Phosphorylation Reaction in cAPK Protein Kinase-Free Energy Quantum Mechanical/Molecular Mechanics Simulations

Hybrid quantum mechanical and molecular mechanics study of the S(N)2 Reaction of CCl4 + OH- in aqueous solution: the potential of mean force, reaction energetics, and rate constants

The bimolecular nucleophilic substitution reaction of CCl(4) and OH(-) in aqueous solution was investigated on the basis of a combined quantum mechanical and molecular mechanics method. A multilayered representation approach is employed to achieve high accuracy results at the CCSD(T) level of theory. The potential of mean force calculations at the DFT level and CCSD(T) level of theory yield reaction barrier heights of 22.7 and 27.9 kcal/mol, respectively. Both the solvation effects and the solvent-induced polarization effect have significant contributions to the reaction energetics, for example, the solvation effect raises the saddle point by 10.6 kcal/mol. The calculated rate constant coefficient is 8.6 × 10(-28) cm(3) molecule(-1) s(-1) at the standard state condition, which is about 17 orders magnitude smaller than that in the gas phase. Among the four chloromethanes (CH(3)Cl, CH(2)Cl(2), CHCl(3), and CCl(4)), CCl(4) has the lowest free energy activation barrier for the reaction with OH(-) in aqueous solution, confirming the trend that substitution of Cl by H in chloromethanes diminishes the reactivity.

Theoretical investigation of the enzymatic phosphoryl transfer of β-phosphoglucomutase: revisiting both steps of the catalytic cycle

Enzyme catalyzed phosphate transfer is a part of almost all metabolic processes. Such reactions are of central importance for the energy balance in all organisms and play important roles in cellular control at all levels. Mutases transfer a phosphoryl group while nucleases cleave the phosphodiester linkages between two nucleotides. The subject of our present study is the Lactococcus lactis β-phosphoglucomutase (β-PGM), which effectively catalyzes the interconversion of β-D-glucose-1-phosphate (β-G1P) to β-D-glucose-6-phosphate (β-G6P) and vice versa via stabile intermediate β-D-glucose-1,6-(bis)phosphate (β-G1,6diP) in the presence of Mg(2+). In this paper we revisited the reaction mechanism of the phosphoryl transfer starting from the bisphosphate β-G1,6diP in both directions (toward β-G1P and β-G6P) combining docking techniques and QM/MM theoretical method at the DFT/PBE0 level of theory. In addition we performed NEB (nudged elastic band) and free energy calculations to optimize the path and to identify the transition states and the energies involved in the catalytic cycle. Our calculations reveal that both steps proceed via dissociative pentacoordinated phosphorane, which is not a stabile intermediate but rather a transition state. In addition to the Mg(2+) ion, Ser114 and Lys145 also play important roles in stabilizing the large negative charge on the phosphate through strong coordination with the phosphate oxygens and guiding the phosphate group throughout the catalytic process. The calculated energy barrier of the reaction for the β-G1P to β-G1,6diP step is only slightly higher than for the β-G1,6diP to β-G6P step (16.10 kcal mol(-1) versus 15.10 kcal mol(-1)) and is in excellent agreement with experimental findings (14.65 kcal mol(-1)).

Solution reaction design: electroaccepting and electrodonating powers of ions in solution

By considering a first-order variation in electroaccepting and electrodonating powers, ω±, induced by a change from gas to aqueous solution phase, the solvent effect on ω± for charged ions is examined. The expression of electroaccepting and electrodonating powers in the solution phase, ω±s, is obtained through establishing the quantitative relationship between the change of the ω± due to the solvation and the hydration free energy. It is shown that cations are poorer electron acceptors and anions are poorer electron donors in solution compared to those in gas phase. We have proven that the scaled aqueous electroaccepting power, ω+s, of cations can act as a good descriptor of the reduction reaction, which is expected to be applied in the design of solution reactions.

