowed the intermediates to be captured, separated on SDS-PAGE, and analyzed by RP-HPLC without the occurrence of undesirable disulfide-exchange reactions during the labeling reactions. The peptide reagent reported herein is a practical tool for investigating the mechanisms of disulfide-coupled folding of mid-size proteins. Full article
(This article belongs to the Special Issue Biophysical Chemistry)
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21 pages, 20337 KiB  
Article
Study of the Sensing Kinetics of G Protein-Coupled Estrogen Receptor Sensors for Common Estrogens and Estrogen Analogs
by Dingqiang Lu, Xinqian Wang, Chunlei Feng, Danyang Liu, Yixuan Liu, Yujiao Liu, Jie Li, Jiayao Zhang, Na Li, Yujing Deng, Ke Wang, Ruijuan Ren and Guangchang Pang
Molecules 2023, 28(8), 3286; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules28083286 - 7 Apr 2023
Cited by 2 | Viewed by 1742
Abstract
Endogenous and exogenous estrogens are widely present in food and food packaging, and high levels of natural estrogens and the misuse or illegal use of synthetic estrogens can lead to endocrine disorders and even cancer in humans. Therefore, it is consequently important to [...] Read more.
Endogenous and exogenous estrogens are widely present in food and food packaging, and high levels of natural estrogens and the misuse or illegal use of synthetic estrogens can lead to endocrine disorders and even cancer in humans. Therefore, it is consequently important to accurately evaluate the presence of food-functional ingredients or toxins with estrogen-like effects. In this study, an electrochemical sensor based on G protein-coupled estrogen receptors (GPERs) was fabricated by self-assembly, modified by double-layered gold nanoparticles, and used to measure the sensing kinetics for five GPER ligands. The interconnected allosteric constants (Ka) of the sensor for 17β-estradiol, resveratrol, G-1, G-15, and bisphenol A were 8.90 × 10−17, 8.35 × 10−16, 8.00 × 10−15, 5.01 × 10−15, and 6.65 × 10−16 mol/L, respectively. The sensitivity of the sensor for the five ligands followed the order of 17β-estradiol > bisphenol A > resveratrol > G-15 > G-1. The receptor sensor also demonstrated higher sensor sensitivity for natural estrogens than exogenous estrogens. The results of molecular simulation docking showed that the residues Arg, Glu, His, and Asn of GPER mainly formed hydrogen bonds with -OH, C-O-C, or -NH-. In this study, simulating the intracellular receptor signaling cascade with an electrochemical signal amplification system enabled us to directly measure GPER–ligand interactions and explore the kinetics after the self-assembly of GPERs on a biosensor. This study also provides a novel platform for the accurate functional evaluation of food-functional components and toxins. Full article
(This article belongs to the Special Issue Biophysical Chemistry)
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17 pages, 1900 KiB  
Article
Volumetric, Compressibility and Viscometric Approach to Study the Interactional Behaviour of Sodium Cholate and Sodium Deoxycholate in Aqueous Glycyl Glycine
by Santosh Kumari, Suvarcha Chauhan, Kuldeep Singh, Ahmad Umar, Hassan Fouad, Mohammed S. Alissawi and Mohammad Shaheer Akhtar
Molecules 2022, 27(24), 8998; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules27248998 - 16 Dec 2022
Cited by 2 | Viewed by 1485
Abstract
Viscosity, speed of sound (u), and density (ρ) have been measured in aqueous glycyl glycine solution over a temperature range from 293.15 to 313.15 K with a 5 K interlude to evaluate the volumetric and compressibility properties of bio-surfactants, [...] Read more.
