Conformational analysis on the wild type and mutated forms of human ORF1p: a molecular dynamics study

2015 ◽  
Vol 11 (7) ◽  
pp. 1987-1999 ◽  
Author(s):  
Rajagopalan Muthukumaran ◽  
Balasubramanian Sangeetha ◽  
Ramaswamy Amutha
Keyword(s):  
Molecular Dynamics ◽  
Complex Formation ◽  
Conformational Analysis ◽  
Structural Dynamics ◽  
Wild Type ◽  
Ribonucleoprotein Complex

Structural dynamics of human ORF1p emphasizes the role of Tyr282 in regulating ribonucleoprotein complex formation.

Role of tryptophan 135 of Chandipura virus phosphoprotein P in dimerization and complex formation with leader RNA: structural aspect using time resolved anisotropy and simulation

RSC Advances ◽  
2015 ◽  
Vol 5 (126) ◽  
pp. 104582-104593
Author(s):  
Manini Mukherjee ◽  
Aditya Sarkar ◽  
Arunava Roy ◽  
Pinki Saha Sardar ◽  
Ansuman Lahiri ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Structural Change ◽  
Complex Formation ◽  
Protein Concentration ◽  
Structural Aspect ◽  
Wild Type ◽  
Time Resolved ◽  
Type Protein ◽  
Wild Type Protein

The nanosecond and picosecond dynamics of wild type protein and its tryptophan mutants have been used to study structural change as a function of protein concentration and binding with leader RNA by time resolved anisotropy and molecular dynamics.

scholarly journals Molecular Dynamics of Chloroplast Membranes Isolated from Wild-Type Barley and a Brassinosteroid-Deficient Mutant Acclimated to Low and High Temperatures

Biomolecules ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 27
Author(s):  
Iwona Sadura ◽  
Dariusz Latowski ◽  
Jana Oklestkova ◽  
Damian Gruszka ◽  
Marek Chyc ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Temperature Stress ◽  
High Temperatures ◽  
Biological Membrane ◽  
Hydrophobic Core ◽  
Wild Type ◽  
Chloroplast Membranes ◽  
Paramagnetic Resonance ◽  
Photosynthetic Membranes

Plants have developed various acclimation strategies in order to counteract the negative effects of abiotic stresses (including temperature stress), and biological membranes are important elements in these strategies. Brassinosteroids (BR) are plant steroid hormones that regulate plant growth and development and modulate their reaction against many environmental stresses including temperature stress, but their role in modifying the properties of the biological membrane is poorly known. In this paper, we characterise the molecular dynamics of chloroplast membranes that had been isolated from wild-type and a BR-deficient barley mutant that had been acclimated to low and high temperatures in order to enrich the knowledge about the role of BR as regulators of the dynamics of the photosynthetic membranes. The molecular dynamics of the membranes was investigated using electron paramagnetic resonance (EPR) spectroscopy in both a hydrophilic and hydrophobic area of the membranes. The content of BR was determined, and other important membrane components that affect their molecular dynamics such as chlorophylls, carotenoids and fatty acids in these membranes were also determined. The chloroplast membranes of the BR-mutant had a higher degree of rigidification than the membranes of the wild type. In the hydrophilic area, the most visible differences were observed in plants that had been grown at 20 °C, whereas in the hydrophobic core, they were visible at both 20 and 5 °C. There were no differences in the molecular dynamics of the studied membranes in the chloroplast membranes that had been isolated from plants that had been grown at 27 °C. The role of BR in regulating the molecular dynamics of the photosynthetic membranes will be discussed against the background of an analysis of the photosynthetic pigments and fatty acid composition in the chloroplasts.

scholarly journals Conformational effects of Lys191 in the human GnRH receptor: mutagenesis and molecular dynamics simulations studies

2009 ◽  
Vol 201 (2) ◽  
pp. 297-307 ◽  
Author(s):  
Eduardo Jardón-Valadez ◽  
Arturo Aguilar-Rojas ◽  
Guadalupe Maya-Núñez ◽  
Alfredo Leaños-Miranda ◽  
Ángel Piñeiro ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Dynamic Behavior ◽  
Gnrh Receptor ◽  
Receptor Trafficking ◽  
Wild Type ◽  
Conformational Effects ◽  
Dynamics Simulations ◽  
And Function

