+ Site Statistics
+ Search Articles
+ PDF Full Text Service
How our service works
Request PDF Full Text
+ Follow Us
Follow on Facebook
Follow on Twitter
Follow on LinkedIn
+ Subscribe to Site Feeds
Most Shared
PDF Full Text
+ Translate
+ Recently Requested

Binding free energies and free energy components from molecular dynamics and Poisson-Boltzmann calculations. Application to amino acid recognition by aspartyl-tRNA synthetase

Binding free energies and free energy components from molecular dynamics and Poisson-Boltzmann calculations. Application to amino acid recognition by aspartyl-tRNA synthetase

Journal of Molecular Biology 306(2): 307-327

Specific amino acid binding by aminoacyl-tRNA synthetases (aaRS) is necessary for correct translation of the genetic code. Engineering a modified specificity into aminoacyl-tRNA synthetases has been proposed as a means to incorporate artificial amino acid residues into proteins in vivo. In a previous paper, the binding to aspartyl-tRNA synthetase of the substrate Asp and the analogue Asn were compared by molecular dynamics free energy simulations. Molecular dynamics combined with Poisson-Boltzmann free energy calculations represent a less expensive approach, suitable for examining multiple active site mutations in an engineering effort. Here, Poisson-Boltzmann free energy calculations for aspartyl-tRNA synthetase are first validated by their ability to reproduce selected molecular dynamics binding free energy differences, then used to examine the possibility of Asn binding to native and mutant aspartyl-tRNA synthetase. A component analysis of the Poisson-Boltzmann free energies is employed to identify specific interactions that determine the binding affinities. The combined use of molecular dynamics free energy simulations to study one binding process thoroughly, followed by molecular dynamics and Poisson-Boltzmann free energy calculations to study a series of related ligands or mutations is proposed as a paradigm for protein or ligand design. The binding of Asn in an alternate, "head-to-tail" orientation observed in the homologous asparagine synthetase is analyzed, and found to be more stable than the "Asp-like" orientation studied earlier. The new orientation is probably unsuitable for catalysis. A conserved active site lysine (Lys198 in Escherichia coli) that recognizes the Asp side-chain is changed to a leucine residue, found at the corresponding position in asparaginyl-tRNA synthetase. It is interesting that the binding of Asp is calculated to increase slightly (rather than to decrease), while that of Asn is calculated, as expected, to increase strongly, to the same level as Asp binding. Insight into the origin of these changes is provided by the component analyses. The double mutation (K198L,D233E) has a similar effect, while the triple mutation (K198L,Q199E,D233E) reduces Asp binding strongly. No binding measurements are available, but the three mutants are known to have no ability to adenylate Asn, despite the "Asp-like" binding affinities calculated here. In molecular dynamics simulations of all three mutants, the Asn ligand backbone shifts by 1-2 A compared to the experimental Asp:AspRS complex, and significant side-chain rearrangements occur around the pocket. These could reduce the ATP binding constant and/or the adenylation reaction rate, explaining the lack of catalytic activity in these complexes. Finally, Asn binding to AspRS with neutral K198 or charged H449 is considered, and shown to be less favorable than with the charged K198 and neutral H449 used in the analysis.

Please choose payment method:

(PDF emailed within 0-6 h: $19.90)

Accession: 009778253

Download citation: RISBibTeXText

PMID: 11237602

DOI: 10.1006/jmbi.2000.4285

Related references

Specific amino acid recognition by aspartyl-tRNA synthetase studied by free energy simulations. Journal of Molecular Biology 275(5): 823-846, 1998

Peptide recognition by the T cell receptor: comparison of binding free energies from thermodynamic integration, Poisson-Boltzmann and linear interaction energy approximations. Philosophical Transactions. Series A Mathematical Physical and Engineering Sciences 363(1833): 2037-2053, 2005

Exploring the inter-molecular interactions in amyloid-β protofibril with molecular dynamics simulations and molecular mechanics Poisson-Boltzmann surface area free energy calculations. Journal of Chemical Physics 136(14): 145101, 2012

Statistical Analysis on the Performance of Molecular Mechanics Poisson-Boltzmann Surface Area versus Absolute Binding Free Energy Calculations: Bromodomains as a Case Study. Journal of Chemical Information and Modeling 57(9): 2203-2221, 2017

Functional asymmetry in the lysyl-tRNA synthetase explored by molecular dynamics, free energy calculations and experiment. Bmc Structural Biology 3: 5, 2003

Poisson-Boltzmann calculations of nonspecific salt effects on protein-protein binding free energies. Biophysical Journal 92(6): 1891-1899, 2007

Free Energy Calculations by the Molecular Mechanics Poisson-Boltzmann Surface Area Method. Molecular Informatics 31(2): 114-122, 2012

Molecular dynamics simulations show that bound Mg2+ contributes to amino acid and aminoacyl adenylate binding specificity in aspartyl-tRNA synthetase through long range electrostatic interactions. Journal of Biological Chemistry 281(33): 23792-23803, 2006

Molecular Dynamics Simulations Show That Bound Mg superscript 2+(B Contributes to Amino Acid and Aminoacyl Adenylate Binding Specificity in Aspartyl-tRNA Synthetase through Long Range Electrostatic Interactions. Journal of biological chemistry18 281(33): 23792-23803, 2006

Changes of binding free energies by substitutions of amino acids around the guanine recognition site of rnase t1 molecular dynamics simulations. Protein Engineering 3(4): 315, 1990

Problems of robustness in Poisson-Boltzmann binding free energies. Journal of Chemical Theory and Computation 11(2): 705-712, 2015

Structure and thermodynamics of RNA-protein binding: using molecular dynamics and free energy analyses to calculate the free energies of binding and conformational change. Journal of Molecular Biology 297(5): 1145-1158, 2000

Solvation free energies of amino acids calculated by molecular dynamics/free energy perturbation method. Chemical & Pharmaceutical Bulletin 43(5): 717-721, 1995

Free Energy Perturbation Hamiltonian Replica-Exchange Molecular Dynamics (FEP/H-REMD) for Absolute Ligand Binding Free Energy Calculations. Journal of Chemical Theory and Computation 6(9): 2559-2565, 2010

Relative binding free energy calculations of inhibitors to two mutants (Glu46----Ala/Gln) of ribonuclease T1 using molecular dynamics/free energy perturbation approaches. Protein Engineering 4(3): 233-243, 1991