Characterizing the hotspots involved in RON-MSPβ complex formation using in silico alanine scanning mutagenesis and molecular dynamics simulation

Zarei, Omid; Hamzeh‐Mivehroud, Maryam; Benvenuti, Silvia; Alkan, Fulya Üstün; Dastmalchi, Siavoush

doi:10.15171/apb.2017.018

Cited by 7 publications

(6 citation statements)

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“…Translation of the obtained sequence showed that the mutation at position 19is silent while the two others have resulted in missense mutation at the positions 18 (S18G) and nonsense mutation of tryptophan at position 39to stop codon ( Figure 1). Previous studies have shown the variation of amino acid sequence of DOF 4.2-ZF MD simulations have been extensively used to virtually investigate proteinprotein/DNA and protein-small molecules interactions [27][28][29] . Different studies have used MD simulation based algorithms to report the interaction of DOF family proteins with DNA 26,30,31 .…”

Section: Discussionmentioning

confidence: 99%

“…MD simulations have been extensively used to virtually investigate protein-protein/DNA and protein-small molecules interactions. 27 - 29 Different studies have used MD simulation based algorithms to report the interaction of DOF family proteins with DNA. 26 , 30 , 31 Pandey et al explored the DNA binding ability of DOF domain from wheat showing that single K29R mutation could adversely affect its binding capability.…”

Section: Discussionmentioning

confidence: 99%

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Identification of Novel Mutations in Arabidopsis thaliana DOF 4.2 Coding Gene

et al. 2020

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Purpose: DOF (DNA-binding with One Finger) proteins are plant-specific transcription factors which mediate numerous biological processes. The purpose of the current study is to report new naturally occurring mutations in the gene encoding for one of the members of DOF proteins named DOF 4.2. Methods: The expression of zinc finger domain of DOF 4.2 (DOF 4.2-ZF) was investigated by first synthesis of cDNA library using different parts of Arabidopsis thaliana plant. Then the coding sequence for zinc finger domain of DOF 4.2 protein was prepared using nested PCR experiment and cloned into pGEX-6P-1 expression vector. Finally, the prepared construct was used for protein expression. Furthermore, molecular dynamics (MD) simulation was carried out to predict DNA binding affinity of DOF 4.2-ZF using AMBER package. Results: For the first time a new variant of DOF 4.2-ZF protein with three mutations was detected. One of the mutations is silent while the other two mutations lead to amino acid replacement (S18G) as well as introduction of a stop codon ultimately resulting in a truncated protein production. In order to investigate whether the truncated form is able to recognize DNA binding motif, MD simulations were carried out and the results showed that the chance of binding of DOF 4.2-ZF protein to cognate DNA in its truncated form is very low. Conclusion: The findings demonstrated that the observed mutations adversely affect the DNA binding ability of the truncated form of DOF4.2 if it is expressed in the mutant variant of A. thaliana used in this study.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Identification of Novel Mutations in Arabidopsis thaliana DOF 4.2 Coding Gene

et al. 2020

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“…The above seven complexes were subsequently prepared for MD simulations with GROMACS v.5.0.6 (GROningen MAChine for Chemical Simulation) software package (Abraham et al, 2015). The AMBER99SB-ILDN forcefield was applied to generate the topology parameters of the structural complexes (Lindorff-Larsen et al, 2010;Venkatesan et al, 2015;Zarei, et al, 2017;Galeazzi et al, 2018). The binary complexes were then surrounded by dodecahedron periodic box of SPCE water molecules (Selent et al, 2013;Venkatesan et al, 2015;Galeazzi et al, 2018;Du et al, 2020).…”

Section: Analysis Of Interaction Dynamicsmentioning

confidence: 99%

Exploring the Binding Interaction of Raf Kinase Inhibitory Protein With the N-Terminal of C-Raf Through Molecular Docking and Molecular Dynamics Simulation

Parate

Rampogu

Lee

et al. 2021

Front. Mol. Biosci.

