The Library

Comparative analysis of rigidity across protein families

Tools

Wells, Stephen A., Jiménez Roldán, J. E. (José Emilio) and Roemer, Rudolf A.. (2009) Comparative analysis of rigidity across protein families. Physical Biology, Vol.6 (No.4). Article 6005. ISSN 1478-3975

PDF
WRAP_Roemer_Comparative_analysis.pdf - Requires a PDF viewer such as GSview, Xpdf or Adobe Acrobat Reader
Download (907Kb)

Official URL: http://dx.doi.org/10.1088/1478-3975/6/4/046005

Abstract

We present a comparative study in which 'pebble game' rigidity analysis is applied to multiple protein crystal structures, for each of six different protein families. We find that the main-chain rigidity of a protein structure at a given hydrogen bond energy cutoff is quite sensitive to small structural variations, and conclude that the hydrogen bond constraints in rigidity analysis should be chosen so as to form and test specific hypotheses about the rigidity of a particular protein. Our comparative approach highlights two different characteristic patterns ('sudden' or 'gradual') for protein rigidity loss as constraints are removed, in line with recent results on the rigidity transitions of glassy networks.

Item Type:	Journal Article
Subjects:	Q Science > QH Natural history > QH301 Biology
Divisions:	Faculty of Science > Centre for Scientific Computing
Library of Congress Subject Headings (LCSH):	Biomolecules -- Research, Conformational analysis, Membranes (Biology) -- Research, Proteins -- Research, Molecule-molecule collisions
Journal or Publication Title:	Physical Biology
Publisher:	Institute of Physics Publishing Ltd.
ISSN:	1478-3975
Date:	December 2009
Volume:	Vol.6
Number:	No.4
Page Range:	Article 6005
Identification Number:	10.1088/1478-3975/6/4/046005
Status:	Peer Reviewed
Access rights to Published version:	Open Access
Funder:	Engineering and Physical Sciences Research Council (EPSRC), Biotechnology and Biological Sciences Research Council (Great Britain) (BBSRC), Leverhulme Trust (LT)
Grant number:	F/00 215/AH (LT), EP/C007042/1 (EPSRC)
References:	[1] Canino LS, Shen T, and McCammon. Changes in flexibility upon binding: application of the self-consistent pair contact probability method to protein-protein interactions. J. Chem. Phys., 117:9927–9933, 2002. [2] Case DA. Molecular dynamics and nomal mode analysis of biomolecular rigidity. in thorpe m. f., duxbury p. m., eds. rigidity theory and applications. New York: Kluwer Academic/Plemum Publishers, pages 329–344, 1999. [3] Bahar I, Atilgan AR, and Erman B. Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. Fold. Des, 2:173–181, 1997. [4] Ming D, Kong Y, We Y, , and Ma J. Substructure synthesis method for simulating large molecular complexes. Proceedings of the National Academy of Sciences of the United States of America, 100:104–109, 2003. [5] Ming D, Kong Y,Wakil SJ, Brink J, and Ma J. Domain movements in human fatty acid synthase by quantized elastic deformational model. Proc Nat Acad Sci USA, 99:7895–7899, 2002. [6] Tama F, Wriggers W, and Brooks CL 3rd. Exploring global distortions of biological macromolecules and assemblies from low- resolution structural information and elastic network theory. J. Mol. Bio, 321:297–305, 2002. [7] Halle B. Flexibility and packing in proteins. Proc Natl Acad Sci USA, 99:1274 1279, 2002. [8] Tirion MM. Large amplitude elastic motions in proteins from single-parameter atomic analysis. prl, 77:1905–1908, 1996. [9] Tama F, Gadea FX, Marques O, and Sanejouand YH. Building-block approach for determining low-frequency normal modes of macromolecules. Proteins, 41:1–7, 2000. [10] Delarue M and Sanejouand YH. Simplified normal mode analysis of conformational transitions in dna-dependant polymerases:the elastic network model. J. Mol. Biol., 320:10111024, 2002. [11] Petrone P and Pande VS. Can conformational change be described by only a few normal modes? Biophys J., 90:p1583–1593, 2006. [12] Vihinene M, Torkkila E, and Riikonen