Label-free screening of drug-protein interactions by time-resolved Fourier transform infrared spectroscopic assays exemplified by Ras interactions

Biophysical approaches for the study of metal-protein interactions

Protein-protein interactions play important roles for a variety of cell functions, often involving metal ions; in fact, metal-ion binding mediates and regulates the activity of a wide range of biomolecules. Enlightening all of the specific features of metal-protein and metal-mediated protein-protein interactions can be a very challenging task; a detailed knowledge of the thermodynamic and spectroscopic parameters and the structural changes of the protein is normally required. For this purpose, many experimental techniques are employed, embracing all fields of Analytical and Bioinorganic Chemistry. In addition, the use of peptide models, reproducing the primary sequence of the metal-binding sites, is also proved to be useful. In this paper, a review of the most useful techniques for studying ligand-protein interactions with a special emphasis on metal-protein interactions is provided, with a critical summary of their strengths and limitations.

Two-Photon Activation of p-Hydroxyphenacyl Phototriggers: Toward Spatially Controlled Release of Diethyl Phosphate and ATP

Two-photon activation of the p-hydroxyphenacyl (pHP) photoactivated protecting group is demonstrated for the first time using visible light at 550 nm from a pulsed laser. Broadband two-photon absorption measurements reveal a strong two-photon transition (>10 GM) near 4.5 eV that closely resembles the lowest-energy band at the same total excitation energy in the one-photon absorption spectrum of the pHP chromophore. The polarization dependence of the two-photon absorption band is consistent with excitation to the same S3 ((1)ππ*) excited state for both one- and two-photon activation. Monitoring the progress of the uncaging reaction under nonresonant excitation at 550 nm confirms a quadratic intensity dependence and that two-photon activation of the uncaging reaction is possible using visible light in the range 500-620 nm. Deprotonation of the pHP chromophore under mildly basic conditions shifts the absorption band to lower energy (3.8 eV) in both the one- and two-photon absorption spectra, suggesting that two-photon activation of the pHP chromophore may be possible using light in the range 550-720 nm. The results of these measurements open the possibility of spatially and temporally selective release of biologically active compounds from the pHP protecting group using visible light from a pulsed laser.

What vibrations tell us about GTPases

In this review, we discuss how time-resolved Fourier transform infrared (FTIR) spectroscopy is used to understand how GTP hydrolysis is catalyzed by small GTPases and their cognate GTPase-activating proteins (GAPs). By interaction with small GTPases, GAPs regulate important signal transduction pathways and transport mechanisms in cells. The GTPase reaction terminates signaling and controls transport. Dysfunctions of GTP hydrolysis in these proteins are linked to serious diseases including cancer. Using FTIR, we resolved both the intrinsic and GAP-catalyzed GTPase reaction of the small GTPase Ras with high spatiotemporal resolution and atomic detail. This provided detailed insight into the order of events and how the active site is completed for catalysis. Comparisons of Ras with other small GTPases revealed conservation and variation in the catalytic mechanisms. The approach was extended to more nearly physiological conditions at a membrane. Interactions of membrane-anchored GTPases and their extraction from the membrane are studied using the attenuated total reflection (ATR) technique.

Metal-ion effects on the polarization of metal-bound water and infrared vibrational modes of the coordinated metal center of Mycobacterium tuberculosis pyrazinamidase via quantum mechanical calculations

Mycobacterium tuberculosis pyrazinamidase (PZAse) is a key enzyme to activate the pro-drug pyrazinamide (PZA). PZAse is a metalloenzyme that coordinates in vitro different divalent metal cofactors in the metal coordination site (MCS). Several metals including Co²⁺, Mn²⁺, and Zn²⁺ are able to reactivate the metal-depleted PZAse in vitro. We use quantum mechanical calculations to investigate the Zn²⁺, Fe²⁺, and Mn²⁺ metal cofactor effects on the local MCS structure, metal–ligand or metal–residue binding energy, and charge distribution. Results suggest that the major metal-dependent changes occur in the metal–ligand binding energy and charge distribution. Zn²⁺ shows the highest binding energy to the ligands (residues). In addition, Zn²⁺ and Mn²⁺ within the PZAse MCS highly polarize the O–H bond of coordinated water molecules in comparison with Fe²⁺. This suggests that the coordination of Zn²⁺ or Mn²⁺ to the PZAse protein facilitates the deprotonation of coordinated water to generate a nucleophile for catalysis as in carboxypeptidase A. Because metal ion binding is relevant to enzymatic reaction, identification of the metal binding event is important. The infrared vibrational mode shift of the C=Nε (His) bond from the M. tuberculosis MCS is the best IR probe to metal complexation.

