scholarly journals Relative Stability of the Scleroglucan Triple-Helix and Single Strand: an Insight from Computational and Experimental Techniques

2016 ◽  
Vol 230 (9) ◽  
Author(s):  
Gianfranco Bocchinfuso ◽  
Claudia Mazzuca ◽  
Paolo Conflitti ◽  
Davide Cori ◽  
Tommasina Coviello ◽  
...  
Keyword(s):  
Relative Stability ◽  
Triple Helix ◽  
Hydrophobic Interactions ◽  
Single Strand ◽  
Single Chain ◽  
Ph Values ◽  
Partial Unfolding ◽  
Triplex Structure ◽  
Partially Unfolded ◽  
The Stability

AbstractScleroglucan (Sclg) is a polysaccharide that exhibits a triple helix conformation (triplex), both in aqueous solution and in the solid state, which is lost in DMSO solution, at high temperature and at high pH values. The triplex conformation is characterized by a high rigidity, responsible of Sclg peculiar properties. Although the relative stability of triplex and single strand has already been investigated, different structural details are still missing.In the present study, we analyse the structural properties and the factors stabilizing the single chain and the triple helix of Sclg in different conditions. To this end, we simulated both systems in water and in DMSO. The triple helix has been also simulated in the presence of chemical damages on one of the three strands (to reproduce in silico the effect of sonication) or by inducing a partial unfolding of the triplex structure. The computational results have been compared with experimental evidences in which the triplex denaturation, at alkaline pH values, has been followed by monitoring the UV and CD spectra of Congo red, used as a probe molecule. Our results indicate that sonication breaks the Sclg chains without appreciably changing the stability of the other tracts of triple helix. The simulated perturbed or partially unfolded triplexes show a clear tendency to form less ordered aggregates. Finally, our simulations put in evidence an important role of the hydrophobic interactions both in the triplex stability and in the aggregation processes observed after induced denaturation.

scholarly journals Stability of an RNA•DNA–DNA triple helix depends on base triplet composition and length of the RNA third strand

2019 ◽  
Vol 47 (14) ◽  
pp. 7213-7222 ◽  
Author(s):  
Charlotte N Kunkler ◽  
Jacob P Hulewicz ◽  
Sarah C Hickman ◽  
Matthew C Wang ◽  
Phillip J McCown ◽  
...  
Keyword(s):  
Relative Stability ◽  
Triple Helix ◽  
Multiple Factors ◽  
Dna And Rna ◽  
Helix Formation ◽  
Canonical Base ◽  
Triple Helix Formation ◽  
Triple Helices ◽  
Dna Triple Helix ◽  
The Stability

AbstractRecent studies suggest noncoding RNAs interact with genomic DNA, forming an RNA•DNA–DNA triple helix that regulates gene expression. However, base triplet composition of pyrimidine motif RNA•DNA–DNA triple helices is not well understood beyond the canonical U•A–T and C•G–C base triplets. Using native gel-shift assays, the relative stability of 16 different base triplets at a single position, Z•X–Y (where Z = C, U, A, G and X–Y = A–T, G–C, T–A, C–G), in an RNA•DNA–DNA triple helix was determined. The canonical U•A–T and C•G–C base triplets were the most stable, while three non-canonical base triplets completely disrupted triple-helix formation. We further show that our RNA•DNA–DNA triple helix can tolerate up to two consecutive non-canonical A•G–C base triplets. Additionally, the RNA third strand must be at least 19 nucleotides to form an RNA•DNA–DNA triple helix but increasing the length to 27 nucleotides does not increase stability. The relative stability of 16 different base triplets in DNA•DNA–DNA and RNA•RNA–RNA triple helices was distinctly different from those in RNA•DNA–DNA triple helices, showing that base triplet stability depends on strand composition being DNA and/or RNA. Multiple factors influence the stability of triple helices, emphasizing the importance of experimentally validating formation of computationally predicted triple helices.

scholarly journals Measurement of the Intestinal pH in Mice under Various Conditions Reveals Alkalization Induced by Antibiotics

Antibiotics ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 180
Author(s):  
Kouki Shimizu ◽  
Issei Seiki ◽  
Yoshiyuki Goto ◽  
Takeshi Murata
Keyword(s):  
Antibiotic Treatment ◽  
High Protein Diet ◽  
Intestinal Bacteria ◽  
High Protein ◽  
Protein Diet ◽  
Germ Free ◽  
Treatment Regimens ◽  
Ph Values ◽  
Specific Pathogen ◽  
The Stability

