Molecular modeling, molecular dynamics simulation, and essential dynamics analysis of grancalcin: An upregulated biomarker in experimental autoimmune encephalomyelitis mice

Paul, Shamrat Kumar; Saddam, Md.; Rahaman, Asiqur; Choi, Jong-Gu; Lee, Sang-Suk; Hasan, Mahbub

doi:10.1016/j.heliyon.2022.e11232

Cited by 15 publications

(18 citation statements)

References 85 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The second component identified accounts for the second-largest amount of variance in the data and is uncorrelated with the first principal component and so on [41] For PC analysis, we employed a 10ns trajectory with 1000 frames. We have followed the PCA analysis protocol described on Paul et al 2022 for this approach [46]. To reveal concerted motions, the trajectory was projected onto a certain eigenvector.…”

Section: Methodsmentioning

confidence: 99%

A computational investigation on Rho-related GTP-binding protein RhoB through molecular modeling and molecular dynamics simulation study

Paul

Metu

Sutihar

et al. 2023

Preprint

Self Cite

View full text Add to dashboard Cite

RhoB is a key member of the Rho family of isoprenylated small GTPases which modulate the cellular cytoskeletal organization. It has a crucial role in the neoplastic apoptotic mechanism after DNA damage. Due to the unavailability of 3D structure in the protein data bank database, in this study, we evaluated the structure of a protein, Rho related GTP binding protein RhoB. RhoB has a predicted pI of 5.10, indicating that it is acidic. The GMQE value was used to compute the target template alignment, and 6hxu.1.A from Homo sapiens was chosen as the template structure, with the model construction task completed using swiss model. The structural compactibility and stability were revealed after a 100ns molecular dynamics simulation using GROMACA employing the OPLSAA force field. PCA analysis found residues that are relevant based on their fluctuation acitivity while their location is between 100 to 110 and 140 to 150. This study will benefit future investigations addressing the association between gene mutation and abnormalities generated by protein Rho-related GTP binding protein RhoB in apoptotic events by offering insight into the biophysical phenomenon of Rho related GTP binding protein RhoB inhibitors.

show abstract

Section: Methodsmentioning

confidence: 99%

A computational investigation on Rho-related GTP-binding protein RhoB through molecular modeling and molecular dynamics simulation study

Paul

Metu

Sutihar

et al. 2023

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

“…The lower the Rg number, the higher the conformational stability. [56,57] However, the constant value of Rg demonstrates stability of the complex over the whole simulation time duration. As shown in Figure 5 (A), the Rg value at 298 K for cortisol showed maximum stability among all other hormones, the least fluctuation can be seen for cortisol from 8340 to 27840 ps in the range of 2.09-2.16 nm.…”

Section: Molecular Dynamics Simulations Trajectories At 298 Kmentioning

confidence: 98%

A Theoretical Study To Understand the Impact of Mpro of nCoV on the Hormones

Babu Singh,

Himani,

Yadav

et al. 2024

ChemistrySelect

View full text Add to dashboard Cite

Amidst the unprecedented 2019 coronavirus outbreak and the substantial loss of lives due to the scarcity of information about the virus and lack of viable drugs, understanding the impact of the nCoV Main Protease (Mpro) on the endocrine system has emerged as a critical topic to pursue. This study explores the potential interactions between four key hormones (cortisol, cortisone, estradiol, and estrone) and the Mpro of nCoV using various in‐silico methodologies. Density Functional Theory (DFT) calculations scrutinized the electron density delocalization of these hormones. Through molecular docking, the molecular‐level binding of Mpro of nCoV with these hormones was studied, revealing cortisol as the hormone exhibiting the most promising binding affinity (−100.05 kcal/mol). Furthermore, molecular dynamics (MD) simulations, emulating human body conditions at distinct temperatures, were employed to study the implications of these interactions. The study analysed the various trajectories such as root mean square deviation (RMSD), root mean square fluctuations (RMSF), radius of gyration (Rg), and H‐bond trajectories to understand the potential impact on biological systems. The findings demonstrate the binding potential of the Mpro of nCoV with these hormones, raising plausible concerns regarding consequential physiological changes within the human body.

show abstract

“…However, within the range of 7000-10000 residues, the amino acid uctuations of the ve polyphenol-myosin complexes undergo drastic changes. It indicated that this part of the amino acid residues was more active and involved in the interaction between polyphenols and myosin (Paul et al, 2022).…”

Section: Analysis Of the Polyphenol-myosin Conformationmentioning

confidence: 99%

“…RMSF was often used to identify the uctuation of amino acids, which was a key indicator for explaining protein activity and conformational stability (Paul et al, 2022). In Fig.…”

Section: Analysis Of the Polyphenol-myosin Conformationmentioning

confidence: 99%

Integrated multi-spectroscopy and molecular dynamics simulations to explore the interaction mechanism of polyphenols and sea bass myofibrillar protein

Zhu,

Li,

Zhong

et al. 2024

Preprint

View full text Add to dashboard Cite

This study aimed to explore the interaction mechanism between five different polyphenols (caffeic acid (CFA), gallic acid (GA), chlorogenic acid (CHA), resveratrol (RES), and catechin (CAT)) with sea bass myofibrillar protein (MP). The multi-spectroscopy results showed that all five polyphenols could spontaneously form new complexes with MP, with a binding molar ratio of 1:1. The interaction between CFA and MP is predominantly electrostatic, while the interaction between GA and MP is mainly hydrophobic. The rest of polyphenols and MP are mediated by hydrogen bonds and van der Waals forces. And molecular dynamics (MD) simulations indicated that CHA-myosin had the strongest structural stability, while CFA-myosin had the tightest binding. In addition, the amino acid Lys-179 was the key residue for the interaction between five polyphenols and myosin. This study contributes to better understanding the interaction between polyphenols and sea bass MP, which could develop the processing of aquatic food products.

show abstract

Molecular modeling, molecular dynamics simulation, and essential dynamics analysis of grancalcin: An upregulated biomarker in experimental autoimmune encephalomyelitis mice

Cited by 15 publications

References 85 publications

A computational investigation on Rho-related GTP-binding protein RhoB through molecular modeling and molecular dynamics simulation study

A computational investigation on Rho-related GTP-binding protein RhoB through molecular modeling and molecular dynamics simulation study

A Theoretical Study To Understand the Impact of Mpro of nCoV on the Hormones

Integrated multi-spectroscopy and molecular dynamics simulations to explore the interaction mechanism of polyphenols and sea bass myofibrillar protein

Contact Info

Product

Resources

About