Variance of a potential of mean force obtained using the weighted histogram analysis method

Studying noncovalent or covalent bond problem between smoothened and cholesterol by molecular dynamics simulation and Markov state model

Smoothened (SMO) is an attractive therapeutic target for the treatment and prevention of several malignant tumors of the nervous system. The crystal structure of SMO shows cholesterol interacts with residue Asp95 via the noncovalent bond. However, some studies indicate that cholesterol covalently binds to residue Asp95 of SMO. To study these contradictory results, we performed molecular dynamics (MD) simulations and Markov state model (MSM) on SMO in complex with noncovalent-bound and covalent-bound cholesterol. The MD simulated results showed that the noncovalent-bound cholesterol was extremely unstable around the position of residue Asp95 of SMO, while the covalent-bound cholesterol could keep the stable connection with residue Asp95 of SMO. The free energy landscape showed that noncovalent-bound cholesterol had more deep energy wells than covalent-bound cholesterol when it dynamically interacted with the extracellular domain of SMO crystal structure. The MSM results showed the noncovalent-bound cholesterol had more dynamic configuration transformation pathways than the covalent-bound cholesterol. These results theoretically revealed cholesterol should have a covalent bond with residue Asp95 if cholesterol could be stable in the near position of residue Asp95 of SMO. Our studies not only elucidate the covalent binding contradictory issue between cholesterol and residue Asp95 of SMO, but also supply helpful information for antagonists design of SMO.

Molecular Dynamics of Oxazole Yellow Dye in its Ground and First Excited Electronic States in Solution and when Intercalated in dsDNA

Oxazole yellow (YOPRO), a cyanine dye consisting of benzoxazole and quinoline rings connected by a linker, is almost nonfluorescent in water, but its fluorescence is greatly enhanced after intercalation in double-stranded DNA, forming the basis of DNA concentration assays. To explore this difference, new potential energy surfaces for the two linker dihedral angles in the ground S0 and first excited S1 electronic states are developed. Umbrella sampling molecular dynamics is used to obtain the free energy of rotation around the two dihedral angles of the linker. The two-dimensional free energy surface of the S1 state, spanning the Franck-Condon transition point from the S0 electronic state minimum (dihedral 1 around 180°, dihedral 2 around 0°) to the S1 state minimum (∼90, ∼0), is obtained in water and when intercalated. In water, YOPRO's S1 free energy surface is completely downhill from the Franck-Condon point, whereas when intercalated, there is a barrier on the path. Thus, when intercalated in DNA, S1 YOPRO is more constrained than in water, supporting the hypothesis that intercalation does inhibit ring rotational motion around the linker and therefore strongly reduces the nonradiative relaxation, resulting in higher fluorescence intensity.