Insights into the phosphoryl transfer mechanism of cyclin-dependent protein kinases from ab initio QM/MM free-energy studies

Phosphorylation reactions catalyzed by kinases and phosphatases play an indispensible role in cellular signaling, and their malfunctioning is implicated in many diseases. A better understanding of the catalytic mechanism will help design novel and effective mechanism-based inhibitors of these enzymes. In this work, ab initio quantum mechanical/molecular mechanical studies are reported for the phosphoryl transfer reaction catalyzed by a cyclin-dependent kinase, CDK2. Our results suggest that an active-site Asp residue, rather than ATP as previously proposed, serves as the general base to activate the Ser nucleophile. The corresponding transition state features a dissociative, metaphosphate-like structure, stabilized by the Mg(2+) ion and several hydrogen bonds. The calculated free-energy barrier is consistent with experimental values. Implications of our results in this and other protein kinases are discussed.

[Modeling the transition state of enzyme-catalyzed phosphoryl transfer reaction using QM/MM method]

Reversible phosphorylation of proteins is a post-translational modification that regulates diverse biological processes. The molecular mechanism underlying phosphoryl transfer catalyzed by enzymes, in particular the nature of transition state (TS), remains a subject of active debate. Structural evidence supports an associative TS, whereas physical organic studies point to a dissociative character. In this article, we briefly introduce our recent effort using the hybrid quantum mechanics/molecular mechanics (QM/MM) simulations to resolve the controversy. We perform QM/MM simulations for the reversible phosphorylation of phosphoserine phosphatase (PSP), which belongs to one of the largest phosphotransferase families characterized to data. Both phosphorylation and dephosphorylation reactions are investigated based on the two-dimensional energy surfaces along phosphoryl and proton transfer coordinates. The resultant structures of the active site at TS in both reactions have compact geometries but a less electron density of the phosphoryl group. This suggests that the TS of PSP has a geometrically associative yet electronically dissociative character and strongly depends on proton transfer being coupled with phosphoryl transfer. Structure and literature database searches on phosphotransferases suggest that such a hybrid TS is consistent with many structures and physical organic studies and likely holds for most enzymes catalyzing phosphoryl transfer.

Cytoskeletal protein kinases: titin and its relations in mechanosensing

Titin, the giant elastic ruler protein of striated muscle sarcomeres, contains a catalytic kinase domain related to a family of intrasterically regulated protein kinases. The most extensively studied member of this branch of the human kinome is the Ca²⁺–calmodulin (CaM)-regulated myosin light-chain kinases (MLCK). However, not all kinases of the MLCK branch are functional MLCKs, and about half lack a CaM binding site in their C-terminal autoinhibitory tail (AI). A unifying feature is their association with the cytoskeleton, mostly via actin and myosin filaments. Titin kinase, similar to its invertebrate analogue twitchin kinase and likely other “MLCKs”, is not Ca²⁺–calmodulin-activated. Recently, local protein unfolding of the C-terminal AI has emerged as a common mechanism in the activation of CaM kinases. Single-molecule data suggested that opening of the TK active site could also be achieved by mechanical unfolding of the AI. Mechanical modulation of catalytic activity might thus allow cytoskeletal signalling proteins to act as mechanosensors, creating feedback mechanisms between cytoskeletal tension and tension generation or cellular remodelling. Similar to other MLCK-like kinases like DRAK2 and DAPK1, TK is linked to protein turnover regulation via the autophagy/lysosomal system, suggesting the MLCK-like kinases have common functions beyond contraction regulation.

Protein kinases: evolution of dynamic regulatory proteins

Eukayotic protein kinases evolved as a family of highly dynamic molecules with strictly organized internal architecture. A single hydrophobic F-helix serves as a central scaffold for assembly of the entire molecule. Two non-consecutive hydrophobic structures termed "spines" anchor all the elements important for catalysis to the F-helix. They make firm, but flexible, connections within the molecule, providing a high level of internal dynamics of the protein kinase. During the course of evolution, protein kinases developed a universal regulatory mechanism associated with a large activation segment that can be dynamically folded and unfolded in the course of cell functioning. Protein kinases thus represent a unique, highly dynamic, and precisely regulated set of switches that control most biological events in eukaryotic cells.

