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Shielding effect in protein folding.

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Title: Shielding effect in protein folding.
Authors: Sieradzan, Adam K.1 adasko@sun1.chem.univ.gda.pl, Lipska, Agnieszka G.1, Lubecka, Emilia A.1,2
Source: Journal of Molecular Graphics & Modelling. Jan2018, Vol. 79, p118-132. 15p.
Subjects: Protein folding, Protein stability, Hydrogen bonding, Hydration, Substituents (Chemistry)
Abstract: One of the most important interactions responsible for protein folding and stability are hydrogen bonds between peptide groups. There is a constant competition between the water molecules and peptide groups in a hydrogen bond formation. Also side-chains take part in this process by reducing hydration of peptide group (shielding effect) that promotes the protein folding. In this paper, a new approach to take into account a shielding effect is presented. A modification of the energy function is derived and incorporated into the UNited RESidue (UNRES) force field. Canonical Molecular Dynamics and Replica Exchange Molecular Dynamics with UNRES force field is applied to study the influence of this effect on protein structure, folding kinetics and free energy landscapes. The results of test calculations suggest that even small contribution of this effect into energy function changes force field behavior as well as speeds up the folding process significantly. [ABSTRACT FROM AUTHOR]
Copyright of Journal of Molecular Graphics & Modelling is the property of Elsevier B.V. and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
Database: Engineering Source
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Header DbId: egs
DbLabel: Engineering Source
An: 127984838
AccessLevel: 6
PubType: Academic Journal
PubTypeId: academicJournal
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  Data: Shielding effect in protein folding.
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  Data: <searchLink fieldCode="AR" term="%22Sieradzan%2C+Adam+K%2E%22">Sieradzan, Adam K.</searchLink><relatesTo>1</relatesTo><i> adasko@sun1.chem.univ.gda.pl</i><br /><searchLink fieldCode="AR" term="%22Lipska%2C+Agnieszka+G%2E%22">Lipska, Agnieszka G.</searchLink><relatesTo>1</relatesTo><br /><searchLink fieldCode="AR" term="%22Lubecka%2C+Emilia+A%2E%22">Lubecka, Emilia A.</searchLink><relatesTo>1,2</relatesTo>
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  Data: <searchLink fieldCode="JN" term="%22Journal+of+Molecular+Graphics+%26+Modelling%22">Journal of Molecular Graphics & Modelling</searchLink>. Jan2018, Vol. 79, p118-132. 15p.
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  Data: <searchLink fieldCode="DE" term="%22Protein+folding%22">Protein folding</searchLink><br /><searchLink fieldCode="DE" term="%22Protein+stability%22">Protein stability</searchLink><br /><searchLink fieldCode="DE" term="%22Hydrogen+bonding%22">Hydrogen bonding</searchLink><br /><searchLink fieldCode="DE" term="%22Hydration%22">Hydration</searchLink><br /><searchLink fieldCode="DE" term="%22Substituents+%28Chemistry%29%22">Substituents (Chemistry)</searchLink>
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  Data: One of the most important interactions responsible for protein folding and stability are hydrogen bonds between peptide groups. There is a constant competition between the water molecules and peptide groups in a hydrogen bond formation. Also side-chains take part in this process by reducing hydration of peptide group (shielding effect) that promotes the protein folding. In this paper, a new approach to take into account a shielding effect is presented. A modification of the energy function is derived and incorporated into the UNited RESidue (UNRES) force field. Canonical Molecular Dynamics and Replica Exchange Molecular Dynamics with UNRES force field is applied to study the influence of this effect on protein structure, folding kinetics and free energy landscapes. The results of test calculations suggest that even small contribution of this effect into energy function changes force field behavior as well as speeds up the folding process significantly. [ABSTRACT FROM AUTHOR]
– Name: AbstractSuppliedCopyright
  Label:
  Group: Ab
  Data: <i>Copyright of Journal of Molecular Graphics & Modelling is the property of Elsevier B.V. and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.</i> (Copyright applies to all Abstracts.)
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RecordInfo BibRecord:
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    Identifiers:
      – Type: doi
        Value: 10.1016/j.jmgm.2017.10.018
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      – Code: eng
        Text: English
    PhysicalDescription:
      Pagination:
        PageCount: 15
        StartPage: 118
    Subjects:
      – SubjectFull: Protein folding
        Type: general
      – SubjectFull: Protein stability
        Type: general
      – SubjectFull: Hydrogen bonding
        Type: general
      – SubjectFull: Hydration
        Type: general
      – SubjectFull: Substituents (Chemistry)
        Type: general
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      – TitleFull: Shielding effect in protein folding.
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            NameFull: Lipska, Agnieszka G.
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            NameFull: Lubecka, Emilia A.
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            – D: 01
              M: 01
              Text: Jan2018
              Type: published
              Y: 2018
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              Value: 79
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            – TitleFull: Journal of Molecular Graphics & Modelling
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