A fluorescence temperature-jump study on Ca2(+)-induced conformational changes in calmodulin

Distinguishing unfolding and functional conformational transitions of calmodulin using ultraviolet resonance Raman spectroscopy

Calmodulin (CaM) is a ubiquitous moderator protein for calcium signaling in all eukaryotic cells. This small calcium-binding protein exhibits a broad range of structural transitions, including domain opening and folding-unfolding, that allow it to recognize a wide variety of binding partners in vivo. While the static structures of CaM associated with its various binding activities are fairly well-known, it has been challenging to examine the dynamics of transition between these structures in real-time, due to a lack of suitable spectroscopic probes of CaM structure. In this article, we examine the potential of ultraviolet resonance Raman (UVRR) spectroscopy for clarifying the nature of structural transitions in CaM. We find that the UVRR spectral change (with 229 nm excitation) due to thermal unfolding of CaM is qualitatively different from that associated with opening of the C-terminal domain in response to Ca(2+) binding. This spectral difference is entirely due to differences in tertiary contacts at the interdomain tyrosine residue Tyr138, toward which other spectroscopic methods are not sensitive. We conclude that UVRR is ideally suited to identifying the different types of structural transitions in CaM and other proteins with conformation-sensitive tyrosine residues, opening a path to time-resolved studies of CaM dynamics using Raman spectroscopy.

Protein analysis by time-resolved measurements with an electro-switchable DNA chip

Measurements in stationary or mobile phases are fundamental principles in protein analysis. Although the immobilization of molecules on solid supports allows for the parallel analysis of interactions, properties like size or shape are usually inferred from the molecular mobility under the influence of external forces. However, as these principles are mutually exclusive, a comprehensive characterization of proteins usually involves a multi-step workflow. Here we show how these measurement modalities can be reconciled by tethering proteins to a surface via dynamically actuated nanolevers. Short DNA strands, which are switched by alternating electric fields, are employed as capture probes to bind target proteins. By swaying the proteins over nanometre amplitudes and comparing their motional dynamics to a theoretical model, the protein diameter can be quantified with Angström accuracy. Alterations in the tertiary protein structure (folding) and conformational changes are readily detected, and even post-translational modifications are revealed by time-resolved molecular dynamics measurements.

The comprehensive bioanalysis of proteins usually requires multi-step surface and mobile phase measurements. Here, the authors use chips functionalized with dynamically actuated nanolevers—DNA strands that can be switched in an electric field—to obtain motional dynamic measurements of proteins on a chip.

Construction of a Ca(2+)-gated artificial channel by fusing alamethicin with a calmodulin-derived extramembrane segment

Using native chemical ligation, we constructed a Ca(2+)-gated fusion channel protein consisting of alamethicin and the C-terminal domain of calmodulin. At pH 5.4 and in the absence of Ca(2+), this fusion protein yielded a burst-like channel current with no discrete channel conductance levels. However, Ca(2+) significantly lengthened the specific channel open state and increased the mean channel current, while Mg(2+) produced no significant changes in the channel current. On the basis of 8-anilinonaphthalene-1-sulfonic acid (ANS) fluorescent measurement, Ca(2+)-stimulated gating may be related to an increased surface hydrophobicity of the extramembrane segment of the fusion protein.

A conformation- and ion-sensitive plasmonic biosensor

The versatile optical and biological properties of a localized surface plasmon resonance (LSPR) sensor that responds to protein conformational changes are illustrated. The sensor detects conformational changes in a surface-bound construct of the calcium-sensitive protein calmodulin. Increases in calcium concentration induce a 0.96 nm red shift in the spectral position of the LSPR extinction maximum (λ(max)). Addition of a calcium chelating agent forces the protein to return to its original conformation and is detected as a reversal of the λ(max) shift. As opposed to previous work, this work demonstrates that these conformational changes produce a detectable shift in λ(max) even in the absence of a protein label, with a signal:noise ratio near 500. In addition, the protein conformational changes reversibly switch both the wavelength and intensity of the resonance peak, representing an example of a bimodal plasmonic component that simultaneously relays two distinct forms of optical information. This highly versatile plasmonic device acts as a biological sensor, enabling the detection of calcium ions with a biologically relevant limit of detection of 23 μM, as well as the detection of calmodulin-specific protein ligands.

Protein-binding assays in biological liquids using microscale thermophoresis

Protein interactions inside the human body are expected to differ from the situation in vitro. This is crucial when investigating protein functions or developing new drugs. In this study, we present a sample-efficient, free-solution method, termed microscale thermophoresis, that is capable of analysing interactions of proteins or small molecules in biological liquids such as blood serum or cell lysate. The technique is based on the thermophoresis of molecules, which provides information about molecule size, charge and hydration shell. We validated the method using immunologically relevant systems including human interferon gamma and the interaction of calmodulin with calcium. The affinity of the small-molecule inhibitor quercetin to its kinase PKA was determined in buffer and human serum, revealing a 400-fold reduced affinity in serum. This information about the influence of the biological matrix may allow to make more reliable conclusions on protein functionality, and may facilitate more efficient drug development.

