Second-harmonic generation for studying structural motion of biological molecules in real time and space

SHG and sum-frequency generation (SFG) are surface-selective, nonlinear optical techniques whose ability to measure the average tilt angle of molecules on surfaces is well known in non-biological systems. By labeling molecules with a second-harmonic-active dye probe, SHG detection is extended to any biological molecule. The method has been used in previous work to detect biomolecules at an interface and their ligand-induced conformational changes. Here I demonstrate that SHG can be used to study structural motion quantitatively using a probe placed at a specific site (Cys-77) in adenylate kinase, a protein. The protein is also labeled non-site-specifically via amines. Labeled protein is absorbed to a surface and a baseline SH signal is measured. Upon introducing ATP, AMP or a specific inhibitor, AP(5)A, the baseline signal changes depending on the ligand and the labeling site. In particular, a substantial change in SH intensity is produced upon binding ATP to the amine-labeled protein, consistent with the X-ray crystal structures. In contrast, SHG polarization measurements are used to quantitatively determine that no rotation occurs at site Cys-77, in agreement with the lack of motion observed at this site in the X-ray crystal structures. A method for building a global map of conformational change in real time and space is proposed using a set of probes placed at different sites in a biomolecule. For this purpose, SH-active unnatural amino acids are attractive complements to exogenous labels.     

A second-harmonic-active unnatural amino acid as a structural probe of biomolecules on surfaces

Second-harmonic generation (SHG) is highly sensitive to the net, average orientation of SH-active molecules on surfaces and has recently emerged as a technique for detecting biomolecules and their conformational changes. As most biomolecules are not intrinsically SH-active, they must be labeled with probes to render them detectable. To date, exogenous probes have been used to do this, but second-harmonic-active unnatural amino acids offer important advantages for the long-range goal of precisely and directly determining structural changes in real time and may be used for both buried and surface sites. Results of the first known SH-active unnatural amino acid, Aladan, are presented here. Aladan is found to be SH-active by detecting it at an interface, both alone and incorporated into the B1 domain of protein G (GB1), a globular immunoglobulin-binding protein, at both buried and exposed sites. The tilt angle of Aladan alone adsorbed on a mica surface is determined by polarization experiments, and its nonlinear polarizability alpha((2)) is found to be ca. 10(-30) esu. Aladan GB1 mutants are detectable by SHG, either when coupled covalently to a derivatized glass surface or bound to IgG immobilized via protein A. Addition of an Fc domain to this GB1 complex causes a small but defined change in the SH signal when Aladan is incorporated at site Ala(24), but not at Leu(7), consistent with a local conformational change of GB1. This structural change is not apparent in either X-ray crystallography or fluorescence studies, demonstrating that SHG can detect subtle orientational changes, including protein-protein interactions in which no significant rearrangements occur.     

Chiroptical effects in the second harmonic signal of collagens I and IV

We performed polarization-resolved surface second harmonic generation (SHG) experiments on thin films of collagen I and IV molecules, as well as conventional CD measurements. We found that collagen IV presents little CD and no SHG optical activity, whereas collagen I exhibits large chiroptical effects involving both one-electron and excitonic coupling mechanisms. We estimated that these chiral components enhance the SHG signal from fibrillar collagen in biological tissues by typically a factor of 2. By comparing the distinct behaviors of collagens I and IV in SHG microscopy and in surface SHG experiments, we concluded that SHG microscopy is a sensitive probe of the micrometer-scale structural organization of collagen in biological tissues.     

Order-Disorder Transition of Carboxyl Terminated Chains in Polydiacetylenes Vesicles Probed by Second Harmonic Generation and Two-Photon Fluorescence

To understand and control the interfacial properties of polydiacetylenes (PDAs) vesicles with π-conjugated backbone is very important for their colorimetric sensing of chemical and biological targets. In this work, we adopted 10, 12-pentacosadiynoic acid (PCDA) as the model molecule to prepare PDAs vesicles in aqueous solution with different forms (from monomer to blue-to-purple-to-red phase) by controlling the UV irradiation dose. The variations of the interfacial conformation of PDAs vesicles during chromatic transitions were inspected by the adsorption behaviors of probe molecules (4-(4-diethylaminostyry)-1-methylpyridinium iodide, D289) on vesicle surface with surface-specific second harmonic generation (SHG) and zeta potential measurements. Resonant SHG signal from D289 adsorbed on vesicle surface attenuated sharply, and the adsorption free energy as well as the corresponding two-photon fluorescence signal decreased slightly in chromatic transitions. While, the change in the surface density of the adsorbed D289 molecules for PDAs vesicles with different forms was relatively small as estimated from zeta potential measurements. The attenuation of the SHG intensity was thus attributed to the overall order-disorder transition and the changed orientation of D289 molecules caused by the gradual distortion of carboxyl head group driven by backbone perturbation.     

