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Collagen and component polypeptides: Low frequency and amide vibrations

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Title: Collagen and component polypeptides: Low frequency and amide vibrations
Authors: Fontaine-Vive, F.1,2, Merzel, F.3, Johnson, M.R.1 johnson@ill.fr, Kearley, G.J.4
Source: Chemical Physics. Jan2009, Vol. 355 Issue 2/3, p141-148. 8p.
Subjects: Polypeptides, Collagen, Amides, Density functionals, Proteins, Simulation methods & models, Biomechanics, Vibrational spectra
Abstract: Abstract: Collagen is a fibrous protein, which exists widely in the human body. The biomechanical properties of collagen depend on its triple helix structure and the corresponding low frequency vibrations. We use first-principles, density functional theory methods and analytical force fields to investigate the molecular vibrations of a model collagen compound, the results being validated by comparison with published, inelastic neutron scattering data. The results from these atomistic simulations are used at higher frequency to study the Amide I and V vibrations and therefore the vibrational signature of secondary and tertiary structure formation. In addition to collagen, its component homopolymers, poly-glycine and poly-proline are also studied. The Amide V vibration of glycine is strongly modified in going from the single helix of poly-glycine II to the triple helix of collagen. The collagen models are hydrated and this work allows us to discuss the relative merits of density functional theory and force field methods when tackling complex, partially crystalline systems. [Copyright &y& Elsevier]
Copyright of Chemical Physics 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: 36194722
AccessLevel: 6
PubType: Academic Journal
PubTypeId: academicJournal
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  Data: Collagen and component polypeptides: Low frequency and amide vibrations
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  Data: <searchLink fieldCode="AR" term="%22Fontaine-Vive%2C+F%2E%22">Fontaine-Vive, F.</searchLink><relatesTo>1,2</relatesTo><br /><searchLink fieldCode="AR" term="%22Merzel%2C+F%2E%22">Merzel, F.</searchLink><relatesTo>3</relatesTo><br /><searchLink fieldCode="AR" term="%22Johnson%2C+M%2ER%2E%22">Johnson, M.R.</searchLink><relatesTo>1</relatesTo><i> johnson@ill.fr</i><br /><searchLink fieldCode="AR" term="%22Kearley%2C+G%2EJ%2E%22">Kearley, G.J.</searchLink><relatesTo>4</relatesTo>
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  Data: <searchLink fieldCode="JN" term="%22Chemical+Physics%22">Chemical Physics</searchLink>. Jan2009, Vol. 355 Issue 2/3, p141-148. 8p.
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  Data: <searchLink fieldCode="DE" term="%22Polypeptides%22">Polypeptides</searchLink><br /><searchLink fieldCode="DE" term="%22Collagen%22">Collagen</searchLink><br /><searchLink fieldCode="DE" term="%22Amides%22">Amides</searchLink><br /><searchLink fieldCode="DE" term="%22Density+functionals%22">Density functionals</searchLink><br /><searchLink fieldCode="DE" term="%22Proteins%22">Proteins</searchLink><br /><searchLink fieldCode="DE" term="%22Simulation+methods+%26+models%22">Simulation methods & models</searchLink><br /><searchLink fieldCode="DE" term="%22Biomechanics%22">Biomechanics</searchLink><br /><searchLink fieldCode="DE" term="%22Vibrational+spectra%22">Vibrational spectra</searchLink>
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  Label: Abstract
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  Data: Abstract: Collagen is a fibrous protein, which exists widely in the human body. The biomechanical properties of collagen depend on its triple helix structure and the corresponding low frequency vibrations. We use first-principles, density functional theory methods and analytical force fields to investigate the molecular vibrations of a model collagen compound, the results being validated by comparison with published, inelastic neutron scattering data. The results from these atomistic simulations are used at higher frequency to study the Amide I and V vibrations and therefore the vibrational signature of secondary and tertiary structure formation. In addition to collagen, its component homopolymers, poly-glycine and poly-proline are also studied. The Amide V vibration of glycine is strongly modified in going from the single helix of poly-glycine II to the triple helix of collagen. The collagen models are hydrated and this work allows us to discuss the relative merits of density functional theory and force field methods when tackling complex, partially crystalline systems. [Copyright &y& Elsevier]
– Name: AbstractSuppliedCopyright
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  Data: <i>Copyright of Chemical Physics 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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        Value: 10.1016/j.chemphys.2008.12.005
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      – Code: eng
        Text: English
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        PageCount: 8
        StartPage: 141
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      – SubjectFull: Polypeptides
        Type: general
      – SubjectFull: Collagen
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      – SubjectFull: Amides
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      – SubjectFull: Density functionals
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      – SubjectFull: Proteins
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      – SubjectFull: Simulation methods & models
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      – SubjectFull: Biomechanics
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      – SubjectFull: Vibrational spectra
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      – TitleFull: Collagen and component polypeptides: Low frequency and amide vibrations
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            NameFull: Fontaine-Vive, F.
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            NameFull: Merzel, F.
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            NameFull: Johnson, M.R.
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              Text: Jan2009
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              Y: 2009
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