Femtosecond studies of protein-DNA binding and dynamics: histone I

Effect of protein binding on ultrafast DNA dynamics: characterization of a DNA:APE1 complex

Synthetic oligonucleotides with a fluorescent coumarin group replacing a basepair have been used in recent time-resolved Stokes-shift experiments to measure DNA dynamics on the femtosecond to nanosecond timescales. Here, we show that the APE1 endonuclease cleaves such a modified oligonucleotide at the abasic site opposite the coumarin with only a fourfold reduction in rate. In addition, a noncatalytic mutant (D210N) binds tightly to the same oligonucleotide, albeit with an 85-fold reduction in binding constant relative to a native oligonucleotide containing a guanine opposite the abasic site. Thus, the modified oligonucleotide retains substantial biological activity and serves as a useful model of native DNA. In the complex of the coumarin-containing oligonucleotide and the noncatalytic APE1, the dye's absorption spectrum is shifted relative to its spectrum in either water or within the unbound oligonucleotide. Thus the dye occupies a site within the DNA:protein complex. This result is consistent with modeling, which shows that the complex accommodates coumarin at the site of the orphaned base with little distortion of the native structure. Stokes-shift measurements of the complex show surprisingly little change in the dynamics within the 40 ps-40 ns time range.

Self-organization of the ternary didecyldimethylammonium bromide/octyl-beta-D-glucopyranoside/water system

The spontaneous and thermodynamically stable mixed vesicles constituted by a double-chain cationic surfactant with 10 carbon atoms hydrophobic tail, didecyldimethylammonium bromide (di-C(10)DMAB), and a nonionic single-chain surfactant, octyl-beta-d-glucopyranoside (OBG), have been characterized in aqueous media by means of a series of experimental techniques, as well as a theoretical approach. Conductivity data allow for the determination of the concentrations at which the monomer-to-vesicle (CVC) and/or vesicle-to-micelle (CMC) transitions occur. Electrophoretic mobilities, obtained from laser-doppler-electrophoresis experiments, permit the determination of zeta-potentials and, from them, the surface charge density of the vesicle aggregates. Cryogenic transmission electron microscopy (cryo-TEM) provides pictures of the vesicles, their size and shape being, thus, determined. Finally, the sensitivity of the emission spectra of some fluorescent probes, such as the cationic TNS and the nonionic PRODAN, to the polarity of the environment, allow for a complete study of different pre- and post-vesicle microdomains, of variable rigidity and micropolarity. This, in turn, yield interesting information about the vesicle surface and bilayer, as well as, about the existence of clusters and/or nanoaggregates prior to the formation of vesicles, as was proposed by us in a previous paper.

Ultrafast relaxation dynamics of a biologically relevant probe dansyl at the micellar surface

We report picosecond-resolved measurement of the fluorescence of a well-known biologically relevant probe, dansyl chromophore at the surface of a cationic micelle (cetyltrimethylammonium bromide, CTAB). The dansyl chromophore has environmentally sensitive fluorescence quantum yields and emission maxima, along with large Stokes shift. In order to study the solvation dynamics of the micellar environment, we measured the fluorescence of dansyl chromophore attached to the micellar surface. The fluorescence transients were observed to decay (with time constant approximately 350 ps) in the blue end and rise with similar timescale in the red end, indicative of solvation dynamics of the environment. The solvation correlation function is measured to decay with time constant 338 ps, which is much slower than that of ordinary bulk water. Time-resolved anisotropy of the dansyl chromophore shows a bi-exponential decay with time constants 413 ps (23%) and 1.3 ns (77%), which is considerably slower than that in free solvents revealing the rigidity of the dansyl-micelle complex. Time-resolved area-normalized emission spectroscopic (TRANES) analysis of the time dependent emission spectra of the dansyl chromophore in the micellar environment shows an isoemissive point at 21066 cm-1. This indicates the fluorescence of the chromophore contains emission from two kinds of excited states namely locally excited state (prior to charge transfer) and charge transfer state. The nature of the solvation dynamics in the micellar environments is therefore explored from the time-resolved anisotropy measurement coupled with the TRANES analysis of the fluorescence transients. The time scale of the solvation is important for the mechanism of molecular recognition.