Viscosity, speed of sound (u), and density (ρ) have been measured in aqueous glycyl glycine solution over a temperature range from 293.15 to 313.15 K with a 5 K interlude to evaluate the volumetric and compressibility properties of bio-surfactants, namely sodium cholate (NaC; 1–20 mmol∙kg−1) and sodium deoxycholate (NaDC; 1–10 mmol∙kg−1). Density and viscosity findings provide information on both solute–solute and solute–solvent types of interactions. Many other metrics, such as apparent molar adiabatic compression (κS,φ), isentropic compressibility (κS), and apparent molar volume (Vφ), have been calculated from speed of sound and density measurements, utilising experimental data. The results show that the zwitterionic end group in the glycyl glycine strongly interacts with NaDC and NaC, promoting its micellization. Since the addition of glycyl glycine causes the bio-surfactant molecules to lose their hydrophobic hydration, the observed concentration-dependent changes in apparent molar volume and apparent molar adiabatic compression are likely attributable to changes in water–water interactions. Viscous relaxation time (τ) increases significantly with a rise in bio-surfactant concentration and decreases with increasing temperature, which may be because of structural relaxation processes resulting from molecular rearrangement. All of the estimated parameters have been analysed for their trends with regard to the different patterns of intermolecular interaction present in an aqueous glycyl glycine solution and bio-surfactant system. Full article
(This article belongs to the Special Issue Biophysical Chemistry)
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18 pages, 1808 KiB  
Article
In Vitro and In Silico Studies for the Identification of Potent Metabolites of Some High-Altitude Medicinal Plants from Nepal Inhibiting SARS-CoV-2 Spike Protein
by Saroj Basnet, Rishab Marahatha, Asmita Shrestha, Salyan Bhattarai, Saurav Katuwal, Khaga Raj Sharma, Bishnu P. Marasini, Salik Ram Dahal, Ram Chandra Basnyat, Simon G. Patching and Niranjan Parajuli
Molecules 2022, 27(24), 8957; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules27248957 - 15 Dec 2022
Cited by 2 | Viewed by 2730
Abstract
Despite ongoing vaccination programs against COVID-19 around the world, cases of infection are still rising with new variants. This infers that an effective antiviral drug against COVID-19 is crucial along with vaccinations to decrease cases. A potential target of such antivirals could be [...] Read more.
Despite ongoing vaccination programs against COVID-19 around the world, cases of infection are still rising with new variants. This infers that an effective antiviral drug against COVID-19 is crucial along with vaccinations to decrease cases. A potential target of such antivirals could be the membrane components of the causative pathogen, SARS-CoV-2, for instance spike (S) protein. In our research, we have deployed in vitro screening of crude extracts of seven ethnomedicinal plants against the spike receptor-binding domain (S1-RBD) of SARS-CoV-2 using an enzyme-linked immunosorbent assay (ELISA). Following encouraging in vitro results for Tinospora cordifolia, in silico studies were conducted for the 14 reported antiviral secondary metabolites isolated from T. cordifolia—a species widely cultivated and used as an antiviral drug in the Himalayan country of Nepal—using Genetic Optimization for Ligand Docking (GOLD), Molecular Operating Environment (MOE), and BIOVIA Discovery Studio. The molecular docking and binding energy study revealed that cordifolioside-A had a higher binding affinity and was the most effective in binding to the competitive site of the spike protein. Molecular dynamics (MD) simulation studies using GROMACS 5.4.1 further assayed the interaction between the potent compound and binding sites of the spike protein. It revealed that cordifolioside-A demonstrated better binding affinity and stability, and resulted in a conformational change in S1-RBD, hence hindering the activities of the protein. In addition, ADMET analysis of the secondary metabolites from T. cordifolia revealed promising pharmacokinetic properties. Our study thus recommends that certain secondary metabolites of T. cordifolia are possible medicinal candidates against SARS-CoV-2. Full article
(This article belongs to the Special Issue Biophysical Chemistry)
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17 pages, 2453 KiB  
Article
Study on Volumetric, Compressibility and Viscometric Behavior of Cationic Surfactants (CTAB and DTAB) in Aqueous Glycyl Dipeptide: A Thermo-Acoustic Approach
by Santosh Kumari, Suvarcha Chauhan, Kuldeep Singh, Ahmad Umar, Hassan Fouad and Mohammad Shaheer Akhtar
Molecules 2022, 27(24), 8767; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules27248767 - 10 Dec 2022
Cited by 3 | Viewed by 1126
Abstract
This study aims to understand how glycyl dipeptide affected the compressibility, volumetric behavior and viscometric behavior of the cationic surfactants CTAB (Cetyltrimethylammonium bromide) and DTAB (dodecyltrimethylammonium bromide). Information on solute–solute, solute–solvent, and solvent–solvent interactions has been inferred using the quantification of density ( [...] Read more.
