Native states of adenylate kinase are two active sub-ensembles

Molecular dynamics studies on the conformational transitions of adenylate kinase: a computational evidence for the conformational selection mechanism

Escherichia coli adenylate kinase (ADK) is a monomeric phosphotransferase enzyme that catalyzes reversible transfer of phosphoryl group from ATP to AMP with a large-scale domain motion. The detailed mechanism for this conformational transition remains unknown. In the current study, we performed long time-scale molecular dynamics simulations on both open and closed states of ADK. Based on the structural analyses of the simulation trajectories, we detected over 20 times conformational transitions between the open and closed states of ADK and identified two novel conformations as intermediate states in the catalytic processes. With these findings, we proposed a possible mechanism for the large-scale domain motion of Escherichia coli ADK and its catalytic process: (1) the substrate free ADK adopted an open conformation; (2) ATP bound with LID domain closure; (3) AMP bound with NMP domain closure; (4) phosphoryl transfer occurred with ATP, and AMP converted into two ADPs, and no conformational transition was detected in the enzyme; (5) LID domain opened with one ADP released; (6) another ADP released with NMP domain open. As both open and closed states sampled a wide range of conformation transitions, our simulation strongly supported the conformational selection mechanism for Escherichia coli ADK.

Hamiltonian replica exchange method study of Escherichia coli and Yersinia pestis HPPK

HPPK (6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase) catalyzes the transfer of pyrophosphate from ATP to HP (6-hydroxymethyl-7,8-dihydropterin). This first reaction in the folate biosynthetic pathway is a potential target for antimicrobial agents. A Hamiltonian replica exchange method (HREM) molecular dynamics (MD) approach is used, with the goal of improving conformational sampling, whereby multiple copies of the system are run without requiring a large number of system copies. For HPPK, the aim is to improve conformational sampling around the HP binding pocket and thereby find near-closed conformations (similar but not identical to the binding pocket of HP, as defined by the ternary crystal structure). Near-closed conformations may be better targets for the design of species-selective inhibitors. Well-populated, near-closed conformations of Escherichia coli HPPK (EcHPPK) and Yersinia pestis HPPK (YpHPPK) were found with HREM by focusing on the interactions involving loops 2 and 3 that are known to be the more flexible regions of HPPK. A small number of systems were found to be sufficient to enlarge the sample space substantially, on the basis of root-mean-square fluctuation measures, relative to the results of a conventional MD simulation. By clustering snapshots on the basis of some of the key residues that form the HP binding pocket, distinct HREM-generated conformations are found. Residue displacements mainly from loop 2 are responsible for the distinct conformers found, relative to the crystal structure, for both EcHPPK and YpHPPK. In contrast, the conventional MD simulations of EcHPPK and YpHPPK each lead essentially to one cluster, with use of the same clustering criterion as for the HREM. The shapes of the HREM near-closed binding pockets are qualitatively investigated and found to be different. Some of these conformations are distinguishable between EcHPPK and YpHPPK, indicating that there may be differing species-selective, near-closed conformations suited to HP binding.

Apo adenylate kinase encodes its holo form: a principal component and varimax analysis

Adenylate kinase undergoes large-scale motions of its LID and AMP-binding (AMPbd) domains when its apo, open form closes over its substrates, AMP and Mg2+-ATP. It may be an example of an enzyme that provides an ensemble of conformations in its apo state from which its substrates can select and bind to produce catalytically competent conformations. In this work, the fluctuations of the enzyme apo Escherichia coli adenylate kinase (AKE) are obtained with molecular dynamics. The resulting trajectory is analyzed with principal component analysis (PCA) that decomposes the atom motions into orthogonal modes ordered by their decreasing contributions to the total protein fluctuation. In apo AKE, a small set of the PCA modes describes the bulk of the fluctuations. Identification of the atom motions that are important contributors to these modes is improved with the use of a varimax rotation method that rotates the PCA modes to a new mode set that concentrates the atom contributions to a smaller set of atoms in these new modes. In this way, the nature of the important motions of the LID and AMPbd domains are clarified. The dominant PCA modes are used to investigate if apo AKE can fluctuate to conformations that are holo-like, even though the apo trajectory is mainly confined to a region around the initial apo structure. This is accomplished by expressing the difference between the protein coordinates, obtained from the holo and apo crystal structures, using as a basis the PCA modes from the apo AKE trajectory. The coherent motion described by a small set of the apo PCA modes is shown to be able to produce protein conformations that are quite similar to the holo conformation of the protein. In this sense, apo AKE does encode in its fluctuations information about holo-like conformations.

