The Experts below are selected from a list of 222 Experts worldwide ranked by ideXlab platform

David Bhella - One of the best experts on this subject based on the ideXlab platform.

  • The respiratory syncytial virus nucleoprotein–RNA complex forms a Left-Handed helical nucleocapsid
    Journal of General Virology, 2013
    Co-Authors: Saskia E. Bakker, Stéphane Duquerroy, Marie Galloux, Colin Loney, Edward Conner, Jean-françois Eléouët, Félix A. Rey, David Bhella
    Abstract:

    Respiratory syncytial virus (RSV) is an important human pathogen. Its nucleocapsid (NC), which comprises the negative sense RNA viral genome coated by the viral nucleoprotein N, is a critical assembly that serves as template for both mRNA synthesis and genome replication. We have previously described the X-ray structure of an NC-like structure: a decameric ring formed of N-RNA that mimics one turn of the helical NC. In the absence of experimental data we had hypothesized that the NC Helix would be right-handed, as the N–N contacts in the ring appeared to more easily adapt to that conformation. We now unambiguously show that the RSV NC is a Left-Handed Helix. We further show that the contacts in the ring can be distorted to maintain key N–N-protein interactions in a Left-Handed Helix, and discuss the implications of the resulting atomic model of the helical NC for viral replication and transcription.

  • The respiratory syncytial virus nucleoprotein-RNA complex forms a Left-Handed helical nucleocapsid.
    The Journal of general virology, 2013
    Co-Authors: Saskia E. Bakker, Stéphane Duquerroy, Marie Galloux, Colin Loney, Edward Conner, Jean-françois Eléouët, Félix A. Rey, David Bhella
    Abstract:

    Respiratory syncytial virus (RSV) is an important human pathogen. Its nucleocapsid (NC), which comprises the negative sense RNA viral genome coated by the viral nucleoprotein N, is a critical assembly that serves as template for both mRNA synthesis and genome replication. We have previously described the X-ray structure of an NC-like structure: a decameric ring formed of N-RNA that mimics one turn of the helical NC. In the absence of experimental data we had hypothesized that the NC Helix would be right-handed, as the N-N contacts in the ring appeared to more easily adapt to that conformation. We now unambiguously show that the RSV NC is a Left-Handed Helix. We further show that the contacts in the ring can be distorted to maintain key N-N-protein interactions in a Left-Handed Helix, and discuss the implications of the resulting atomic model of the helical NC for viral replication and transcription.

Fan Sha - One of the best experts on this subject based on the ideXlab platform.

  • Protein loops, solitons and side-chain visualization with applications to the Left-Handed Helix region
    Physical Review E, 2012
    Co-Authors: Martin Lundgren, Antti J. Niemi, Fan Sha
    Abstract:

    Proteins in nature fold to one dominant native structure. Despite being a heavily studied field, predicting the native structure from the amino acid sequence and modeling the folding process can still be considered unsolved problems. In this thesis I present a new approach to this problem with methods borrowed from theoretical physics. In the first part I show how it is possible to use a discrete Frenet frame to define the discrete curvature and torsion of the main chain of the protein. This method is then extended to the side chains as well. In particular I show how to use the discrete Frenet frame to produce a statistical distribution of angles that works in similar fashion as the commonly used Ramachandran plot and side chain rotamers. The discrete Frenet frame displays a gauge symmetry, in the choice of basis vectors on the normal plane, that is reminiscent of features of Abelian-Higgs theory. In the second part of the thesis I show how this similarity with Abelian-Higgs theory can be translated into an effective energy for a protein. The loops of the proteins are shown to correspond to solitons so that the whole protein can be constructed by gluing together any number of solitons. I present results of simulating proteins by minimizing the energy, starting from a real line or straight Helix, where the correct native fold is attained. Finally the model is shown to display the same phase structure as real proteins.

  • Protein loops, solitons, and side-chain visualization with applications to the Left-Handed Helix region.
    Physical review. E Statistical nonlinear and soft matter physics, 2012
    Co-Authors: Martin Lundgren, Antti J. Niemi, Fan Sha
    Abstract:

    Folded proteins have a modular assembly. They are constructed from regular secondary structures like α helices and β strands that are joined together by loops. Here we develop a visualization technique that is adapted to describe this modular structure. In complement to the widely employed Ramachandran plot that is based on toroidal geometry, our approach utilizes the geometry of a two sphere. Unlike the more conventional approaches that describe only a given peptide unit, ours is capable of describing the entire backbone environment including the neighboring peptide units. It maps the positions of each atom to the surface of the two-sphere exactly how these atoms are seen by an observer who is located at the position of the central C_{α} atom. At each level of side-chain atoms we observe a strong correlation between the positioning of the atom and the underlying local secondary structure with very little if any variation between the different amino acids. As a concrete example we analyze the Left-Handed Helix region of nonglycyl amino acids. This region corresponds to an isolated and highly localized residue independent sector in the direction of the C_{β} carbons on the two-sphere. We show that the residue independent localization extends to C_{γ} and C_{δ} carbons and to side-chain oxygen and nitrogen atoms in the case of asparagine and aspartic acid. When we extend the analysis to the side-chain atoms of the neighboring residues, we observe that Left-Handed β turns display a regular and largely amino acid independent structure that can extend to seven consecutive residues. This collective pattern is due to the presence of a backbone soliton. We show how one can use our visualization techniques to analyze and classify the different solitons in terms of selection rules that we describe in detail.

