Protein: nucleic acid interactions. I. Electronic structures of cytosine, indole, and guanine complexes

Optical activity of a nucleotide-sensitive tryptophan in myosin subfragment 1 during ATP hydrolysis

The xanthene probes 5'-iodoacetamido-fluorescein and -tetramethylrhodamine specifically modify skeletal muscle myosin subfragment 1 (S1) at the reactive thiol residue (SH1) and fully quench the fluorescence emission from tryptophan residue 510 (Trp510) in S1 (T.P. Burghardt and K. Ajtai, Biophys. Chem., 60 (1996) 119; K. Ajtai and T.P. Burghardt, Biochemistry, 34 (1995) 15943). The difference between the fluorescence intensity obtained from S1 and probe-modified S1 comes solely from Trp510 in chymotryptic S1, a protein fragment that contains five tryptophan residues. The rotary strength and quantum efficiency of Trp510 were measured using difference signals from fluorescence detected circular dichroism (FDCD) and fluorescence emission spectroscopy. These structure-sensitive signals indicate that the binding of nucleotide or nucleotide analogs to the active site of S1 causes structural changes in S1 at Trp510 and that a one-to-one correspondence exists between Trp510 conformation and transient states of myosin during contraction. The Trp510 rotary strength and quantum efficiency were interpreted structurally in terms of the indole side-chain conformation using model structures and established computational methods.

The conformation of xanthene dyes in the myosin sulfhydryl one binding site. Part I. Methods and model systems

Derivatives of the fluorescent probes fluorescein and rhodamine specifically and covalently modify the highly reactive thiol (SH1) of myosin subfragment 1 (S1). Both probes develop circular dichroism (CD) upon modification of SH1 at the visible absorption band of the chromophore. A model system of chiral complexing agents (aromatic chiral amines) interacting with fluorescein in solvent develops a CD signal that mimics that produced by S1. The model system suggests that a specific interaction of the probe with an aromatic chiral residue in the SH1 binding pocket induces the CD signal. Several other spectroscopic signals, including absorption and fluorescence intensity and anisotropy, characterize the fluorescein or rhodamine binding to SH1. A coupled dipole method is adapted to interpret these spectroscopic signals in terms of the probe-S1 complex conformation. The computation of the orientation of the principal hydrodynamic frame (PHF) of S1 from its crystallographic alpha-carbon backbone structure permits the known orientation of the probe in the PHF of S1 to further constrain the conformation of the probe-S1 complex. The coupled dipole interpretation of spectroscopic data combined with constraints relating the probe dipole orientation to the PHF of S1 determines the conformation of the probe-S1 complex. The methods developed here are applied to the spectroscopic signals from fluorescein or rhodamine in the SH1 binding site of S1 to obtain an atomic resolution model of the probe-S1 conformation [Ajtai and Burghardt, Biochemistry, 34 (1995) 15943-15952].