Chemical approaches towards unravelling kinase-mediated signalling pathways

Protein kinases control the function of about one third of cellular proteins by catalysing the transfer of the γ-phosphate group of ATP onto their substrate proteins. Protein phosphatases counter this action and also control the activation status of many kinases. Cellular responses to environmental changes, or signalling events, temporarily tilt the balance of protein phosphorylation and dephosphorylation to one side or the other. The identification of protein-kinase-substrate pairs and substrate-phosphatase pairs is critical to understanding cell function and how cells respond to environmental changes. Identification of these substrate-enzyme pairs is non-trivial, because of the structural and mechanistic conservation of the catalytic cores of protein kinases. In this tutorial review we review recent progress towards identifying protein-kinase-substrate pairs by emphasising the use of chemical genetics and purpose-designed ATP analogues that target one particular protein kinase. In addition, we discuss activity-based chemical profiling approaches, based on ATP analogues, for the detection of active kinases.

A QM/MM study of the phosphoryl transfer to the Kemptide substrate catalyzed by protein kinase A. The effect of the phosphorylation state of the protein on the mechanism

We present here a theoretical study of the phosphoryl transfer catalytic mechanism of protein kinase A, which is the best known member of the large protein kinase family. We have built different theoretical models of the complete PKA-Mg(2)-ATP-substrate system to explore the two most accepted reaction pathways, using for the first time in a reaction mechanism theoretical study, the heptapeptide substrate Kemptide, which is relevant for its high efficiency and small size. The effect of the protein configuration, as modeled by two different X-ray structures with different phosphorylation states and degrees of flexibility, has been analyzed. The results indicate that the environmental conditions can influence the availability of the pathways and thus the choice of the mechanism to be followed. In addition, the roles of the two active site conserved residues, Asp166 and Lys168, have been analyzed for each reaction mechanism.

High-resolution structure of the nitrile reductase QueF combined with molecular simulations provide insight into enzyme mechanism

Here, we report the 1.53-Å crystal structure of the enzyme 7-cyano-7-deazaguanine reductase (QueF) from Vibrio cholerae, which is responsible for the complete reduction of a nitrile (CN) bond to a primary amine (H(2)C-NH(2)). At present, this is the only example of a biological pathway that includes reduction of a nitrile bond, establishing QueF as particularly noteworthy. The structure of the QueF monomer resembles two connected ferrodoxin-like domains that assemble into dimers. Ligands identified in the crystal structure suggest the likely binding conformation of the native substrates NADPH and 7-cyano-7-deazaguanine. We also report on a series of numerical simulations that have shed light on the mechanism by which this enzyme affects the transfer of four protons (and electrons) to the 7-cyano-7-deazaguanine substrate. In particular, the simulations suggest that the initial step of the catalytic process is the formation of a covalent adduct with the residue Cys194, in agreement with previous studies. The crystal structure also suggests that two conserved residues (His233 and Asp102) play an important role in the delivery of a fourth proton to the substrate.

Structure and dynamics of the hydration shells of the Zn(2+) ion from ab initio molecular dynamics and combined ab initio and classical molecular dynamics simulations

