Domain Closure in Adenylate Kinase

Sinev, Michael A.; Sineva, Elena V.; Ittah, Varda; Haas, Elisha

doi:10.1021/bi952687j

Cited by 104 publications

(149 citation statements)

References 58 publications

Supporting

Mentioning

134

Contrasting

Order By: Relevance

“…The WHAM provides a convenient, statistically based approach to combine trajectory data from multiple windows with their different biasing potentials and obtain the PMF along a reaction coordinate. Here, we use it to calculate the PMF along our selected reaction coordinate, the distance between the mass centers of residues 55 and 169, which are the residues that were labeled in the energy transfer experiments 7 and serve as a monitor of the Amp-bd domain-to-core distance. To make sure of the convergence of the PMF, we calculated the PMF for the time corresponding to the first half and the second half of the trajectory for the DREMA and DREMB data.…”

Section: Resultsmentioning

confidence: 99%

“…5 The importance of domain conformational changes has been emphasized by recent experiments showing that they, versus the chemical, phosphoryl transfer step, are rate limiting in AKE and can rationalize differences in activity between mesophiles and thermophiles. 6 Crystallography 1 and time-resolved dynamic nonradiative excitation energy transfer experiments 7 show that binding AMP is associated with an initial conformational change. Binding of the next substrate, usually modeled with a binary substrate, mimics AP 5 A (ATP and AMP linked by a fifth phosphate group), resulting in the formation of the closed, catalytically competent form.…”

Section: Introductionmentioning

confidence: 99%

“…Harmonic potentials are used as the window potentials along a reaction coordinate, which is the distance between the mass centers of residues Ala 55 and Val 169, to match the residues used in the energy transfer experiments. 7 The potential of mean force along this reaction coordinate over a range of approximately 35 Å is obtained with use of the DREM. The large range of the reaction coordinate spans the open and closed X-ray structure values.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Molecular Dynamics of Apo-Adenylate Kinase: A Distance Replica Exchange Method for the Free Energy of Conformational Fluctuations

2006

View full text Add to dashboard Cite

A large domain motion in adenylate kinase from E. coli (AKE) is studied with molecular dynamics. AKE undergoes a large-scale rearrangement of its lid and AMP-binding domains when the open form closes over its substrates, AMP, and Mg 2+ -ATP, whereby the AMP-binding and lid domains come closer to the core. The third domain, the core, is relatively stable during this motion. A reaction coordinate that monitors the distance between the AMP-binding and core domains is selected to be able to compare with the results of energy transfer experiments. Sampling along this reaction coordinate is carried out by using a distance replica exchange method (DREM), where systems that differ by a restraint potential enforcing different reaction coordinate values are independently simulated with periodic attempts at exchange of these systems. Several methods are used to study the efficiency and convergence properties of the DREM simulation and compared with an analogous non-DREM simulation. The DREM greatly accelerates the rate and extent of configurational sampling and leads to equilibrium sampling as measured by monitoring collective modes obtained from a principal coordinate analysis. The potential of mean force along the reaction coordinate reveals a rather flat region for distances from the open to a relatively closed AKE conformation. The potential of mean force for smaller distances has a distinct minimum that is quite close to that found in the closed form X-ray structure. In concert with a decrease in the reaction coordinate distance (AMP-binding-to-core distance) the lid-to-core distance of AKE also decreases. Therefore, apo AKE can fluctuate from its open form to conformations that are quite similar to its closed form X-ray structure, even in the absence of its substrates.

show abstract

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Molecular Dynamics of Apo-Adenylate Kinase: A Distance Replica Exchange Method for the Free Energy of Conformational Fluctuations

