BCL::Fold - De Novo Prediction of Complex and Large Protein Topologies by Assembly of Secondary Structure Elements

Karakaş, Mert; Woetzel, Nils; Staritzbichler, René; Alexander, Nathan; Weiner, Brian E.; Meiler, Jens

doi:10.1371/journal.pone.0049240

Cited by 43 publications

(94 citation statements)

References 87 publications

(109 reference statements)

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“…To highlight the conformational changes induced by protonation in a structural context, we carried out detailed de novo modeling of the pH 5 conformation using BCL::Fold and Rosetta (22)(23)(24)(25). The conformational search was restrained by the experimental distances at pH 5 (22,23).…”

Section: Discussionmentioning

confidence: 99%

“…The conformational search was restrained by the experimental distances at pH 5 (22,23). A twofold symmetry was imposed such that both protomers have similar conformations, in contrast to the crystal structure, where the two protomers have distinct conformations and form an asymmetric dimer.…”

Section: Discussionmentioning

confidence: 99%

“…The initial model of the EmrE structure at pH 5 was predicted by a two-step approach using BCL::Fold (22,23) to assemble the secondary structure elements (SSEs) in 3D space and Rosetta (24,25) to construct loop regions and predict sidechain conformations. See SI Methods for more details on BCL/Rosetta modeling.…”

Section: Methodsmentioning

confidence: 99%

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Protonation-dependent conformational dynamics of the multidrug transporter EmrE

Dastvan

Fischer

Mishra

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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The small multidrug transporter from Escherichia coli, EmrE, couples the energetically uphill extrusion of hydrophobic cations out of the cell to the transport of two protons down their electrochemical gradient. Although principal mechanistic elements of proton/substrate antiport have been described, the structural record is limited to the conformation of the substrate-bound state, which has been shown to undergo isoenergetic alternating access. A central but missing link in the structure/mechanism relationship is a description of the protonbound state, which is an obligatory intermediate in the transport cycle. Here we report a systematic spin labeling and double electron electron resonance (DEER) study that uncovers the conformational changes of EmrE subsequent to protonation of critical acidic residues in the context of a global description of ligand-induced structural rearrangements. We find that protonation of E14 leads to extensive rotation and tilt of transmembrane helices 1-3 in conjunction with repacking of loops, conformational changes that alter the coordination of the bound substrate and modulate its access to the binding site from the lipid bilayer. The transport model that emerges from our data posits a proton-bound, but occluded, resting state. Substrate binding from the inner leaflet of the bilayer releases the protons and triggers alternating access between inward-and outward-facing conformations of the substrate-loaded transporter, thus enabling antiport without dissipation of the proton gradient.EmrE | SMR | EPR | DEER | multidrug transport P owered by the proton electrochemical gradient across the inner membrane of prokaryotes, small multidrug resistance (SMR) transporters extrude a spectrum of cytotoxic molecules that are primarily hydrophobic cations (1). The functional unit is typically a homodimer wherein each protomer consists of four hydrophobic transmembrane helices (TM). TM1-3 cradle a substrate binding pocket, whereas TM4 is involved in the contacts that stabilize the dimer. EmrE, the SMR transporter from Escherichia coli, has been a focal point of structural, spectroscopic, and mechanistic investigations (2-7). Seminal work from the Schuldiner laboratory over the last two decades has unlocked mechanistic principles of substrate-ionantiport (1,(8)(9)(10). EmrE binds hydrophobic substrates in a membrane-embedded chamber coordinated by glutamate 14 (E14), an absolutely conserved, membrane-embedded, acidic residue in the middle of TM1. Coupling between substrate and proton arises from the principle of mutual exclusion between the two ligands at the binding site (8,10).In contrast to the elaborate understanding of the EmrE antiport mechanism, the conformational changes that enable binding and release of ligands have not been elucidated. Although the general framework of antiport is presumed to follow the principles of alternating access, the only structure available is of EmrE bound to the substrate tetraphenylphosphonium (TPP) (3). EM analysis of 2D crystals established an antiparallel ...

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Protonation-dependent conformational dynamics of the multidrug transporter EmrE

Dastvan

Fischer

Mishra

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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“…23,24 The secondary structure is the three-dimensional form of local segments of proteins, which consists of local inter-residue interactions mediated by hydrogen bonds. Amino acids vary in their ability to form the various secondary structure elements.…”

Section: -15mentioning

confidence: 99%

Protein Structure Prediction: Assembly of Secondary Structure Elements by Basin‐Hopping

et al. 2014

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The prediction of protein tertiary structure from primary structure remains a challenging task. A possible approach to this problem is the application of basin-hopping global optimization combined with an all-atom force field. In this work, we further improve the efficiency of basin-hopping by introducing an approach that derives tertiary structures from the secondary structure assignments of individual residues. We term this approach secondary-to-tertiary basin-hopping and benchmark it for three miniproteins, trpzip, trp-cage and ER-10. For each of the the three miniproteins the secondaryto-tertiary basin-hopping approach successfully and reliably predicts the three-dimensional structure.When it is applied to larger proteins we also obtain correctly folded structures. We thus conclude that the assembly of secondary structure elements using basin-hopping is a promising tool for de novo protein structure prediction.1 These authors contributed equally to this work.

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“…The search for the native structure starts from randomly placed helices oriented perpendicular to the membrane plane. As a next step, folding is performed with simulated annealing [63].…”

Section: Forcefield-based Approachesmentioning

confidence: 99%