Proton transfer dynamics of GART: the pH-dependent catalytic mechanism examined by electrostatic calculations

pH Effects and Cooperativity among Key Titratable Residues for Escherichia coli Glycinamide Ribonucleotide Transformylase

Human glycinamide ribonucleotide transformylase (GAR Tfase) is a regulatory enzyme in the de novo purine biosynthesis pathway that has been extensively studied as an anticancer target. To some extent, inhibition of GAR Tfase selectively targets cancer cells over normal cells and inhibits purine formation and DNA replication. In this study, we investigated E. coli GAR Tfase, which shares high sequence similarity with the human GAR Tfase, and most functional residues are conserved. Herein, we aim to predict the pH-activity curve through a computational approach. We carried out pH-replica exchange molecular dynamics (pH-REMD) simulations to investigate pH-dependent functions such as structural changes, ligand binding, and catalytic activity. To compute the pH-activity curve, we identified the catalytic residues in specific protonation states, referred to as the catalytic competent protonation states (CCPS), which maintain the structure, keep ligands bound, and facilitate catalysis. Our computed population of CCPS with respect to pH matches well with the experimental pH-activity curve. To compute the microscopic pK_a values in the catalytically active conformation, we devised a thermodynamic model that considers the coupling between protonation states of CCPS residues and conformational states. These results allow us to correctly identify the general acid and base catalysts and interpret the pH-activity curve at an atomistic level.

Automated computational framework for the analysis of electrostatic similarities of proteins

Charge plays an important role in protein-protein interactions. In the case of excessively charged proteins, their electrostatic potentials contribute to the processes of recognition and binding with other proteins or ligands. We present an automated computational framework for determining the contribution of each charged amino acid to the electrostatic properties of proteins, at atomic resolution level. This framework involves computational alanine scans, calculation of Poisson-Boltzmann electrostatic potentials, calculation of electrostatic similarity distances (ESDs), hierarchical clustering analysis of ESDs, calculation of solvation free energies of association, and visualization of the spatial distributions of electrostatic potentials. The framework is useful to classify families of mutants with similar electrostatic properties and to compare them with the parent proteins in the complex. The alanine scan mutants introduce perturbations in the local electrostatic properties of the proteins and aim in delineating the contribution of each mutated amino acid in the spatial distribution of electrostatic potential, and in biological function when electrostatics is a dominant contributing factor in protein-protein interactions. The framework can be used to design new proteins with tailored electrostatic properties, such as immune system regulators, inhibitors, and vaccines, and in guiding experimental studies. We present an example for the interaction of the immune system protein C3d (the d-fragment of complement protein C3) with its receptor CR2, and we discuss our data in view of a binding site controversy.

Protein preparation, crystallization and preliminary crystallographic studies of Bacillus subtilis glycinamide ribonucleotide transformylase

Glycinamide ribonucleotide transformylase (GART) catalyzes the transfer of a formyl group from formyl tetrahydrofolate (FTHF) to glycinamide ribonucleotide (GAR), which is an essential step in the de novo synthesis pathway of purines. In Bacillus subtilis, GART is encoded by the gene purN. In order to study the structure and function of B. subtilis GART, the purN gene was amplified, cloned into an expression vector and expressed in soluble form in Escherichia coli. The protein was purified to homogeneity and crystals suitable for X-ray data collection were obtained. These crystals diffracted to 2.5 A resolution and belonged to space group P3(1)21, with unit-cell parameters a = b = 95.5, c = 64.0 A.

Active site dynamics and combined quantum mechanics/molecular mechanics (QM/MM) modelling of a HIV-1 reverse transcriptase/DNA/dTTP complex