This study aims to understand how glycyl dipeptide affected the compressibility, volumetric behavior and viscometric behavior of the cationic surfactants CTAB (Cetyltrimethylammonium bromide) and DTAB (dodecyltrimethylammonium bromide). Information on solute–solute, solute–solvent, and solvent–solvent interactions has been inferred using the quantification of density (ρ), speed of sound (u) and viscosity in aqueous media containing glycyl dipeptide in the temperature range 293.15–313.15 K at an interval of 5 K. The data from the aforementioned research have been used to enumerate numerous volumetric and compressibility metrics that aid in the collection of information about the interactional behavior of the system under consideration. The study suggests that CTAB interacts strongly compared to DTAB with dipeptide, and it also significantly dehydrates glycyl dipeptide. The difference in water–water interactions caused by the loss of hydrophobic hydration of the surfactant molecules upon the addition of cationic surfactants may be the cause of the variation in determined parameters with surfactant concentration. Consideration of the structural rearrangement of molecules that may occur in the system has been used to explain the results of viscosity and computed factors related to viscosity. The patterns of competitive intermolecular interactions in the ternary (dipeptide + water + surfactant) system have been used to analyze the trends of all the parameters. The study may be helpful to understand the stability and structural changes in protein–surfactant systems mediated through various interactions that may be present in the system. Full article
(This article belongs to the Special Issue Biophysical Chemistry)
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24 pages, 2873 KiB  
Article
Phosphorylation of Thr9 Affects the Folding Landscape of the N-Terminal Segment of Human AGT Enhancing Protein Aggregation of Disease-Causing Mutants
by Jose L. Neira, Athi N. Naganathan, Noel Mesa-Torres, Eduardo Salido and Angel L. Pey
Molecules 2022, 27(24), 8762; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules27248762 - 10 Dec 2022
Cited by 2 | Viewed by 1101
Abstract
The mutations G170R and I244T are the most common disease cause in primary hyperoxaluria type I (PH1). These mutations cause the misfolding of the AGT protein in the minor allele AGT-LM that contains the P11L polymorphism, which may affect the folding of the [...] Read more.
The mutations G170R and I244T are the most common disease cause in primary hyperoxaluria type I (PH1). These mutations cause the misfolding of the AGT protein in the minor allele AGT-LM that contains the P11L polymorphism, which may affect the folding of the N-terminal segment (NTT-AGT). The NTT-AGT is phosphorylated at T9, although the role of this event in PH1 is unknown. In this work, phosphorylation of T9 was mimicked by introducing the T9E mutation in the NTT-AGT peptide and the full-length protein. The NTT-AGT conformational landscape was studied by circular dichroism, NMR, and statistical mechanical methods. Functional and stability effects on the full-length AGT protein were characterized by spectroscopic methods. The T9E and P11L mutations together reshaped the conformational landscape of the isolated NTT-AGT peptide by stabilizing ordered conformations. In the context of the full-length AGT protein, the T9E mutation had no effect on the overall AGT function or conformation, but enhanced aggregation of the minor allele (LM) protein and synergized with the mutations G170R and I244T. Our findings indicate that phosphorylation of T9 may affect the conformation of the NTT-AGT and synergize with PH1-causing mutations to promote aggregation in a genotype-specific manner. Phosphorylation should be considered a novel regulatory mechanism in PH1 pathogenesis. Full article
(This article belongs to the Special Issue Biophysical Chemistry)
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9 pages, 2185 KiB  
Article
Excited-State Dynamics of Proflavine after Intercalation into DNA Duplex
by Jie Zhou, Yanyan Jia, Xueli Wang, Menghui Jia, Haifeng Pan, Zhenrong Sun and Jinquan Chen
Molecules 2022, 27(23), 8157; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules27238157 - 23 Nov 2022
Cited by 1 | Viewed by 1457
Abstract
Proflavine is an acridine derivative which was discovered as one of the earliest antibacterial agents, and it has been proven to have potential application to fields such as chemotherapy, photobiology and solar-energy conversion. In particular, it is well known that proflavine can bind [...] Read more.
