Long-range electrostatic interactions in proteins/peptides associating to nucleic acids are reflected in the salt-dependence of the binding process.According to the oligocationic binding model,which is based on counte...Long-range electrostatic interactions in proteins/peptides associating to nucleic acids are reflected in the salt-dependence of the binding process.According to the oligocationic binding model,which is based on counterion condensation theory,only the cationic residues of peptides/proteins near the binding interface are assumed to affect the salt dependence in the association of peptides and proteins to nucleic acids.This model has been used to interpret and predict the binding of oligocationic chains-such as oligoarginines/lysines-to nucleic acids,and does an excellent job in these kinds of systems.This simple relationship,which is used to compare or count the number of ionic interactions in protein-nucleic acid complexes,does not hold when acidic residues,i.e.glutamate and aspartate,are incorporated in the protein matrix.Here,we report a combined molecular mechanics(by means of energy-minimization of the structure under the influence of an empirical energy function)and Poisson-Boltzmann(PB)study on the salt-dependence in binding to tRNA of two important enzymes that are involved in the seminal step of peptide formation in the ribosome:Glutamine synthetase(GluRS)and Glutaminyl synthetase(GlnRS)bound to their cognate tRNA.These two proteins are anionic and contain a significant number of acidic residues distributed over the entire protein.Some of these residues are located in the binding interface to tRNA.We computed the salt-dependence in association,SKpred,of these enzyme-tRNA complexes using both the linear and nonlinear solution to the PoissonBoltzmann Equation(PBE).Our findings demonstrate that the SKpred obtained with the nonlinear PBE is in good agreement with the experimental SKobs,while use of the linear PBE resulted in the SKpred being anomalous.We conclude that electrostatic interactions between the binding partners in these systems are less favorable by means of charge-charge repulsion between negatively charged protein residues and phosphateoxygens in the tRNA backbone but also play a significant role in the association process of proteins to tRNA.Some unfavorable electrostatic interactions are probably compensated by hydrogen-bonds between the carboxylate group of the side chain in the interfacial acidic protein residues and the tRNA backbone.We propose that the low experimentally observed SKobs values for both GlnRS-and GluRS-tRNA depend on the distribution and number of anionic residues that exist in these tRNA synthetases.Our computed electrostatic binding free energies were large and unfavorable due to the Coulombic and de-solvation contribution for the GlnRS-tRNA and GluRS-tRNA complexes,respectively.Thus,low SKobs values may not reflect small contributions from the electrostatic contribution in complex-formation,as is often suggested in the literature.When charges are”turned off”in a computer-experiment,our results indicated that”turning off”acidic residues far from a phosphate group significantly influences SKpred.If cationic residues are“turned off”,less impact on SKpred is observed with respect to the distance to the nearest phosphate-group。展开更多
The nonlinear Poisson-Boltzmann predictions of the salt-dependent association of proteins to DNA,SKpred,are fairly insensitive to the choice of atomic charges,radii,interior dielectric constant and treatment of the bo...The nonlinear Poisson-Boltzmann predictions of the salt-dependent association of proteins to DNA,SKpred,are fairly insensitive to the choice of atomic charges,radii,interior dielectric constant and treatment of the boundary between a biomolecule and the solvent.In this study we show that the SKpred is highly correlated with the conformational adaptability of the partners involved in the biomolecular binding process.This is demonstrated for the wild-type and mutant forms of the archaeon Pyrococcus woesi TATA-binding protein(PwTBP)in complex with DNA,on which we performed molecular mechanics energy minimizations with different protocols,and molecular dynamics simulations and then computed the SKpred on the resulting structures.It was found that the inter-molecular non bonded force field energy between the DNA and protein correlates linearly and significantly well with the SKpred.This correlation encompasses the wild-type and mutant variants of the PwTBP and provides us with a quick way to estimate the SKpred from a large ensemble of structures generated with Molecular Dynamics or Monte Carlo simulations.The corresponding experimental SKobs should also correlate with the inter-molecular non bonded force field energy between the protein and DNA,given that the underlying mechanisms in binding and salt-dependent effects are in fact the main contributors in the association of proteins/peptides to nucleic acids.We show that it is possible to fit experiments versus the inter-molecular non bonded force field energy between the protein and DNA,and use this relation to predict the SKobs in absolute numbers.Thus,we present two novel approaches to estimate both the SKpred and the SKobs for in silico modelled PwTBP novel mutants and even for TBPs from other organisms.This is a simple but powerful tool to suggest new experiments on the TBP-DNA type of macromolecular assemblies.We conclude by suggesting some mutants and a possible biological interpretation of how changes in solvent salinity affect the binding of proteins to DNA.展开更多
基金NSF-CHEM-0137961(to MOF)and in part by the Institute for Mathematics and its Applications with funds provided by the National Science Foundation.
