QM/MM MD and free energy simulations of the methylation reactions catalyzed by protein arginine methyltransferase PRMT3

2013 ◽  
Vol 91 (7) ◽  
pp. 605-612 ◽  
Author(s):  
Yuzhuo Chu ◽  
Guohui Li ◽  
Hong Guo
Keyword(s):  
Free Energy ◽  
Mammalian Cells ◽  
Experimental Investigations ◽  
Type I ◽  
Active Site Residues ◽  
Product Specificity ◽  
Proton Transfers ◽  
Eukaryotic Proteins ◽  
Energy Simulations ◽  
Concerted Processes

Protein arginine N-methyltransferases (PRMTs) catalyze the transfer of methyl group(s) from S-adenosyl-l-methionine (AdoMet) to the guanidine group of arginine residue in abundant eukaryotic proteins. Two major types of PRMTs have been identified in mammalian cells. Type I PRMTs catalyze the formation of asymmetric ω-NG, NG-dimethylarginine (ADMA), while Type II PRMTs catalyze the formation of symmetric ω-NG, N′G-dimethylarginine (SDMA). The two different methylation products (ADMA or SDMA) of the substrate could lead to different biological consequences. Although PRMTs have been the subject of extensive experimental investigations, the origin of the product specificity remains unclear. In this study, quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) and free energy simulations are performed to study the reaction mechanism for one of Type I PRMTs, PRMT3, and to gain insights into the energetic origin of its product specificity (ADMA). Our simulations have identified some important interactions and proton transfers involving the active site residues. These interactions and proton transfers seem to be responsible, at least in part, in making the Nη2 atom of the substrate arginine the target of the both 1st and 2nd methylations, leading to the asymmetric dimethylation product. The simulations also suggest that the methyl transfer and proton transfer appear to be somehow concerted processes and that Glu326 is likely to function as the general base during the catalysis.

scholarly journals A glutamate/aspartate switch controls product specificity in a protein arginine methyltransferase

2016 ◽  
Vol 113 (8) ◽  
pp. 2068-2073 ◽  
Author(s):  
Erik W. Debler ◽  
Kanishk Jain ◽  
Rebeccah A. Warmack ◽  
You Feng ◽  
Steven G. Clarke ◽  
...  
Keyword(s):  
Active Site ◽  
Catalytic Mechanism ◽  
Structural Basis ◽  
Titration Calorimetry ◽  
Type I ◽  
Histone H4 ◽  
Active Site Residues ◽  
Protein Arginine Methyltransferase ◽  
Arginine Methyltransferase ◽  
Product Specificity

Trypanosoma brucei PRMT7 (TbPRMT7) is a protein arginine methyltransferase (PRMT) that strictly monomethylates various substrates, thus classifying it as a type III PRMT. However, the molecular basis of its unique product specificity has remained elusive. Here, we present the structure of TbPRMT7 in complex with its cofactor product S-adenosyl-l-homocysteine (AdoHcy) at 2.8 Å resolution and identify a glutamate residue critical for its monomethylation behavior. TbPRMT7 comprises the conserved methyltransferase and β-barrel domains, an N-terminal extension, and a dimerization arm. The active site at the interface of the N-terminal extension, methyltransferase, and β-barrel domains is stabilized by the dimerization arm of the neighboring protomer, providing a structural basis for dimerization as a prerequisite for catalytic activity. Mutagenesis of active-site residues highlights the importance of Glu181, the second of the two invariant glutamate residues of the double E loop that coordinate the target arginine in substrate peptides/proteins and that increase its nucleophilicity. Strikingly, mutation of Glu181 to aspartate converts TbPRMT7 into a type I PRMT, producing asymmetric dimethylarginine (ADMA). Isothermal titration calorimetry (ITC) using a histone H4 peptide showed that the Glu181Asp mutant has markedly increased affinity for monomethylated peptide with respect to the WT, suggesting that the enlarged active site can favorably accommodate monomethylated peptide and provide sufficient space for ADMA formation. In conclusion, these findings yield valuable insights into the product specificity and the catalytic mechanism of protein arginine methyltransferases and have important implications for the rational (re)design of PRMTs.

scholarly journals Large-scale QM/MM free energy simulations of enzyme catalysis reveal the influence of charge transfer

2018 ◽  
Author(s):  
Heather Kulik
Keyword(s):  
Free Energy ◽  
Electronic Structure ◽  
Charge Transfer ◽  
Ab Initio ◽  
Density Functional ◽  
Large Scale ◽  
Active Site Residues ◽  
Functional Theory ◽  
Energy Simulations ◽  
Electrostatic Embedding

