Allostery without conformation change: Modelling protein dynamics at multiple scales

Physical Biology

Volumn 10, Issue 5, 2013, Pages

  McLeish, T C B ^a   Rodgers, T L ^b   Wilson, M R ^a  

^a DURHAM UNIVERSITY   (United Kingdom)

^b UNIVERSITY OF MANCHESTER   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

ALLOSTERISM; ARTICLE; CHEMISTRY; ELASTICITY; PROTEIN CONFORMATION; THEORETICAL MODEL; THERMODYNAMICS;

ALLOSTERIC REGULATION; ELASTICITY; MODELS, THEORETICAL; PROTEIN CONFORMATION; PROTEINS; THERMODYNAMICS;

EID: 84887037245     PISSN: 14783967     EISSN: 14783975     Source Type: Journal    
DOI: 10.1088/1478-3975/10/5/056004     Document Type: Article

References (25)

1. Changeux J P and Edelstein S J 2005 Allosteric mechanisms of signal transduction Science 308 1424-8
2. Monod J, Wyman J and Changeux J P 1965 On the nature of allosteric transitions: a plausible model J. Mol. Biol. 12 88-118
3. Canals M, Lane J R, Wen A, Scammells P J, Sexton P M and Christopoulos A 2012 A Monod-Wyman-Changeux mechanism can explain G protein-coupled receptor (GPCR) allosteric modulation J. Biol. Chem. 287 650-9
4. Hwang T-C and Kirk K L 2013 The CFTR ion channel: gating, regulation, and anion permeation Cold Spring Harb. Perspect. Med. 3 a009498
5. Popovych N, Sun S H, Ebright R H and Kalodimos C G 2006 Dynamically driven protein allostery Nature Struct. Mol. Biol. 13 831-8
6. Cooper A, McAlpine A and Stockley P G 1944 Calorimetric studies of the energetics of protein-DNA interactions in the E. coli methionine repressor (MetJ) system FEBS Lett. 348 41-5
7. Cooper A and Dryden D T F 1984 Allostery without conformational change Eur. Biophys. J. 11 103-9
8. Tsai C J, del Sol A and Nussinov R 2008 Allostery: absence of a change in shape does not imply that allostery is not at play J. Mol. Biol. 378 1-11
9. Hilser V J, Wrabl J O and Motlagh H M 2012 Structural and energetic basis of allostery Anal. Rev. Biophys. 41 585-609
10. Tirion K M 1996 Low-amplitude elastic motions in proteins from a single-parameter atomic analysis Phys. Rev. Lett. 77 1905-8
11. Bahar I, Lezon T R, Bakan A and Shrivastava I H 2010 Normal mode analysis of biomolecular structures: functional mechanisms of membrane proteins Chem. Rev. 110 1463-97
12. Hawkins R J and McLeish T C B 2004 Coarse-grained model of entropic allostery Phys. Rev. Lett. 93 098104
13. Delarue M and Sanejouand Y H 2002 Simplified normal mode analysis of conformational transitions in DNA-dependent polymerases: the elastic network model J. Mol. Biol. 320 1011-24
14. Goulian M, Bruinsma R and Pincus P 1993 Long-range forces in heterogeneous fluid membranes Europhys. Lett. 22 145
15. Wickstrom L, Okur A and Simmerling C 2009 Evaluating the performance of the FF99SB force field based on NMR scalar coupling data Biophys. J. 97 853-6
16. Frank D E, Saecker R M, Bond J P, Capp M W, Tsodikov O V, Melcher S E, Levandoski M M and Record M T J 1997 Thermodynamics of the interactions of lac repressor with variants of the symmetric lac operator: effects of converting a consensus site to a non-specific site J. Mol. Biol. 267 1186-206
17. Hawkins R J and McLeish T C B 2006 Coupling of global and local vibrational modes in dynamic allostery of proteins Biophys. J. 91 2055-62
18. Toncrova H and McLeish T C B 2010 Substrate-modulated thermal fluctuations affect long-range allosteric signalling in protein homodimers: exemplified in CAP Biophys. J. 98 2317-26
19. Hawkins R J and McLeish T C B 2005 Dynamic allostery of protein alpha helical coiled-coils J. R. Soc. Interface 3 125-38
20. Rodgers T L et al 2013 ΔΔPT: a comprehensive toolbox for the analysis of protein motion BMC Bioinform. 14 183
21. Gorke B and Stulke J 2008 Carbon catabolite repression in bacteria: many ways to make the most out of nutrients Nature Rev. Microbiol. 6 613-24
22. Green J, Scott C and Guest J R 2001 Functional versatility in the CRP-FNR superfamily of transcription factors: FNR and FLP Adv. Microbiol. Physiol. 44 1-34
23. Rodgers T L, Townsend P D, Burnell D, Jones M L, Richards S A, McLeish T C B, Pohl E, Wilson M R and Cann M J 2013 Modulation of global low-frequency motions underlies allosteric regulation; demonstration in the CRP/FNR family transcription factor PLoS Biol. 11 e1001651
24. Ahmed A, Villinger S and Gohlke H 2010 Large-scale comparison of protein essential dynamics from molecular dynamics simulations and coarse-grained normal mode analyses Proteins 78 3341-52
25. Moritsugu K, Brigitte N and Smith J C 2010 Theory and normal mode analysis of change in protein vibrational dynamics on ligand binding J. Phys. Chem. B 114 1479-85