scholarly journals Molecular basis of Arginine and Lysine DNA sequence-dependent thermo-stability modulation

2022 ◽  
Vol 18 (1) ◽  
pp. e1009749
Author(s):  
Benjamin Martin ◽  
Pablo D. Dans ◽  
Milosz Wieczór ◽  
Nuria Villegas ◽  
Isabelle Brun-Heath ◽  
...  
Keyword(s):  
Amino Acids ◽  
Double Helix ◽  
Dna Oligomers ◽  
Organic Ions ◽  
Sequence Dependent ◽  
Structure Flexibility ◽  
The Difference ◽  
The Stability ◽  
Thermo Stability

We have used a variety of theoretical and experimental techniques to study the role of four basic amino acids–Arginine, Lysine, Ornithine and L-2,4-Diaminobutyric acid–on the structure, flexibility and sequence-dependent stability of DNA. We found that the presence of organic ions stabilizes the duplexes and significantly reduces the difference in stability between AT- and GC-rich duplexes with respect to the control conditions. This suggests that these amino acids, ingredients of the primordial soup during abiogenesis, could have helped to equalize the stability of AT- and GC-rich DNA oligomers, facilitating a general non-catalysed self-replication of DNA. Experiments and simulations demonstrate that organic ions have an effect that goes beyond the general electrostatic screening, involving specific interactions along the grooves of the double helix. We conclude that organic ions, largely ignored in the DNA world, should be reconsidered as crucial structural elements far from mimics of small inorganic cations.

scholarly journals Pengaruh Biopolimer Pada Stabilitas Lereng Swelling soil

2021 ◽  
Vol 5 (3) ◽  
pp. 307-316
Author(s):  
Dewi Amalia ◽  
Bagus Guritno ◽  
Geni Firuliadhim
Keyword(s):  
Stability Analysis ◽  
Slope Stability ◽  
Safety Factor ◽  
Soil Type ◽  
Analysis Program ◽  
Swelling Soil ◽  
The Difference ◽  
The Stability ◽  
Cracked Soil

Many studies have begun to develop the concept of cracked soil. The results of research related to cracked soil are able to answer the irregularities that occur, such as the difference in the results of the stability analysis which is considered safe with the conventional bishop method, while the conditions in the field are landslides. Swelling soil is soil that is susceptible to changes in water content. This type of soil is very prone to cracking. To build infrastructure on the swelling soil type, an improvement must be made, one of which is by mixing the swelling soil with biopolymer. The results of this biopolymer mixing are then modeled in the New Slope Stability Analysis Program (NSSAP) 1.0 which refers to the concept of cracked soil. From the analysis, it was found that the slope safety factor before improvement with biopolymer was 0.305 and the safety factor after improvement with biopolymer was 2.006. From the results of this study, it can be seen that the role of biopolymers in stabilizing swelling soil is quite large, which is around 558%.

The role of divalent cations in the activation of the NADP+-specific isocitrate dehydrogenase from Pisum sativum L.

1977 ◽  
Vol 55 (9) ◽  
pp. 928-934 ◽  
Author(s):  
Robert J. Maloney ◽  
David T. Dennis
Keyword(s):  
Ionic Strength ◽  
Stability Constants ◽  
Isocitrate Dehydrogenase ◽  
Divalent Cations ◽  
Free Form ◽  
Saturation Kinetics ◽  
The Difference ◽  
The Stability ◽  
Kinetics Of