Hybrid quantum mechanical-molecular mechanical (QM/MM) simulations provide key insights into enzyme structure–function relationships. Numerous studies have demonstrated that large QM regions are needed to systematically converge ground state, zero temperature properties with electrostatic embedding QM/MM. However, it is not well known if <i>ab initio </i>QM/MM free energy simulations have this same dependence, in part due to the hundreds of thousands of energy evaluations required for free energy estimations that in turn limit QM region size. Here, we leverage recent advances in electronic structure efficiency and accuracy to carry out range-separated hybrid density functional theory free energy simulations in a representative methyltransferase. By studying 200 ps of <i>ab initio </i>QM/MM dynamics for each of five QM regions from minimal (64 atoms) to one-sixth of the protein (544 atoms), we identify critical differences between large and small QM region QM/MM in charge transfer between substrates and active site residues as well as in geometric structure and dynamics that coincide with differences in predicted free energy barriers. Distinct geometric and electronic structure features in the largest QM region indicate that important aspects of enzymatic rate enhancement in methyltransferases are identified with large-scale electronic structure.<br>

scholarly journals Large-scale QM/MM free energy simulations of enzyme catalysis reveal the influence of charge transfer

2018 ◽  
Author(s):  
Heather Kulik
Keyword(s):  
Free Energy ◽  
Electronic Structure ◽  
Charge Transfer ◽  
Ab Initio ◽  
Density Functional ◽  
Large Scale ◽  
Active Site Residues ◽  
Functional Theory ◽  
Energy Simulations ◽  
Electrostatic Embedding

Hybrid quantum mechanical-molecular mechanical (QM/MM) simulations provide key insights into enzyme structure–function relationships. Numerous studies have demonstrated that large QM regions are needed to systematically converge ground state, zero temperature properties with electrostatic embedding QM/MM. However, it is not well known if <i>ab initio </i>QM/MM free energy simulations have this same dependence, in part due to the hundreds of thousands of energy evaluations required for free energy estimations that in turn limit QM region size. Here, we leverage recent advances in electronic structure efficiency and accuracy to carry out range-separated hybrid density functional theory free energy simulations in a representative methyltransferase. By studying 200 ps of <i>ab initio </i>QM/MM dynamics for each of five QM regions from minimal (64 atoms) to one-sixth of the protein (544 atoms), we identify critical differences between large and small QM region QM/MM in charge transfer between substrates and active site residues as well as in geometric structure and dynamics that coincide with differences in predicted free energy barriers. Distinct geometric and electronic structure features in the largest QM region indicate that important aspects of enzymatic rate enhancement in methyltransferases are identified with large-scale electronic structure.<br>

Charge Transfer Effects in Enzyme Catalysis Observed with Large-Scale QM/MM Free Energy Simulations

2018 ◽  
Author(s):  
Heather Kulik
Keyword(s):  
Free Energy ◽  
Electronic Structure ◽  
Charge Transfer ◽  
Ab Initio ◽  
Density Functional ◽  
Large Scale ◽  
Active Site Residues ◽  
Functional Theory ◽  
Energy Simulations ◽  
Electrostatic Embedding

Hybrid quantum mechanical-molecular mechanical (QM/MM) simulations provide key insights into enzyme structure–function relationships. Numerous studies have demonstrated that large QM regions are needed to systematically converge ground state, zero temperature properties with electrostatic embedding QM/MM. However, it is not well known if ab initio QM/MM free energy simulations have this same dependence, in part due to the hundreds of thousands of energy evaluations required for free energy estimations that in turn limit QM region size. Here, we leverage recent advances in electronic structure efficiency and accuracy to carry out range-separated hybrid density functional theory free energy simulations in a representative methyltransferase. By studying for 200 ps each of ab initio QM/MM dynamics in five QM regions from minimal (64 atoms) to one-sixth of the protein (544 atoms), we identify critical differences between large and small QM region QM/MM in charge transfer between substrates and active site residues as well as in geometric structure and dynamics that coincide with differences in predicted free energy barriers. Distinct geometric and electronic structure features in the largest QM region indicate that fundamental aspects of enzymatic rate enhancement are identified with large-scale electronic structure.

Prediction of Alkanolamine pKa Values by Combined Molecular Dynamics Free Energy Simulations and ab initio Calculations

2019 ◽  
Author(s):  
Javad Noroozi ◽  
William Smith
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Ab Initio Calculations ◽  
Gas Phase ◽  
Quantum Chemical ◽  
Phase Reaction ◽  
Pka Values ◽  
Gas Phase Reaction ◽  
Reaction Free Energy ◽  
Energy Simulations

We use molecular dynamics free energy simulations in conjunction with quantum chemical calculations of gas phase reaction free energy to predict alkanolamines pka values. <br>

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