Results of ab initio molecular dynamics (AIMD) simulations (density functional theory+PBE96) of the dynamics of waters in the hydration shells surrounding the Zn(2+) ion (T approximately 300 K, rho approximately 1 gm/cm(3)) are compared to simulations using a combined quantum and classical molecular dynamics [AIMD/molecular mechanical (MM)] approach. Both classes of simulations were performed with 64 solvating water molecules ( approximately 15 ps) and used the same methods in the electronic structure calculation (plane-wave basis set, time steps, effective mass, etc.). In the AIMD/MM calculation, only six waters of hydration were included in the quantum mechanical (QM) region. The remaining 58 waters were treated with a published flexible water-water interaction potential. No reparametrization of the water-water potential was attempted. Additional AIMD/MM simulations were performed with 256 water molecules. The hydration structures predicted from the AIMD and AIMD/MM simulations are found to agree in detail with each other and with the structural results from x-ray data despite the very limited QM region in the AIMD/MM simulation. To further evaluate the agreement of these parameter-free simulations, predicted extended x-ray absorption fine structure (EXAFS) spectra were compared directly to the recently obtained EXAFS data and they agree in remarkable detail with the experimental observations. The first hydration shell contains six water molecules in a highly symmetric octahedral structure is (maximally located at 2.13-2.15 A versus 2.072 A EXAFS experiment). The widths of the peak of the simulated EXAFS spectra agree well with the data (8.4 A(2) versus 8.9 A(2) in experiment). Analysis of the H-bond structure of the hydration region shows that the second hydration shell is trigonally bound to the first shell water with a high degree of agreement between the AIMD and AIMD/MM calculations. Beyond the second shell, the bonding pattern returns to the tetrahedral structure of bulk water. The AIMD/MM results emphasize the importance of a quantum description of the first hydration shell to correctly describe the hydration region. In these calculations the full d(10) electronic structure of the valence shell of the Zn(2+) ion is retained. The simulations show substantial and complex charge relocation on both the Zn(2+) ion and the first hydration shell. The dipole moment of the waters in the first hydration shell is 3.4 D (3.3 D AIMD/MM) versus 2.73 D bulk. Little polarization is found for the waters in the second hydration shell (2.8 D). No exchanges were seen between the first and the second hydrations shells; however, many water transfers between the second hydration shell and the bulk were observed. For 64 waters, the AIMD and AIMD/MM simulations give nearly identical results for exchange dynamics. However, in the larger particle simulations (256 waters) there is a significant reduction in the second shell to bulk exchanges.

Atomistic details of the associative phosphodiester cleavage in human ribonuclease H

During translation of the genetic information of DNA into proteins, mRNA is synthesized by RNA polymerase and after the transcription process degraded by RNase H. The endoribonuclease RNase H is a member of the nucleotidyl-transferase (NT) superfamily and is known to hydrolyze the phosphodiester bonds of RNA which is hybridized to DNA. Retroviral RNase H is part of the viral reverse transcriptase enzyme that is indispensable for the proliferation of retroviruses, such as HIV. Inhibitors of this enzyme could therefore provide new drugs against diseases like AIDS. In our study we investigated the molecular mechanism of RNA cleavage by human RNase H using a comprehensive high level DFT/B3LYP QM/MM theoretical method for the calculation of the stationary points and nudged elastic band (NEB) and free energy calculations to identify the transition state structures, the rate limiting step and the reaction barrier. Our calculations reveal that the catalytic mechanism proceeds in two steps and that the nature of the nucleophile is a water molecule. In the first step, the water attack on the scissile phosphorous is followed by a proton transfer from the water to the O2P oxygen and a trigonal bipyramidal pentacoordinated phosphorane is formed. Subsequently, in the second step the proton is shuttled to the O3' oxygen to generate the product state. During the reaction mechanism two Mg(2+) ions support the formation of a stable associated in-line S(N)2-type phosphorane intermediate. Our calculated energy barrier of 19.3 kcal mol(-1) is in excellent agreement with experimental findings (20.5 kcal mol(-1)). These results may contribute to the clarification and understanding of the RNase H reaction mechanism and of further enzymes from the RNase family.

