Analysis of the low-frequency normal modes of the R state of aspartate transcarbamylase and a comparison with the T state modes - PubMed (original) (raw)
. 1996 Aug 23;261(3):490-506.
doi: 10.1006/jmbi.1996.0478.
Affiliations
- PMID: 8780788
- DOI: 10.1006/jmbi.1996.0478
Analysis of the low-frequency normal modes of the R state of aspartate transcarbamylase and a comparison with the T state modes
A Thomas et al. J Mol Biol. 1996.
Abstract
Aspartate transcarbamylase (ATCase) is a classic example of an allosteric enzyme. It catalyzes the conversion of aspartate to carbamyl aspartate, which is the first substrate in the biosynthesis of pyrimidines. Although ATCase is well characterized, both structurally and biochemically, little is known at the atomic level about the large amplitude motions that govern its T-->R quaternary transition. We present the results of calculations of the very-low-frequency normal modes of the CTP-ligated R state ATCase, and we compare them with the equivalent modes in the CTP-ligated T state ATCase. The large-amplitude, delocalized modes of frequencies below 4 cm-1 contribute a large fraction of the atomic fluctuations observed experimentally. They show some ability to drive the R-state structure towards the T-state structure, by promoting some of the quaternary structure rearrangements that take place during the allosteric process. Their potential role in the T-->R transition is quantified and compared with the role of the low-frequency modes of the T state in the quaternary rearrangement.
Similar articles
- Analysis of the low frequency normal modes of the T-state of aspartate transcarbamylase.
Thomas A, Field MJ, Mouawad L, Perahia D. Thomas A, et al. J Mol Biol. 1996 Apr 19;257(5):1070-87. doi: 10.1006/jmbi.1996.0224. J Mol Biol. 1996. PMID: 8632469 - Influence of nucleotide effectors on the kinetics of the quaternary structure transition of allosteric aspartate transcarbamylase.
Tsuruta H, Kihara H, Sano T, Amemiya Y, Vachette P. Tsuruta H, et al. J Mol Biol. 2005 Apr 22;348(1):195-204. doi: 10.1016/j.jmb.2005.02.041. J Mol Biol. 2005. PMID: 15808863 - Crystal structure of T state aspartate carbamoyltransferase of the hyperthermophilic archaeon Sulfolobus acidocaldarius.
De Vos D, Van Petegem F, Remaut H, Legrain C, Glansdorff N, Van Beeumen JJ. De Vos D, et al. J Mol Biol. 2004 Jun 11;339(4):887-900. doi: 10.1016/j.jmb.2004.03.079. J Mol Biol. 2004. PMID: 15165857 - Folding funnels and conformational transitions via hinge-bending motions.
Kumar S, Ma B, Tsai CJ, Wolfson H, Nussinov R. Kumar S, et al. Cell Biochem Biophys. 1999;31(2):141-64. doi: 10.1007/BF02738169. Cell Biochem Biophys. 1999. PMID: 10593256 Review. - [Dynamic study of allosteric proteins].
Kihara H. Kihara H. Tanpakushitsu Kakusan Koso. 1994 May;39(7):1078-82. Tanpakushitsu Kakusan Koso. 1994. PMID: 8016335 Review. Japanese. No abstract available.
Cited by
- New advances in normal mode analysis of supermolecular complexes and applications to structural refinement.
Ma J. Ma J. Curr Protein Pept Sci. 2004 Apr;5(2):119-23. doi: 10.2174/1389203043486892. Curr Protein Pept Sci. 2004. PMID: 15078222 Free PMC article. Review. - Conformational change in the activation of lipase: an analysis in terms of low-frequency normal modes.
Jääskeläinen S, Verma CS, Hubbard RE, Linko P, Caves LS. Jääskeläinen S, et al. Protein Sci. 1998 Jun;7(6):1359-67. doi: 10.1002/pro.5560070612. Protein Sci. 1998. PMID: 9655340 Free PMC article. - Building Biological Relevance Into Integrative Modelling of Macromolecular Assemblies.
Molza AE, Westermaier Y, Moutte M, Ducrot P, Danilowicz C, Godoy-Carter V, Prentiss M, Robert CH, Baaden M, Prévost C. Molza AE, et al. Front Mol Biosci. 2022 Apr 11;9:826136. doi: 10.3389/fmolb.2022.826136. eCollection 2022. Front Mol Biosci. 2022. PMID: 35480882 Free PMC article. - The allosteric mechanism of the chaperonin GroEL: a dynamic analysis.
Ma J, Karplus M. Ma J, et al. Proc Natl Acad Sci U S A. 1998 Jul 21;95(15):8502-7. doi: 10.1073/pnas.95.15.8502. Proc Natl Acad Sci U S A. 1998. PMID: 9671707 Free PMC article. - The role of shape in determining molecular motions.
Lu M, Ma J. Lu M, et al. Biophys J. 2005 Oct;89(4):2395-401. doi: 10.1529/biophysj.105.065904. Epub 2005 Jul 29. Biophys J. 2005. PMID: 16055547 Free PMC article.