Kevin J. McConnell

Nucleic acids: theory and computer simulation, Y2K.

Molecular dynamics simulations on DNA and RNA that include solvent are now being performed under realistic environmental conditions of water activity and salt. Improvements to force-fields and treatments of long-range interactions have significantly increased the reliability of simulations. New studies of sequence effects, axis bending, solvation and conformational transitions have appeared.

Free-Energy Component Analysis of 40 Protein-DNA Complexes: A Consensus View on the Thermodynamics of Binding at the Molecular Level

Noncovalent association of proteins to specific target sites on DNA—a process central to gene expression and regulation—has thus far proven to be idiosyncratic and elusive to generalizations on the nature of the driving forces. The spate of structural information on protein—DNA complexes sets the stage for theoretical investigations on the molecular thermodynamics of binding aimed at identifying forces responsible for specific macromolecular recognition. Computation of absolute binding free energies for systems of this complexity transiting from structural information is a stupendous task. Adopting some recent progresses in treating atomic level interactions in proteins and nucleic acids including solvent and salt effects, we have put together an energy component methodology cast in a phenomenological mode and amenable to systematic improvements and developed a computational first atlas of the free energy contributors to binding in ∼40 protein–DNA complexes representing a variety of structural motifs and functions. Illustrating vividly the compensatory nature of the free energy components contributing to the energetics of recognition for attaining optimal binding, our results highlight unambiguously the roles played by packing, electrostatics including hydrogen bonds, ion and water release (cavitation) in protein–DNA binding. Cavitation and van der Waals contributions without exception favor complexation. The electrostatics is marginally unfavorable in a consensus view. Basic residues on the protein contribute favorably to binding despite the desolvation expense. The electrostatics arising from the acidic and neutral residues proves unfavorable to binding. An enveloping mode of binding to short stretches of DNA makes for a strong unfavorable net electrostatics but a highly favorable van der Waals and cavitation contribution. Thus, noncovalent protein–DNA association is a system‐specific fine balancing act of these diverse competing forces. With the advances in computational methods as applied to macromolecular recognition, the challenge now seems to be to correlate the differential (initial vs. final) energetics to substituent effects in drug design and to move from affinity to specificity.

Molecular Dynamics Simulations of DNA and a Protein-DNA Complex Including Solvent

The results of a recent nanosecond (ns) molecular dynamics (MD) simulation of the d(CGCGAATTCGCG) double helix in water and a 100 ps MD study of the λ repressor-operator complex are described. The DNA simulations are analyzed in terms of the structural dynamics, fluctuations in the groove width and bending of the helical axis. The results indicate that the ns dynamical trajectory progresses through a series of three substates of B form DNA, with lifetimes of the order of hundreds of picoseconds (ps). An incipient dynamical equilibrium is evident. A comparison of the calculated axis bending with that observed in corresponding crystal structure data is presented. Simulation of the DNA in complex with the protein and that of the free DNA in solution, starting from the crystal conformation, reveal the dynamical changes that occur on complex formation.

Calculation of the Affinity of the λ Repressor-Operator Complex Based on Free Energy Component Analysis

A calculation of the binding free energy of the u repressor-operator complex is described based on free energy component analysis. The calculations are based on a thermodynamic cycle of seven steps decomposed into a total of 24 individual components. The values of these terms are estimated using a combination of empirical potential functions from AMBER, generalized Born - solvent accessibility calculations, elementary statistical mechanics and semiempirical physicochemical properties. Two alternative approaches are compared, one based on the crystal structure of the complex and the other based on the molecular dynamics simulation of the u repressor-operator complex. The calculated affinity is m 19.7 kcal/mol from the crystal structure calculation and m 17.9 kcal/mol from the MD method. The corresponding experimental affinity of the complex is about m 12.6 kcal/mol, indicating reasonable agreement between theory and experiment, considering the approximations involved in the computational methodology. The results are analyzed in terms of contributions from electrostatics, van der Waal interactions, the hydrophobic effect and solvent release. The capabilities and limitations of free energy component methodology are assessed and discussed on the basis of these results.