First principles simulation of the bonding, vibrational, and electronic properties of the hydration shells of the high-spin Fe(3+) ion in aqueous solutions

Results of parameter-free first principles simulations of a spin up 3d(5) Fe(3+) ion hydrated in an aqueous solution (64 waters, 30 ps, 300 K) are reported. The first hydration shell associated with the first maximum of the radial distribution function, g(FeO)(r), at d(Fe-O(I)) = 2.11-2.15 A, contains 6 waters with average d(OH) = 0.99 A, in good agreement with observations. A second shell with average coordination number 13.3 can be identified with average shell radius of d(Fe-O(II)) = 4.21-4.32 A. The waters in this hydration shell are coordinated to the first shell via a trigonal H-bond network with d(O(I)-O(II)) = 2.7-2.9 A, also in agreement with experimental measurements. The first shell tilt angle average is 33.4 degrees as compared to the reported value of 41 degrees . Wannier-Boys orbitals (WBO) show an interaction between the unoccupied 3d orbitals of the Fe(3+) valence (spin up, 3d(5)) and the occupied spin down lone pair orbitals of first shell waters. The effect of the spin ordering of the Fe(3+) ion on the WBO is not observed beyond the first shell. From this local bond analysis and consistent with other observations, the electronic structure of waters in the second shell is similar to that of a bulk water even in this strongly interacting system. H-bond decomposition shows significant bulk-like structure within the second shell for Fe(3+). The vibrational density of states shows a first shell red shift of 230 cm(-1) for the v(1),2v(2),v(3) overtone, in reasonable agreement with experimental estimates for trivalent cations (300 cm(-1)). No exchanges between first and second shell were observed. Waters in the second shell exchanged with bulk waters via dissociative and associative mechanisms. Results are compared with an AIMD study of Al(3+) and 64 waters. For Fe(3+) the average first shell tilt angle is larger and the tilt angle distribution wider. H-bond decomposition shows that second shell to second shell H-bonding is enhanced in Fe(3+) suggesting an earlier onset of bulk-like water structure.

Evolution of CASK into a Mg2+-sensitive kinase

All known protein kinases, except CASK [calcium/calmodulin (CaM)-activated serine-threonine kinase], require magnesium ions (Mg(2+)) to stimulate the transfer of a phosphate from adenosine 5'-triphosphate (ATP) to a protein substrate. The CaMK (calcium/calmodulin-dependent kinase) domain of CASK shows activity in the absence of Mg(2+); indeed, it is inhibited by divalent ions including Mg(2+). Here, we converted the Mg(2+)-inhibited wild-type CASK kinase (CASK(WT)) into a Mg(2+)-stimulated kinase (CASK(4M)) by substituting four residues within the ATP-binding pocket. Crystal structures of CASK(4M) with and without bound nucleotide and Mn(2+), together with kinetic analyses, demonstrated that Mg(2+) accelerates catalysis of CASK(4M) by stabilizing the transition state, enhancing the leaving group properties of adenosine 5'-diphosphate, and indirectly shifting the position of the gamma-phosphate of ATP. Phylogenetic analysis revealed that the four residues conferring Mg(2+)-mediated stimulation were substituted from CASK during early animal evolution, converting a primordial, Mg(2+)-coordinating form of CASK into a Mg(2+)-inhibited kinase. This emergence of Mg(2+) sensitivity (inhibition by Mg(2+)) conferred regulation of CASK activity by divalent cations, in parallel with the evolution of the animal nervous systems.

ErbB3/HER3 intracellular domain is competent to bind ATP and catalyze autophosphorylation

ErbB3/HER3 is one of four members of the human epidermal growth factor receptor (EGFR/HER) or ErbB receptor tyrosine kinase family. ErbB3 binds neuregulins via its extracellular region and signals primarily by heterodimerizing with ErbB2/HER2/Neu. A recently appreciated role for ErbB3 in resistance of tumor cells to EGFR/ErbB2-targeted therapeutics has made it a focus of attention. However, efforts to inactivate ErbB3 therapeutically in parallel with other ErbB receptors are challenging because its intracellular kinase domain is thought to be an inactive pseudokinase that lacks several key conserved (and catalytically important) residues-including the catalytic base aspartate. We report here that, despite these sequence alterations, ErbB3 retains sufficient kinase activity to robustly trans-autophosphorylate its intracellular region--although it is substantially less active than EGFR and does not phosphorylate exogenous peptides. The ErbB3 kinase domain binds ATP with a K(d) of approximately 1.1 microM. We describe a crystal structure of ErbB3 kinase bound to an ATP analogue, which resembles the inactive EGFR and ErbB4 kinase domains (but with a shortened alphaC-helix). Whereas mutations that destabilize this configuration activate EGFR and ErbB4 (and promote EGFR-dependent lung cancers), a similar mutation conversely inactivates ErbB3. Using quantum mechanics/molecular mechanics simulations, we delineate a reaction pathway for ErbB3-catalyzed phosphoryl transfer that does not require the conserved catalytic base and can be catalyzed by the "inactive-like" configuration observed crystallographically. These findings suggest that ErbB3 kinase activity within receptor dimers may be crucial for signaling and could represent an important therapeutic target.

