The role of dynamics in allosteric regulation
Introduction
Dynamic processes in biomolecules cover a large timescale regime, including very fast fluctuations of individual atoms on the picosecond timescale, loop and domain motions on the nanosecond timescale, conformational rearrangements on the millisecond timescale and breathing modes on a timescale slower than seconds. Several excellent reviews summarize the functional role of dynamics in catalysis 1., 2.. Here, we review the role of dynamics in allostery. Allostery (‘allo-steric = other-space’) means that action in one part of the molecule causes an effect at another site. Allosteric processes are closely associated with ligand-induced conformational changes that propagate between the allosterically coupled binding sites [3]. The allosteric molecule thus changes its coordinates as a function of time, which constitutes dynamics. Hence, dynamics and allosteric processes are almost tautologically linked. In addition, changes in the dynamic properties of the different conformations of the allosteric protein may contribute to the free energy of allosteric coupling through entropic effects [4]. This review focuses on the different types of dynamics of allosteric proteins. Purists may associate only quasi-harmonic motions on the shortest timescales with the word dynamics. In this review, however, we will consider all motions — quasi-harmonic, diffusive rearrangements or fluctuations in populations over an ensemble of subconformations — as dynamics. The review ignores the role of allosteric proteins in systemic dynamic processes, such as the dynamic changes of gene expression and neuron proliferation.
It is often stated that allosteric systems are oligomeric and symmetric (e.g. [5]); for this review, we want to take a broader point of view. We define here as allosteric those systems in which the binding of one ligand affects the affinity of another ligand (Figure 1). This includes, in addition to the classical homotropic oligomeric systems such as hemoglobin and aspartate transcarbamylase, heterotropic monomeric systems such as Hsp70 chaperones, whereby allosteric coupling exists between ATP binding in one domain and protein substrate binding in another domain [6], and single-domain proteins, whereby phosphorylation at one site affects the structure of the protein in a remote area 7., 8.••. Our definition also includes those proteins for which at least one of the ligands is a biological macromolecule; good examples are the Trp- and RNA-binding attenuation protein repressor, for which tryptophan binding affects RNA binding at a remote site [9••], and processes such as ligand-coupled oligomerization 10., 11..
We want to mention a few developments that have made many of the exciting recent discoveries in allosteric dynamics feasible. Improvements in mutagenesis and site-specific labeling techniques extended the applicability of fluorescence lifetime methods beyond naturally available tryptophan residues [12]. Ultrafast laser technologies can resolve many time steps in dynamic processes [13]. The measurement of site-resolved quasi-harmonic dynamics on the picosecond to nanosecond timescale by NMR relaxation methods is feasible for both protein backbone and protein sidechains 14., 15., 16.. Fluctuations between conformational substates on the millisecond to microsecond timescale can now be measured quantitatively and site resolved by NMR as well [17]. Importantly, NMR dynamic measurements can now be combined with TROSY detection methods [18], which extends its application to larger systems, such as a 91 kDa allosteric protein [9••]. The NMR measurement of residual dipolar couplings in solution has recently been applied to characterize dynamic process as well [19]. The commercial availability of precise microcalorimeters allows a quantitative assessment of entropic effects, which, in some cases, can be related to changes in dynamic processes [20]. A new, unsuspected source of dynamic information is ultra-high resolution low-temperature X-ray crystallography; anisotropic B-factors allow motional models for atomic and collective motions to be developed, and the observation of multiple conformations is suggestive of fluctuations over conformational substates [21•]. Comprehensive synthetic approaches make it possible to design small allosteric systems [22•]. Last but not least, the steady increase in computational power and the development of new computational approaches for the study of protein dynamics push simulations into time regimes that have previously not been accessible [23]. This permits the comparison of simulated and experimental dynamics, ultimately allowing predictions of allosteric dynamic pathways.
To the best of our knowledge, this subject has been reviewed systematically only once before [24]. That work is an excellent source for an overview of movements in allosteric proteins as inferred from static structures, NMR methods for the detection of picosecond to nanosecond backbone dynamics, and the dynamic properties of the allosteric Trp repressor system. In the following, we selected several representative examples from the enormous volume of literature that has been reported since then and have organized the information in four sections.
Section snippets
Allosteric dynamics as inferred from static limit structures
To date, the vast majority of allosteric dynamic processes are still investigated by comparing the structures of allosteric molecules in their limiting states. Classical examples include hemoglobin and aspartate transcarbamylase, in which an up to 20° subunit reorientation occurs upon ligation 25., 26., leading to changes in the atomic coordinates of up to 10 Å. An extensive body of literature has been devoted to describing the dynamic pathway of such conformational changes; one of the best
Experimental observation of motions relevant to allosteric conformational change
Evidence is mounting that allosteric motions take place not only when the allosteric conformational change is induced upon ligand binding but also in the absence of this process, confirming the early realization that proteins should be described as a dynamic ensemble of conformational substates [29]. A mechanical realization of a thermodynamic allosteric model is depicted for homotropic oligomeric (Figure 1a) and heterotropic monomeric (Figure 1b) systems. This is a generalization of the Monod,
Dynamics as an intrinsic carrier of allosteric free energy
Proteins are generally tightly packed, except around ligand-binding sites, which may be viewed as packing deficiencies. These packing deficiencies allow mobility of their perimeters, which propagates through other parts of the protein because they are so tightly packed. Ligand binding ‘repairs’ the packing defect, leading to global protein rigidification with concomitant entropy loss. In many of the above-described studies, such rigidification upon ligand binding was experimentally detected.