  • On universal aspects of the Left-Handed Helix region
    arXiv: Biomolecules, 2011
    Co-Authors: Martin Lundgren, Antti J. Niemi, Fan Sha
    Abstract:

    We inspect the geometry of proteins by identifying their backbones as framed polygons. We find that the Left-Handed Helix region of the Ramachandran map for non-glycyl residues corresponds to an isolated and highly localized sector in the orientation of the Cβ carbons, when viewed in a Frenet frame that is centered at the corresponding Cα carbons. We show that this localization in the orientation persists to Cγ and Cδ carbons. Furthermore, when we extend our analysis to the neighboring residues we conclude that the Left-Handed Helix region reflects a very regular and apparently residue independent collective interplay of at least seven consecutive amino acids.

Saskia E. Bakker - One of the best experts on this subject based on the ideXlab platform.

  • The respiratory syncytial virus nucleoprotein–RNA complex forms a Left-Handed helical nucleocapsid
    Journal of General Virology, 2013
    Co-Authors: Saskia E. Bakker, Stéphane Duquerroy, Marie Galloux, Colin Loney, Edward Conner, Jean-françois Eléouët, Félix A. Rey, David Bhella
    Abstract:

    Respiratory syncytial virus (RSV) is an important human pathogen. Its nucleocapsid (NC), which comprises the negative sense RNA viral genome coated by the viral nucleoprotein N, is a critical assembly that serves as template for both mRNA synthesis and genome replication. We have previously described the X-ray structure of an NC-like structure: a decameric ring formed of N-RNA that mimics one turn of the helical NC. In the absence of experimental data we had hypothesized that the NC Helix would be right-handed, as the N–N contacts in the ring appeared to more easily adapt to that conformation. We now unambiguously show that the RSV NC is a Left-Handed Helix. We further show that the contacts in the ring can be distorted to maintain key N–N-protein interactions in a Left-Handed Helix, and discuss the implications of the resulting atomic model of the helical NC for viral replication and transcription.

  • The respiratory syncytial virus nucleoprotein-RNA complex forms a Left-Handed helical nucleocapsid.
    The Journal of general virology, 2013
    Co-Authors: Saskia E. Bakker, Stéphane Duquerroy, Marie Galloux, Colin Loney, Edward Conner, Jean-françois Eléouët, Félix A. Rey, David Bhella
    Abstract:

    Respiratory syncytial virus (RSV) is an important human pathogen. Its nucleocapsid (NC), which comprises the negative sense RNA viral genome coated by the viral nucleoprotein N, is a critical assembly that serves as template for both mRNA synthesis and genome replication. We have previously described the X-ray structure of an NC-like structure: a decameric ring formed of N-RNA that mimics one turn of the helical NC. In the absence of experimental data we had hypothesized that the NC Helix would be right-handed, as the N-N contacts in the ring appeared to more easily adapt to that conformation. We now unambiguously show that the RSV NC is a Left-Handed Helix. We further show that the contacts in the ring can be distorted to maintain key N-N-protein interactions in a Left-Handed Helix, and discuss the implications of the resulting atomic model of the helical NC for viral replication and transcription.

Martin Lundgren - One of the best experts on this subject based on the ideXlab platform.

  • Protein loops, solitons and side-chain visualization with applications to the Left-Handed Helix region
    Physical Review E, 2012
    Co-Authors: Martin Lundgren, Antti J. Niemi, Fan Sha
    Abstract:

    Proteins in nature fold to one dominant native structure. Despite being a heavily studied field, predicting the native structure from the amino acid sequence and modeling the folding process can still be considered unsolved problems. In this thesis I present a new approach to this problem with methods borrowed from theoretical physics. In the first part I show how it is possible to use a discrete Frenet frame to define the discrete curvature and torsion of the main chain of the protein. This method is then extended to the side chains as well. In particular I show how to use the discrete Frenet frame to produce a statistical distribution of angles that works in similar fashion as the commonly used Ramachandran plot and side chain rotamers. The discrete Frenet frame displays a gauge symmetry, in the choice of basis vectors on the normal plane, that is reminiscent of features of Abelian-Higgs theory. In the second part of the thesis I show how this similarity with Abelian-Higgs theory can be translated into an effective energy for a protein. The loops of the proteins are shown to correspond to solitons so that the whole protein can be constructed by gluing together any number of solitons. I present results of simulating proteins by minimizing the energy, starting from a real line or straight Helix, where the correct native fold is attained. Finally the model is shown to display the same phase structure as real proteins.

