Understanding the apparent stator-rotor connections in the rotary ATPase family using coarse-grained computer modeling

• Published in: Proteins, structure, function, and bioinformatics Vol. 82; no. 12; pp. 3298 - 3311
• Main Authors: Richardson, Robin A., Papachristos, Konstantinos, Read, Daniel J., Harlen, Oliver G., Harrison, Michael, Paci, Emanuele, Muench, Stephen P., Harris, Sarah A.
• Format: Journal Article
• Language: English
• Published: United States Blackwell Publishing Ltd 01.12.2014; Wiley Subscription Services, Inc
• Subjects: Animals; Bacterial Proteins - chemistry; Bacterial Proteins - metabolism; Biocatalysis; Bioinformatics; Cryo-EM; Databases, Protein; Elastic Modulus; ENM; FFEA; Finite Element Analysis; Insect Proteins - chemistry; Insect Proteins - metabolism; Manduca - enzymology; Models, Molecular; Molecular Dynamics Simulation; PCA; Principal Component Analysis; Protein Conformation; Protein Interaction Domains and Motifs; Protein Multimerization; Protein Subunits - chemistry; Protein Subunits - metabolism; Proton-Translocating ATPases - chemistry; Proton-Translocating ATPases - metabolism; Saccharomyces cerevisiae - enzymology; Saccharomyces cerevisiae Proteins - chemistry; Saccharomyces cerevisiae Proteins - metabolism; simulation; Thermus thermophilus - enzymology; Vacuolar Proton-Translocating ATPases - chemistry; Vacuolar Proton-Translocating ATPases - metabolism; FFEA; finite element analysis; ENM; Cryo-EM; simulation; PCA
• ISSN: 0887-3585; 1097-0134; 1097-0134
• DOI: 10.1002/prot.24680

ABSTRACT Advances in structural biology, such as cryo‐electron microscopy (cryo‐EM) have allowed for a number of sophisticated protein complexes to be characterized. However, often only a static snapshot of a protein complex is visualized despite the fact that conformational change is frequently inherent to biological function, as is the case for molecular motors. Computer simulations provide valuable insights into the different conformations available to a particular system that are not accessible using conventional structural techniques. For larger proteins and protein complexes, where a fully atomistic description would be computationally prohibitive, coarse‐grained simulation techniques such as Elastic Network Modeling (ENM) are often employed, whereby each atom or group of atoms is linked by a set of springs whose properties can be customized according to the system of interest. Here we compare ENM with a recently proposed continuum model known as Fluctuating Finite Element Analysis (FFEA), which represents the biomolecule as a viscoelastic solid subject to thermal fluctuations. These two complementary computational techniques are used to answer a critical question in the rotary ATPase family; implicit within these motors is the need for a rotor axle and proton pump to rotate freely of the motor domain and stator structures. However, current single particle cryo‐EM reconstructions have shown an apparent connection between the stators and rotor axle or pump region, hindering rotation. Both modeling approaches show a possible role for this connection and how it would significantly constrain the mobility of the rotary ATPase family. Proteins 2014; 82:3298–3311. © 2014 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.