A divalent cation electrode was used to measure the stability constants (association constants) for the magnesium and manganese complexes of the substrates for the NADP+-specific isocitrate dehydrogenase (EC 1.1.1.42) from pea stems. At an ionic strength of 26.5 mM and at pH 7.4 the stability constants for the Mg2+–isocitrate and Mg2+–NADP+ complexes were 0.85 ± 0.2 and 0.43 ± 0.04 mM−1 respectively and for the Mn2+–isocitrate and Mn2+–NADP+ complexes they were 1.25 ± 0.07 and 0.75 ± 0.09 mM−1 respectively. At the same ionic strength but at pH 6.0 the Mg2+–NADPH and Mn2+–NADPH complexes had stability constants of 0.95 ± 0.23 and 1.79 ± 0.34 mM−1 respectively. Oxalosuccinate and α-ketoglutarate do not form measureable complexes under these conditions. Saturation kinetics of the enzyme with respect to isocitrate and metal ions are consistent with the metal–isocitrate complex being the substrate for the enzyme. NADP+ binds to the enzyme in the free form. Saturation kinetics of NADPH and Mn2+ indicate that the metal–NADPH complex is the substrate in the reverse reaction. In contrast the pig heart enzyme appears to bind free NADPH and Mn2+. A scheme for the reaction mechanism is presented and the difference between the reversibility of the NAD+ and NADP+ enzyme is discussed in relation to the stability of the NADH and NADPH metal complexes.

scholarly journals DNA partitions into triplets under tension in the presence of organic cations, with sequence evolutionary age predicting the stability of the triplet phase

2017 ◽  
Vol 50 ◽  
Author(s):  
Amirhossein Taghavi ◽  
Paul van der Schoot ◽  
Joshua T. Berryman
Keyword(s):  
Amino Acids ◽  
Double Helix ◽  
Phase 1 ◽  
Weak Form ◽  
Organic Salt ◽  
Atomistic Calculations ◽  
Function Relationship ◽  
The Stability ◽  
World Hypothesis ◽  
Alignment Errors

AbstractUsing atomistic simulations, we show the formation of stable triplet structure when particular GC-rich DNA duplexes are extended in solution over a timescale of hundreds of nanoseconds, in the presence of organic salt. We present planar-stacked triplet disproportionated DNA (Σ DNA) as a possible solution phase of the double helix under tension, subject to sequence and the presence of stabilising co-factors. Considering the partitioning of the duplexes into triplets of base pairs as the first step of operation of recombinase enzymes like RecA, we emphasise the structure–function relationship in Σ DNA. We supplement atomistic calculations with thermodynamic arguments to show that codons for ‘phase 1’ amino acids (those appearing early in evolution) are more likely than a lower entropy GC-rich sequence to form triplets under tension. We further observe that the four amino acids supposed (in the ‘GADV world’ hypothesis) to constitute the minimal set to produce functional globular proteins have the strongest triplet-forming propensity within the phase 1 set, showing a series of decreasing triplet propensity with evolutionary newness. The weak form of our observation provides a physical mechanism to minimise read frame and recombination alignment errors in the early evolution of the genetic code.

Deciphering role of amino acids for the stability of Staphylococcus aureus lipase (SAL3)

2010 ◽  
Vol 2 (3) ◽  
pp. 271-279 ◽  
Author(s):  
Saravanan Patameswaran ◽  
Alpana Ankush Throat ◽  
Sanjukta Patra
Keyword(s):  
Amino Acids ◽  
Staphylococcus Aureus ◽  
The Stability

scholarly journals Arginine-Amino Acid Interactions and Implications to Protein Solubility and Aggregation

2015 ◽  
Vol 12 (2) ◽  
pp. 1 ◽  
Author(s):  
A. R. Shaikh ◽  
D. Shah
Keyword(s):  
Amino Acids ◽  
Protein Interactions ◽  
Density Functional ◽  
Protein Solubility ◽  
Aromatic Amino Acids ◽  
Hydrogen Bond Interactions ◽  
Stable Clusters ◽  
Pharmaceutical Industries ◽  
The Stability