文摘Long-range electrostatic interactions in proteins/peptides associating to nucleic acids are reflected in the salt-dependence of the binding process.According to the oligocationic binding model,which is based on counterion condensation theory,only the cationic residues of peptides/proteins near the binding interface are assumed to affect the salt dependence in the association of peptides and proteins to nucleic acids.This model has been used to interpret and predict the binding of oligocationic chains-such as oligoarginines/lysines-to nucleic acids,and does an excellent job in these kinds of systems.This simple relationship,which is used to compare or count the number of ionic interactions in protein-nucleic acid complexes,does not hold when acidic residues,i.e.glutamate and aspartate,are incorporated in the protein matrix.Here,we report a combined molecular mechanics(by means of energy-minimization of the structure under the influence of an empirical energy function)and Poisson-Boltzmann(PB)study on the salt-dependence in binding to tRNA of two important enzymes that are involved in the seminal step of peptide formation in the ribosome:Glutamine synthetase(GluRS)and Glutaminyl synthetase(GlnRS)bound to their cognate tRNA.These two proteins are anionic and contain a significant number of acidic residues distributed over the entire protein.Some of these residues are located in the binding interface to tRNA.We computed the salt-dependence in association,SKpred,of these enzyme-tRNA complexes using both the linear and nonlinear solution to the PoissonBoltzmann Equation(PBE).Our findings demonstrate that the SKpred obtained with the nonlinear PBE is in good agreement with the experimental SKobs,while use of the linear PBE resulted in the SKpred being anomalous.We conclude that electrostatic interactions between the binding partners in these systems are less favorable by means of charge-charge repulsion between negatively charged protein residues and phosphateoxygens in the tRNA backbone but also play a significant role in the association process of proteins to tRNA.Some unfavorable electrostatic interactions are probably compensated by hydrogen-bonds between the carboxylate group of the side chain in the interfacial acidic protein residues and the tRNA backbone.We propose that the low experimentally observed SKobs values for both GlnRS-and GluRS-tRNA depend on the distribution and number of anionic residues that exist in these tRNA synthetases.Our computed electrostatic binding free energies were large and unfavorable due to the Coulombic and de-solvation contribution for the GlnRS-tRNA and GluRS-tRNA complexes,respectively.Thus,low SKobs values may not reflect small contributions from the electrostatic contribution in complex-formation,as is often suggested in the literature.When charges are”turned off”in a computer-experiment,our results indicated that”turning off”acidic residues far from a phosphate group significantly influences SKpred.If cationic residues are“turned off”,less impact on SKpred is observed with respect to the distance to the nearest phosphate-group。
文摘The nonlinear Poisson-Boltzmann predictions of the salt-dependent association of proteins to DNA,SKpred,are fairly insensitive to the choice of atomic charges,radii,interior dielectric constant and treatment of the boundary between a biomolecule and the solvent.In this study we show that the SKpred is highly correlated with the conformational adaptability of the partners involved in the biomolecular binding process.This is demonstrated for the wild-type and mutant forms of the archaeon Pyrococcus woesi TATA-binding protein(PwTBP)in complex with DNA,on which we performed molecular mechanics energy minimizations with different protocols,and molecular dynamics simulations and then computed the SKpred on the resulting structures.It was found that the inter-molecular non bonded force field energy between the DNA and protein correlates linearly and significantly well with the SKpred.This correlation encompasses the wild-type and mutant variants of the PwTBP and provides us with a quick way to estimate the SKpred from a large ensemble of structures generated with Molecular Dynamics or Monte Carlo simulations.The corresponding experimental SKobs should also correlate with the inter-molecular non bonded force field energy between the protein and DNA,given that the underlying mechanisms in binding and salt-dependent effects are in fact the main contributors in the association of proteins/peptides to nucleic acids.We show that it is possible to fit experiments versus the inter-molecular non bonded force field energy between the protein and DNA,and use this relation to predict the SKobs in absolute numbers.Thus,we present two novel approaches to estimate both the SKpred and the SKobs for in silico modelled PwTBP novel mutants and even for TBPs from other organisms.This is a simple but powerful tool to suggest new experiments on the TBP-DNA type of macromolecular assemblies.We conclude by suggesting some mutants and a possible biological interpretation of how changes in solvent salinity affect the binding of proteins to DNA.
