scholarly journals Computing the Structural Dynamics of RVFV L Protein Domain in Aqueous Glycerol Solutions

Biomolecules ◽  
2021 ◽  
Vol 11 (10) ◽  
pp. 1427
Author(s):  
Gideon K. Gogovi ◽  
Swabir Silayi ◽  
Amarda Shehu
Keyword(s):  
Structural Dynamics ◽  
Rift Valley Fever Virus ◽  
Protein Domain ◽  
Solvent Accessible Surface Area ◽  
Radius Of Gyration ◽  
Atomic Charges ◽  
Glycerol Concentration ◽  
Solvent Interactions ◽  
Amber Force Field ◽  
L Protein

Many biological and biotechnological processes are controlled by protein–protein and protein–solvent interactions. In order to understand, predict, and optimize such processes, it is important to understand how solvents affect protein structure during protein–solvent interactions. In this study, all-atom molecular dynamics are used to investigate the structural dynamics and energetic properties of a C-terminal domain of the Rift Valley Fever Virus L protein solvated in glycerol and aqueous glycerol solutions in different concentrations by molecular weight. The Generalized Amber Force Field is modified by including restrained electrostatic potential atomic charges for the glycerol molecules. The peptide is considered in detail by monitoring properties like the root-mean-squared deviation, root-mean-squared fluctuation, radius of gyration, hydrodynamic radius, end-to-end distance, solvent-accessible surface area, intra-potential energy, and solvent–peptide interaction energies for hundreds of nanoseconds. Secondary structure analysis is also performed to examine the extent of conformational drift for the individual helices and sheets. We predict that the peptide helices and sheets are maintained only when the modeling strategy considers the solvent with lower glycerol concentration. We also find that the solvent-peptide becomes more cohesive with decreasing glycerol concentrations. The density and radial distribution function of glycerol solvent calculated when modeled with the modified atomic charges show a very good agreement with experimental results and other simulations at 298.15K.

scholarly journals Modeling the Tertiary Structure of the Rift Valley Fever Virus L Protein

Molecules ◽  
2019 ◽  
Vol 24 (9) ◽  
pp. 1768
Author(s):  
Gideon K. Gogovi ◽  
Fahad Almsned ◽  
Nicole Bracci ◽  
Kylene Kehn-Hall ◽  
Amarda Shehu ◽  
...  
Keyword(s):  
Amino Acids ◽  
Rift Valley ◽  
Rift Valley Fever ◽  
Tertiary Structure ◽  
Rift Valley Fever Virus ◽  
Fever Virus ◽  
Radius Of Gyration ◽  
Computational Molecular Biology ◽  
Valley Fever ◽  
L Protein

A tertiary structure governs, to a great extent, the biological activity of a protein in the living cell and is consequently a central focus of numerous studies aiming to shed light on cellular processes central to human health. Here, we aim to elucidate the structure of the Rift Valley fever virus (RVFV) L protein using a combination of in silico techniques. Due to its large size and multiple domains, elucidation of the tertiary structure of the L protein has so far challenged both dry and wet laboratories. In this work, we leverage complementary perspectives and tools from the computational-molecular-biology and bioinformatics domains for constructing, refining, and evaluating several atomistic structural models of the L protein that are physically realistic. All computed models have very flexible termini of about 200 amino acids each, and a high proportion of helical regions. Properties such as potential energy, radius of gyration, hydrodynamics radius, flexibility coefficient, and solvent-accessible surface are reported. Structural characterization of the L protein enables our laboratories to better understand viral replication and transcription via further studies of L protein-mediated protein–protein interactions. While results presented a focus on the RVFV L protein, the following workflow is a more general modeling protocol for discovering the tertiary structure of multidomain proteins consisting of thousands of amino acids.

scholarly journals X-ray structure and activities of an essential Mononegavirales L-protein domain

2015 ◽  
Vol 6 (1) ◽  
Author(s):  
Guido C. Paesen ◽  
Axelle Collet ◽  
Corinne Sallamand ◽  
Françoise Debart ◽  
Jean-Jacques Vasseur ◽  
...  
Keyword(s):  
Protein Domain ◽  
X Ray ◽  
L Protein