Ultrafast surface solvation dynamics and functionality of an enzyme α-chymotrypsin upon interfacial binding to a cationic micelle

In this contribution we report studies on enzymatic activity of alpha-chymotrypsin (CHT) upon complexation with cationic cetyltrimethylammonium bromide (CTAB) micelle. With picosecond time resolution, we examined solvation dynamics at the interface of CHT-micelle complex, and rigidity of the binding. We have used 5-(dimethyl amino) naphthalene-1-sulfonyl chloride (dansyl chloride; DC) that is covalently attached to the enzyme at the surface sites. The solvation processes at the surface of CHT in buffer solution are found to be mostly in the sub-50 ps time scale. However, at the interface the solvation correlation function decays with time constant 150 ps (65%) and 500 ps (35%), which is significantly different from those found at the enzyme and micellar surfaces. The binding structure of the enzyme-micelle complex was examined by local orientational motion of the probe DC and compared with the case without micelle. The orientational dynamics of the probe DC in the complex reveals a structural perturbation at the surface sites of CHT upon complexation, consistent with other reported structural studies. We also found possible entanglement of charge transfer dynamics of the probe DC on the measured solvation processes by using time-resolved area normalized emission spectroscopic technique. The interfacial solvation process and complex rigidity elucidate the strong recognition mechanism between CHT and the micelle, which is important to understand the biological function of CHT upon complexation with the micelle.

Piezoluminescence at the air-water interface through dynamic molecular recognition driven by lateral pressure application

The steroid cyclophanes with a cyclic core consisting of a 1,6,20,25-tetraaza[6.1.6.1]paracyclophane connected to four steroid moieties (cholic acid or cholanic acid) through a flexible l-lysine spacer were spread on water as Langmuir monolayers. The pi-A isotherm of the cholic-type steroid cyclophane includes a transition to the condensed phase with a limiting area of approximately 2 nm(2). This value is close to the cross-sectional area of the steroid cyclophane with a standing-up conformation of the cholic acid moieties, strongly suggesting that the cavity converts from a two-dimensional cavity to a three-dimensional cavity upon compressing the monolayer. Surface-reflective fluorescence spectroscopy of the monolayer using an aqueous fluorescent probe (6-(p-toluidino)naphthalene-2-sulfonate (TNS)) showed an abrupt increase in the TNS fluorescence intensity at a molecular area of 2 nm(2). Efficient binding of the guest probe would occur upon the completion of the three-dimensional cavity. Repeated compression and expansion induces periodic changes in the fluorescence intensity. This indicates a piezoluminescence effect through the catch and release of the TNS guest upon dynamic cavity formation. Analyses of the binding behavior of TNS to the steroid cyclophane resulted in binding constants in the range of approximately (5-9) x 10(4) M(-1) which are similar to that observed in lipid bilayer media (K = 5.1 x 10(4) M(-1)). The fluorescence intensity within the condensed phase was significantly increased with increasing pressure, suggesting that suppression of the molecular motion of the bound TNS may retard the nonemission process. Similar monolayer experiments were carried out with the monolayer of the cholanic-type steroid cyclophane that cannot form an open conformation on water. Both the phase transition in the pi-A isotherm and the change in the fluorescence intensity were negligible, confirming that the dynamic characteristic of the cavity is indispensable for the efficient pressure-induced binding of the guest and the consequent luminescence.

Water at DNA surfaces: ultrafast dynamics in minor groove recognition

Water molecules at the surface of DNA are critical to its equilibrium structure, DNA-protein function, and DNA-ligand recognition. Here we report direct probing of the dynamics of hydration, with femtosecond resolution, at the surface of a DNA dodecamer duplex whose native structure remains unperturbed on recognition in minor groove binding with the bisbenzimide drug (Hoechst 33258). By following the temporal evolution of fluorescence, we observed two well separated hydration times, 1.4 and 19 ps, whereas in bulk water the same drug is hydrated with time constants of 0.2 and 1.2 ps. For comparison, we also studied calf thymus DNA for which the hydration exhibits similar time scales to that of dodecamer DNA. However, the time-resolved polarization anisotropy is very different for the two types of DNA and clearly elucidates the rigidity in drug binding and difference in DNA rotational motions. These results demonstrate that hydration at the surface of the groove is a dynamical process with two general types of trajectories; the slowest of them (approximately 20 ps) are those describing dynamically ordered water. Because of their ultrafast time scale, the "ordered" water molecules are the most weakly bound and are accordingly involved in the entropic (hydration/dehydration) process of recognition.

Solvation dynamics and proton transfer in supramolecular assemblies

Water molecules confined in a supramolecular assembly control reactivity and dynamics of biological systems in a unique way. In a confined system, water molecules display an ultraslow component of solvation which is slower than that in bulk water by 2-4 orders of magnitude. The ultraslow component arises mainly from the disruption of the hydrogen-bond network of water and the binding of water molecules to a macromolecule. The ultraslow component of solvation markedly retards polar reactions. Many examples of slow dynamics in complex systems, and their implications in biological and natural processes are discussed.

