An Exhaustive Search Algorithm to Aid NMR-Based Structure Determination of Rotationally Symmetric Transmembrane Oligomers

Jing Yang,Alessandro Piai,Hong-Bin Shen,James J Chou

doi:10.1038/s41598-017-17639-w

Jing Yang, Alessandro Piai + Show 2 more

Open Access

https://doi.org/10.1038/s41598-017-17639-w

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Abstract

Nuclear magnetic resonance (NMR) has been an important source of structural restraints for solving structures of oligomeric transmembrane domains (TMDs) of cell surface receptors and viral membrane proteins. In NMR studies, oligomers are assembled using inter-protomer distance restraints. But, for oligomers that are higher than dimer, these distance restraints all have two-fold directional ambiguity, and resolving such ambiguity often requires time-consuming trial-and-error calculations using restrained molecular dynamics (MD) with simulated annealing (SA). We report an Exhaustive Search algorithm for Symmetric Oligomer (ExSSO), which can perform near-complete search of the symmetric conformational space in a very short time. In this approach, the predetermined protomer model is subject to full angular and spatial search within the symmetry space. This approach, which can be applied to any rotationally symmetric oligomers, was validated using the structures of the Fas death receptor, the HIV-1 gp41 fusion protein, the influenza proton channel, and the MCU pore. The algorithm is able to generate approximate oligomer solutions quickly as initial inputs for further refinement using the MD/SA method.

Highlights

In Nuclear magnetic resonance (NMR)-based structure determination of transmembrane (TM) oligomers, the key structural restraints are inter-protomer distance restraints derived from nuclear Overhauser enhancement (NOE)
In the case of small transmembrane domains (TMDs), e.g., a TM helix, the protomer backbone structure can be initially constructed with the backbone dihedral angles derived from chemical shifts
The distance r is set to the range 3–15 Å and the step size Δr = 0.5 Å is used, because these values were found optimal for the sizes of most TM oligomers investigated by NMR

Summary

Introduction

In NMR-based structure determination of transmembrane (TM) oligomers, the key structural restraints are inter-protomer distance restraints derived from nuclear Overhauser enhancement (NOE). Algorithms that do not depend on restraint-derived energy landscape are more suitable for resolving ambiguous restraints, and several exhaustive search methods have been proposed previously, including the AmbiPack[14] and SYMBRANE15. These methods are based on the branch-and-bound algorithm to exhaustively search molecular symmetry axis – which is translated to the oligomer structure – by recursively dividing a cell representing the symmetry space into smaller sub-cells until finding a cell in which the symmetry axes satisfy all the restraints. The representative conformations from this program can be further refined in the standard restrained MD and SA programs

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