Two-intermediate model to characterize the structure of fast-folding proteins
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| Title: | Two-intermediate model to characterize the structure of fast-folding proteins |
|---|---|
| Authors: | Roterman, I.1 myroterm@cyf-kr.edu.pl, Konieczny, L.1,2, Jurkowski, W.1, Prymula, K.1,3, Banach, M.1,4 |
| Source: | Journal of Theoretical Biology. Aug2011, Vol. 283 Issue 1, p60-70. 11p. |
| Subjects: | Mathematical models, Protein structure, Protein folding, Information theory, Simulation methods & models, Entropy, Peptides |
| Abstract: | Abstract: This paper introduces a new model that enables researchers to conduct protein folding simulations. A two-step in silico process is used in the course of structural analysis of a set of fast-folding proteins. The model assumes an early stage (ES) that depends solely on the backbone conformation, as described by its geometrical properties—specifically, by the V-angle between two sequential peptide bond planes (which determines the radius of curvature, also called R-radius, according to a second-degree polynomial form). The agreement between the structure under consideration and the assumed model is measured in terms of the magnitude of dispersion of both parameters with respect to idealized values. The second step, called late-stage folding (LS), is based on the “fuzzy oil drop” model, which involves an external hydrophobic force field described by a three-dimensional Gauss function. The degree of conformance between the structure under consideration and its idealized model is expressed quantitatively by means of the Kullback–Leibler entropy, which is a measure of disparity between the observed and expected hydrophobicity distributions. A set of proteins, representative of the fast-folding group – specifically, cold shock proteins – is shown to agree with the proposed model. [Copyright &y& Elsevier] |
| Copyright of Journal of Theoretical Biology is the property of Academic Press Inc. 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 |
| FullText | Text: Availability: 0 |
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| Header | DbId: egs DbLabel: Engineering Source An: 63185599 AccessLevel: 6 PubType: Academic Journal PubTypeId: academicJournal PreciseRelevancyScore: 0 |
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| Items | – Name: Title Label: Title Group: Ti Data: Two-intermediate model to characterize the structure of fast-folding proteins – Name: Author Label: Authors Group: Au Data: <searchLink fieldCode="AR" term="%22Roterman%2C+I%2E%22">Roterman, I.</searchLink><relatesTo>1</relatesTo><i> myroterm@cyf-kr.edu.pl</i><br /><searchLink fieldCode="AR" term="%22Konieczny%2C+L%2E%22">Konieczny, L.</searchLink><relatesTo>1,2</relatesTo><br /><searchLink fieldCode="AR" term="%22Jurkowski%2C+W%2E%22">Jurkowski, W.</searchLink><relatesTo>1</relatesTo><br /><searchLink fieldCode="AR" term="%22Prymula%2C+K%2E%22">Prymula, K.</searchLink><relatesTo>1,3</relatesTo><br /><searchLink fieldCode="AR" term="%22Banach%2C+M%2E%22">Banach, M.</searchLink><relatesTo>1,4</relatesTo> – Name: TitleSource Label: Source Group: Src Data: <searchLink fieldCode="JN" term="%22Journal+of+Theoretical+Biology%22">Journal of Theoretical Biology</searchLink>. Aug2011, Vol. 283 Issue 1, p60-70. 11p. – Name: Subject Label: Subjects Group: Su Data: <searchLink fieldCode="DE" term="%22Mathematical+models%22">Mathematical models</searchLink><br /><searchLink fieldCode="DE" term="%22Protein+structure%22">Protein structure</searchLink><br /><searchLink fieldCode="DE" term="%22Protein+folding%22">Protein folding</searchLink><br /><searchLink fieldCode="DE" term="%22Information+theory%22">Information theory</searchLink><br /><searchLink fieldCode="DE" term="%22Simulation+methods+%26+models%22">Simulation methods & models</searchLink><br /><searchLink fieldCode="DE" term="%22Entropy%22">Entropy</searchLink><br /><searchLink fieldCode="DE" term="%22Peptides%22">Peptides</searchLink> – Name: Abstract Label: Abstract Group: Ab Data: Abstract: This paper introduces a new model that enables researchers to conduct protein folding simulations. A two-step in silico process is used in the course of structural analysis of a set of fast-folding proteins. The model assumes an early stage (ES) that depends solely on the backbone conformation, as described by its geometrical properties—specifically, by the V-angle between two sequential peptide bond planes (which determines the radius of curvature, also called R-radius, according to a second-degree polynomial form). The agreement between the structure under consideration and the assumed model is measured in terms of the magnitude of dispersion of both parameters with respect to idealized values. The second step, called late-stage folding (LS), is based on the “fuzzy oil drop” model, which involves an external hydrophobic force field described by a three-dimensional Gauss function. The degree of conformance between the structure under consideration and its idealized model is expressed quantitatively by means of the Kullback–Leibler entropy, which is a measure of disparity between the observed and expected hydrophobicity distributions. A set of proteins, representative of the fast-folding group – specifically, cold shock proteins – is shown to agree with the proposed model. [Copyright &y& Elsevier] – Name: AbstractSuppliedCopyright Label: Group: Ab Data: <i>Copyright of Journal of Theoretical Biology is the property of Academic Press Inc. 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: BibEntity: Identifiers: – Type: doi Value: 10.1016/j.jtbi.2011.05.027 Languages: – Code: eng Text: English PhysicalDescription: Pagination: PageCount: 11 StartPage: 60 Subjects: – SubjectFull: Mathematical models Type: general – SubjectFull: Protein structure Type: general – SubjectFull: Protein folding Type: general – SubjectFull: Information theory Type: general – SubjectFull: Simulation methods & models Type: general – SubjectFull: Entropy Type: general – SubjectFull: Peptides Type: general Titles: – TitleFull: Two-intermediate model to characterize the structure of fast-folding proteins Type: main BibRelationships: HasContributorRelationships: – PersonEntity: Name: NameFull: Roterman, I. – PersonEntity: Name: NameFull: Konieczny, L. – PersonEntity: Name: NameFull: Jurkowski, W. – PersonEntity: Name: NameFull: Prymula, K. – PersonEntity: Name: NameFull: Banach, M. IsPartOfRelationships: – BibEntity: Dates: – D: 21 M: 08 Text: Aug2011 Type: published Y: 2011 Identifiers: – Type: issn-print Value: 00225193 Numbering: – Type: volume Value: 283 – Type: issue Value: 1 Titles: – TitleFull: Journal of Theoretical Biology Type: main |
| ResultId | 1 |