We have investigated the structure and dynamics of the HIV-1 reverse transcriptase (HIV-RT) active site, by modelling the active conformation of the HIV-1 RT/DNA/deoxythymidine triphosphate (dTTP) ternary complex. This has included molecular dynamics simulations with the CHARMM27 force field, and combined quantum mechanics/molecular mechanics (QM/MM) calculations. Three different ternary systems were studied to investigate the effects of different protonation states of the dTTP substrate (a deprotonated and two different mono-protonated triphosphate forms of dTTP at the active site), and the effects of different possible protonation state of potentially catalytic aspartate residues (Asp185 and Asp186) were tested. Several potentially important hydrogen-bonding interactions with amino acids and bound water molecules in the deoxyribonucleoside triphosphate (dNTP) binding pocket were examined. The model of the deprotonated form of the dTTP substrate with the two aspartates in their charged (basic) form seemed to be the most stable and its orientation was in good agreement with X-ray crystallographic structure. In addition, two different semiempirical (AM1/CHARMM and PM3/CHARMM) QM/MM methods were tested for the HIV-RT system, in structural optimizations. Both methods provided conformations of the triphosphate moiety in either fully deprotonated or mono-protonated forms, which agreed well with the experimental structure of dTTP. The only significant difference between the AM1/CHARMM and PM3/CHARMM minimized structures is that the PM3/CHARMM Palpha-O3' optimized distance (important for nucleotide addition) is longer by 0.66 A in the deprotonated system but shorter by 0.37 A in the mono-protonated triphosphate system as compared with those obtained from AM1/CHARMM minimized structure. The obtained results suggest that both of these QM/MM methods, and the stochastic boundary molecular dynamics approach applied in this work, can give reasonable results for modelling the catalytically active complex of this important enzyme. The results provide insight into the structure and interactions of the active site of this important enzyme, with implications for its mechanism, which may be useful in inhibitor design.

Thermodynamic studies on the interaction of the third complement component and its inhibitor, compstatin

Compstatin is a 13-residue cyclic peptide that inhibits complement activation by binding to complement component, C3. Although the activity of compstatin has been improved severalfold using combinatorial and rational design approaches, the molecular basis for its interaction with C3 is not yet fully understood. In the present study, isothermal titration calorimetry was employed to dissect the molecular forces that govern the interaction of compstatin with C3 using four different compstatin analogs. Our studies indicate that the C3-compstatin interaction is an enthalpy-driven process. Substitution of the valine and histidine residues at positions 4 and 9 with tryptophan and alanine, respectively, resulted in the increase of enthalpy of the interaction, thereby increasing the binding affinity for C3. The data also suggest that the interaction is mediated by water molecules. These interfacial water molecules could be the source for unfavorable entropy and large negative heat capacity changes observed in the interaction. Although part of the negative heat capacity changes could be accounted for by the water molecules, the rest might be resulting from the conformational changes in C3 and/or compstatin up on binding. Finally, we propose based on the pK(a) values determined from the protonation studies that histidine on compstatin participates in protonation changes and contributes to the specificity of the interaction between compstatin and C3. These protonation changes vary significantly between the binding of different compstatin analogs to C3.

The electrostatic nature of C3d-complement receptor 2 association

The association of complement component C3d with B or T cell complement receptor 2 (CR2 or CD21) is a link between innate and adaptive immunity. It has been recognized in experimental studies that the C3d-CR2 association is pH- and ionic strength-dependent. This led us to perform electrostatic calculations to obtain a theoretical understanding of the mechanism of C3d-CR2 association. We used the crystallographic structures of human free C3d, free CR2 (short consensus repeat (SCR)1-2), and the C3d-CR2(SCR1-2) complex, and continuum solvent representation, to obtain a detailed atomic-level picture of the components of the two molecules that contribute to association. Based on the calculation of electrostatic potentials for the free and bound species and apparent pK(a) values for each ionizable residue, we show that C3d-CR2(SCR1-2) recognition is electrostatic in nature and involves not only the association interface, but also the whole molecules. Our results are in qualitative agreement with experimental data that measured the ionic strength and pH dependence of C3d-CR2 association. Also, our results for the native molecules and a number of theoretical mutants of C3d explain experimental mutagenesis studies of amino acid replacements away from the association interface that modulate binding of iC3b with full-length CR2. Finally, we discuss the packing of the two SCR domains. Overall, our data provide global and site-specific explanations of the physical causes that underlie the ionic strength dependence of C3d-CR2 association in a unified model that accounts for all experimental data, some of which were previously thought to be contradictory.

