A normal mode analysis of structural plasticity in the biomolecular motor F(1)-ATPase - PubMed (original) (raw)
A normal mode analysis of structural plasticity in the biomolecular motor F(1)-ATPase
Qiang Cui et al. J Mol Biol. 2004.
Abstract
Normal modes have been used to explore the inherent flexibility of the alpha, beta and gamma subunits of F(1)-ATPase in isolation and as part of the alpha(3)beta(3)gamma complex. It was found that the structural plasticity of the gamma and beta subunits, in particular, correlates with their functions. The N and C-terminal helices forming the coiled-coil domain of the gamma subunit are highly flexible in the isolated subunit, but more rigid in the alpha(3)beta(3)gamma complex due to interactions with other subunits. The globular domain of the gamma subunit is structurally relatively rigid when isolated and in the alpha(3)beta(3)gamma complex; this is important for its functional role in coupling the F(0) and F(1) complex of ATP synthase and in inducing the conformational changes of the beta subunits in synthesis. Most important, the character of the lowest-frequency modes of the beta(E) subunit is highly correlated with the large beta(E) --> beta(TP) transition. This holds for the C-terminal domain and the nucleotide-binding domain, which undergo significant conformational transitions in the functional cycle of F(1)-ATPase. This is most evident in the ligand-free beta(E) subunit; the flexibility in the nucleotide-binding domain is reduced somewhat in the beta(TP) subunit in the presence of Mg(2+).ATP. The low-frequency modes of the alpha(3)beta(3)gamma complex show that the motions of the globular domain of the gamma subunit and of the C-terminal and nucleotide binding domains of the beta(E) subunits are coupled, in accord with their function. Overall, the normal mode analysis reveals that F(1)-ATPase, like other macromolecular assemblies, has the intrinsic structural flexibility required for its function encoded in its sequence and three-dimensional structure. This inherent plasticity is an essential aspect of assuring a small free energy cost for the large-scale conformational transition that occurs in molecular motors.
Similar articles
- Structural fluctuation and concerted motions in F(1)-ATPase: A molecular dynamics study.
Ito Y, Ikeguchi M. Ito Y, et al. J Comput Chem. 2010 Aug;31(11):2175-85. doi: 10.1002/jcc.21508. J Comput Chem. 2010. PMID: 20336770 - Structure of the catalytic nucleotide-binding subunit A of A-type ATP synthase from Pyrococcus horikoshii reveals a novel domain related to the peripheral stalk.
Maegawa Y, Morita H, Iyaguchi D, Yao M, Watanabe N, Tanaka I. Maegawa Y, et al. Acta Crystallogr D Biol Crystallogr. 2006 May;62(Pt 5):483-8. doi: 10.1107/S0907444906006329. Epub 2006 Apr 19. Acta Crystallogr D Biol Crystallogr. 2006. PMID: 16627940 - [Electrostatic interactions in catalytic centers of F1-ATPase].
Tikhonov AN, Pogrebnaia AF, Romanovskiĭ IuM. Tikhonov AN, et al. Biofizika. 2003 Nov-Dec;48(6):1052-70. Biofizika. 2003. PMID: 14714522 Review. Russian. - Regulation of the F0F1-ATP synthase: the conformation of subunit epsilon might be determined by directionality of subunit gamma rotation.
Feniouk BA, Junge W. Feniouk BA, et al. FEBS Lett. 2005 Sep 26;579(23):5114-8. doi: 10.1016/j.febslet.2005.08.030. FEBS Lett. 2005. PMID: 16154570 Review.
Cited by
- Domain motions of Argonaute, the catalytic engine of RNA interference.
Ming D, Wall ME, Sanbonmatsu KY. Ming D, et al. BMC Bioinformatics. 2007 Nov 30;8:470. doi: 10.1186/1471-2105-8-470. BMC Bioinformatics. 2007. PMID: 18053142 Free PMC article. - Allosteric communication in myosin V: from small conformational changes to large directed movements.
Cecchini M, Houdusse A, Karplus M. Cecchini M, et al. PLoS Comput Biol. 2008 Aug 15;4(8):e1000129. doi: 10.1371/journal.pcbi.1000129. PLoS Comput Biol. 2008. PMID: 18704171 Free PMC article. - The effect of medium viscosity on kinetics of ATP hydrolysis by the chloroplast coupling factor CF1.
Malyan AN. Malyan AN. Photosynth Res. 2016 May;128(2):163-8. doi: 10.1007/s11120-015-0213-y. Epub 2016 Jan 12. Photosynth Res. 2016. PMID: 26754050 - Mechanochemical coupling in the myosin motor domain. II. Analysis of critical residues.
Yu H, Ma L, Yang Y, Cui Q. Yu H, et al. PLoS Comput Biol. 2007 Feb 16;3(2):e23. doi: 10.1371/journal.pcbi.0030023. Epub 2006 Dec 22. PLoS Comput Biol. 2007. PMID: 17305418 Free PMC article. - Molecular dynamics and protein function.
Karplus M, Kuriyan J. Karplus M, et al. Proc Natl Acad Sci U S A. 2005 May 10;102(19):6679-85. doi: 10.1073/pnas.0408930102. Epub 2005 May 3. Proc Natl Acad Sci U S A. 2005. PMID: 15870208 Free PMC article.