Arginine, useful in protein refolding, solubilization of proteins, and suppression of protein aggregation and non-specific adsorption during formulation and purification, is a ubiquitous additive in the biotechnology and pharmaceutical industries. In order to provide a framework for analyzing the molecular level mechanisms behind arginine/protein interactions in the above context, density functional theory was used to systematically examine how arginine interacts with naturally occurring amino acids. The results show that the most favorable interaction of arginine is with acidic amino acids and arises from charge interactions and hydrogen-bond interactions. Arginine is also shown to form stacking and T-shaped structures with aromatic amino acids, the types of cation–p and N–H…p interactions, respectively, known to be important contributors to protein stability. The analysis also shows that arginine-arginine interactions lead to stable clusters, with the stability of the clusters arising from the stacking of the guanidinium part of arginine. The results show that the unique ability of arginine to form clusters with itself makes it an effective aggregation suppressant and support the interpretations of the current study using experimental and molecular dynamics results available in the literature. The results also contribute to understanding the role of arginine in increasing protein solubility, imparting thermal stability of important enzymes, and designing better additives.  

Characterization and Prediction of Presynaptic and Postsynaptic Neurotoxin by Reduced Amino Acid and Biological Property.

2020 ◽  
Vol 15 ◽  
Author(s):  
Yiyin Cao ◽  
Chunlu Yu ◽  
Shenghui Huang ◽  
Shiyuan Wang ◽  
Yongchun Zuo ◽  
...  
Keyword(s):  
Amino Acids ◽  
Support Vector Machine ◽  
Amino Acid ◽  
Biological Properties ◽  
Statistical Test ◽  
Support Vector ◽  
Reduced Amino Acid Alphabet ◽  
The Difference ◽  
Amino Acid Alphabet

Background: Presynaptic and postsynaptic neurotoxins are two important neurotoxins. Due to the important role of presynaptic and postsynaptic neurotoxins in pharmacology and neuroscience, identification of them becomes very important in biology. Method: In this study, the statistical test and F-score were used to calculate the difference between amino acids and biological properties. The support vector machine was used to predict the presynaptic and postsynaptic neurotoxins by using the reduced amino acid alphabet types. Results: By using the reduced amino acid alphabet as the input parameters of support vector machine, the overall accuracy of our classifier had increased to 91.07%, which was the highest overall accuracy in this study. When compared with the other published methods, better predictive results were obtained by our classifier. Conclusion: In summary, we analyzed the differences between two neurotoxins in amino acids and biological properties, and constructed a classifier that could predict these two neurotoxins by using the reduced amino acid alphabet.

scholarly journals The role of OX40L and ICAM-1 in the stability of coronary atherosclerotic plaques and their relationship with sudden coronary death

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Yu Wang ◽  
Xiaoyu Sun ◽  
Bing Xia ◽  
Cuiyun Le ◽  
Zhu Li ◽  
...  
Keyword(s):  
Atherosclerotic Plaque ◽  
Control Group ◽  
Coronary Death ◽  
Sudden Coronary Death ◽  
Increasing Trend ◽  
Coronary Atherosclerotic Plaque ◽  
The Difference ◽  
The Stability ◽  
Experimental Group

Abstract Background Coronary heart disease is related to sudden death caused by multi-factors and a major threat to human health.This study explores the role of OX40L and ICAM-1 in the stability of coronary plaques and their relationship with sudden coronary death. Methods A total of 118 human coronary arteries with different degrees of atherosclerosis and/or sudden coronary death comprised the experimental group and 28 healthy subjects constituted the control group were isolated from patients. The experimental group was subdivided based on whether the cause of death was sudden coronary death and whether it was accompanied by thrombosis, plaque rupture, plaque outflow and other secondary changes: group I: patients with coronary atherosclerosis but not sudden coronary death, group II: sudden coronary death without any of the secondary changes mentioned above, group III: sudden coronary death with coronary artery atherosclerotic lesions accompanied by either of the above secondary changes. The histological structure of the coronary artery was observed under a light microscope after routine HE staining, and the related indexes of atherosclerotic plaque lesions were assessed by image analysis software. The expressions of OX40L and ICAM-1 were detected by real-time quantitative PCR (RT-PCR), immunohistochemistry (IHC) and Western blotting, and the correlations between the expressions and the stability of coronary atherosclerotic plaque and sudden coronary death were analyzed. Results (1) The expression of OX40L protein in the control group and the three experimental groups showed an increasing trend, and the difference between groups was statistically significant (P < 0.05). (2) The expression of the ICAM-1 protein in the control group and the three experimental groups showed a statistically significant (P < 0.05) increasing trend. (3) The expression of OX40L and ICAM-1 mRNAs increased in the control and the three experimental groups and the difference was statistically significant (P < 0.05). Conclusion The expression of OX40L and ICAM-1 proteins and mRNAs is positively correlated with the stability of coronary atherosclerotic plaque and sudden coronary death.

