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Computational reconstruction of multidomain proteins using atomic force microscopy data.


ABSTRACT: Classical structural biology techniques face a great challenge to determine the structure at the atomic level of large and flexible macromolecules. We present a novel methodology that combines high-resolution AFM topographic images with atomic coordinates of proteins to assemble very large macromolecules or particles. Our method uses a two-step protocol: atomic coordinates of individual domains are docked beneath the molecular surface of the large macromolecule, and then each domain is assembled using a combinatorial search. The protocol was validated on three test cases: a simulated system of antibody structures; and two experimentally based test cases: Tobacco mosaic virus, a rod-shaped virus; and Aquaporin Z, a bacterial membrane protein. We have shown that AFM-intermediate resolution topography and partial surface data are useful constraints for building macromolecular assemblies. The protocol is applicable to multicomponent structures connected in the polypeptide chain or as disjoint molecules. The approach effectively increases the resolution of AFM beyond topographical information down to atomic-detail structures.

SUBMITTER: Trinh MH 

PROVIDER: S-EPMC3264848 | biostudies-literature | 2012 Jan

REPOSITORIES: biostudies-literature

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Computational reconstruction of multidomain proteins using atomic force microscopy data.

Trinh Minh-Hieu MH   Odorico Michael M   Pique Michael E ME   Teulon Jean-Marie JM   Roberts Victoria A VA   Ten Eyck Lynn F LF   Getzoff Elizabeth D ED   Parot Pierre P   Chen Shu-Wen W SW   Pellequer Jean-Luc JL  

Structure (London, England : 1993) 20120101 1


Classical structural biology techniques face a great challenge to determine the structure at the atomic level of large and flexible macromolecules. We present a novel methodology that combines high-resolution AFM topographic images with atomic coordinates of proteins to assemble very large macromolecules or particles. Our method uses a two-step protocol: atomic coordinates of individual domains are docked beneath the molecular surface of the large macromolecule, and then each domain is assembled  ...[more]

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