Structural assembly of multidomain proteins and protein complexes guided by the overall rotational diffusion tensor.

Structural assembly of multidomain proteins and protein complexes guided by the overall rotational diffusion tensor. Research Abstract Details 

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Structural assembly of multidomain proteins and protein complexes guided by the overall rotational diffusion tensor. Abstract Text:

Yaroslav Ryabov,David Fushman,

We present a simple and robust approach that uses the overall rotational diffusion tensor as a structural constraint for domain positioning in multidomain proteins and protein-protein complexes. This method offers the possibility to use NMR relaxation data for detailed structure characterization of such systems provided the structures of individual domains are available. The proposed approach extends the concept of using long-range information contained in the overall rotational diffusion tensor. In contrast to the existing approaches, we use both the principal axes and principal values of protein's rotational diffusion tensor to determine not only the orientation but also the relative positioning of the individual domains in a protein. This is achieved by finding the domain arrangement in a molecule that provides the best possible agreement with all components of the overall rotational diffusion tensor derived from experimental data. The accuracy of the proposed approach is demonstrated for two protein systems with known domain arrangement and parameters of the overall tumbling: the HIV-1 protease homodimer and Maltose Binding Protein. The accuracy of the method and its sensitivity to domain positioning are also tested using computer-generated data for three protein complexes, for which the experimental diffusion tensors are not available. In addition, the proposed method is applied here to determine, for the first time, the structure of both open and closed conformations of a Lys48-linked diubiquitin chain, where domain motions render impossible accurate structure determination by other methods. The proposed method opens new avenues for improving structure characterization of proteins in solution.

Structural assembly of multidomain proteins and protein complexes guided by the overall rotational diffusion tensor. Publishing Authors By Initials

Y Ryabov,D Fushman,

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Structural assembly of multidomain proteins and protein complexes guided by the overall rotational diffusion tensor. Journal Published:

PUBLICATION TYPE: Research Support, N.I.H., Extr

Journal: Journal of the American Chemical Society

VOLUME: 129

Page Numbers: 7894-902

Journal Abbreviation: J. Am. Chem. Soc.

ISSN: 0002-7863

DAY: 6

MONTH: 06

YEAR: 2007

Structural assembly of multidomain proteins and protein complexes guided by the overall rotational diffusion tensor. Information

Number of References:

LANGUAGE: eng

NlmUniqueID: 7503056

Structural assembly of multidomain proteins and protein complexes guided by the overall rotational diffusion tensor. Keywords Mesh Terms:

KEYWORDS: Proteins

MESH TERMS: chemistry

Chemical & Substance for Abstract: Structural assembly of multidomain proteins and protein complexes guided by the overall rotational diffusion tensor. Information

Substance Name: Proteins

Registry Number: 0

Grant and Affiliation Information for Structural assembly of multidomain proteins and protein complexes guided by the overall rotational diffusion tensor.

AFFILIATION: Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, Maryland 20742, USA.

Country: United States

AGENCY: United States NIGMS

GRANT: GM065334

ACRONYM: GM

MEDLINETA: J Am Chem Soc

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Structural assembly of multidomain proteins and protein complexes guided by the overall rotational diffusion tensor Related Publications

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• Analysis of interdomain dynamics in a two-domain protein using residual dipolar couplings together with 15N relaxation data.
• Effects of cyclization on conformational dynamics and binding properties of Lys48-linked di-ubiquitin.
• Mapping the interactions between Lys48 and Lys63-linked di-ubiquitins and a ubiquitin-interacting motif of S5a.
• Measurement of 15N relaxation in deuterated amide groups in proteins using direct nitrogen detection.
• Mutations in the hydrophobic core of ubiquitin differentially affect its recognition by receptor proteins.
• Structural assembly of multidomain proteins and protein complexes guided by the overall rotational diffusion tensor.