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Effects of the binding of calcium ions on the structure and dynamics of the ?X174 virus investigated using molecular dynamics.

ABSTRACT: It is known that the presence of calcium ions (Ca(2?+?)) is necessary for the enterobacterial virus ?X174 to inject its DNA into the host cell, and that some mutations in the major capsid proteins lead to better survivability at higher temperatures. Our goal in the current study is to determine the physical changes in both the wild-type and mutant virus due to the binding of Ca(2?+?). Thus, we performed molecular dynamics simulations of the ?X174 major capsid protein complex with and without Ca(2?+?) bound. Our results show that binding of Ca(2?+?) leads to energetic and dynamical changes in the virus proteins. In particular, the results suggest that binding of Ca(2?+?) is energetically favorable and that the mutation leads to increased fluctuations of the protein complex (especially with the calcium ions bound to the complex), which may increase the rate of genome packaging and ejection for ?X174.

SUBMITTER: Pina JE

PROVIDER: S-EPMC3388200 | biostudies-literature | 2012 Jun

REPOSITORIES: biostudies-literature

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Effects of the binding of calcium ions on the structure and dynamics of the ΦX174 virus investigated using molecular dynamics.

Pina Jason E JE Lee Kuo Hao KH Ytreberg F Marty FM

Journal of biological physics 20120121 3

It is known that the presence of calcium ions (Ca(2 + )) is necessary for the enterobacterial virus ΦX174 to inject its DNA into the host cell, and that some mutations in the major capsid proteins lead to better survivability at higher temperatures. Our goal in the current study is to determine the physical changes in both the wild-type and mutant virus due to the binding of Ca(2 + ). Thus, we performed molecular dynamics simulations of the ΦX174 major capsid protein complex with and without Ca( ...[more]

PMID: 23729905

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Project description:We have studied the structure of (Ala)5, a model unfolded peptide, using a combination of 2D IR spectroscopy and molecular dynamics (MD) simulation. Two different isotopomers, each bis-labeled with (13)C?O and (13)C?(18)O, were strategically designed to shift individual site frequencies and uncouple neighboring amide-I' modes. 2D IR spectra taken under the double-crossed ??/4, -?/4, Y, Z? polarization show that the labeled four-oscillator systems can be approximated by three two-oscillator systems. By utilizing the different polarization dependence of diagonal and cross peaks, we extracted the coupling constants and angles between three pairs of amide-I' transition dipoles through spectral fitting. These parameters were related to the peptide backbone dihedral angles through DFT calculated maps. The derived dihedral angles are all located in the polyproline-II (ppII) region of the Ramachandran plot. These results were compared to the conformations sampled by Hamiltonian replica-exchange MD simulations with three different CHARMM force fields. The C36 force field predicted that ppII is the dominant conformation, consistent with the experimental findings, whereas C22/CMAP predicted similar population for ?+, ?, and ppII, and the polarizable Drude-2013 predicted dominating ? structure. Spectral simulation based on MD representative conformations and structure ensembles demonstrated the need to include multiple 2D spectral features, especially the cross-peak intensity ratio and shape, in structure determination. Using 2D reference spectra defined by the C36 structure ensemble, the best spectral simulation is achieved with nearly 100% ppII population, although the agreement with the experimental cross-peak intensity ratio is still insufficient. The dependence of population determination on the choice of reference structures/spectra and the current limitations on theoretical modeling relating peptide structures to spectral parameters are discussed. Compared with the previous results on alanine based oligopeptides, the dihedral angles of our fitted structure, and the most populated ppII structure from the C36 simulation are in good agreement with those suggesting a major ppII population. Our results provide further support for the importance of ppII conformation in the ensemble of unfolded peptides.

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Effects of the binding of calcium ions on the structure and dynamics of the ?X174 virus investigated using molecular dynamics.

Publications

Effects of the binding of calcium ions on the structure and dynamics of the ΦX174 virus investigated using molecular dynamics.

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