Proflavine is an acridine derivative which was discovered as one of the earliest antibacterial agents, and it has been proven to have potential application to fields such as chemotherapy, photobiology and solar-energy conversion. In particular, it is well known that proflavine can bind to DNA with different modes, and this may open addition photochemical-reaction channels in DNA. Herein, the excited-state dynamics of proflavine after intercalation into DNA duplex is studied using femtosecond time-resolved spectroscopy, and compared with that in solution. It is demonstrated that both fluorescence and the triplet excited-state generation of proflavine were quenched after intercalation into DNA, due to ultrafast non-radiative channels. A static-quenching mechanism was identified for the proflavine-DNA complex, in line with the spectroscopy data, and the excited-state deactivation mechanism was proposed. Full article
(This article belongs to the Special Issue Biophysical Chemistry)
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15 pages, 2866 KiB  
Article
Conductometric and Fluorescence Probe Analysis to Investigate the Interaction between Bioactive Peptide and Bile Salts: A Micellar State Study
by Santosh Kumari, Suvarcha Chauhan, Ahmad Umar, Hassan Fouad and Mohammad Shaheer Akhtar
Molecules 2022, 27(21), 7561; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules27217561 - 4 Nov 2022
Cited by 6 | Viewed by 2170
Abstract
The present work deals with the micellar state study of sodium cholate and sodium deoxycholate in the aqueous solution of a bioactive peptide, namely glycyl dipeptide, having different concentrations through conductivity and fluorescence methods at different temperatures. The data obtained from conductivity is [...] Read more.
The present work deals with the micellar state study of sodium cholate and sodium deoxycholate in the aqueous solution of a bioactive peptide, namely glycyl dipeptide, having different concentrations through conductivity and fluorescence methods at different temperatures. The data obtained from conductivity is plotted against the concentration of Bile salts, and CMC (critical micelle concentration) values are calculated. The results realized have been elucidated with reference to Glycyl dipeptide–bile salts hydrophobic/hydrophilic interactions existing in solution. In addition, the CMC values converted to mole fraction (Xcmc) values have been used to evaluate the standard thermodynamic factors of micellization viz., enthalpy H, free energy ΔGm0, and entropy (ΔSm0) which extract information regarding thermodynamic feasibility of micellar state, energy alteration, and the assorted interactions established in the existing (bile salts–water–glycyl dipeptide) system. Furthermore, the pyrene fluorescence spectrum has also been utilized to study the change in micro polarity induced by the interactions of bile salts with glycyl dipeptide and the aggregation action of bile salts. The decrease in modification in the ratio of intensities of first and third peaks i.e., (I1/I3) for the pyrene molecules in aqueous bile salts solution by the addition of dipeptide, demonstrates that the micelle polarity is affected by glycyl dipeptide. This ratio has also been utilized to determine CMC values for the studied system, and the results have been found to be in good correlation with observations made in conductivity studies. Full article
(This article belongs to the Special Issue Biophysical Chemistry)
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16 pages, 2541 KiB  
Article
Effect of Laser-Induced Optical Breakdown on the Structure of Bsa Molecules in Aqueous Solutions: An Optical Study
by Egor I. Nagaev, Ilya V. Baimler, Alexey S. Baryshev, Maxim E. Astashev and Sergey V. Gudkov
Molecules 2022, 27(19), 6752; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules27196752 - 10 Oct 2022
Cited by 9 | Viewed by 1895
Abstract
The influence of laser radiation of a typical surgical laser on the physicochemical properties of the Bovine Serum Albumin (BSA) protein was studied. It was established that the physicochemical characteristics of optical breakdown weakly depend on the concentration of protein molecules. At the [...] Read more.