The intestinal pH can greatly influence the stability and absorption of oral drugs. Therefore, knowledge of intestinal pH is necessary to understand the conditions for drug delivery. This has previously been measured in humans and rats. However, information on intestinal pH in mice is insufficient despite these animals being used often in preclinical testing. In this study, 72 female ICR mice housed in SPF (specific pathogen-free) conditions were separated into nine groups to determine the intestinal pH under conditions that might cause pH fluctuations, including high-protein diet, ageing, proton pump inhibitor (PPI) treatment, several antibiotic treatment regimens and germ-free mice. pH was measured in samples collected from the ileum, cecum and colon, and compared to control animals. An electrode, 3 mm in diameter, enabled accurate pH measurements with a small amount of gastrointestinal content. Consequently, the pH values in the cecum and colon were increased by high-protein diet, and the pH in the ileum was decreased by PPI. Drastic alkalization was induced by antibiotics, especially in the cecum and colon. The alkalized pH values in germ-free mice suggested that the reduction in the intestinal bacteria caused by antibiotics led to alkalization. Alkalization of the intestinal pH caused by antibiotic treatment was verified in mice. We need further investigations in clinical settings to check whether the same phenomena occur in patients.

scholarly journals Hoogsteen-position pyrimidines promote the stability and function of the MALAT1 RNA triple helix

RNA ◽  
2016 ◽  
Vol 22 (5) ◽  
pp. 743-749 ◽  
Author(s):  
Jessica A. Brown ◽  
Charles G. Kinzig ◽  
Suzanne J. DeGregorio ◽  
Joan A. Steitz
Keyword(s):  
Triple Helix ◽  
The Stability ◽  
And Function ◽  
Rna Triple Helix

Study on Influence of Silicate Morphology Based on pH Value

2012 ◽  
Vol 454 ◽  
pp. 324-328
Author(s):  
Yan He ◽  
Ya Jing Liu ◽  
Yong Lin Cao ◽  
Li Xia Zhou
Keyword(s):  
Silicic Acid ◽  
Ph Value ◽  
Colorimetric Method ◽  
Absorption Spectrometry ◽  
Degree Of Polymerization ◽  
Raw Material ◽  
X Ray Diffraction ◽  
X Ray ◽  
Ph Values ◽  
The Stability

Infra-red absorption spectrometry, X-ray diffraction observations and characterization tests based on silicon molybdenum colorimetric method were used to investigate the optimal pH value controlling the stability of the silicic acid form. The experiment process was done by using sodium silicate as raw material. The results showed that the solution of silicate influenced the polymerization. The active silicic acid solution with a certain degree of polymerization was obtained by controlling the pH values.

USING MALIC ACID SOLUTIONS FOR THE HYDRATION OF VEGETABLE OILS AND LECITHIN PRODUCTION

2020 ◽  
Author(s):  
Л.А. МАРЧЕНКО ◽  
Т.Н. БОКОВИКОВА ◽  
Е.В. ЛИСОВАЯ ◽  
С.А. ИЛЬИНОВА ◽  
Е.П. ВИКТОРОВА
Keyword(s):  
Malic Acid ◽  
Complex Compounds ◽  
Point Of View ◽  
Magnesium Ions ◽  
Ph Values ◽  
Calcium And Magnesium ◽  
The Stability ◽  
The Cost ◽  
Calcium And Magnesium Ions