In the present study, we analyzed the role of Lys191 on function, structure, and dynamic behavior of the human GnRH receptor (hGnRHR) and the formation of the Cys14–Cys200 bridge, which is essential for receptor trafficking to the plasma membrane. Several mutants were studied; mutants lacked either the Cys14–Cys200 bridge, Lys191 or both. The markedly reduced expression and function of a Cys14Ser mutant lacking the 14–200 bridge, was nearly restored to wild-type/ΔLys191 levels upon deletion of Lys191. Lys191 removal resulted in changes in the dynamic behavior of the mutants as disclosed by molecular dynamics simulations: the distance between the sulfur- (or oxygen-) sulfur groups of Cys (or Ser)14 and Cys200 was shorter and more constant, and the conformation of the NH2-terminus and the exoloop 2 exhibited fewer fluctuations than when Lys191 was present. These data provide novel information on the role of Lys191 in defining an optimal configuration for the hGnRHR intracellular trafficking and function.

scholarly journals Molecular Dynamics of SARS-CoV-2 Nsp1 Structural Changes Associated with Variant Mutations

2021 ◽  
Author(s):  
Shokouh Rezaei ◽  
Yahya Sefidbakht ◽  
Filipe Pereira
Keyword(s):  
Molecular Dynamics ◽  
Conformational Changes ◽  
Structural Changes ◽  
Structure And Function ◽  
Dynamics Simulation ◽  
Structural Protein ◽  
Wild Type ◽  
Deletion Mutations ◽  
And Function

Abstract SARS-CoV-2 non-structural protein 1 (Nsp1) is a virulence factor that inhibits the translation of host mRNAs and interact with viral RNA. Despite the relevance of Nsp1, few studies have been conducted to understand the effect of mutations on Nsp1 structure and function. Here, we provide a molecular dynamics simulation of SARS-CoV-2 Nsp1, wild type and variants. We found that SARS-CoV-2 Nsp1 has a more Rg value than SARS-CoV-1 Nsp1, with indicate an effect on the folding protein. This result suggest that SARS-CoV-2 Nsp1 can more easily approach the active site of the ribosome compared to SARS-CoV-1 Nsp1. In addition, we found that the C-terminal of the SARS-CoV-2 Nsp1, in particular residues 164 to 170, are more flexible than other regions of SARS-CoV-2 Nsp1 and SARS-CoV-1 Nsp1, confirming the role of this region in the interaction with the 40S subunit. Moreover, multiple deletion mutations have been found in the N/C-terminal of the SARS-CoV-2 Nsp1, which seems the effect of SARS-CoV-2 Nsp1 multiple deletions is greater than that of substitutions. Among all deletions, D156-158 and D80-90 may destabilize the protein structure and possibly increase the virulence of the SARS-CoV-2. Overall, our findings reinforce the importance of studying Nsp1 conformational changes in new variants and its effect on virulence of SARS-CoV-2.

scholarly journals Influence of Disulfide Bridge on the Structural Stability of Human Neuroglobin: A Molecular Dynamics Simulation Using Latest Data Entry

2016 ◽  
Vol 26 (2) ◽  
pp. 151
Author(s):  
Bui Thi Le Quyen ◽  
Nguyen Thi Lam Hoai ◽  
Ngo Van Thanh
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Structural Stability ◽  
Data Entry ◽  
Disulfide Bridge ◽  
Dynamics Simulation ◽  
Wild Type ◽  
Heme Group ◽  
Classical Simulation

In this paper, we investigated the role of the disulfide bridge in the structural stability of wild-type human neuroglobin. The classical simulation of the neuroglobin without the disulfide bridge was performed for a long simulation run of 240~ns   using a new parameter set of Gromos96 force field and the latest data entry as the initial topologies. We used the analyzed data of original neuroglobin with the remained disulfide bridge to compare to the ones from this simulation. Our results showed that, the structure of neuroglobin was still very stable although the disulfide bridge was absent. There was only a few residues in B and C helices having a higher mobility. The most interesting result we obtained was that the increasing distance between the distal histidine and heme group could allow oxygen to bind more easily.

Computational insights into active site shaping for substrate specificity and reaction regioselectivity in the EXTL2 retaining glycosyltransferase

2017 ◽  
Vol 15 (43) ◽  
pp. 9095-9107 ◽  
Author(s):  
Fernanda Mendoza ◽  
José M. Lluch ◽  
Laura Masgrau
Keyword(s):  
Molecular Dynamics ◽  
Substrate Specificity ◽  
Molecular Dynamics Simulations ◽  
Active Site ◽  
Wild Type ◽  
Dynamics Simulations

QM(DFT)/MM calculations and molecular dynamics simulations on wild-type retaining α1,4-N-acetylhexosaminyltransferase (EXTL2) and Arg293Ala, Asp246Ala, Arg293Ala/Asp246Ala and Asp246Glu mutants are used to understand the role of these two residues.

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