2006

View full text Add to dashboard Cite

show abstract

“…Time-resolved fluorescence energy transfer studies of fluorescent AKeco derivatives confirmed domain closure in solution upon inhibitor binding (23,24). These studies also indicated that large-amplitude segmental mobility of AMPbd and LID is in effect in the ligand-free form (23). AKeco is the only adenylate kinase for which crystal structures corresponding to the extreme stages of the catalytic cycle are available (17,21,22), with the closed form represented by AKeco*AP 5 A.…”

mentioning

confidence: 85%

Domain Flexibility in Ligand-Free and Inhibitor-BoundEscherichia coliAdenylate Kinase Based on a Mode-Coupling Analysis of¹⁵N Spin Relaxation

et al. 2002

View full text Add to dashboard Cite

Adenylate kinase from Escherichia coli (AKeco), consisting of a 23.6-kDa polypeptide chain folded into domains CORE, AMPbd, and LID catalyzes the reaction AMP + ATP T 2ADP. The domains AMPbd and LID execute large-amplitude movements during catalysis. Backbone dynamics of ligandfree and AP 5 A-inhibitor-bound AKeco is studied with slowly relaxing local structure (SRLS) 15 N relaxation, an approach particularly suited when the global (τ m ) and the local (τ) motions are likely to be coupled. For AKeco τ m ) 15.1 ns, whereas for AKeco*AP 5 A τ m ) 11.6 ns. The CORE domain of AKeco features an average squared order parameter, , of 0.84 and correlation times τ f ) 5-130 ps. Most of the AKeco*AP 5 A backbone features ) 0.90 and τ f ) 33-193 ps. These data are indicative of relative rigidity. Domains AMPbd and LID of AKeco, and loops 1 /R 1 , R 2 /R 3 , R 4 / 3 , R 5 / 4 , and 8 /R 7 of AKeco*AP 5 A, feature a novel type of protein flexibility consisting of nanosecond peptide plane reorientation about the C i-1 R -C i R axis, with correlation time τ ⊥ ) 5.6-11.3 ns. The other microdynamic parameters underlying this dynamic model include S 2 ) 0.13-0.5, τ || on the ps time scale, and a diffusion tilt MD ranging from 12 to 21°. For the ligand-free enzyme the τ ⊥ mode was shown to represent segmental domain motion, accompanied by conformational exchange contributions R ex e 4.4 s -1 . Loop R 4 / 3 and R 5 / 4 dynamics in AKeco*AP 5 A is related to the "energetic counter-balancing of substrate binding" effect apparently driving kinase catalysis. The other flexible AKeco*AP 5 A loops may relate to domain motion toward product release.The ability to interpret nuclear spin relaxation properties in terms of microdynamic parameters turned NMR into a powerful method for elucidating protein dynamics (1, 2). The amide 15 N spin in proteins is a particularly useful probe, relaxed predominantly by dipolar coupling to the amide proton and 15 N chemical shift anisotropy (CSA) 1 (3). The experimental NMR observables are controlled by the global and local dynamic processes experienced by protein N-H bond vectors, which determine the spectral density function, J(ω). 15 N relaxation data in proteins are commonly analyzed with the model-free (MF) approach, where the global and local motions are assumed to be decoupled (4-6). In a recent study (7), we applied the two-body slowly relaxing local structure (SRLS) approach developed by Freed and coworkers (8, 9) to 15 N relaxation in proteins. SRLS accounts rigorously for dynamical coupling between the local and global motions, and treats the global diffusion, the local diffusion, the local ordering, and the magnetic interactions as tensors that may be tilted relative to one another, providing thereby important information related to protein structure (10-12). The MF spectral density functions constitute asymptotic solutions of the SRLS spectral densities (7,8,13). It was found that currently available experimental 15 N relaxation data are sensitive to the coupling-induce...

~~show abstract~~

“…AK was chosen for this study because many aspects of this enzyme have been studied both experimentally (11)(12)(13)(14)(15)(16)(17)(18)(19) and theoretically (20)(21)(22)(23)(24). It is an ubiquitous enzyme that helps maintain the energy balance in cells by catalyzing the reversible reaction, Mg 2ϩ ⅐ATP ϩ AMP º Mg 2ϩ ⅐ADP ϩ ADP.…”

mentioning
confidence: 99%

Illuminating the mechanistic roles of enzyme conformational dynamics
Hanson
¹
,
Duderstadt
²
,
Watkins
³

et al. 2007
Proc. Natl. Acad. Sci. U.S.A.
277
41
434
5
View full text Add to dashboard Cite

