Temperature-induced unfolding pathway of a type III antifreeze protein: Insight from molecular dynamics simulation

Kundu, Subrata; Roy, Dilip

doi:10.1016/j.jmgm.2008.03.002

Cited by 29 publications

(21 citation statements)

References 22 publications

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“…The RMSD of protein backbone atoms measured over the course of simulation is usually used as a measure of the conformational stability of the protein [33,34]. RMSD plots of Hirudin and the mutants are shown in Fig.…”

Section: Rmsdmentioning

confidence: 99%

“…The radius of gyration (Rg) gives an insight into the overall dimensions of the protein [33,34]. The radius of gyration of the proteins versus time is shown in Fig.…”

Section: Radius Of Gyrationmentioning

confidence: 99%

“…Specific details on differences in residue mobility can be obtained from graphs of the root mean-square fluctuations (RMSF) of Ca atoms relative to the average structure [33,34]. These fluctuations have been calculated for native and mutants (Fig.…”

Section: Rmsfmentioning

confidence: 99%

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Rational design of stable and functional hirudin III mutants with lower antigenicity

et al. 2015

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Section: Rmsdmentioning

confidence: 99%

“…The radius of gyration (Rg) gives an insight into the overall dimensions of the protein [33,34]. The radius of gyration of the proteins versus time is shown in Fig.…”

Section: Radius Of Gyrationmentioning

confidence: 99%

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Rational design of stable and functional hirudin III mutants with lower antigenicity

et al. 2015

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“…The radius of gyration (Rg) is defined as the mass-weight root mean square distance of a collection of atoms from their common center of mass (Kundu and Roy, 2008). Hence, this analysis gives us insight into the overall dimensions of the proteins.…”

Section: Rgmentioning

confidence: 99%

Insights into the human A1 adenosine receptor from molecular dynamics simulation: structural study in the presence of lipid membrane

et al. 2015

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Homology modeling, molecular docking and molecular dynamics (MD) simulation methods were used to build a reliable model for A 1 AR (as one of the G protein-coupled receptors-GPCRs) and to explore the structural features and binding mechanism of ligands to this receptor. A model of A 1 AR was built and inserted in a hydrated lipid bilayer, and 20-ns MD simulation was performed to examine the stability of the best model. In this study, RG-14718 as the best A 1 AR agonist and bamifylline as a selective antagonist of A 1 AR have been docked into the active site of the A 1 AR. After docking, two 20-ns MD simulation was performed on the A 1 ARligand complex to explore effects of the presence of lipid membrane in the vicinity of the A 1 AR-ligand complex. At the end of the MD simulation, a change in the position and orientation of the ligand in the binding site was observed. This important observation indicated that the application of MD simulation after docking of ligands is useful. Thr270, His278 and Asn70 were crucial residues for hydrogen bonds with these ligands. Phe171, Glu172, Tyr271 and Ile274 were determined to be involved in ligand-receptor binding. The results obtained are in good agreement with most of the site-directed mutagenesis data reported by others. Our results show that molecular modeling and rational drug design for adenosine targets is a possible approach.

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“…The TxT sequence of most insect AFPs is a good example of such a repeated region. The hydroxyl groups found on the Thr residues are able to create hydrogen bonds (Jia et al, 1996;Chen and Jia, 1999;Kundu and Roy, 2008) with the water molecules found at the surface of hexagonal ice crystals. The binding affinity between AFP and ice differs in insects and fish.…”

Section: Binding To Icementioning

confidence: 99%

Controlling the Freezing Process with Antifreeze Proteins

Ramløv

Johnsen

2014

Emerging Technologies for Food Processing

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Temperature-induced unfolding pathway of a type III antifreeze protein: Insight from molecular dynamics simulation

Cited by 29 publications

References 22 publications

Rational design of stable and functional hirudin III mutants with lower antigenicity

Rational design of stable and functional hirudin III mutants with lower antigenicity

Insights into the human A1 adenosine receptor from molecular dynamics simulation: structural study in the presence of lipid membrane

Controlling the Freezing Process with Antifreeze Proteins

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