P. Accuracy of protein flexibility predictions. Proteins, 19:141–149, 1994. [13] Holm L and Sander C. Parser for protein folding units. Proteins, 19:256 268, 1994. [14] Zehfus MH and Rose GD. Compact units in proteins. Biochemistry, 25:5759 5765, 1986. [15] Karplus PA and Schulz GE. Prediction of chain exibility in proteins. Naturwissenschaten, 72:212213, 1985. [16] Maiorov V and Abagyan R. A new method for modeling large-scale rearrangements of protein domains. Proteins, 27:410 424, 1997. [17] Flores M, Echols N, Milburn D, Hespenheide BM, Keating K, Lu J, Wells SA, Yu EZ, Thorpe MF, and Gerstein M. The database of macromolecular motions: new features added at the decade mark. Nucleic Acid Research, 34:D296–D301, 2005. [18] Jacobs DJ and Thorpe MF. Generic rigidity percolation: The pebble game. Phys. Rev. Lett., 75:4051–4054, 1995. [19] Jacobs DJ, Rader AJ, Kuhn LA, and Thorpe MF. Protein flexibility predictions using graph theory. PROTEINS: Struct., Func. and Gen., 44:150–165, 2001. [20] Hespenheide BM, Jacobs DJ, and Thorpe MF. Structural rigidity and the capsid assembly of cowpea chlorotic mottle virus. J. Phys.: Condens. Matter, 16:S5055–S5064, 2004. [21] Rader AJ, Hespenheide BM, Kuhn LA, and Thorpe MF. Protein unfolding: Rigidity lost. Proc. Natl. Acad. Sci., 99:3540–3545, 2002. [22] Hespenheide BM, Rader AJ, Thorpe MF, and Kuhn LA. Identifying protein folding cores: Observing the evolution of rigid and flexible regions during unfolding. J. Mol. Graph. & Model., 21:195–207, 2002. [23] Thorpe MF, Lei M, Rader AJ, Jacobs DJ, and Kuhn LA. Protein flexibility and dynamics using constraint theory. J. Mol. Graph. & Model., 19:60–69, 2001. [24] Wells SA, Menor S, Hespenheide BM, and Thorpe MF. Constrained geometric simulation of diffusive motion in proteins. Phys. Biol., 2:S127–S136, 2005. [25] Jolley CC, Wells SA, Hespenheide BM, Thorpe MF, and Fromme P. Docking of photosystem i subunit c using a constrained geometric simulation. J. Am. Chem. Soc., 128:8803–8812, 2006. [26] Hemberg M, Yaliraki SN, and Barahona M. Stocastik kinetics of viral capsid assembly based on detailed protein structures. Biophysical journal, 90:3029–3042, 2006. [27] Jolley CC, Wells SA, Fromme P, and Thorpe MF. Fitting low-resolution cryo-em maps of proteins using constrained geometric simulations. Biophys. J., 94:1613–1621, 2008. [28] Macchiarulo A, Nuti R, Bellochi D, Camaioni E, and Pellicciari R. Molecular docking and spatial coarse graining simulations as tools to investigate substrate recognition, enhancer binding and conformational transitions in indoleamine-2,3-dioxygenase (ido). Biochim. et Biophys. Acta- Proteins and Proteomics, 1774:1058–1068, 2007. [29] Sun M, Rose MB, Ananthanarayanan SK, Jacobs DJ, and Yengo CM. Characterisation of the pre-force-generation state in the actomyosin cross-bridge cycle. Proc. Nat. Acad. Sci., 105:8631–8636, 2008. [30] Gohlke H and Thorpe MF. A natural coarse graining for simulating large biomolecular motion. Biophys. J., 91:2115–2120, 2006. [31] Sartbaeva A, Wells SA, Huerta A, and Thorpe MF. Local structural variability and the intermediate phase window in network glasses. Phys. Rev. B, 75:224204, 2007. [32] Berman HM,Westbrook J, Feng Z, Gilliland G, Bhat TN,Weissig H, Shindyalov IN, and Bourne PE. The protein data bank. Nucl. Acids Res., 28:235–242, 2000. http://www.rcsb.org. [33] DeLano W. The pymol molecular graphics system. www.pymol.org. [34] Word JM, Lovell SC, Richardson JS, and Richardson DC. Asparagine and glutamine: Using hydrogen atoms contacts in the choice of side-chain amide orientation. J. Mol. Biol., 285:1735–1747, 1999. http://kinemage.biochem.duke.edu/software/reduce.php. [35] Dahiyat BI, Gordon DB, and Mayo SL. Automated design of the surface positions of protein helices. Protein Sci., 6:1333–1337, 1997. [36] Minary P and Levitt M. Probing protein fold space with a simplified model. J. Mol. Biol., 375:920–933, 2008.
URI:	http://wrap.warwick.ac.uk/id/eprint/3169