Oscillating bubble SHG on surface elastic and surface viscoelastic systems: new insights in the dynamics of adsorption layers

Surface rheology governs a great variety of interfacial phenomena such as foams or emulsions and plays a dominant role in several technological processes such as high-speed coating. Its major difference with bulk rheology resides in the high compressibility of the surface phase, which is the direct consequence of the molecular exchange between adsorbed and dissolved species. In analogy to bulk rheology, a complex surface dilational modulus, epsilon, which captures surface tension changes upon defined area changes of the surface layer, can be defined. The module epsilon is complex, and the molecular interpretation of the dissipative process that gives rise to the imaginary part of the module is subject to some controversy. In this contribution, we used the oscillating bubble technique to study the surface dilational modulus in the mid-frequency range. The dynamic state of the surface layer was monitored by a pressure sensor and by surface second-harmonic generation (SHG). The pressure sensor measures the real and imaginary part of the modulus while SHG monitors independently the surface composition under dynamic conditions. The experiment allows the assessment of the contribution of the compositional term to the surface dilational modulus epsilon. Two aqueous surfactant solutions have been characterized: a surface elastic and a surface viscoelastic solution. The elastic surface layer can be described within the framework of the extended Lucassen-van den Tempel Hansen model. The change in surface concentration is in phase with the relative area change of the surface layer, which is in strong contrast with the results obtained from the surface viscoelastic solution. Here, surface tension, area change, and surface composition are phase-shifted, providing evidence for a nonequilibrium state within the surface phase. The data are used to assess existing surface rheology models.     

DNA single strands tethered to fused quartz/water interfaces studied by second harmonic generation

Second harmonic generation (SHG) is used to study oligonucleotides at aqueous/solid interfaces for the first time. Detailed thermodynamic state information for interfacial DNA single strands, namely, the interfacial charge density, the interfacial potential, and the change in the interfacial energy density, is obtained. The phosphate groups on the DNA backbone serve as intrinsic labels that do not require DNA modification other than surface attachment. This approach is broadly applicable for the investigation of DNA during its interaction with biological targets, as well as charged biopolymers in general, and has important implications for predicting and controlling macromolecular interactions, improving biodiagnostics, and understanding life processes.     

Second-harmonic spectroscopy of surface immobilized gold nanospheres above a gold surface supported by self-assembled monolayers

We have investigated linear and nonlinear optical properties of surface immobilized gold nanospheres (SIGNs) above a gold surface with a gap distance of a few nanometers. The nanogap was supported by amine or merocyanine terminated self-assembled monolayers (SAMs) of alkanethiolates. A large second-harmonic generation (SHG) was observed from the SIGN systems at localized surface plasmon resonance condition. The maximum enhancement factor of SHG intensity was found to be 3 x 10(5) for the SIGN system of nanospheres 100 nm in diameter with a gap distance of 0.8 nm. The corresponding susceptibility was estimated to be chi((2))=750 pmV (1.8 x 10(-6) esu). In the SIGN system supported with the merocyanine terminated SAMs, the SHG response was also resonant to the merocyanine in the nanogap. It was found that the SHG response of the SIGN systems is strongly frequency dependent. This leads us to conclude that the large chi((2)) is caused by enhanced electric fields at the localized surface plasmon resonance condition and is not due to an increase of the surface susceptibility following from the presence of the gold nanospheres. The observed SHG was consistent with the theoretical calculations involving Fresnel correction factors, based on the quasistatic approximation.     

SPIN LABELED CYSTEINES AS SENSORS FOR PROTEIN-LIPID INTERACTION AND CONFORMATION IN RHODOPSIN

In stoichiometric amounts, the spin label N-tempoyl-(p-chloromercuribenzamide) reacts rapidly with one cysteine residue in membrane-bound bovine rhodopsin. This residue is distinct from the two reactive cysteines previously used as attachment sites for spectroscopic labels, and is on the external surface of the protein near the cytoplasmic membrane/aqueous interface. The spin-labeled side chain has revealed a light-induced conformational change in membrane-bound rhodopsin that is apparently not associated with protein aggregation. The changes are reversible upon the addition of 11-cis retinal, and the magnitude of the change is dependent on the identity of the phospholipid in the surrounding bilayer. Alteration of lipid composition has a much larger effect on bleached rhodopsin than rhodopsin itself, indicating that the former is more readily deformable in response to changes in bilayer properties. This is consistent with the loss of 11-cis retinal binding energy in opsin compared to rhodopsin. These results provide direct structural evidence that the conformation of a membrane protein can be modulated by the lipid properties.     

Distance measurements on spin-labelled biomacromolecules by pulsed electron paramagnetic resonance

The biological function of protein, DNA, and RNA molecules often depends on relative movements of domains with dimensions of a few nanometers. This length scale can be accessed by distance measurements between spin labels if pulsed electron paramagnetic resonance (EPR) techniques such as electron-electron double resonance (ELDOR) and double-quantum EPR are used. The approach does not require crystalline samples and is well suited to biomacromolecules with an intrinsic flexibility as distributions of distances can be measured. Furthermore, oligomerization or complexation of biomacromolecules can also be studied, even if it is incomplete. The sensitivity of the technique and the reliability of the measured distance distribution depend on careful optimization of the experimental conditions and procedures for data analysis. Interpretation of spin-to-spin distance distributions in terms of the structure of the biomacromolecules furthermore requires a model for the conformational distribution of the spin labels.     

