Predicting receptor functionality of signaling lymphocyte activation molecule for measles virus hemagglutinin by docking simulation

Suzuki, Yoshiyuki

doi:10.1111/1348-0421.12484

Cited by 3 publications

(2 citation statements)

References 22 publications

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“…It is essential to elucidate the details of intermolecular interactions quantitatively in order to understand the molecular recognition mechanisms involved in the complexes of MVH and the respective receptors. The interaction between MVH and SLAM has been analyzed by using the docking analysis and expressed in terms of docking scores [ 14 ]. However, the interaction energies of respective amino acid residues of the receptor and MVH remain to be studied more accurately.…”

Section: Introductionmentioning

confidence: 99%

“…The important point to be considered is that the three receptors bind to MVH at somewhat overlapping interfaces, thus indicating some similarities and differences in the mechanism of their molecular recognition (or binding energy) which can be utilized for artificially controlling the (relative) strength of respective binding affinity. Thus, the present quantum-chemical approach can provide a more dependable theoretical tool than conventional docking simulations [ 14 ].…”

Section: Introductionmentioning

confidence: 99%

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Computational Analysis of the Interaction Energies between Amino Acid Residues of the Measles Virus Hemagglutinin and Its Receptors

Tanaka

Watanabe

et al. 2018

Viruses

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Measles virus (MV) causes an acute and highly devastating contagious disease in humans. Employing the crystal structures of three human receptors, signaling lymphocyte-activation molecule (SLAM), CD46, and Nectin-4, in complex with the measles virus hemagglutinin (MVH), we elucidated computationally the details of binding energies between the amino acid residues of MVH and those of the receptors with an ab initio fragment molecular orbital (FMO) method. The calculated inter-fragment interaction energies (IFIEs) revealed a number of significantly interacting amino acid residues of MVH that played essential roles in binding to the receptors. As predicted from previously reported experiments, some important amino-acid residues of MVH were shown to be common but others were specific to interactions with the three receptors. Particularly, some of the (non-polar) hydrophobic residues of MVH were found to be attractively interacting with multiple receptors, thus indicating the importance of the hydrophobic pocket for intermolecular interactions (especially in the case of Nectin-4). In contrast, the electrostatic interactions tended to be used for specific molecular recognition. Furthermore, we carried out FMO calculations for in silico experiments of amino acid mutations, finding reasonable agreements with virological experiments concerning the substitution effect of residues. Thus, the present study demonstrates that the electron-correlated FMO method is a powerful tool to search exhaustively for amino acid residues that contribute to interactions with receptor molecules. It is also applicable for designing inhibitors of MVH and engineered MVs for cancer therapy.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Computational Analysis of the Interaction Energies between Amino Acid Residues of the Measles Virus Hemagglutinin and Its Receptors

Tanaka

Watanabe

et al. 2018

Viruses

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Protein–Protein Docking in Drug Design and Discovery

Kaczor

Bartuzi

Stępniewski

et al. 2018

Methods in Molecular Biology

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Protein-protein interactions (PPIs) are responsible for a number of key physiological processes in the living cells and underlie the pathomechanism of many diseases. Nowadays, along with the concept of so-called "hot spots" in protein-protein interactions, which are well-defined interface regions responsible for most of the binding energy, these interfaces can be targeted with modulators. In order to apply structure-based design techniques to design PPIs modulators, a three-dimensional structure of protein complex has to be available. In this context in silico approaches, in particular protein-protein docking, are a valuable complement to experimental methods for elucidating 3D structure of protein complexes. Protein-protein docking is easy to use and does not require significant computer resources and time (in contrast to molecular dynamics) and it results in 3D structure of a protein complex (in contrast to sequence-based methods of predicting binding interfaces). However, protein-protein docking cannot address all the aspects of protein dynamics, in particular the global conformational changes during protein complex formation. In spite of this fact, protein-protein docking is widely used to model complexes of water-soluble proteins and less commonly to predict structures of transmembrane protein assemblies, including dimers and oligomers of G protein-coupled receptors (GPCRs). In this chapter we review the principles of protein-protein docking, available algorithms and software and discuss the recent examples, benefits, and drawbacks of protein-protein docking application to water-soluble proteins, membrane anchoring and transmembrane proteins, including GPCRs.

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Herpes Simplex Virus Type 1 Human Cervical Dorsal Root Ganglionitis

Vályi-Nagy¹,

Rathore²,

Rakic³

et al. 2017

Case Rep Neurol

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We present a case of a 34-year-old right-handed Caucasian male with chronic occipital neuralgia refractory to medical therapies and minimally invasive pain procedures who underwent surgical cervical dorsal root ganglionectomy which completely relieved his headaches. The histopathological and immunohistochemical findings of the resected cervical dorsal root ganglia were consistent with active herpes simplex virus type 1 (HSV-1) infection causing ganglionitis. To the best of our knowledge, this case represents the first histopathologically proven HSV-1 cervical dorsal root ganglionitis in humans. This case provides an insight into a possible etiology of occipital neuralgia.

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Predicting receptor functionality of signaling lymphocyte activation molecule for measles virus hemagglutinin by docking simulation

Cited by 3 publications

References 22 publications

Computational Analysis of the Interaction Energies between Amino Acid Residues of the Measles Virus Hemagglutinin and Its Receptors

Computational Analysis of the Interaction Energies between Amino Acid Residues of the Measles Virus Hemagglutinin and Its Receptors

Protein–Protein Docking in Drug Design and Discovery

Herpes Simplex Virus Type 1 Human Cervical Dorsal Root Ganglionitis

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