Исследована возможность применения яблочной кислоты (ЯК) в качестве гидратирующего агента для перевода негидратируемых форм фосфолипидов в гидратируемые. Выбор ЯК обусловлен ее стоимостью, которая в 1,5 раза меньше стоимости янтарной кислоты, широко применяемой в качестве гидратирующего агента, а также большей доступностью с точки зрения промышленного производства. Исследование процесса комплексообразования и определение состава комплексных соединений ЯК с ионами кальция и магния осуществляли методом потенциометрического титрования. Установлено, что внесение в раствор ЯК ионов кальция и магния приводит к снижению значений рН, что свидетельствует о наличии комплексообразования в указанных системах. Наиболее устойчивыми являются комплексы ионов кальция и магния с непротонированным лигандом при соотношении Ме2 : лиганд 1 : 1. В процессе комплексообразования ионы Ca2 и Mg2 вытесняют протоны только карбоксильных групп ЯК, которая с ионами кальция образует более устойчивые комплексы, чем с ионами магния. Показано, что устойчивость комплексов ЯК с ионами кальция и магния значительно выше, чем устойчивость комплексов фосфатидилсеринов и фосфатидных кислот с указанными ионами. Использование водных растворов ЯК в качестве гидратирующего агента позволит повысить эффективность процесса гидратации и увеличить выход фосфолипидов и, следовательно, готового продукта лецитина. The possibility of using malic acid (MA) as a hydrating agent for converting non-hydrated forms of phospholipids into hydrated ones has been investigated. The choice of MA is due to its cost, which is 1,5 times less than the cost of succinic acid, as well as greater availability from the point of view of industrial production. The study of the complexation process and determination of the composition of complex compounds of MA with calcium and magnesium ions was carried out by the method of potentiometric titration. It was found that the introduction of calcium and magnesium ions into the MA solution leads to a decrease in pH values, which indicates the presence of complexation in these systems. Complexes of calcium and magnesium ions with an unprotected ligand at a ratio of ME2 : ligand 1 : 1 are the most stable. In the process of complexing, Ca2 and Mg2 ions displace protons only of the carboxyl groups of MA, which forms more stable complexes with calcium ions than with magnesium ions. It is shown that the stability of MA complexes with calcium and magnesium ions is significantly higher than the stability of phosphatidylserine and phosphatidic acid complexes with these ions. Using water solutions of MA as a hydrating agent will increase the efficiency of the hydration process and increase the yield of phospholipids and, consequently, the finished product lecithin.

scholarly journals A model of nonlinear DNA-protein interaction system with Cornell potential and its stability

2017 ◽  
Vol 1 (1) ◽  
pp. 62
Author(s):  
Edy Syahroni ◽  
A Suparmi ◽  
C Cari ◽  
Fuad Anwar
Keyword(s):  
Protein Interaction ◽  
Interaction Model ◽  
The State ◽  
Hamiltonian Equation ◽  
Single Chain ◽  
Cornell Potential ◽  
Interaction System ◽  
Dna Protein Interaction ◽  
Dna Chain ◽  
The Stability

<p class="Abstract">The purpose of this study was to determine the model of a interaction system between the DNA with protein. The interaction system consisted of a molecule of protein bound with a single chain of DNA. The interaction between DNA chain, especially adenine and thymine, and DNA-protein bound to glutamine and adenine. The forms of these bonds are adapted from the hydrogen bonds. The Cornell potential was used to describe both of the interactions. We proposed the Hamiltonian equation to describe the general model of interaction. Interaction system is divided into three parts. The interaction model is satisfied when a protein molecule triggers pulses on a DNA chain. An initial shift in position of protein xm should trigger the shift in position of DNA ym, or alter the state. However, an initial shift in DNA, yn, should not alter the state of a rest protein (i.e. xm = 0), otherwise, the protein would not steadily bind. We also investigated the stability of the model from the DNA-protein interaction with Lyapunov function. The stability of system can be determined when we obtained the equilibrium point.</p>

Abstract 434: A Novel 5-Step Model for the Mechanism of ABCA1-Mediated Nascent HDL Biogenesis

2012 ◽  
Vol 32 (suppl_1) ◽  
Author(s):  
Shuhui Wang ◽  
Gregory Brubaker ◽  
Kailash Gulshan ◽  
Jonathan D Smith
Keyword(s):  
Plasma Membrane ◽  
Membrane Lipids ◽  
Sodium Taurocholate ◽  
Hek293 Cells ◽  
Membrane Remodeling ◽  
Fluorescent Indicators ◽  
Step Model ◽  
Partial Unfolding ◽  
Cell Membrane Protein ◽  
Partially Unfolded