The influence of laser radiation of a typical surgical laser on the physicochemical properties of the Bovine Serum Albumin (BSA) protein was studied. It was established that the physicochemical characteristics of optical breakdown weakly depend on the concentration of protein molecules. At the same time, the patterns observed for an aqueous solution of BSA irradiated with a laser for different time periods were extremely similar to the classical ones. It was established that after exposure to laser radiation, the optical density of protein solutions increases. At the same time, the intensity of BSA fluorescence due to aromatic amino acid residues decreases insignificantly after exposure to laser radiation. In this case, the position of the excitation and emission maximum does not change, and the shape of the fluorescence spot on 3D maps also does not change significantly. On the Raman spectrum after exposure to laser radiation, a significant decrease in 1570 cm−1 was observed, which indicates the degradation of α-helices and, as a result, partial denaturation of BSA molecules. Partial denaturation did not significantly change the total area of protein molecules, since the refractive index of solutions did not change significantly. However, in BSA solutions, after exposure to laser radiation, the viscosity increased, and the pseudoplasticity of aqueous solutions decreased. In this case, there was no massive damage to the polypeptide chain; on the contrary, when exposed to optical breakdown, intense aggregation was observed, while aggregates with a size of 400 nm or more appeared in the solution. Thus, under the action of optical breakdown induced by laser radiation in a BSA solution, the processes of partial denaturation and aggregation prevail, aromatic amino acid residues are damaged to a lesser extent, and fragmentation of protein molecules is not observed. Full article
(This article belongs to the Special Issue Biophysical Chemistry)
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Review

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29 pages, 1388 KiB  
Review
Setting Boundaries for Statistical Mechanics
by Bob Eisenberg
Molecules 2022, 27(22), 8017; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules27228017 - 18 Nov 2022
Cited by 3 | Viewed by 1468
Abstract
Statistical mechanics has grown without bounds in space. Statistical mechanics of noninteracting point particles in an unbounded perfect gas is widely used to describe liquids like concentrated salt solutions of life and electrochemical technology, including batteries. Liquids are filled with interacting molecules. A [...] Read more.
Statistical mechanics has grown without bounds in space. Statistical mechanics of noninteracting point particles in an unbounded perfect gas is widely used to describe liquids like concentrated salt solutions of life and electrochemical technology, including batteries. Liquids are filled with interacting molecules. A perfect gas is a poor model of a liquid. Statistical mechanics without spatial bounds is impossible as well as imperfect, if molecules interact as charged particles, as nearly all atoms do. The behavior of charged particles is not defined until boundary structures and values are defined because charges are governed by Maxwell’s partial differential equations. Partial differential equations require boundary structures and conditions. Boundary conditions cannot be defined uniquely ‘at infinity’ because the limiting process that defines ‘infinity’ includes such a wide variety of structures and behaviors, from elongated ellipses to circles, from light waves that never decay, to dipolar fields that decay steeply, to Coulomb fields that hardly decay at all. Boundaries and boundary conditions needed to describe matter are not prominent in classical statistical mechanics. Statistical mechanics of bounded systems is described in the EnVarA system of variational mechanics developed by Chun Liu, more than anyone else. EnVarA treatment does not yet include Maxwell equations. Full article
(This article belongs to the Special Issue Biophysical Chemistry)
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Other

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22 pages, 989 KiB  
Perspective
Review of the Role of Nanotechnology in Overcoming the Challenges Faced in Oral Cancer Diagnosis and Treatment
by Vidhya Rekha Umapathy, Prabhu Manickam Natarajan and Bhuminathan Swamikannu
Molecules 2023, 28(14), 5395; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules28145395 - 14 Jul 2023
Cited by 3 | Viewed by 1842
Abstract
Throughout the world, oral cancer is a common and aggressive malignancy with a high risk of morbidity, mortality, and recurrence. The importance of early detection in cancer prevention and disease treatment cannot be overstated. Conventional therapeutic strategies have minor difficulties but considerable side [...] Read more.