Free-Solution, Label-Free Molecular Interactions Studied by Back-Scattering Interferometry

Free-solution, label-free molecular interactions were investigated with back-scattering interferometry in a simple optical train composed of a helium-neon laser, a microfluidic channel, and a position sensor. Molecular binding interactions between proteins, ions and protein, and small molecules and protein, were determined with high dynamic range dissociation constants (Kd spanning six decades) and unmatched sensitivity (picomolar Kd's and detection limits of 10,000s of molecules). With this technique, equilibrium dissociation constants were quantified for protein A and immunoglobulin G, interleukin-2 with its monoclonal antibody, and calmodulin with calcium ion Ca2+, a small molecule inhibitor, the protein calcineurin, and the M13 peptide. The high sensitivity of back-scattering interferometry and small volumes of microfluidics allowed the entire calmodulin assay to be performed with 200 picomoles of solute.

Competitive Binding Assay Using Fluorescence Resonance Energy Transfer for the Identification of Calmodulin Antagonists

The ubiquitous calcium regulating protein calmodulin (CaM) has been utilized as a model drug target in the design of a competitive binding fluorescence resonance energy transfer assay for pharmacological screening. The protein was labeled by covalently attaching the thiol-reactive fluorophore, N-[2-(1-maleimidyl)ethyl]-7-(diethylamino)coumarin-3-carboxamide (MDCC) to an engineered C-terminal cysteine residue. Binding of the environmentally sensitive hydrophobic probe 2,6-anilinonaphthalene sulfonate (2,6-ANS) to CaM could be monitored by an increase in the fluorescence emission intensity of the 2,6-ANS. Evidence of fluorescence resonance energy transfer (FRET) from 2,6-ANS (acting as a donor) to MDCC (the acceptor in this system) was also observed; fluorescence emission representative of MDCC could be seen after samples were excited at a wavelength specific for 2,6-ANS. The FRET signal was monitored as a function of the concentration of calmodulin antagonists in solution. Calibration curves for both a selection of small molecules and a series of peptides based upon known CaM-binding domains were obtained using this system. The assay demonstrated dose-dependent antagonism by analytes known to hinder the biological activity of CaM. These data indicate that the presence of molecules known to bind CaM interfere with the ability of FRET to occur, thus leading to a concentration-dependent decrease of the ratio of acceptor:donor fluorescence emission. This assay can serve as a general model for the development of other protein binding assays intended to screen for molecules with preferred binding activity.

Mechanism of 2-chloro-(epsilon-amino-Lys75)-[6-[4-(N,N- diethylamino)phenyl]-1,3,5-triazin-4-yl]calmodulin interactions with smooth muscle myosin light chain kinase and derived peptides

The mechanism of the interactions of 2-chloro-(epsilon-amino-Lys75)-[6-[4-(N,N-diethylamino)phenyl]- 1,3,5-triazin-4-yl]calmodulin (TA-calmodulin) with smooth muscle myosin light-chain kinase (MLCK) and two 17-residue peptides, Ac-R-R-K-W-Q-K-T-G-H-A-V-R-A-I-G-R-L-CONH2 (Trp peptide) and Tyr peptide, in which W is replaced by Y, were studied by measurements of equilibrium and transient fluorescence changes in the nanomolar range. Most reactions were carried out in 100 microM CaCl2 at ionic strength 0.15 M, pH 7.0, and 21 degrees C. In each case association of MLCK or peptide to TA-calmodulin could be described by a two-step process, a bimolecular step and an isomerization. In the case of the interaction between TA-calmodulin and Tyr peptide it was shown that the isomerization involved the binary complex of TA-calmodulin and Tyr peptide as opposed to an isomerization of either TA-calmodulin or Tyr peptide in isolation. These distinctions depended in part on development for transient kinetic experiments of a general theory to quantify relative phase amplitudes in two-step mechanisms. The kinetics for all three association reactions were then interpreted in terms of a bimolecular association (rate constants k+1 and k-1) followed by an isomerization of the binary complex (rate constants k+2 and k-2). For the interaction of TA-calmodulin and Tyr peptide, values of the rate constants are k+1, 8.8 x 10(8) M-1 s-1; k-1, 5.7 s-1; k+2, 0.38 s-1; and k-2, 0.65 s-1. The fluorescence intensities (lambda ex 365 nm, lambda ex 365 nm, lambda em > 400 nm) of TA-calmodulin, the initial binary complex of TA-calmodulin and Tyr peptide, and the isomerized binary complex are in the ratio 1:2.8:1.3. Analogous mechanisms were found for TA-calmodulin binding to Trp peptide and to MLCK, but values for the rate constants and relative fluorescence intensities of the binary complexes were generally not so completely defined. Values for the Trp peptide and MLCK, respectively, are k+1, 8.8 x 10(8) M-1 s-1 and 1.1 x 10(8) M-1 s-1; (k+2 + k-2), 0.97 s-1 and 1.3 s-1; and k-1k-2/(k+2 + k-2), 0.0079 s-1 and 0.025-0.056 s-1. Equilibrium dissociation constants (Kd) for interactions of TA-calmodulin and targets determined from these data are Tyr peptide, 4.1 nM; Trp peptide, 0.011 nM; and MLCK, 0.23-0.51 nM.(ABSTRACT TRUNCATED AT 400 WORDS)