A transition path ensemble study reveals a linchpin role for Mg(2+) during rate-limiting ADP release from protein kinase A

Protein kinases are key regulators of diverse signaling networks critical for growth and development. Protein kinase A (PKA) is an important kinase prototype that phosphorylates protein targets at Ser and Thr residues by converting ATP to ADP. Mg²⁺ ions play a crucial role in regulating phosphoryl transfer and can limit overall enzyme turnover by affecting ADP release. However, the mechanism by which Mg²⁺ participates in ADP release is poorly understood. Here we use a novel transition path ensemble technique, the harmonic Fourier beads method, to explore the atomic and energetic details of the Mg²⁺-dependent ADP binding and release. Our studies demonstrate that adenine-driven ADP binding to PKA creates three ion-binding sites at the ADP/PKA interface that are absent otherwise. Two of these sites bind the previously characterized Mg²⁺ ions, whereas the third site binds a monovalent cation with high affinity. This third site can bind the P-3 residue of substrate proteins and may serve as a reporter of the active site occupation. Binding of Mg²⁺ ions restricts mobility of the Gly-rich loop that closes over the active site. We find that simultaneous release of ADP with Mg²⁺ ions from the active site is unfeasible. Thus, we conclude that Mg²⁺ ions act as a linchpin and that at least one ion must be removed prior to pyrophosphate-driven ADP release. The results of the present study enhance understanding of Mg²⁺-dependent association of nucleotides with protein kinases.

Low temperature 65Cu NMR spectroscopy of the Cu+ site in azurin

(65)Cu central-transition NMR spectroscopy of the blue copper protein azurin in the reduced Cu(I) state, conducted at 18.8 T and 10 K, gave a strongly second order quadrupole perturbed spectrum, which yielded a (65)Cu quadrupole coupling constant of +/-71.2 +/- 1 MHz, corresponding to an electric field gradient of +/-1.49 atomic units at the copper site, and an asymmetry parameter of approximately 0.2. Quantum chemical calculations employing second order Møller-Plesset perturbation theory and large basis sets successfully reproduced these experimental results. Sensitivity and relaxation times were quite favorable, suggesting that NMR may be a useful probe of the electronic state of copper sites in proteins.

Defining the conserved internal architecture of a protein kinase

Protein kinases constitute a large protein family of important regulators in all eukaryotic cells. All of the protein kinases have a similar bilobal fold, and their key structural features have been well studied. However, the recent discovery of non-contiguous hydrophobic ensembles inside the protein kinase core shed new light on the internal organization of these molecules. Two hydrophobic "spines" traverse both lobes of the protein kinase molecule, providing a firm but flexible connection between its key elements. The spine model introduces a useful framework for analysis of intramolecular communications, molecular dynamics, and drug design.