Monitoring protein-ligand interactions by time-resolved FTIR difference spectroscopy

Time-resolved FTIR difference spectroscopy is a valuable tool to monitor the dynamics and exact molecular details of protein-ligand interactions. FTIR difference spectroscopy selects, out of the background absorbance of the whole sample, the absorbance bands of the protein groups and of the ligands that are involved in the protein reaction. The absorbance changes can be monitored with time-resolutions down to nanoseconds and followed for time periods ranging over nine orders of magnitude even in membrane proteins with a size of 100,000 Da. Here, we discuss the various experimental setups. The rapid scan technique allows a time resolution in the millisecond regime, whereas the step scan technique allows nanosecond time resolution. We show appropriate sample cells and how to trigger a reaction within these cells. The kinetic analysis of the data is discussed. A crucial step in the data analysis is the reliable assignment of bands to chemical groups of the protein and the ligand. This is done either by site directed mutagenesis, where the absorbance bands of the exchanged amino acids disappear or by isotopically labeling, where the band of the labelled group is frequency shifted.

Applications of p-hydroxyphenacyl (pHP) and coumarin-4-ylmethyl photoremovable protecting groups

Most applications of photoremovable protecting groups have used o-nitrobenzyl compounds and their (often commercially available) derivatives that, however, have several disadvantages. The focus of this review is on applications of the more recently developed title compounds, which are especially well suited for time-resolved biochemical and physiological investigations, because they release the caged substrates in high yield within a few nanoseconds or less. Together, these two chromophores cover the action spectrum for photorelease from >700 nm to 250 nm.

Achieving broad molecular insights into dynamic protein interactions by integrated structural-kinetic approaches

A network of dynamic protein interactions with their protein partners, substrates, and ligands is known to be crucial for biological function. Revealing molecular and structural-based mechanisms at atomic resolution and in real-time is fundamental for achieving a basic understanding of cellular processes. These technically challenging goals may be achieved by combining time-resolved spectroscopic and structural-kinetic tools, thus providing broad insights into specific molecular events over a wide range of timescales. Here we review representative studies utilizing such an integrated real-time structural approach designed to reveal molecular mechanisms underlying protein interactions at atomic resolution.

Time-resolved mid-IR spectroscopy of (bio)chemical reactions in solution utilizing a new generation of continuous-flow micro-mixers

A specially designed micro-mixer made of silicon, calcium fluoride, and silicone with an optical transmission path of 8 μm has been used for mid-IR spectroscopy monitoring of mixing-induced chemical reactions in the low millisecond time regime. The basic principle of the proposed continuous-flow technique is to mix two liquids introduced in two times two alternatingly stacked layers through diffusion at the entrance of a 200 μm wide, 1 cm long micro-fluidic channel also serving as measurement area. By using this special, dedicated arrangement, diffusion lengths and hence the mixing times can be significantly shortened and the overall performance improved in comparison to previous systems and alternative methods. Measurements were carried out in transmission mode using an Fourier transform infrared (FTIR) microscope, recording spectra with spot sizes of 180 × 100 μm(2) each at defined spots along this channel. Each of these spots corresponds to a specific reaction time: moving the measurement spot towards the entry yields shorter reaction times, moving it towards the channel's end gives longer reaction times. This principle is generic in nature and provides a solution for accurate, chemically induced triggering of reactions requiring the mixing of two liquid reagents or reagent solutions. A typical experiment thus yields up to 85 time-coded data points, covering a time span from 1 to 80 ms at a total reagent consumption of only about 125 μL. Using the fast neutralization reaction of acetic acid with sodium hydroxide as a model, the time required for 90% mixing was determined to be around 4 ms. Additionally, first experiments on ubiquitin changing its secondary structure from native to "A-state" were carried out, illustrating the potential for time-resolved measurements of proteins in aqueous solutions.