scholarly journals The C-terminal region affects the activity of photoactivated adenylyl cyclase from Oscillatoria acuminata

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Minako Hirano ◽  
Masumi Takebe ◽  
Tomoya Ishido ◽  
Toru Ide ◽  
Shigeru Matsunaga
Keyword(s):  
Amino Acids ◽  
Adenylyl Cyclase ◽  
Light Exposure ◽  
Terminal Region ◽  
Light Sensing ◽  
Spectral Shifts ◽  
The Difference ◽  
High Degree ◽  
Photoactivated Adenylyl Cyclase

AbstractPhotoactivated adenylyl cyclase (PAC) is a unique protein that, upon blue light exposure, catalyzes cAMP production. The crystal structures of two PACs, from Oscillatoria acuminata (OaPAC) and Beggiatoa sp. (bPAC), have been solved, and they show a high degree of similarity. However, the photoactivity of OaPAC is much lower than that of bPAC, and the regulatory mechanism of PAC photoactivity, which induces the difference in activity between OaPAC and bPAC, has not yet been clarified. Here, we investigated the role of the C-terminal region in OaPAC, the length of which is the only notable difference from bPAC. We found that the photoactivity of OaPAC was inversely proportional to the C-terminal length. However, the deletion of more than nine amino acids did not further increase the activity, indicating that the nine amino acids at the C-terminal critically affect the photoactivity. Besides, absorption spectral features of light-sensing domains (BLUF domains) of the C-terminal deletion mutants showed similar light-dependent spectral shifts as in WT, indicating that the C-terminal region influences the activity without interacting with the BLUF domain. The study characterizes new PAC mutants with modified photoactivities, which could be useful as optogenetics tools.

scholarly journals D-Retro Inverso (DRI) Amylin and the Stability of Amylin Fibrils

2020 ◽  
Author(s):  
Preeti Pandey ◽  
Natalie Nguyen ◽  
Ulrich H.E. Hansmann
Keyword(s):  
Molecular Dynamics ◽  
Amino Acids ◽  
Type Ii Diabetes ◽  
Type Ii ◽  
Fibril Structure ◽  
Elongation Process ◽  
The Stability ◽  
Dynamics Simulations ◽  
Potential Use

AbstractMotivated by the role that amylin aggregates pay in type-II diabetes, we compare the stability of regular amylin fibrils with the stability of fibrils where L-amino acid chains are replaced by D-Retro Inverso (DRI) amylin, i.e., peptides where the sequence of amino acids is reversed, and at the same time the L-amino acids are replaced by their mirror images. Our molecular dynamics simulations show that despite leading to only marginal difference in fibril structure and stability, aggregating DRI-amylin peptides have different pattern of contacts and hydrogen bonding. Because of these differences does DRI-amylin, when interacting with regular (L) amylin, alter the elongation process and lowers the stability of hybrid amylin fibrils. Our results suggest not only a potential use of DRI-amylin as inhibitor of amylin fibril-formation, but points also to the possibility of using insertion of DRI-proteins in L-assemblies as a way to probe the role of certain kinds of hydrogen bonds in supra-molecular assemblies or aggregates.

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