An investigation of the catalytic mechanism of S-adenosylmethionine synthetase by QM/MM calculations

Catalysis by S-adenosylmethionine synthetase has been investigated by quantum mechanical/molecular mechanical calculations, exploiting structures of the active crystalline enzyme. The transition state energy of +19.1 kcal/mol computed for a nucleophilic attack of the methionyl sulfur on carbon-5' of the nucleotide was indistinguishable from the experimental (solution) value when the QM residues were an uncharged histidine that hydrogen bonds to the leaving oxygen-5' and an aspartate that chelates a Mg2+ ion, and was similar (+18.8 kcal/mol) when the QM region also included the active site arginine and lysines. The computed energy difference between reactant and product was also consistent with their equimolar abundance in co-crystals. The calculated geometrical changes support catalysis of a S(N)2 reaction through hydrogen bonding of the liberated oxygen-5' to the histidine, charge neutralization by the two Mg2+ ions, and stabilization of the product sulfonium cation through a close, non-bonded, contact between the sulfur and the ribose oxygen-4'.

A computational study of the phosphorylation mechanism of the insulin receptor tyrosine kinase

Although various groups have studied the phosphorylation mechanism of the insulin receptor tyrosine kinase (IRK), an unanimous picture has not yet emerged. In this work, we performed a computational study to gain further insights. We first built a structural model of the reactant complex with the guide of several crystal structures and previous computational studies of the cyclic AMP-dependent protein kinase. We then optimized the structure by performing geometry optimization using a quantum mechanical model containing nearly 300 atoms. A reaction path was then traced between the reactant and the product by using a multiple coordinate-driven method. The calculations mapped out a sequence of structural changes depicting the conversion of the reactant to the product. Analysis of the structural changes revealed the formation of a dissociative transition state and the involvement of a proton transfer from the hydroxyl group of the tyrosyl residue of the peptide substrate to a conserved aspartate in the active site of the enzyme. The proton transfer began well before the transition state was reached and finished only shortly before the product was completely formed. In addition, the formation of a hydrogen bonding network among Arg1136, Asp1132, the gamma-phosphate of ATP, and the tyrosine residue of the substrate appeared to hold the latter two in a near-attack position for reaction. The model estimated a reaction barrier of 14 kcal/mol, semiquantitatively in accord with experiment.

Quantum mechanics/molecular mechanics investigation of the mechanism of phosphate transfer in human uridine-cytidine kinase 2

The mechanisms of enzyme-catalyzed phosphate transfer and hydrolysis reactions are of great interest due to their importance and abundance in biochemistry. The reaction may proceed in a stepwise fashion, with either a pentavalent phosphorane or a metaphosphate anion intermediate, or by a concerted SN2 mechanism. Despite much theoretical work focused on a few key enzymes, a consensus for the mechanism has not been reached, and examples of all three possibilities have been demonstrated. We have investigated the mechanism of human uridine-cytidine kinase 2 (UCK2, EC 2.7.1.48), which catalyzes the transfer of a phosphate group from ATP to the ribose 5'-hydroxyl of cytidine and uridine. UCK2 is normally expressed in human placenta, but is overexpressed in certain cancer cells, where it is responsible for activating a class of antitumor prodrugs. The UCK2 mechanism was investigated by generating a 2D potential energy surface as a function of the P-O bonds forming and breaking, with energies calculated using a quantum mechanics/molecular mechanics potential (B3LYP/6-31G(d):AMBER). The mechanism of phosphate transfer is shown to be concerted, and is accompanied by concerted proton transfer from the 5'-hydroxyl to a conserved active site aspartic acid that serves as a catalytic base. The calculated barrier for this reaction is 15.1 kcal/mol, in relatively good agreement with the experimental barrier of 17.5 kcal/mol. The interactions of the enzyme active site with the reactant, transition state, and product are examined for their implications on the design of anticancer prodrugs or positron emission tomography (PET) reporter probes for this enzyme.

