The effect of hydration on the dynamics of trimethoprim bound to dihydrofolate reductase. A deuterium NMR study

Hydration effects on the protein dynamics in stratum corneum as evaluated by EPR spectroscopy

The uppermost layer of the epidermis, the stratum corneum (SC), was spin-labeled with a sulfhydryl-specific nitroxide reagent to investigate the water content effects upon the protein dynamics directly in the intact tissue. A two-state model for the nitroxide side chain described the coexistence of two spectral components in the electron paramagnetic resonance (EPR) spectra. The so-called strongly immobilized component, S, is associated with the EPR signal of a motionally restricted nitroxide fraction having its N-O group hydrogen bonded to protein (rigid structure) while the weakly immobilized component, W, corresponds to the signal provided by the spin labels with higher mobility (approximately 10 times greater) exposed to the aqueous environment. The relative populations between these two mobility states, S and W, are in thermodynamic equilibrium. The standard Gibbs free energy, enthalpy and entropy changes for transferring the nitroxide side chain from the state contacting the solvent, W, to the one contacting protein, S, indicated that the reduction of the SC water content to below approximately h 0.69 g H(2)O/g dry SC, stabilizes the protein interacting state, S. Upon decreasing the SC hydration level below approximately h 0.69 the segmental motion of the polypeptide chains and the rotational motion of the spin-labeled side chain were also constrained. This work can also be useful to improve the spectral analysis of site-directed spin labeling, especially for a more quantitative description in terms of thermodynamic parameters.

Dynamics of trimethoprim bound to dihydrofolate reductase--a deuterium NMR study

We have employed deuterium NMR techniques to determine the dynamics of trimethoprim (TMP) in a binary complex with dihydrofolate reductase (DHFR) or in a ternary complex with DHFR and cofactor NADP+ in the fully hydrated state. TMP was deuterated at the following positions: (2',6'-D2)TMP, (3'-Ome-D3)TMP and (3',4'-Ome-D6)TMP. Dynamics of TMP were deduced from lineshape simulation and relaxation measurements of the deuterium NMR powder spectra of the three samples obtained at various temperatures. The results showed that in the polycrystalline state the TMP molecule is very rigid. The only detectable motion is the methyl group rotation at a rate of 10(10) s-1 at 25 degrees C, as determined from simulation of the partially relaxed powder patterns. When bound to DHFR a residual deuterium quadrupole splitting of 140 kHz was observed for (2',6'-D2)TMP at temperatures up to 30 degrees C, suggesting that the benzyl ring in the bound state is also very rigid. In contrast, in the binary complex with DHFR the methoxyl groups of TMP undergo librational motion of 10(7) s-1 about the C3-O bond at an amplitude of 54 degrees for the meta methoxyl group and about the C4-O bond at an amplitude of 70 degrees and similar rate for the para methoxyl group at 30 degrees C. The presence of the cofactor, NADP+, appears to tighten up the binding pocket such that the motion freedom of TMP is more restricted. The rigidity of TMP in a protein complex as revealed by our deuterium NMR results is in accord with the tight binding of TMP to DHFR.

Effect of probe force on the resolution of atomic force microscopy of DNA

Experimental results are presented to show that the adhesion force is the single most important limiting factor in high-resolution atomic force microscopy of DNA in air, prepared by the cytochrome-C-assisted spreading method. It is also shown that humidity plays a minor role in the control of probe force. Using a pure carbon film as the substrate to clean the AFM tip prior to imaging, it is demonstrated that 4-6 nm resolution on DNA can be routinely obtained by the atomic force microscope with commercial Si3N4 pyramid cantilevers. We also show that in organic solvents a resolution of up to 3 nm can be obtained under optimal conditions.