RosettaRemodel: A Generalized Framework for Flexible Backbone Protein Design

Huang, Po-Ssu; Ban, Yih-En Andrew; Richter, Florian; André, Ingemar; Vernon, Robert; Schief, William R.; Baker, David

doi:10.1371/journal.pone.0024109

Cited by 341 publications

(336 citation statements)

References 43 publications

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“…**p < 0.01. e Representative total fluorescence intensity (I || + 2I ⊥ , left) and anisotropy (right). Scale bars: 5 µm orientations of the two connections between LFA-1 and GFP was effectively sampled using polypeptide segments from the protein databank, selecting those that enabled connections at both the N and C termini of GFP to be closed, and then minimizing the energy of the system with respect to the degrees of freedom of the connecting linkers 23 . The distribution of dipole orientations in the resulting ensembles (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…We also use negative stain EM class averages showing the bent-closed, extended-closed, and extended-open conformations of the αLβ2 and αXβ2 ectodomains 2 . These structures together with those of green fluorescent protein (GFP) have guided development here of constrained integrin-GFP fusions and prediction of the orientation of GFP and its fluorescent excitation/emission transition dipole relative to the integrin using Rosetta 23 . Two different types of fluorescent microscopes provide similar measurements of the orientation of the transition dipole relative to the direction of actin flow.…”

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confidence: 99%

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Direction of actin flow dictates integrin LFA-1 orientation during leukocyte migration

Nordenfelt

Moore

Mehta

et al. 2016

Preprint

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Integrin αβ heterodimer cell surface receptors mediate adhesive interactions that provide traction for cell migration. Here, we test whether the integrin, when engaged to an extracellular ligand and the cytoskeleton, adopts a specific orientation dictated by the direction of actin flow on the surface of migrating cells. We insert GFP into the rigid, ligand-binding head of the integrin, model with Rosetta the orientation of GFP and its transition dipole relative to the integrin head, and measure orientation with fluorescence polarization microscopy. Cytoskeleton and ligand-bound integrins orient in the same direction as retrograde actin flow with their cytoskeleton-binding β-subunits tilted by applied force. The measurements demonstrate that intracellular forces can orient cell surface integrins and support a molecular model of integrin activation by cytoskeletal force. Our results place atomic, Å-scale structures of cell surface receptors in the context of functional and cellular, μm-scale measurements.

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Section: Resultsmentioning

confidence: 99%

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confidence: 99%

Direction of actin flow dictates integrin LFA-1 orientation during leukocyte migration

Nordenfelt

Moore

Mehta

et al. 2016

Preprint

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“…19 Initially, conformational sampling was carried with a low-resolution description of the side-chains, which were represented as centroids, and in the final stage the sampled conformations were refined and scored using a full atom description of the protein. 8 The generated models were clustered according to the rmsd of the designed loop using a hierarchical cluster algorithm as implemented in Rosetta, with a cluster radius of 0.1 Å . The lowest full atom energy 21 structure from the largest cluster was selected to establish structural comparisons with the solved crystal structure.…”

Section: Methodsmentioning

confidence: 99%

High‐resolution structure prediction of a circular permutation loop

et al. 2011

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Methods for rapid and reliable design and structure prediction of linker loops would facilitate a variety of protein engineering applications. Circular permutation, in which the existing termini of a protein are linked by the polypeptide chain and new termini are created, is one such application that has been employed for decreasing proteolytic susceptibility and other functional purposes. The length and sequence of the linker can impact the expression level, solubility, structure and function of the permuted variants. Hence it is desirable to achieve atomic-level accuracy in linker design. Here, we describe the use of RosettaRemodel for design and structure prediction of circular permutation linkers on a model protein. A crystal structure of one of the permuted variants confirmed the accuracy of the computational prediction, where the all-atom rmsd of the linker region was 0.89 Å between the model and the crystal structure. This result suggests that RosettaRemodel may be generally useful for the design and structure prediction of protein loop regions for circular permutations or other structure-function manipulations.

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“…The best known modeling platform, Rosetta, has now a lot of dierent subdomains, including RosettaDesign [37]. Recent release, RosettaRemodel [38], deals with exible proteins. However, the same rule which is written into heptad repeat is of high importance for every computer designed helix, and physicochemical intuition towards computational design is not in the opposition; design based only on experiments and intuition provide proofs for understanding of rules, which may become codied into computer algorithms [11].…”

Section: Strategy Of Computational Designmentioning

confidence: 99%

De Novo Designed Proteins - Perspective Materials for Nanotechnology

Grzyb

2012

Acta Phys. Pol. A

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The paper explores the eld of de novo protein design, as a source of material for eective hybrid nanostructures. Main design approaches, namely the intuitional and the computational strategy, are briey overviewed. The achievements in the eld are illustrated with several examples, starting from historical heme binding maquettes to novel non-natural enzymes. Separate paragraph covers the problem of designing peptides, which may act as anchor between biological and non-biological parts of nanostructures. The advantages of de novo designed proteins and still existing problems of the eld are discussed.

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RosettaRemodel: A Generalized Framework for Flexible Backbone Protein Design

Cited by 341 publications

References 43 publications

Direction of actin flow dictates integrin LFA-1 orientation during leukocyte migration

Direction of actin flow dictates integrin LFA-1 orientation during leukocyte migration

High‐resolution structure prediction of a circular permutation loop

De Novo Designed Proteins - Perspective Materials for Nanotechnology

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