In Silico Study on Retinoid-binding Modes in Human RBP and ApoD Lipocalins.
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| Authors: | Munussami, Ganapathiraman1, Sokalingam, Sriram1, Kim, Jung Rae1, Lee, Sun-Gu1 sungulee@pusan.ac.kr |
| Source: | Biotechnology & Bioprocess Engineering. Mar2018, Vol. 23 Issue 2, p158-167. 10p. |
| Subjects: | Retinoids, Lipocalins, Apolipoproteins, Ligands (Biochemistry), Crystallization |
| Abstract: | Lipocalins are proteins with highly homologous structures but diverse sequences that are potential candidates for scaffold protein engineering with novel ligand-binding functions. Numerous crystal structures of lipocalin-ligand complexes have been identified and used in the study of their binding modes. On the other hand, crystallization studies cannot meet the increasing demand for novel lipocalin-ligand complexes in scaffold engineering, which requires rapid computational analyses of their binding modes in parallel. Human retinol-binding protein (RBP) and apolipoprotein D (apoD) are sequentially very distant proteins, but they show tight binding against retinoids, such as retinol and retinoic acid. In the present study, complexes of the two lipocalins with retinol and retinoic acid were modeled computationally by a molecular docking simulation, and their ligand-binding modes were analyzed at a molecular level. The models identified the crucial residues of lipocalins that interact with the ligands and revealed the similarities and differences in their retinoid-binding modes as well as in the specific interactions of the retinoid species within the same lipocalin. An analysis of the amino acid propensity of the retinoid-binding residues suggested that the evolutionary preference of the residues is restricted to the binding pocket rather than the entire protein. The distribution of charged residues around the terminus of retinoic acid showed a huge difference between RBP and ApoD, which might be a factor for the different binding affinities of lipocalins against retinoic acid. This |
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| Items | – Name: Title Label: Title Group: Ti Data: <italic>In Silico</italic> Study on Retinoid-binding Modes in Human RBP and ApoD Lipocalins. – Name: Author Label: Authors Group: Au Data: <searchLink fieldCode="AR" term="%22Munussami%2C+Ganapathiraman%22">Munussami, Ganapathiraman</searchLink><relatesTo>1</relatesTo><br /><searchLink fieldCode="AR" term="%22Sokalingam%2C+Sriram%22">Sokalingam, Sriram</searchLink><relatesTo>1</relatesTo><br /><searchLink fieldCode="AR" term="%22Kim%2C+Jung+Rae%22">Kim, Jung Rae</searchLink><relatesTo>1</relatesTo><br /><searchLink fieldCode="AR" term="%22Lee%2C+Sun-Gu%22">Lee, Sun-Gu</searchLink><relatesTo>1</relatesTo><i> sungulee@pusan.ac.kr</i> – Name: TitleSource Label: Source Group: Src Data: <searchLink fieldCode="JN" term="%22Biotechnology+%26+Bioprocess+Engineering%22">Biotechnology & Bioprocess Engineering</searchLink>. Mar2018, Vol. 23 Issue 2, p158-167. 10p. – Name: Subject Label: Subjects Group: Su Data: <searchLink fieldCode="DE" term="%22Retinoids%22">Retinoids</searchLink><br /><searchLink fieldCode="DE" term="%22Lipocalins%22">Lipocalins</searchLink><br /><searchLink fieldCode="DE" term="%22Apolipoproteins%22">Apolipoproteins</searchLink><br /><searchLink fieldCode="DE" term="%22Ligands+%28Biochemistry%29%22">Ligands (Biochemistry)</searchLink><br /><searchLink fieldCode="DE" term="%22Crystallization%22">Crystallization</searchLink> – Name: Abstract Label: Abstract Group: Ab Data: Lipocalins are proteins with highly homologous structures but diverse sequences that are potential candidates for scaffold protein engineering with novel ligand-binding functions. Numerous crystal structures of lipocalin-ligand complexes have been identified and used in the study of their binding modes. On the other hand, crystallization studies cannot meet the increasing demand for novel lipocalin-ligand complexes in scaffold engineering, which requires rapid computational analyses of their binding modes in parallel. Human retinol-binding protein (RBP) and apolipoprotein D (apoD) are sequentially very distant proteins, but they show tight binding against retinoids, such as retinol and retinoic acid. In the present study, complexes of the two lipocalins with retinol and retinoic acid were modeled computationally by a molecular docking simulation, and their ligand-binding modes were analyzed at a molecular level. The models identified the crucial residues of lipocalins that interact with the ligands and revealed the similarities and differences in their retinoid-binding modes as well as in the specific interactions of the retinoid species within the same lipocalin. An analysis of the amino acid propensity of the retinoid-binding residues suggested that the evolutionary preference of the residues is restricted to the binding pocket rather than the entire protein. The distribution of charged residues around the terminus of retinoic acid showed a huge difference between RBP and ApoD, which might be a factor for the different binding affinities of lipocalins against retinoic acid. This <italic>in silico</italic> study is expected to be applied to scaffold protein engineering for novel retinoid-binding lipocalins. [ABSTRACT FROM AUTHOR] – Name: AbstractSuppliedCopyright Label: Group: Ab Data: <i>Copyright of Biotechnology & Bioprocess Engineering is the property of Springer Nature 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: 10.1007/s12257-018-0032-z Languages: – Code: eng Text: English PhysicalDescription: Pagination: PageCount: 10 StartPage: 158 Subjects: – SubjectFull: Retinoids Type: general – SubjectFull: Lipocalins Type: general – SubjectFull: Apolipoproteins Type: general – SubjectFull: Ligands (Biochemistry) Type: general – SubjectFull: Crystallization Type: general Titles: – TitleFull: <italic>In Silico</italic> Study on Retinoid-binding Modes in Human RBP and ApoD Lipocalins. Type: main BibRelationships: HasContributorRelationships: – PersonEntity: Name: NameFull: Munussami, Ganapathiraman – PersonEntity: Name: NameFull: Sokalingam, Sriram – PersonEntity: Name: NameFull: Kim, Jung Rae – PersonEntity: Name: NameFull: Lee, Sun-Gu IsPartOfRelationships: – BibEntity: Dates: – D: 01 M: 03 Text: Mar2018 Type: published Y: 2018 Identifiers: – Type: issn-print Value: 12268372 Numbering: – Type: volume Value: 23 – Type: issue Value: 2 Titles: – TitleFull: Biotechnology & Bioprocess Engineering Type: main |
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