Journal of Biophysical Chemistry

Journal Information
ISSN / EISSN : 2153-036X / 2153-0378
Current Publisher: Scientific Research Publishing, Inc. (10.4236)
Total articles ≅ 187
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Latest articles in this journal

Henk M. Buck
Journal of Biophysical Chemistry, Volume 11, pp 27-42; doi:10.4236/jbpc.2020.113003

At the moment, we see a great interest for application of Anti Sense Oligonucleotides (ASOs) in order to regulate the expression of genes related to certain diseases. These nucleotides obtained a number of fascinating properties by means of chemical manipulation of natural DNA and RNA under conservation of Watson-Crick base-pairing. About 35 years ago for our research in this field, we selected synthetically (short) phosphate-methylated DNA and RNA. It was concluded that there is an exclusive selection in hybridization affinity with natural DNA and RNA. These (bio)chemical and physical-chemical properties are extensively published. ASOs have found their way in public health as is clearly shown in the treatment of (progressive) neurological diseases. We focus specifically on the past, present and future of the phosphate-methylated oligonucleotides, illustrated with different research studies in chemistry and biophysics. A new field of application of modified DNAs is based on interactive improvements of sensitivity and specificity of nanowire field effect transistor gene chip by designing phosphate-methylated DNA as probe.
Gad Degani
Journal of Biophysical Chemistry, Volume 11, pp 43-50; doi:10.4236/jbpc.2020.114004

In the present study, a model is suggested to describe hormone control in male blue gourami (Trichogaster trichopterus) along the gonadotropic brain-pituitary- gonad axis (BPG axis) and the hypothalamic-pituitary-somatotropic axis (HPS axis). This model is based on the cloning and transcription of genes encoding hormones of the two axes involved in spermatogenesis during blue gourami reproduction. Gene transcription is affected by environmental, biological, and behavioral factors. Mature males were examined in two different stages—nonreproductive in high-density habitats and reproductive in low-density habitats. Based on gene transcription, gonadotropin-releasing hormone 1 (GnRH1) was involved in controlling spermatogenesis (spermatogonia to spermatids) via the BPG axis in nonreproductive and reproductive stages by controlling follicle-stimulating hormone (FSH), 11-ketotestosterone (11KT) and 17β-estradiol (E2). However, GnRH3 had a larger effect during the reproductive stage via the BPG axis (spermatids to sperm) on luteinizing hormone (LH), 11KT, and 17α-hydroxyprogesterone (17P). At the same time, the HPS axis was involved in spermatogenesis via pituitary adenylate cyclase-activating polypeptide (PACAP) and its related peptide PRP (formerly known as GHRH-like peptide) in the brain, and growth hormone (GH) in the pituitary affected synthesis of insulin-like growth factor 1 (IGF1) in the liver.
M. Baskar, N. Sathyan
Journal of Biophysical Chemistry, Volume 11, pp 15-25; doi:10.4236/jbpc.2020.112002

Endohedral fullerene studies are the fascinating one, particularly with Carbon 60 and Carbon 70. Water molecules inside fullerenes alter their cage structure, reorientations make them to play a lot in charge distribution. In this line we are presenting our work on Carbon 70 with three water molecules inside. Ab initio SCF calculations are carried out for the fullerene Carbon 70 and Carbon 70 with three water molecules. Carbon 70 is a rugby ball structure, when three water molecules are added inside it, dissociation of charges takes place. Unusual flip flop circular hydrogen bond formation takes place inside Carbon 70. The dipole moment of endohedral C70 with three water molecules has been found to be 0.53 Debye, 0.49 Debye and 0.71 Debye respectively for STO-3G, 3-21G and 6-31G basis sets. Total energies for this molecule are reported in addition to the Hydrogen bond length and bond angles of the three water molecules trapped inside C70.
Ganame Abdou-Salam, Ouoba Kondia Honore, Zougmore François
Journal of Biophysical Chemistry, Volume 11, pp 1-13; doi:10.4236/jbpc.2020.111001

In this paper, we perform experiments on the drying of widely consumed food products in Africa. Tomatoes and peppers are considered as products with a complex structure. Zucchini, cucumber, eggplant and cabbages are the other products used in these drying experiments, having different intrinsic parameters. Most food products have three components, namely skin, flesh containing seeds and the central spongy structure, that do not have the same behavior during their convective drying. Skin is the component that significantly reduces drying while the flesh is easy to dry. By drying the samples considering their intrinsic parameters, one quickly realizes the complex nature of mass and heat transfers during the drying of biological products.
Daiki Ito, Takanari Ikeda, Keijiro Taga, Yasushi Yamamoto, Zameer Shervani, Masato Yamamoto
Journal of Biophysical Chemistry, Volume 10, pp 15-29; doi:10.4236/jbpc.2019.102002

We have investigated the morphology of dimyristoyl phosphatidyl choline (DMPC)—cholesterol mixed monolayer formed on the water surface by dropping method using surface tension measurement (STm), Brewster angle microscopy (BAM), and infrared external reflection spectroscopy (IERS). STm results showed negative deviation of the limiting molecular area (A0) of cholesterol occurred when cholesterol was added to the DMPC monolayer. BAM images showed the expandable DMPC monolayer changed to the condensed rigid monolayer at more than cholesterol mole fraction (xChol) 0.4. IERS recordings showed that the addition of cholesterol at xChol = 0.4 occurred structural change from gauche- to trans- conformation of two DMPC molecule alkyl chains. From these results, it is found that cholesterol molecule has specific properties that cause structural transition of DMPC molecule alkyl chains.
Elena Alvareda, Federico Iribarne, Victoria Espinosa, Pablo Miranda, Daniela Santi, Sara Aguilera, S. Bustos, Margot Paulino Zunini
Journal of Biophysical Chemistry, Volume 10, pp 1-14; doi:10.4236/jbpc.2019.101001

