Structural stability of myoglobin and glycomyoglobin: a comparative molecular dynamics simulation study

Alizadeh-Rahrovi, Joulia; Shayesteh, Alireza; Ebrahim‐Habibi, Azadeh

doi:10.1007/s10867-015-9383-2

Cited by 17 publications

(8 citation statements)

References 32 publications

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“…The different behavior of myoglobin versus hemoglobin glycation is interesting to note since it was previously highlighted by a comparative study on the structural stability of myoglobin and glycomyoglobin [ 33 ]. The molecular dynamics simulation study revealed an increased stability in the glycomyoglobin molecule as a consequence of increased contacts with water molecules.…”

Section: Resultsmentioning

confidence: 99%

Modifications of hemoglobin and myoglobin by Maillard reaction products (MRPs)

Ioannou¹,

Varotsis²

2017

PLoS ONE

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High performance liquid chromatography (HPLC) coupled with a Fraction Collector was employed to isolate Maillard reaction products (MRPs) formed in model systems comprising of asparagine and monosaccharides in the 60–180°C range. The primary MRP which is detected at 60°C is important for Acrylamide content and color/aroma development in foods and also in the field of food biotechnology for controlling the extent of the Maillard reaction with temperature. The discrete fractions of the reaction products were reacted with Hemoglobin (Hb) and Myoglobin (Mb) at physiological conditions and the reaction adducts were monitored by UV-vis and Attenuated Total Reflection-Fourier transform infrared (FTIR) spectrophotometry. The UV-vis kinetic profiles revealed the formation of a Soret transition characteristic of a low-spin six-coordinated species and the ATR-FTIR spectrum of the Hb-MRP and Mb-MRP fractions showed modifications in the protein Amide I and II vibrations. The UV-vis and the FTIR spectra of the Hb-MRPs indicate that the six-coordinated species is a hemichrome in which the distal E7 Histidine is coordinated to the heme Fe and blocks irreversibly the ligand binding site. Although the Mb-MRPs complex is a six-coordinated species, the 1608 cm-1 FTIR band characteristic of a hemichrome was not observed.

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Section: Resultsmentioning

confidence: 99%

Modifications of hemoglobin and myoglobin by Maillard reaction products (MRPs)

Ioannou¹,

Varotsis²

2017

PLoS ONE

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“…It is suggested that enzymes keep their structural stability by various kinds of non-covalent interactions, such as hydrogen bonds, salt bridges, disulfide bonds, and hydrophobic interaction (Nick Pace et al, 2014;Nilofer et al, 2017). Recently, molecular dynamics (MD) simulation, as a useful tool, has been widely applied to find important characteristics of protein stability (Alizadeh-Rahrovi et al, 2015;Sharma and Sastry, 2015;Jiang et al, 2016;Idrees et al, 2017;Gu et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

Understanding Thermostability Factors of Barley Limit Dextrinase by Molecular Dynamics Simulations

Dong²,

et al. 2020

Front. Mol. Biosci.

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Limit dextrinase (LD) is the only endogenous starch-debranching enzyme in barley (Hordeum vulgare, Hv), which is the key factor affecting the production of a high degree of fermentation. Free LD will lose its activity in the mashing process at high temperature in beer production. However, there remains a lack of understanding on the factor affecting the themostability of HvLD at the atomic level. In this work, the molecular dynamics simulations were carried out for HvLD to explore the key factors affecting the thermal stability of LD. The higher value of root mean square deviation (RMSD), radius of gyration (R g), and surface accessibility (SASA) suggests the instability of HvLD at high temperatures. Intra-protein hydrogen bonds and hydrogen bonds between protein and water decrease at high temperature. Long-lived hydrogen bonds, salt bridges, and hydrophobic contacts are lost at high temperature. The salt bridge interaction analysis suggests that these salt bridges are important for the thermostability of HvLD, including E568-R875, D317-R378, D803-R884, D457-R214, D468-R395, D456-R452, D399-R471, and D541-R542. Root mean square fluctuation (RMSF) analysis identified the thermal-sensitive regions of HvLD, which will facilitate enzyme engineering of HvLD for enhanced themostability.

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“…A longer trajectory ensures investigation over well-thermalized systems [ 25 ]. Alizadeh-Rahrovi et al also reported a lower value of RMSD contributed to structural stability [ 26 ]. The influence of terminal moiety to the enzyme stability also been study by the L1 lipase using the same method (MD).…”

Section: Resultsmentioning

confidence: 99%

The Effect of N-Terminal Domain Removal towards the Biochemical and Structural Features of a Thermotolerant Lipase from an Antarctic Pseudomonas sp. Strain AMS3

Latip

Rahman

Leow

et al. 2018

IJMS

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Lipase plays an important role in industrial and biotechnological applications. Lipases have been subject to modification at the N and C terminals, allowing better understanding of lipase stability and the discovery of novel properties. A thermotolerant lipase has been isolated from Antarctic Pseudomonas sp. The purified Antarctic AMS3 lipase (native) was found to be stable across a broad range of temperatures and pH levels. The lipase has a partial Glutathione-S-transferase type C (GST-C) domain at the N-terminal not found in other lipases. To understand the influence of N-terminal GST-C domain on the biochemical and structural features of the native lipase, the deletion of the GST-C domain was carried out. The truncated protein was successfully expressed in E. coli BL21(DE3). The molecular weight of truncated AMS3 lipase was approximately ~45 kDa. The number of truncated AMS3 lipase purification folds was higher than native lipase. Various mono and divalent metal ions increased the activity of the AMS3 lipase. The truncated AMS3 lipase demonstrated a similarly broad temperature range, with the pH profile exhibiting higher activity under alkaline conditions. The purified lipase showed a substrate preference for a long carbon chain substrate. In addition, the enzyme activity in organic solvents was enhanced, especially for toluene, Dimethylsulfoxide (DMSO), chloroform and xylene. Molecular simulation revealed that the truncated lipase had increased structural compactness and rigidity as compared to native lipase. Removal of the N terminal GST-C generally improved the lipase biochemical characteristics. This enzyme may be utilized for industrial purposes.

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Structural stability of myoglobin and glycomyoglobin: a comparative molecular dynamics simulation study

Cited by 17 publications

References 32 publications

Modifications of hemoglobin and myoglobin by Maillard reaction products (MRPs)

Modifications of hemoglobin and myoglobin by Maillard reaction products (MRPs)

Understanding Thermostability Factors of Barley Limit Dextrinase by Molecular Dynamics Simulations

The Effect of N-Terminal Domain Removal towards the Biochemical and Structural Features of a Thermotolerant Lipase from an Antarctic Pseudomonas sp. Strain AMS3

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