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Protein-protein interactions are indispensable physiological processes regulating several biological functions. Despite the availability of structural information on protein-protein complexes, deciphering their complex topology remains an outstanding challenge. Raf kinase inhibitory protein (RKIP) has gained substantial attention as a favorable molecular target for numerous pathologies including cancer and Alzheimer’s disease. RKIP interferes with the RAF/MEK/ERK signaling cascade by endogenously binding with C-Raf (Raf-1 kinase) and preventing its activation. In the current investigation, the binding of RKIP with C-Raf was explored by knowledge-based protein-protein docking web-servers including HADDOCK and ZDOCK and a consensus binding mode of C-Raf/RKIP structural complex was obtained. Molecular dynamics (MD) simulations were further performed in an explicit solvent to sample the conformations for when RKIP binds to C-Raf. Some of the conserved interface residues were mutated to alanine, phenylalanine and leucine and the impact of mutations was estimated by additional MD simulations and MM/PBSA analysis for the wild-type (WT) and constructed mutant complexes. Substantial decrease in binding free energy was observed for the mutant complexes as compared to the binding free energy of WT C-Raf/RKIP structural complex. Furthermore, a considerable increase in average backbone root mean square deviation and fluctuation was perceived for the mutant complexes. Moreover, per-residue energy contribution analysis of the equilibrated simulation trajectory by HawkDock and ANCHOR web-servers was conducted to characterize the key residues for the complex formation. One residue each from C-Raf (Arg398) and RKIP (Lys80) were identified as the druggable “hot spots” constituting the core of the binding interface and corroborated by additional long-time scale (300 ns) MD simulation of Arg398Ala mutant complex. A notable conformational change in Arg398Ala mutant occurred near the mutation site as compared to the equilibrated C-Raf/RKIP native state conformation and an essential hydrogen bonding interaction was lost. The thirteen binding sites assimilated from the overall analysis were mapped onto the complex as surface and divided into active and allosteric binding sites, depending on their location at the interface. The acquired information on the predicted 3D structural complex and the detected sites aid as promising targets in designing novel inhibitors to block the C-Raf/RKIP interaction.

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“…In this paper, a novel method, namely, interaction entropy (IE) (Duan et al, 2016b), is used to calculate the entropy change, which is theoretically rigorous. It can yield more accurate results than the traditional Nmode method, which has been applied successfully to the calculation of the binding free energy in many studies (Duan et al, 2016a, 2017a,b; Aldeghi et al, 2017; Ben-Shalom et al, 2017; Cebrián-Prats et al, 2017; Chen et al, 2017a,b; Gao et al, 2017; Khammari et al, 2017; Nguyen Quoc et al, 2017; Sun et al, 2017; Wang et al, 2017; Yan et al, 2017; Yang et al, 2017; Zarei et al, 2017; Zou et al, 2017; Cong et al, 2018; Liu et al, 2018; Qiu et al, 2018; Song et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

Insight Into the Binding Mechanism of p53/pDIQ-MDMX/MDM2 With the Interaction Entropy Method

Cong

et al. 2019

Front. Chem.

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The study of the p53-MDMX/MDM2 binding sites is a research hotspot for tumor drug design. The inhibition of p53-targeted MDMX/MDM2 has become an effective approach in anti-tumor drug development. In this paper, a theoretically rigorous and computationally accurate method, namely, the interaction entropy (IE) method, combined with the polarized protein-specific charge (PPC) force field, is used to explore the difference in the binding mechanism between p53-MDMX and p53-MDM2. The interaction of a 12mer peptide inhibitor (pDIQ), which is similar to p53 in structure, with MDMX/MDM2 is also studied. The results demonstrate that p53/pDIQ with MDM2 generates a stronger interaction than with MDMX. Compared to p53, pDIQ has larger binding free energies with MDMX and MDM2. According to the calculated binding free energies, the differences in the binding free energy among the four complexes that are obtained from the combination of PPC and IE are more consistent with the experimental values than with the results from the combination of the non-polarizable AMBER force field and IE. In addition, according to the decomposition of the binding free energy, the van der Waals (vdW) interactions are the main driving force for the binding of the four complexes. They are also the main source of the weaker binding affinity of p53/pDIQ-MDMX relative to p53/pDIQ-MDM2. Compared with p53-MDMX/MDM2, according to the analysis of the residue decomposition, the predicated total residue contributions are higher in pDIQ-MDMX/MDM2 than in p53-MDMX/MDM2, which explains why pDIQ has higher binding affinity than p53 with MDMX/MDM2. The current study provides theoretical guidance for understanding the binding mechanisms and designing a potent dual inhibitor that is targeted to MDMX/MDM2.

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Characterizing the hotspots involved in RON-MSPβ complex formation using in silico alanine scanning mutagenesis and molecular dynamics simulation

Cited by 7 publications

References 84 publications

Identification of Novel Mutations in Arabidopsis thaliana DOF 4.2 Coding Gene

Identification of Novel Mutations in Arabidopsis thaliana DOF 4.2 Coding Gene

Exploring the Binding Interaction of Raf Kinase Inhibitory Protein With the N-Terminal of C-Raf Through Molecular Docking and Molecular Dynamics Simulation

Insight Into the Binding Mechanism of p53/pDIQ-MDMX/MDM2 With the Interaction Entropy Method

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