How mitogen-activated protein kinases recognize and phosphorylate their targets: A QM/MM study

Mitogen-activated protein kinase (MAPK) signaling pathways play an essential role in the transduction of environmental stimuli to the nucleus, thereby regulating a variety of cellular processes, including cell proliferation, differentiation, and programmed cell death. The components of the MAPK extracellular activated protein kinase (ERK) cascade represent attractive targets for cancer therapy, as their aberrant activation is a frequent event among highly prevalent human cancers. To understand how MAPKs recognize and phosphorylate their targets is key to unravel their function. However, these events are still poorly understood because of the lack of complex structures of MAPKs with their bound targets in the active site. Here we have modeled the interaction of ERK with a target peptide and analyzed the specificity toward Ser/Thr-Pro motifs. By using a quantum mechanics/molecular mechanics (QM/MM) approach, we propose a mechanism for the phosphoryl transfer catalyzed by ERK that offers new insights into MAPK function. Our results suggest that (1) the proline residue has a role in both specificity and phospho transfer efficiency, (2) the reaction occurs in one step, with ERK2 Asp(147) acting as the catalytic base, (3) a conserved Lys in the kinase superfamily that is usually mutated to check kinase activity strongly stabilizes the transition state, and (4) the reaction mechanism is similar with either one or two Mg(2+) ions in the active site. Taken together, our results provide a detailed description of the molecular events involved in the phosphorylation reaction catalyzed by MAPK and contribute to the general understanding of kinase activity.

QM/MM methods for biomolecular systems

Combined quantum-mechanics/molecular-mechanics (QM/MM) approaches have become the method of choice for modeling reactions in biomolecular systems. Quantum-mechanical (QM) methods are required for describing chemical reactions and other electronic processes, such as charge transfer or electronic excitation. However, QM methods are restricted to systems of up to a few hundred atoms. However, the size and conformational complexity of biopolymers calls for methods capable of treating up to several 100,000 atoms and allowing for simulations over time scales of tens of nanoseconds. This is achieved by highly efficient, force-field-based molecular mechanics (MM) methods. Thus to model large biomolecules the logical approach is to combine the two techniques and to use a QM method for the chemically active region (e.g., substrates and co-factors in an enzymatic reaction) and an MM treatment for the surroundings (e.g., protein and solvent). The resulting schemes are commonly referred to as combined or hybrid QM/MM methods. They enable the modeling of reactive biomolecular systems at a reasonable computational effort while providing the necessary accuracy.

A helix scaffold for the assembly of active protein kinases

Structures of set of serine-threonine and tyrosine kinases were investigated by the recently developed bioinformatics tool Local Spatial Patterns (LSP) alignment. We report a set of conserved motifs comprised mostly of hydrophobic residues. These residues are scattered throughout the protein sequence and thus were not previously detected by traditional methods. These motifs traverse the conserved protein kinase core and play integrating and regulatory roles. They are anchored to the F-helix, which acts as an organizing "hub" providing precise positioning of the key catalytic and regulatory elements. Consideration of these discovered structures helps to explain previously inexplicable results.

Residue ionization in LpxC directly observed by 67Zn NMR spectroscopy

The pH dependence of the solid-state (67)Zn NMR lineshapes has been measured for both the wild type (WT) and the H265A mutant of Aquifex aeolicus LpxC, each in the absence of substrate (resting state). The (67)Zn NMR spectrum of WT LpxC at pH 6 (prepared at 0 degrees C) contains two overlapping quadrupole lineshapes with C q values of 10 and 12.9 MHz, while the spectrum measured for the sample prepared at a pH near 9 (at 0 degrees C) is dominated by the appearance of a third species with a C q of 14.3 MHz. These findings are consistent with the two p K a values previously observed by the bell-shaped dependence of the LpxC-catalyzed reaction. On the basis of comparison of the experimental results with predictions from quantum mechanical/molecular mechanical (QM/MM) modeling, we suggest that p K a1 (low pH) represents the ionization of Glu78 and p K a2 (high pH) reflects the ionization of another active site residue located near the zinc ion, such as His265. These results are also consistent with water being bound to the Zn (2+) ion throughout this pH range. The (67)Zn NMR spectra of the H265A mutant appear to be pH independent, with a C q of 9.55 MHz being sufficient to describe both low- and high-pH data. The QM/MM models of the H265A mutant suggest that over this pH range water is bound to the zinc ion while Glu78 is protonated.