Xanthine oxidase inhibitory activity of Euphorbia peplus L. phenolics

2021 ◽  
Vol 24 ◽  
Author(s):  
Emadeldin M. Kamel ◽  
Noha A. Ahmed ◽  
Ashraf A. El-Bassuony ◽  
Omnia E. Hussein ◽  
Barakat Alrashdi ◽  
...  
Keyword(s):  
Xanthine Oxidase ◽  
Active Site ◽  
Inhibitory Activity ◽  
Drug Binding ◽  
Dynamics Simulation ◽  
Solvent Accessible Surface Area ◽  
Radius Of Gyration ◽  
Euphorbia Peplus

Background: Various phenolics show inhibitory activity towards xanthine oxidase (XO), an enzyme that generates reactive oxygen species which cause oxidative damage. Objective: This study investigated the XO inhibitory activity of Euphorbia peplus phenolics. Methods: The dried powdered aerial parts of E. peplus were extracted, fractioned and phenolics were isolated and identified. The XO inhibitory activity of E. peplus extract (EPE) and the isolated phenolics was investigated in vitro and in vivo. Results: Three phenolics were isolated from the ethyl acetate fraction of E. peplus. All isolated compounds and the EPE showed inhibitory activity towards XO in vitro. In hyperuricemic rats, EPE and the isolated phenolics decreased uric acid and XO activity. Molecular docking showed the binding modes of isolated phenolics with XO, depicting significant interactions with the active site amino acid residues. Molecular dynamics simulation trajectories confirmed the interaction of isolated phenolics with XO by forming hydrogen bonds with the active site residues. Also, the root mean square (RMS) deviations of XO and phenolics-XO complexes achieved equilibrium and fluctuated during the 10 ns MD simulations. The radius of gyration and solvent accessible surface area investigations showed that different systems were stabilized at ≈ 2500 ps. The RMS fluctuations profile depicted that the drug binding site exhibited a rigidity behavior during the simulation. Conclusion: In vitro, in vivo and computational investigations showed the XO inhibitory activity of E. peplus phenolics. These phenolics might represent promising candidates for the development of XO inhibitors.

scholarly journals Structure of a functional cap-binding domain in Rift Valley fever virus L protein

2019 ◽  
Vol 15 (5) ◽  
pp. e1007829 ◽  
Author(s):  
Nadja Gogrefe ◽  
Sophia Reindl ◽  
Stephan Günther ◽  
Maria Rosenthal
Keyword(s):  
Rift Valley ◽  
Rift Valley Fever ◽  
Rift Valley Fever Virus ◽  
Binding Domain ◽  
Fever Virus ◽  
Valley Fever ◽  
L Protein

scholarly journals Screening of Potent Phytochemical Inhibitors Against SARS-CoV-2 Main Protease: An Integrative Computational Approach

2021 ◽  
Vol 1 ◽  
Author(s):  
Shafi Mahmud ◽  
Md. Robiul Hasan ◽  
Suvro Biswas ◽  
Gobindo Kumar Paul ◽  
Shamima Afrose ◽  
...  
Keyword(s):  
Root Mean Square ◽  
Global Economy ◽  
Transmission Rate ◽  
Accessible Surface Area ◽  
Dynamics Simulation ◽  
Solvent Accessible Surface Area ◽  
Radius Of Gyration ◽  
Mean Square ◽  
Protease Inhibition ◽  
Main Protease