Conjugated polyelectrolyte based real-time fluorescence assay for adenylate kinase

Addition of adenosine 5'-triphosphate (ATP) to a solution of the anionic conjugated polyelectrolyte PPECO2 and copper(II) ion (Cu2+) recovers the Cu2+-quenched fluorescence of PPECO(2) to a significantly greater extent compared with the addition of adenosine 5'-diphosphate (ADP) or adenosine 5'-monophosphate (AMP) at the same concentration levels. Taking advantage of the differential response of the PPECO2-Cu2+ system to ATP, ADP and AMP, we have developed fluorescence turn-off and turn-on assays that monitor the catalytic activity of adenylate kinase (ADK) in the equilibrium transphosphorylation reaction (ATP + AMP <--> 2ADP). The fluorescence turn-on and turn-off assays monitor the forward and reverse transphosphorylation reactions, respectively. The forward assay operates with ATP substrate present at the submillimolar concentration range and offers a straightforward and rapid detection of ADK catalytic activity with the enzyme present in the nanomolar range, in either end-point or real-time formats. The real-time fluorescence intensity from PPECO2 can be converted to substrate (ATP) concentration in the forward reaction assay by using an ex-situ calibration curve, allowing ADK catalyzed reaction rates and kinetic parameters to be determined. ADK activation by Mg2+ and inhibition by Ag+ and product are analyzed using the optimized assay system. Non-specific interactions are observed between the assay complex and other proteins, but the signal response to the ADK assay is demonstrated to mainly arise from the specific enzyme catalyzed transphosphorylation reaction.

Small- and large-scale conformational changes of adenylate kinase: a molecular dynamics study of the subdomain motion and mechanics

Adenylate kinase, an enzyme that catalyzes the phosphoryl transfer between ATP and AMP, can interconvert between the open and catalytically potent (closed) forms even without binding ligands. Several aspects of the enzyme elasticity and internal dynamics are analyzed here by atomistic molecular dynamics simulations covering a total time span of 100 ns. This duration is sufficiently long to reveal a partial conversion of the enzyme that proceeds through jumps between structurally different substates. The intra- and intersubstates contributions to the enzyme's structural fluctuations are analyzed and compared both in magnitude and directionality. It is found that, despite the structural heterogeneity of the visited conformers, the generalized directions accounting for conformational fluctuations within and across the substates are mutually consistent and can be described by a limited set of collective modes. The functional-oriented nature of the consensus modes is suggested by their good overlap with the deformation vector bridging the open and closed crystal structures. The consistency of adenylate kinase's internal dynamics over timescales wide enough to capture intra- and intersubstates fluctuations adds elements in favor of the recent proposal that the free (apo) enzyme possesses an innate ability to sustain the open/close conformational changes.

C-terminal effect of Thermoanaerobacter tengcongensis ribosome recycling factor on its activity and conformation changes

The in vivo activities and conformational changes of ribosome recycling factor from Thermoanaerobacter tengcongensis (TteRRF) with 12 successive C-terminal deletions were compared. The results showed that TteRRF mutants lacking one to four amino acid residues are inactive, those lacking five to nine are reactivated to a similar or a little higher level than wild-type TteRRF, and those lacking ten to twelve are inactivated again gradually. Conformational studies indicated that only the ANS binding fluorescence change is correlated well with the RRF in vivo activity change, while the secondary structure and local structure at the aromatic residues are not changed significantly. Trypsin cleavage site identification and protein stability measurement suggested that mutation only induced subtle conformation change and increased flexibility of the protein. Our results indicated that the ANS-detected local conformation changes of TteRRF and mutants are one verified direct reason of the in vivo inactivation and reactivation in Escherichia coli.

Molecular dynamics of apo-adenylate kinase: a distance replica exchange method for the free energy of conformational fluctuations

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 Mg2+-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.

Molecular Dynamics of Apo-Adenylate Kinase: A Principal Component Analysis

Adenylate kinase from E. coli (AKE) is studied with molecular dynamics. AKE undergoes large-scale motions of its Lid and AMP-binding domains when its open form closes over its substrates, AMP and Mg2+-ATP. The third domain, the Core, is relatively stable during closing. The resulting trajectory is analyzed with a principal component analysis method that decomposes the atom motions into modes ordered by their decreasing contributions to the total protein fluctuation. Simulations at 303 K (normal T) and 500 K (high T) reveal that at both temperatures the first three modes account for 70% of the total fluctuation. The residues that contribute the most to these three modes are concentrated in the Lid and AMP-binding domains. Analysis of the normal T modes indicates that the Lid and AMP-binding domains sample a broad distribution of conformations indicating that AKE is designed to provide its substrates with a large set of conformations. The high T results show that the Lid initially closes toward the Core. Subsequently, the Lid rotates to a new stable conformation that is different from what is observed in the substrate-bound AKE. These results are discussed in the context of experimental data that indicate that adenylate kinases do sample more than one conformational state in solution and that each of these conformational states undergoes substantial fluctuations. A pair of residues is suggested for labeling that would be useful for monitoring distance fluctuations by energy transfer experiments.