A new force field for molecular mechanical simulation of nucleic acids and proteins

• Published in: Journal of the American Chemical Society 1984-02, Vol.106 (3), p.765-784
• Main Authors: Weiner, Scott J, Kollman, Peter A, Case, David A, Singh, U. Chandra, Ghio, Caterina, Alagona, Guliano, Profeta, Salvatore, Weiner, Paul
• Format: Article
• Language: English
• Subjects: Biological and medical sciences; energetics; Fundamental and applied biological sciences. Psychology; Molecular biophysics; oligonucleotides; proteins; Structure in molecular biology; Tridimensional structure
• ISSN: 0002-7863; 1520-5126
• DOI: 10.1021/ja00315a051

The authors present the development of a force field for simulation of nucleic acids and proteins. They obtained equilibrium bond lengths and angles, torsional constants, nonbonded parameters, and atomic charges. The parameters were then refined with molecular mechanical studies on the structures and energies of model compounds. For nucleic acids, bond, angle, torsional, nonbonded, and hydrogen-bond parameters were varied to optimize the agreement between calculated and experimental values for sugar pucker energies and structures, vibrational frequencies of dimethyl phosphate and tetrahydrofuran, and energies for base pairing and base stacking. For proteins, they focused on Phi , psi maps of glycyl and alanyl dipeptides, hydrogen-bonding interactions involving the various protein polar groups, and energy refinement calculations on insulin. Unlike the models for hydrogen bonding involving nitrogen and oxygen electron donors, an adequate description of sulfur hydrogen bonding required explicit inclusion of lone pairs.