Coronavirus disease 2019 (COVID-19) is a potentially lethal and devastating disease that has quickly become a public health threat worldwide. Due to its high transmission rate, many countries were forced to implement lockdown protocols, wreaking havoc on the global economy and the medical crisis. The main protease (Mpro) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative virus for COVID-19, represent an effective target for the development of a new drug/vaccine because it is well-conserved and plays a vital role in viral replication. Mpro inhibition can stop the replication, transcription as well as recombination of SARS-CoV-2 after the infection and thus can halt the formation of virus particles, making Mpro a viable therapeutic target. Here, we constructed a phytochemical dataset based on a rigorous literature review and explored the probability that various phytochemicals will bind with the main protease using a molecular docking approach. The top three hit compounds, medicagol, faradiol, and flavanthrin, had binding scores of −8.3, −8.6, and −8.8 kcal/mol, respectively, in the docking analysis. These three compounds bind to the active groove, consisting of His41, Cys45, Met165, Met49, Gln189, Thr24, and Thr190, resulting in main protease inhibition. Moreover, the multiple descriptors from the molecular dynamics simulation, including the root-mean-square deviation, root-mean-square fluctuation, solvent-accessible surface area, radius of gyration, and hydrogen bond analysis, confirmed the stable nature of the docked complexes. In addition, absorption, distribution, metabolism, excretion, and toxicity (ADMET) analysis confirmed a lack of toxicity or carcinogenicity for the screened compounds. Our computational analysis may contribute toward the design of an effective drug against the main protease of SARS-CoV-2.

scholarly journals Phytochemicals from Leucas zeylanica Targeting Main Protease of SARS-CoV-2: Chemical Profiles, Molecular Docking, and Molecular Dynamics Simulations

Biology ◽  
2021 ◽  
Vol 10 (8) ◽  
pp. 789
Author(s):  
Mycal Dutta ◽  
Abu Montakim Tareq ◽  
Ahmed Rakib ◽  
Shafi Mahmud ◽  
Saad Ahmed Sami ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Molecular Dynamics Simulation ◽  
Surface Area ◽  
Dynamics Simulation ◽  
Solvent Accessible Surface Area ◽  
Gas Chromatography Mass Spectrometry ◽  
Radius Of Gyration ◽  
Hydrogen Bond Formation ◽  
Main Protease

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a contemporary coronavirus, has impacted global economic activity and has a high transmission rate. As a result of the virus’s severe medical effects, developing effective vaccinations is vital. Plant-derived metabolites have been discovered as potential SARS-CoV-2 inhibitors. The SARS-CoV-2 main protease (Mpro) is a target for therapeutic research because of its highly conserved protein sequence. Gas chromatography–mass spectrometry (GC-MS) and molecular docking were used to screen 34 compounds identified from Leucas zeylanica for potential inhibitory activity against the SARS-CoV-2 Mpro. In addition, prime molecular mechanics–generalized Born surface area (MM-GBSA) was used to screen the compound dataset using a molecular dynamics simulation. From molecular docking analysis, 26 compounds were capable of interaction with the SARS-CoV-2 Mpro, while three compounds, namely 11-oxa-dispiro[4.0.4.1]undecan-1-ol (−5.755 kcal/mol), azetidin-2-one 3,3-dimethyl-4-(1-aminoethyl) (−5.39 kcal/mol), and lorazepam, 2TMS derivative (−5.246 kcal/mol), exhibited the highest docking scores. These three ligands were assessed by MM-GBSA, which revealed that they bind with the necessary Mpro amino acids in the catalytic groove to cause protein inhibition, including Ser144, Cys145, and His41. The molecular dynamics simulation confirmed the complex rigidity and stability of the docked ligand–Mpro complexes based on the analysis of mean radical variations, root-mean-square fluctuations, solvent-accessible surface area, radius of gyration, and hydrogen bond formation. The study of the postmolecular dynamics confirmation also confirmed that lorazepam, 11-oxa-dispiro[4.0.4.1]undecan-1-ol, and azetidin-2-one-3, 3-dimethyl-4-(1-aminoethyl) interact with similar Mpro binding pockets. The results of our computerized drug design approach may assist in the fight against SARS-CoV-2.

scholarly journals Evolution of structural dynamics in bilobed proteins

2020 ◽  
Author(s):  
Giorgos Gouridis ◽  
Yusran A. Muthahari ◽  
Marijn de Boer ◽  
Konstantinos Tassis ◽  
Alexandra Tsirigotaki ◽  
...  
Keyword(s):  
Structural Dynamics ◽  
Protein Evolution ◽  
Single Molecule ◽  
Protein Function ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Protein Domain ◽  
Divergent Evolution ◽  
Exchange Mass Spectrometry ◽  
Cytoplasmic Transport