Description and modeling of the dynamics of allosteric conformational change
It appears to be generally assumed that the timescale of global allosteric conformational change is relatively slow. Hammes [50], reviewing the role of conformational change in enzyme catalysis, mentions that the rate of allosteric conformational change in aspartate transcarbamylase is a millisecond process. NMR studies indicate that the interconversion of allosteric subconformations takes place on the millisecond to microsecond timescale 8.••, 9.••, 47.•. Allosteric transitions in hemoglobin
Conclusions
Many outstanding publications now demonstrate the central role of a dynamic equilibrium between conformational substates in the allosteric process. Moreover, it has become clear that changes in entropy upon ligand binding are a common, not often recognized, contribution to allosteric free energy. Consequently, dynamics constitutes not only the move from ‘T’ to ‘R’, but also an integral part of the allosteric system in all of its states. We anticipate that this awareness will inspire new studies
References and recommended reading
Papers of particular interest, published within the annual period of review, have been highlighted as:
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of special interest
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of outstanding interest
Acknowledgements
DK acknowledges support by National Institutes of Health (NIH) grant GM62117 and instrumentation grants from the National Science Foundation (NSF) and Keck foundation. ERPZ thanks the NIH (GM52421 and GM63027) and NSF (MCB 0135330) for continued support, and instrumentation grants from the NIH, NSF and Keck foundation.
References (59)
- et al.
Conformational dynamics and enzyme activity
Biochimie
(1998) - et al.
Collective protein dynamics in relation to function
Curr. Opin. Struct. Biol.
(2000) - et al.
On the nature of allosteric transitions: a plausible model
J. Mol. Biol.
(1965) - et al.
Tetramer-dimer conversion of phosphofructokinase from Thermus thermophilus induced by its allosteric effectors
J. Mol. Biol.
(1990) - et al.
Backbone dynamics of Tet repressor alpha8-alpha9 loop
Biochemistry
(2000) Protein dynamics from NMR
Nat. Struct. Biol.
(1998)Dynamic activation of protein function: a view emerging from NMR spectroscopy
Nat. Struct. Biol.
(2001)- et al.
Structural and dynamic analysis of residual dipolar coupling data for proteins
J. Am. Chem. Soc.
(2001) - et al.
Role of coupling entropy in establishing the nature and magnitude of allosteric response
Proc. Natl. Acad. Sci. USA
(1989) - et al.
MolMovDB: analysis and visualization of conformational change and structural flexibility
Nucleic Acids Res.
(2003)
NMR order parameters and free energy: an analytical approach and its application to cooperative Ca2+ binding by calbindin D9k
J. Am. Chem. Soc.
Configurational entropy and cooperativity between ligand binding and dimerization in glycopeptide antibiotics
J. Am. Chem. Soc.
Multiple conformational changes in enzyme catalysis
Biochemistry
Allostery without conformational change. A plausible model
Eur. Biophys. J.
Structural symmetry and protein function
Annu. Rev. Biophys. Biomol. Struct.
Multistep mechanism of substrate binding determines chaperone activity of Hsp70
Nat. Struct. Biol.
Control by protein phosphorylation
Nat. Struct. Biol.
Two-state allosteric behavior in a single-domain signaling protein
Science
TROSY-NMR studies of the 91 kDa TRAP protein reveal allosteric control of a gene regulatory protein by ligand-altered flexibility
J. Mol. Biol.
Enthalpic and entropic components of cooperativity for the partially ligated intermediates of hemoglobin support a ‘symmetry rule’ mechanism
Biochemistry
Structural dynamics of myoglobin
Biophys. Chem.
Protein NMR relaxation: theory, applications and outlook
Prog. NMR Spectrosc.
Nuclear magnetic resonance methods for quantifying microsecond-to-millisecond motions in biological macromolecules
Methods Enzymol.
TROSY and CRINEPT: NMR with large molecular and supramolecular structures in solution
Trends Biochem. Sci.
Atomic resolution structure of prokaryotic phospholipase A2: analysis of internal motion and implication for a catalytic mechanism
Proteins
Molecular design of artificial molecular and ion recognition systems with allosteric guest responses
Acc. Chem. Res.
Molecular dynamics simulations of biomolecules
Nat. Struct. Biol.
Protein dynamics and conformational transitions in allosteric proteins
Prog. Biophys. Mol. Biol.
Stereochemistry of cooperative effects in haemoglobin
Nature
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