Throughout the world, oral cancer is a common and aggressive malignancy with a high risk of morbidity, mortality, and recurrence. The importance of early detection in cancer prevention and disease treatment cannot be overstated. Conventional therapeutic strategies have minor difficulties but considerable side effects and unfavourable consequences in clinical applications. Hence, there is a requirement for effective ways for early detection and treatment of oral cancer. At present, numerous forms of nanoparticles have piqued researchers’ interest as a potentially useful tool for diagnostic probes and medicinal devices. Because of their inherent physicochemical properties and customizable surface modification, they are able to circumvent some of restrictions and accomplish the intended diagnostic and therapeutic impact. Nanotechnology is a unique field that has revolutionised the industry and is paving the way for new treatments for oral cancer. It can help with a better diagnosis with less harmful substances and is setting current guidelines for treatment. The use of nanotechnology in cancer diagnosis, therapy, and care improves clinical practise dramatically. The different types of nanoparticles that have been developed for the diagnosis and therapy of oral cancers will be covered in this study. The difficulties and potential uses of nanoparticles in the treatment and diagnosis of oral cancer are then highlighted. In order to emphasise existing difficulties and potential remedies for oral cancer, a prospective view of the future is also provided. Full article
(This article belongs to the Special Issue Biophysical Chemistry)
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Perspective
Review Insights on Salivary Proteomics Biomarkers in Oral Cancer Detection and Diagnosis
by Vidhya Rekha Umapathy, Prabhu Manickam Natarajan and Bhuminathan Swamikannu
Molecules 2023, 28(13), 5283; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules28135283 - 7 Jul 2023
Cited by 2 | Viewed by 2185
Abstract
Early detection is crucial for the treatment and prognosis of oral cancer, a potentially lethal condition. Tumor markers are abnormal biological byproducts produced by malignant cells that may be found and analyzed in a variety of bodily fluids, including saliva. Early detection and [...] Read more.
Early detection is crucial for the treatment and prognosis of oral cancer, a potentially lethal condition. Tumor markers are abnormal biological byproducts produced by malignant cells that may be found and analyzed in a variety of bodily fluids, including saliva. Early detection and appropriate treatment can increase cure rates to 80–90% and considerably improve quality of life by reducing the need for costly, incapacitating medicines. Salivary diagnostics has drawn the interest of many researchers and has been proven to be an effective tool for both medication monitoring and the diagnosis of several systemic diseases. Since researchers are now searching for biomarkers in saliva, an accessible bodily fluid, for noninvasive diagnosis of oral cancer, measuring tumor markers in saliva is an interesting alternative to blood testing for early identification, post-treatment monitoring, and monitoring high-risk lesions. New molecular markers for oral cancer detection, treatment, and prognosis have been found as a result of developments in the fields of molecular biology and salivary proteomics. The numerous salivary tumor biomarkers and how they relate to oral cancer and pre-cancer are covered in this article. We are optimistic that salivary protein biomarkers may one day be discovered for the clinical detection of oral cancer because of the rapid advancement of proteomic technology. Full article
(This article belongs to the Special Issue Biophysical Chemistry)
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