AbstractNovel biophysical tools allow the structural dynamics of proteins, and the regulation of such dynamics by binding partners, to be explored in unprecedented detail. Although this has provided critical insights into protein function, the means by which structural dynamics direct protein evolution remains poorly understood. Here, we investigated how proteins with a bilobed structure, composed of two related domains from the type-II periplasmic binding protein domain family, have undergone divergent evolution leading to modification of their structural dynamics and function. We performed a structural analysis of ~600 bilobed proteins with a common primordial structural core, which we complemented with biophysical studies to explore the structural dynamics of selected examples by single-molecule Förster resonance energy transfer and Hydrogen-Deuterium exchange mass spectrometry. We show that evolutionary modifications of the structural core, largely at its termini, enables distinct structural dynamics, allowing the diversification of these proteins into transcription factors, enzymes, and extra-cytoplasmic transport-related proteins. Structural embellishments of the core created new interdomain interactions that stabilized structural states, reshaping the active site geometry, and ultimately, altered substrate specificity. Our findings reveal an as yet unrecognized mechanism for the emergence of functional promiscuity during long periods of protein evolution and are applicable to a large number of domain architectures.

scholarly journals Identification of Sendai Virus L Protein Amino Acid Residues Affecting Viral mRNA Cap Methylation

2008 ◽  
Vol 83 (4) ◽  
pp. 1669-1681 ◽  
Author(s):  
Andrea M. Murphy ◽  
Valery Z. Grdzelishvili
Keyword(s):  
Amino Acid ◽  
Host Range ◽  
Sendai Virus ◽  
Experimental System ◽  
Protein Domain ◽  
Amino Acid Substitutions ◽  
Viral Mrna ◽  
Amino Acid Residues ◽  
Viral Mrnas ◽  
L Protein

ABSTRACT Viruses of the order Mononegavirales all encode a large (L) polymerase protein responsible for the replication and transcription of the viral genome as well as all posttranscriptional modifications of viral mRNAs. The L protein is conserved among all members of the Mononegavirales and has six conserved regions (“domains”). Using vesicular stomatitis virus (VSV) (family Rhabdoviridae) experimental system, we and others recently identified several conserved amino acid residues within L protein domain VI which are required for viral mRNA cap methylation. To verify that these critical amino acid residues have a similar function in other members of the Mononegavirales, we examined the Sendai virus (SeV) (family Paramyxoviridae) L protein by targeting homologous amino acid residues important for cap methylation in VSV which are highly conserved among all members of the Mononegavirales and are believed to constitute the L protein catalytic and S-adenosylmethionine-binding sites. In addition, an SeV L protein mutant with a deletion of the entire domain VI was generated. First, L mutants were tested for their abilities to synthesize viral mRNAs. While the domain VI deletion completely inactivated L, most of the amino acid substitutions had minor effects on mRNA synthesis. Using a reverse genetics approach, these mutations were introduced into the SeV genome, and recombinant infectious SeV mutants with single alanine substitutions at L positions 1782, 1804, 1805, and 1806 or a double substitution at positions 1804 and 1806 were generated. The mutant SeV virions were purified, detergent activated, and analyzed for their abilities to synthesize viral mRNAs methylated at their cap structures. In addition, further studies were done to examine these SeV mutants for a possible host range phenotype, which was previously shown for VSV cap methylation-defective mutants. In agreement with a predicted role of the SeV L protein invariant lysine 1782 as a catalytic residue, the recombinant virus with a single K1782A substitution was completely defective in cap methylation and showed a host range phenotype. In addition, the E1805A mutation within the putative S-adenosylmethionine-binding site of L resulted in a 60% reduction in cap methylation. In contrast to the homologous VSV mutants, other recombinant SeV mutants with amino acid substitutions at this site were neither defective in cap methylation nor host range restricted. The results of this initial study using an SeV experimental system demonstrate similarities as well as differences between the L protein cap methylation domains in different members of the Mononegavirales.

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