  • Protein loops, solitons, and side-chain visualization with applications to the Left-Handed Helix region.
    Physical review. E Statistical nonlinear and soft matter physics, 2012
    Co-Authors: Martin Lundgren, Antti J. Niemi, Fan Sha
    Abstract:

    Folded proteins have a modular assembly. They are constructed from regular secondary structures like α helices and β strands that are joined together by loops. Here we develop a visualization technique that is adapted to describe this modular structure. In complement to the widely employed Ramachandran plot that is based on toroidal geometry, our approach utilizes the geometry of a two sphere. Unlike the more conventional approaches that describe only a given peptide unit, ours is capable of describing the entire backbone environment including the neighboring peptide units. It maps the positions of each atom to the surface of the two-sphere exactly how these atoms are seen by an observer who is located at the position of the central C_{α} atom. At each level of side-chain atoms we observe a strong correlation between the positioning of the atom and the underlying local secondary structure with very little if any variation between the different amino acids. As a concrete example we analyze the Left-Handed Helix region of nonglycyl amino acids. This region corresponds to an isolated and highly localized residue independent sector in the direction of the C_{β} carbons on the two-sphere. We show that the residue independent localization extends to C_{γ} and C_{δ} carbons and to side-chain oxygen and nitrogen atoms in the case of asparagine and aspartic acid. When we extend the analysis to the side-chain atoms of the neighboring residues, we observe that Left-Handed β turns display a regular and largely amino acid independent structure that can extend to seven consecutive residues. This collective pattern is due to the presence of a backbone soliton. We show how one can use our visualization techniques to analyze and classify the different solitons in terms of selection rules that we describe in detail.

  • On universal aspects of the Left-Handed Helix region
    arXiv: Biomolecules, 2011
    Co-Authors: Martin Lundgren, Antti J. Niemi, Fan Sha
    Abstract:

    We inspect the geometry of proteins by identifying their backbones as framed polygons. We find that the Left-Handed Helix region of the Ramachandran map for non-glycyl residues corresponds to an isolated and highly localized sector in the orientation of the Cβ carbons, when viewed in a Frenet frame that is centered at the corresponding Cα carbons. We show that this localization in the orientation persists to Cγ and Cδ carbons. Furthermore, when we extend our analysis to the neighboring residues we conclude that the Left-Handed Helix region reflects a very regular and apparently residue independent collective interplay of at least seven consecutive amino acids.

Félix A. Rey - One of the best experts on this subject based on the ideXlab platform.

  • The respiratory syncytial virus nucleoprotein–RNA complex forms a Left-Handed helical nucleocapsid
    Journal of General Virology, 2013
    Co-Authors: Saskia E. Bakker, Stéphane Duquerroy, Marie Galloux, Colin Loney, Edward Conner, Jean-françois Eléouët, Félix A. Rey, David Bhella
    Abstract:

    Respiratory syncytial virus (RSV) is an important human pathogen. Its nucleocapsid (NC), which comprises the negative sense RNA viral genome coated by the viral nucleoprotein N, is a critical assembly that serves as template for both mRNA synthesis and genome replication. We have previously described the X-ray structure of an NC-like structure: a decameric ring formed of N-RNA that mimics one turn of the helical NC. In the absence of experimental data we had hypothesized that the NC Helix would be right-handed, as the N–N contacts in the ring appeared to more easily adapt to that conformation. We now unambiguously show that the RSV NC is a Left-Handed Helix. We further show that the contacts in the ring can be distorted to maintain key N–N-protein interactions in a Left-Handed Helix, and discuss the implications of the resulting atomic model of the helical NC for viral replication and transcription.

  • The respiratory syncytial virus nucleoprotein-RNA complex forms a Left-Handed helical nucleocapsid.
    The Journal of general virology, 2013
    Co-Authors: Saskia E. Bakker, Stéphane Duquerroy, Marie Galloux, Colin Loney, Edward Conner, Jean-françois Eléouët, Félix A. Rey, David Bhella
    Abstract:

    Respiratory syncytial virus (RSV) is an important human pathogen. Its nucleocapsid (NC), which comprises the negative sense RNA viral genome coated by the viral nucleoprotein N, is a critical assembly that serves as template for both mRNA synthesis and genome replication. We have previously described the X-ray structure of an NC-like structure: a decameric ring formed of N-RNA that mimics one turn of the helical NC. In the absence of experimental data we had hypothesized that the NC Helix would be right-handed, as the N-N contacts in the ring appeared to more easily adapt to that conformation. We now unambiguously show that the RSV NC is a Left-Handed Helix. We further show that the contacts in the ring can be distorted to maintain key N-N-protein interactions in a Left-Handed Helix, and discuss the implications of the resulting atomic model of the helical NC for viral replication and transcription.