The use of food additives with xanthine oxidase (XO) inhibitory activity offers an alternative approach to hyperuricemic and gout disease treatment, and provides an example of antioxidant nutraceutics. The in vitro and in silico XO inhibitory activity of polyphenols from Uruguayan Tannat grape pomaces and propolis extracts was evaluated as well as the scavenging capacity of said compounds. When comparing propolis and grape pomace samples, the in vitro studies demonstrated that polyphenols extracted from propolis are more active as free radical scavengers than those from Tannat grape pomace. Both natural products effectively inhibited XO but the capacity of phenols present in GP is higher than the one present in P. The high content of anthocyanins in GP, absent in P, could account for this observation. In silico assays allowed us to determine relevant ligand-receptor interactions between polyphenols, from a database built with previously reported polyphenols from both natural products, and the active site of XO. The in silico results showed that compound (E)-isoprenylcaffeate from propolis was the best potential XO inhibitor displaying hydrophobic aromatic interaction between the conjugated ring of the caffeate moiety and polar interactions between hydroxyl groups from caffeate with the active site polar residues. Among grape pomaces, the Cyanidin-3-O-(6-(E)-p-coumaroyl)-glucoside was the best XO inhibitor; its moiety oxychromenyl being relevant to the docking stabilization. All these results lead us to propose Uruguayan propolis and Tannat grape pomace extracts as food additives as well as phytopharmaceuticals to decrease the uric acid levels in gout disease and to act against oxidative stress.
C. Leigh Broadhurst, Walter Schmidt, Julie K. Nguyen, Jianwei Qin, Kuanglin Chao, Moon Sung Kim
Journal of Biophysical Chemistry, Volume 9, pp 1-14; doi:10.4236/jbpc.2018.91001

Specialized pro-resolving mediators provide promising targets for new drugs and natural products. Much work has been accomplished on the structure/ function of the lipoxygenase and cyclooxygenase enzymes but not on the substrates. A better visualization of three-dimensional lipid structures will allow increased refinement of the interactions that produce the pro-resolving mediators, and lead to improvements in synthetic pathways. We present systematic analysis of oleic (18:1n-9), linoleic (18:2n-6), alpha-linolenic (18:3n-3), arachidonic (20:4n-6), docosapentaenoic (22:5n-3), and docosahexaenoic (22:6n-3) acids. Continuous gradient temperature Raman spectroscopy (GTRS) applies the temperature gradients utilized in differential scanning calorimetry to Raman spectroscopy. GTRS can identify and differentiate specific carbon chain sites, finally allowing Raman analysis to explain why the long-chain polyunsaturated fatty acids (LC-PUFA) exhibit such extreme functional differences despite minimal changes in chemical structure. Detailed vibrational analysis of the important frequency ranges 1450 - 1200 cm-1 (includes CH2 bending and twisting) and 1750 - 1425 cm-1 (includes C=C stretching and C-C stretching plus H-C in-plane rocking) shows for the first time that each molecule has its own characteristic set of modes with only some redundancy/commonality. The number and frequency of modes correlates with three-dimensional molecular structure, not the degree of unsaturation. The high degree of specificity of lipoxygenase and cyclooxygenase enzymes should be reconsidered in light of the fact that individual sites on the polyunsaturated fatty acid chain are nonequivalent, and each LC-PUFA molecule has an individual, specific three dimensional structure incorporating torsion.
M. Baskar, N. Sathyan, T. R. Gopalakrishnan Nair
Journal of Biophysical Chemistry, Volume 9, pp 15-21; doi:10.4236/jbpc.2018.92002

Experimental scenario of the world being successful in planting water molecule at binary level in fullerene C70 is of utmost importance to pursue the theoretical properties of predictive triple water molecules and poly water molecules in Vander Waals confined space like fullerenes. Here, we present a paper in these lines of exploration of embedding triple water molecules in a Carbon confined space through the studies of behavior of three water molecules in Fullerene C60 by ab-initio methods. This heterogeneous system manifests cyclic hydrogen bonds which may be working with flipping actions. The unusual structural property of water trimers is reported. There exists a dipole moment of 0.9 ± 0.1 Debye which indicates the probable semiconductor properties.
Isaiah A. Adejoro, Sodiq O. Waheed, Omolara O. Adeboye, Frederick U. Akhigbe
Journal of Biophysical Chemistry, Volume 8, pp 1-11; doi:10.4236/jbpc.2017.81001

Ulcer is one of the life threatening diseases. It is an open sore on an external or internal surface of the body caused by a break in the skin or mucous membrane which fails to heal. In this work, specific ligands that are suitable for ulcer have been studied computationally. Docking of the triterpenoids of Lonchocarpus cyanescens with target proteins of PDB codes 1AFC, 1AXM and 2AXM were performed using AutoDock Vina and Pymol for docking and post-docking analysis, respectively. In this study, the triterpenoid ligands with binding affinity/inhibitory constants -7.2/5.21, -6.5/16.99 and -6.2/28.20 for OH, and -6.7/12.12, -6.3/23.82 and -6.1/33.40 for OCH3 were compared with the standard ligands. Our study indicates that the results corresponding to triterpenoid ligands are close to standard ligands.
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