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Structural analysis of cross ?-helical nanotubes provides insight into the designability of filamentous peptide nanomaterials.

ABSTRACT: The exquisite structure-function correlations observed in filamentous protein assemblies provide a paradigm for the design of synthetic peptide-based nanomaterials. However, the plasticity of quaternary structure in sequence-space and the lability of helical symmetry present significant challenges to the de novo design and structural analysis of such filaments. Here, we describe a rational approach to design self-assembling peptide nanotubes based on controlling lateral interactions between protofilaments having an unusual cross-? supramolecular architecture. Near-atomic resolution cryo-EM structural analysis of seven designed nanotubes provides insight into the designability of interfaces within these synthetic peptide assemblies and identifies a non-native structural interaction based on a pair of arginine residues. This arginine clasp motif can robustly mediate cohesive interactions between protofilaments within the cross-? nanotubes. The structure of the resultant assemblies can be controlled through the sequence and length of the peptide subunits, which generates synthetic peptide filaments of similar dimensions to flagella and pili.

SUBMITTER: Wang F

PROVIDER: S-EPMC7814010 | biostudies-literature | 2021 Jan

REPOSITORIES: biostudies-literature

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Structural analysis of cross α-helical nanotubes provides insight into the designability of filamentous peptide nanomaterials.

Wang Fengbin F Gnewou Ordy O Modlin Charles C Beltran Leticia C LC Xu Chunfu C Su Zhangli Z Juneja Puneet P Grigoryan Gevorg G Egelman Edward H EH Conticello Vincent P VP

Nature communications 20210118 1

The exquisite structure-function correlations observed in filamentous protein assemblies provide a paradigm for the design of synthetic peptide-based nanomaterials. However, the plasticity of quaternary structure in sequence-space and the lability of helical symmetry present significant challenges to the de novo design and structural analysis of such filaments. Here, we describe a rational approach to design self-assembling peptide nanotubes based on controlling lateral interactions between prot ...[more]

PMID: 33462223

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Project description:Because the space of folded protein structures is highly degenerate, with recurring secondary and tertiary motifs, methods for representing protein structure in terms of collective physically relevant coordinates are of great interest. By collapsing structural diversity to a handful of parameters, such methods can be used to delineate the space of designable structures (i.e., conformations that can be stabilized with a large number of sequences)-a crucial task for de novo protein design. We first demonstrate this on natural ?-helical coiled coils using the Crick parameterization. We show that over 95% of known coiled-coil structures are within 1-Å C(?) root mean square deviation of a Crick-ideal backbone. Derived parameters show that natural geometric space of coiled coils is highly restricted and can be represented by "allowed" conformations amidst a potential continuum of conformers. Allowed structures have (1) restricted axial offsets between helices, which differ starkly between parallel and anti-parallel structures; (2) preferred superhelical radii, which depend linearly on the oligomerization state; (3) pronounced radius-dependent a- and d-position amino acid propensities; and (4) discrete angles of rotation of helices about their axes, which are surprisingly independent of oligomerization state or orientation. In all, we estimate the space of designable coiled-coil structures to be reduced at least 160-fold relative to the space of geometrically feasible structures. To extend the benefits of structural parameterization to other systems, we developed a general mathematical framework for parameterizing arbitrary helical structures, which reduces to the Crick parameterization as a special case. The method is successfully validated on a set of non-coiled-coil helical bundles, frequent in channels and transporter proteins, which show significant helix bending but not supercoiling. Programs for coiled-coil parameter fitting and structure generation are provided via a web interface at http://www.gevorggrigoryan.com/cccp/, and code for generalized helical parameterization is available upon request.

Dataset Information

Structural analysis of cross ?-helical nanotubes provides insight into the designability of filamentous peptide nanomaterials.

Publications

Structural analysis of cross α-helical nanotubes provides insight into the designability of filamentous peptide nanomaterials.

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