Objective— Lipid-poor apoA-I acts as an acceptor for cell cholesterol and phospholipids via the cell membrane protein ABCA1, generating nascent HDL. However, the mechanism of this process is not understood at the molecular level. Methods and Results— We propose a novel five-step model of nascent HDL biogenesis: ABCA1 remodeling of the plasma membrane lipids exposing phosphatidylserine and apoA-I binding to ABCA1 are the first two independent steps; third, ABCA1 facilitates apoA-I partial unfolding; forth, partially unfolded apoA-I inserts into the modified plasma membrane resulting in apoA-I lipidation; and fifth, nascent HDL is released from the cell. We created fluorescent apoA-I indicators that can monitor apoA-I unfolding and lipidation states. In cell free assays of reconstituted HDL (rHDL) generation from apoAI and DMPC liposomes, the fluorescent indicators demonstrated apoA-I unfolding and lipidation concurrent with rHDL formation. Next, HEK293 cells were stably transfected with different ABCA1 vectors encoding wild type (WT) and W590S and C1477R Tangier disease mutation isoforms. WT ABCA1 mediated cholesterol efflux to apoA-I (requires all steps) and sodium taurocholate (NaTC, requires only the membrane remodeling step,). Although neither mutant could efflux cholesterol efficiently to apoA-I, they were blocked at different steps. The W590S mutant bound apoAI but could not efflux cholesterol to NaTC, thus it was blocked at the membrane remodeling step. However, the C1477R mutant could not bind apoAI but could efflux cholesterol to NaTC, thus its activity was blocked at the apoAI binding step. When the lipidation indicator apoA-I was incubated with stably transfected HEK cells, we observed cell associated lipidated apoA-I in cells expressing WT ABCA1, but mostly unlipidated apoA-I was associated with the cells expressing W590S ABCA1. Conclusion— Our results support a novel five-step model for nascent HDL biogenesis: 1, 2) ABCA1 remodeling of the plasma membrane and apoA-I binding to ABCA1, which facilitate 3) apoA-I partial unfolding and 4) and lipidation by the remodeled membrane, followed by 5) the release of nascent HDL.

Stability and Complexation of Cyanidin-3-Giucoside and Raspberry Juice Extract in the Presence of Selected Cations

1981 ◽  
Vol 44 (7) ◽  
pp. 516-523 ◽  
Author(s):  
D. G. COFFEY ◽  
F. M. CLYDESDALE ◽  
F. J. FRANCIS ◽  
R. A. DAMON
Keyword(s):  
Complex Formation ◽  
Metal Ions ◽  
Ph Values ◽  
Hue Angle ◽  
The Stability ◽  
Similar Complex

The stability and color of purified cyanidin-3-glucoside and raspberry juice extract in the presence of selected metal ions was investigated. Production of metal-anthocyanin complexes was suggested by changes in color of the samples as shown by L, a, and hue angle values. Complex formation was indicated by HPLC in raspberry juice samples treated with Sn++ but not in samples of purified cyanidin-3-glucoside. According to the colorimetric values, complex formation occurs with cyanidin-3-glucoside and A1+++ at pH 2.0 and 3.0 and with Sn++ at pH 4.0 and 3.0. Similar complex formation occurs with these metals and raspberry juice extract at the same respective pH values.

scholarly journals Stability of Kiwi Varieties of ‘Hayward’ in Powder During Storage

2020 ◽  
Vol 8 (2) ◽  
pp. 150
Author(s):  
Inacia Dos Santos Moreira ◽  
Jacinete Pereira Lima ◽  
Deise Souza de Castro ◽  
Wilton Pereira da Silva ◽  
Josivanda Palmeira Gomes ◽  
...  
Keyword(s):  
Water Activity ◽  
Bioactive Compounds ◽  
Titratable Acidity ◽  
Physicochemical Characteristics ◽  
Soluble Solids ◽  
Total Chlorophyll ◽  
Lower Content ◽  
Total Water ◽  
Ph Values ◽  
The Stability

For the preservation of products obtained by dehydration, it is necessary to evaluate their physicochemical characteristics during storage. It was proposed, in the present study, to evaluate the stability of the kiwi cv. ‘Hayward’ powder, obtained at temperatures of 60 and 70 °C during its storage in laminated packages under controlled conditions of temperature (25 ºC) and relative humidity (75%) for 90 days. The parameter’s evaluated were: moisture content, ashes, soluble solids, titratable acidity (% citric acid), pH, water activity at 25 ºC, color for the parameters lightness (L*) and chromaticity (+a* red; -a* green; +b* yellow; and -b* blue), phenolic compounds, flavonoids, total chlorophyll and carotenoids. It was observed that, after the 90 days, for the powder obtained at 70 °C, the soluble solids and pH values were altered by the storage, which did not occur for the powder obtained at 60 °C. For both powders, the content of ash and bioactive compounds were not affected by storage. The parameter of lightness decreased in both powders. The powder obtained at 70 ºC proved to be better, showing lower content of moisture and total water activity, as well as the highest values of bioactive compounds.

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