Ultrafast surface hydration dynamics and expression of protein functionality: alpha -Chymotrypsin

We report studies of hydration dynamics at the surface of the enzyme protein bovine pancreatic alpha-chymotrypsin. The probe is the well known 1-anilinonaphthalene-8-sulfonate, which binds selectively in the native state of the protein, not the molten globule, as shown by x-ray crystallography. With femtosecond time resolution, we examined the hydration dynamics at two pHs, when the protein is physiologically in the inactive state (pH 3.6) or the active state (pH 6.7); the global structure and the binding site remain the same. The hydration correlation function, C(t), whose decay is governed by the rotational and translational motions of water molecules at the site, shows the behavior observed in this laboratory for other proteins, Subtilisin Carlsberg and Monellin, using the intrinsic amino acid tryptophan as a probe for surface hydration. However, the time scales and amplitudes vary drastically at the two pHs. For the inactive protein state, C(t) decays with an ultrafast component, close to bulk-type behavior, but 50% of the C(t) decays at a much slower rate, tau = 43 ps. In contrast, for the active state, the ultrafast component becomes dominant (90%) and the slow component changes to a faster decay, tau = 28 ps. These results indicate that in the active state water molecules in the hydration layer around the site have a high degree of mobility, whereas in the inactive state the water is more rigidly structured. For the substrate-enzyme complex, the function and dynamics at the probe site are correlated, and the relevance to the enzymatic action is clear.

Biological water at the protein surface: dynamical solvation probed directly with femtosecond resolution

Biological water at the interface of proteins is critical to their equilibrium structures and enzyme function and to phenomena such as molecular recognition and protein-protein interactions. To actually probe the dynamics of water structure at the surface, we must examine the protein itself, without disrupting the native structure, and the ultrafast elementary processes of hydration. Here we report direct study, with femtosecond resolution, of the dynamics of hydration at the surface of the enzyme protein Subtilisin Carlsberg, whose single Trp residue (Trp-113) was used as an intrinsic biological fluorescent probe. For the protein, we observed two well separated dynamical solvation times, 0.8 ps and 38 ps, whereas in bulk water, we obtained 180 fs and 1.1 ps. We also studied a covalently bonded probe at a separation of approximately 7 A and observed the near disappearance of the 38-ps component, with solvation being practically complete in (time constant) 1.5 ps. The degree of rigidity of the probe (anisotropy decay) and of the water environment (protein vs. micelle) was also studied. These results show that hydration at the surface is a dynamical process with two general types of trajectories, those that result from weak interactions with the selected surface site, giving rise to bulk-type solvation (approximately 1 ps), and those that have a stronger interaction, enough to define a rigid water structure, with a solvation time of 38 ps, much slower than that of the bulk. At a distance of approximately 7 A from the surface, essentially all trajectories are bulk-type. The theoretical framework for these observations is discussed.

Femtosecond dynamics of flavoproteins: charge separation and recombination in riboflavine (vitamin B2)-binding protein and in glucose oxidase enzyme

Flavoproteins can function as hydrophobic sites for vitamin B(2) (riboflavin) or, in other structures, with cofactors for catalytic reactions such as glucose oxidation. In this contribution, we report direct observation of charge separation and recombination in two flavoproteins: riboflavin-binding protein and glucose oxidase. With femtosecond resolution, we observed the ultrafast electron transfer from tryptophan(s) to riboflavin in the riboflavin-binding protein, with two reaction times: approximately 100 fs (86% component) and 700 fs (14%). The charge recombination was observed to take place in 8 ps, as probed by the decay of the charge-separated state and the recovery of the ground state. The time scale for charge separation and recombination indicates the local structural tightness for the dynamics to occur that fast and with efficiency of more than 99%. In contrast, in glucose oxidase, electron transfer between flavin-adenine-dinucleotide and tryptophan(s)/tyrosine(s) takes much longer times, 1.8 ps (75%) and 10 ps (25%); the corresponding charge recombination occurs on two time scales, 30 ps and nanoseconds, and the efficiency is still more than 97%. The contrast in time scales for the two structurally different proteins (of the same family) correlates with the distinction in function: hydrophobic recognition of the vitamin in the former requires a tightly bound structure (ultrafast dynamics), and oxidation-reduction reactions in the latter prefer the formation of a charge-separated state that lives long enough for chemistry to occur efficiently. Finally, we also studied the influence on the dynamics of protein conformations at different ionic strengths and denaturant concentrations and observed the sharp collapse of the hydrophobic cleft and, in contrast, the gradual change of glucose oxidase.