The pH dependence of stability of the activation helix and the catalytic site of GART

We have predicted the free energy of unfolding for the pH-dependent helix-coil transition of the activation helix of GART using continuum electrostatic calculations and structural modeling. We have assigned the contributions of each element of secondary structure and of each ionizable residue, within and in the vicinity of the activation helix, to the stability of several fragments of GART that participate in the formation of the catalytic site. We demonstrate that the interaction of His121-His132 contributes 2.2 kcal/mol to the ionization free energy between pH 0 and approximately 6. We also show that the ionization state of a network of five histidines, His108, His119, His121, His132 and His137, and two aspartic acids Asp141 and Asp144, contributes approximately 12 kcal/mol to the stability of the catalytic site of GART, out of a total stability of 16 kcal/mol of the whole enzyme. These interactions are important for the formation of the catalytic site of GART.

On the evaluation and optimization of protein X-ray structures for pKa calculations

The calculation of the physical properties of a protein from its X-ray structure is of importance in virtually every aspect of modern biology. Although computational algorithms have been developed for calculating everything from the dynamics of a protein to its binding specificity, only limited information is available on the ability of these methods to give accurate results when used with a particular X-ray structure. We examine the ability of a pKa calculation algorithm to predict the proton-donating residue in the catalytic mechanism of hen egg white lysozyme. We examine the correlation between the ability of the pKa calculation method to obtain the correct result and the overall characteristics of 41 X-ray structures such as crystallization conditions, resolution, and the output of structure validation software. We furthermore examine the ability of energy minimizations (EM), molecular dynamics (MD) simulations, and structure-perturbation methods to optimize the X-ray structures such that these give correct results with the pKa calculation algorithm. We propose a set of criteria for identifying the proton donor in a catalytic mechanism, and demonstrate that the application of these criteria give highly accurate prediction results when using unmodified X-ray structures. More specifically, we are able to successfully identify the proton donor in 85% of the X-ray structures when excluding structures with crystal contacts near the active site. Neither the use of the overall characteristics of the X-ray structures nor the optimization of the structure by EM, MD, or other methods improves the results of the pKa calculation algorithm. We discuss these results and their implications for the design of structure-based energy calculation algorithms in general.

Native-state conformational dynamics of GART: a regulatory pH-dependent coil-helix transition examined by electrostatic calculations

Glycinamide ribonucleotide transformylase (GART) undergoes a pH-dependent coil-helix transition with pK(a) approximately 7. An alpha-helix is formed at high pH spanning 8 residues of a 21-residue-long loop, comprising the segment Thr120-His121-Arg122-Gln123-Ala124-Leu125-Glu126-Asn127. To understand the electrostatic nature of this loop-helix, called the activation loop-helix, which leads to the formation and stability of the alpha-helix, pK(a) values of all ionizable residues of GART have been calculated, using Poisson-Boltzmann electrostatic calculations and crystallographic data. Crystallographic structures of high and low pH E70A GART have been used in our analysis. Low pK(a) values of 5.3, 5.3, 3.9, 1.7, and 4.7 have been calculated for five functionally important histidines, His108, His119, His121, His132, and His137, respectively, using the high pH E70A GART structure. Ten theoretical single and double mutants of the high pH E70A structure have been constructed to identify pairwise interactions of ionizable residues, which have aided in elucidating the multiplicity of electrostatic interactions of the activation loop-helix, and the impact of the activation helix on the catalytic site. Based on our pK(a) calculations and structural data, we propose that: (1) His121 forms a molecular switch for the coil-helix transition of the activation helix, depending on its protonation state; (2) a strong electrostatic interaction between His132 and His121 is observed, which can be of stabilizing or destabilizing nature for the activation helix, depending on the relative orientation and protonation states of the rings of His121 and His132; (3) electrostatic interactions involving His119 and Arg122 play a role in the stability of the activation helix; and (4) the activation helix contains the helix-promoting sequence Arg122-Gln123-Ala124-Leu125-Glu126, but its alignment relative to the N and C termini of the helix is not optimal, and is possibly of a destabilizing nature. Finally, we provide electrostatic evidence that the formation and closure of the activation helix create a hydrophobic environment for catalytic-site residue His108, to facilitate catalysis.