Many enzymes mold their structures to enclose substrates in their active sites such that conformational remodeling may be required during each catalytic cycle. In adenylate kinase (AK), this involves a large-amplitude rearrangement of the enzyme's lid domain. Using our method of high-resolution single-molecule FRET, we directly followed AK's domain movements on its catalytic time scale. To quantitatively measure the enzyme's entire conformational distribution, we have applied maximum entropy-based methods to remove photon-counting noise from single-molecule data. This analysis shows unambiguously that AK is capable of dynamically sampling two distinct states, which correlate well with those observed by x-ray crystallography. Unexpectedly, the equilibrium favors the closed, active-site-forming configurations even in the absence of substrates. Our experiments further showed that interaction with substrates, rather than locking the enzyme into a compact state, restricts the spatial extent of conformational fluctuations and shifts the enzyme's conformational equilibrium toward the closed form by increasing the closing rate of the lid. Integrating these microscopic dynamics into macroscopic kinetics allows us to model lid opening-coupled product release as the enzyme's rate-limiting step.conformational equilibrium ͉ rate-limiting step ͉ single-molecule FRET ͉ adenylate kinase P roteins such as enzymes are flexible with a range of motions spanning from picoseconds for localized vibrations to seconds for concerted global conformational rearrangements (1). Despite their randomly fluctuating environment, in which stochastic collisions with solvent molecules drive changes in tertiary structure, enzymes have evolved to catalyze reactions efficiently and specifically. Indeed, conformational transitions have been postulated to play a central role in enzyme functions in a wide variety of ways, including direct contribution to catalysis (2), allosteric regulation (3), and large-scale conformational changes in response to ligand binding (4). Most of our current understanding of structural motions in solution comes from NMR experiments (5) as well as from molecular dynamics simulations (6), approaches that are best suited to study dynamics in the picoto millisecond time scales. Because catalysis in enzymes frequently occurs in the submillisecond to minute time regime, our current understanding of the relationship between enzyme function and conformational dynamics comes from NMR experiments involving relatively localized motions of active site forming loops on the submillisecond time scale (7-10). However, many enzymes contain active sites located in between domains in which large-amplitude, low-frequency domain motions are required to complete their Michaelis-Menten enzyme-substrate complexes. Even simple questions regarding these transitions remain generally unanswered: What is the number and range of conformational states accessible to enzymes during their catalytic cycle? How does the enzyme's conformation respond to interac...

~~show abstract~~

Domain Closure in Adenylate Kinase

Cited by 104 publications

References 58 publications

Molecular Dynamics of Apo-Adenylate Kinase: A Distance Replica Exchange Method for the Free Energy of Conformational Fluctuations

Molecular Dynamics of Apo-Adenylate Kinase: A Distance Replica Exchange Method for the Free Energy of Conformational Fluctuations

Domain Flexibility in Ligand-Free and Inhibitor-BoundEscherichia coliAdenylate Kinase Based on a Mode-Coupling Analysis of¹⁵N Spin Relaxation

Illuminating the mechanistic roles of enzyme conformational dynamics

Contact Info

Product

Resources

About

Domain Closure in Adenylate Kinase

Cited by 104 publications

References 58 publications

Molecular Dynamics of Apo-Adenylate Kinase: A Distance Replica Exchange Method for the Free Energy of Conformational Fluctuations

Molecular Dynamics of Apo-Adenylate Kinase: A Distance Replica Exchange Method for the Free Energy of Conformational Fluctuations

Domain Flexibility in Ligand-Free and Inhibitor-BoundEscherichia coliAdenylate Kinase Based on a Mode-Coupling Analysis of15N Spin Relaxation

Illuminating the mechanistic roles of enzyme conformational dynamics

Contact Info

Product

Resources

About

Domain Flexibility in Ligand-Free and Inhibitor-BoundEscherichia coliAdenylate Kinase Based on a Mode-Coupling Analysis of¹⁵N Spin Relaxation