Influence of rotational energy barriers to the conformational search of protein loops in molecular dynamics and ranking the conformations

    Research output: Contribution to journalArticleScientificpeer-review

    17 Citations (Scopus)

    Abstract

    An adjustable-barrier dihedral angle potential was added as an extension to a novel, previously presented soft-core potential to study its contribution to the efficacy of the search of the conformational space in molecular dynamics. As opposed to the conventional soft-core potential functions, the leading principle in the design of the new soft-core potential, as well as of its extension, the soft-core and adjustable-barrier dihedral angle (SCADA) potential (referred as the SCADA potential), was to maintain the main equilibrium properties of the original force field. This qualifies the methods for a variety of a priori modeling problems without need for additional restraints typically required with the conventional soft-core potentials. In the present study, the different potential energy functions are applied to the problem of predicting loop conformations in proteins. Comparison of the performance of the soft-core and SCADA potential showed that the main hurdles for the efficient sampling of the conformational space of (loops in) proteins are related to the high-energy barriers caused by the Lennard-Jones and Coulombic energy terms, and not to the rotational barriers, although the conformational search can be further enhanced by lowering the rotational barriers of the dihedral angles. Finally, different evaluation methods were studied and a few promising criteria found to distinguish the near-native loop conformations from the wrong ones.
    Original languageEnglish
    Pages (from-to)167-179
    Number of pages13
    JournalProteins
    Volume44
    Issue number3
    Publication statusPublished - 2001
    MoE publication typeA1 Journal article-refereed

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    Energy barriers
    Dihedral angle
    Molecular Dynamics Simulation
    Conformations
    Molecular dynamics
    Protein Conformation
    Proteins
    Potential energy functions
    Sampling

    Cite this

    @article{fa74427ef92942c794a0612dd1f3a2be,
    title = "Influence of rotational energy barriers to the conformational search of protein loops in molecular dynamics and ranking the conformations",
    abstract = "An adjustable-barrier dihedral angle potential was added as an extension to a novel, previously presented soft-core potential to study its contribution to the efficacy of the search of the conformational space in molecular dynamics. As opposed to the conventional soft-core potential functions, the leading principle in the design of the new soft-core potential, as well as of its extension, the soft-core and adjustable-barrier dihedral angle (SCADA) potential (referred as the SCADA potential), was to maintain the main equilibrium properties of the original force field. This qualifies the methods for a variety of a priori modeling problems without need for additional restraints typically required with the conventional soft-core potentials. In the present study, the different potential energy functions are applied to the problem of predicting loop conformations in proteins. Comparison of the performance of the soft-core and SCADA potential showed that the main hurdles for the efficient sampling of the conformational space of (loops in) proteins are related to the high-energy barriers caused by the Lennard-Jones and Coulombic energy terms, and not to the rotational barriers, although the conformational search can be further enhanced by lowering the rotational barriers of the dihedral angles. Finally, different evaluation methods were studied and a few promising criteria found to distinguish the near-native loop conformations from the wrong ones.",
    author = "Kirsi Tappura",
    year = "2001",
    language = "English",
    volume = "44",
    pages = "167--179",
    journal = "Proteins",
    issn = "0887-3585",
    publisher = "Wiley",
    number = "3",

    }

    Influence of rotational energy barriers to the conformational search of protein loops in molecular dynamics and ranking the conformations. / Tappura, Kirsi.

    In: Proteins, Vol. 44, No. 3, 2001, p. 167-179.

    Research output: Contribution to journalArticleScientificpeer-review

    TY - JOUR

    T1 - Influence of rotational energy barriers to the conformational search of protein loops in molecular dynamics and ranking the conformations

    AU - Tappura, Kirsi

    PY - 2001

    Y1 - 2001

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    AB - An adjustable-barrier dihedral angle potential was added as an extension to a novel, previously presented soft-core potential to study its contribution to the efficacy of the search of the conformational space in molecular dynamics. As opposed to the conventional soft-core potential functions, the leading principle in the design of the new soft-core potential, as well as of its extension, the soft-core and adjustable-barrier dihedral angle (SCADA) potential (referred as the SCADA potential), was to maintain the main equilibrium properties of the original force field. This qualifies the methods for a variety of a priori modeling problems without need for additional restraints typically required with the conventional soft-core potentials. In the present study, the different potential energy functions are applied to the problem of predicting loop conformations in proteins. Comparison of the performance of the soft-core and SCADA potential showed that the main hurdles for the efficient sampling of the conformational space of (loops in) proteins are related to the high-energy barriers caused by the Lennard-Jones and Coulombic energy terms, and not to the rotational barriers, although the conformational search can be further enhanced by lowering the rotational barriers of the dihedral angles. Finally, different evaluation methods were studied and a few promising criteria found to distinguish the near-native loop conformations from the wrong ones.

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    SP - 167

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    JO - Proteins

    JF - Proteins

    SN - 0887-3585

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