Ellipsometric approach for the real-time detection of label-free protein adsorption by second harmonic generation

Second harmonic generation (SHG) was performed using a novel ellipsometric detection approach to selectively probe the real-time surface binding kinetics of an unlabeled protein. The coherence of nonlinear optical processes introduces new possibilities for exploiting polarization that are unavailable with incoherent methods, such as absorbance and fluorescence. Adsorption of bovine serum albumin (BSA) at silica/aqueous solution interfaces resulted in changes in the polarization state of the frequency-doubled light through weak, dynamic interactions with a coadsorbed nonlinear optical probe molecule (rhodamine 6G). Using a remarkably simple instrumental approach, signals arising exclusively from surface interactions with BSA were spatially isolated and selectively detected with high signal-to-noise. The relative intensities acquired during the kinetics experiments using both circularly and linearly polarized incident beams were in excellent agreement with the responses predicted from SHG ellipsometry polarization measurements. Analysis of the polarization-dependent SHG generated during BSA adsorption at glass/aqueous solution interfaces provided direct evidence for slow conformational changes within the protein layer after adsorption, consistent with protein denaturation. This polarization selection approach is sufficiently general to be easily extended to virtually all coherent nonlinear optical processes and a variety of different surface interactions and architectures.     

Amphiphilic dyes for NLO in LB-films

The influence of structural variations of phenyl-hydrazones and stilbazium salts on monolayer behaviour and second-harmonic generation in LB-monolayers is discussed. In contrast to the stilbazium salts the variation of the substituents of the phenylhydrazones does not influence the absorption maximum of the dyes in resonance enhancement of the nonlinearity. This allows a direct comparison of the substitution pattern on SHG.     

Selective High‐Resolution Detection of Membrane Protein–Ligand Interaction in Native Membranes Using Trityl–Nitroxide PELDOR

The orchestrated interaction of transmembrane proteins with other molecules mediates several crucial biological processes. Detergent solubilization may significantly alter or even abolish such hetero‐oligomeric interactions, which makes observing them at high resolution in their native environment technically challenging. Dipolar electron paramagnetic resonance (EPR) techniques such as pulsed electro–electron double resonance (PELDOR) can provide very precise distances within biomolecules. To concurrently determine the inter‐subunit interaction and the intra‐subunit conformational changes in hetero‐oligomeric complexes, a combination of different spin labels is required. Orthogonal spin labeling using a triarylmethyl (TAM) label in combination with a nitroxide label is used to detect protein–ligand interactions in native lipid bilayers. This approach provides a higher sensitivity and total selectivity and will greatly facilitate the investigation of multimeric transmembrane complexes employing different spin labels in the native lipid environment.     

Induction of protein conformational change inside the charged electrospray droplet

The behavior of the analyte molecules inside the neutral core of the charged electrospray (ES) droplet is not unambiguously known to date. The possibility of protein conformational change inside the charged ES droplet has been investigated. The ES droplets encapsulating the protein molecules were exposed to the acetic acid vapor in the ionization chamber to absorb the acetic acid vapor. Because of the faster evaporation of water than that of acetic acid, the droplets became enriched with acetic acid and thus altered the solvent environment (e.g. pH and polarity) of the final charged droplets from where the naked charged analytes (proteins) are formed. Thus, the perturbation of the ES droplet solvent environment resulted in the protein conformational change (unfolding) during the short lifespan of the ES droplet and that is reflected by the multimodal charge state distribution in the corresponding mass spectra. Further, the extent of this conformational change inside the ES droplet was found to be related to the structural flexibility of the protein. Although the protein conformational change inside the ES droplet has been driven by using acetic acid vapor in the present study, the results would help in the near future to understand the spontaneity of the conformational change of the analyte on the millisecond timescale of phase transition in the natural way of ES process. Copyright © 2013 John Wiley & Sons, Ltd.     

The Influence of Two‐Dimensional Organization on Peptide Conformation

Molecular crowding plays a significant role in regulating molecular conformation in cellular environments. It is also likely to be important wherever high molecular densities are required, for example in surface‐phase studies, in which molecular densities generally far exceed those observed in solution. Using on‐surface circular dichroism (CD) spectroscopy, we have investigated the structure of a synthetic peptide assembled into a highly packed monolayer. The immobilized peptide undergoes a structural transition between α‐helical and random coil conformation upon changes in pH and ionic concentration, but critically the threshold for conformational change is altered dramatically by molecular crowding within the peptide monolayer. This study highlights the often overlooked role molecular crowding plays in regulating molecular structure and function in surface‐phase studies of biological molecules.     

Monitoring biological membrane-potential changes: a CI QM/MM study

In recent decades, new less-invasive, nonlinear optical methods have been proposed and optimized for monitoring fast physiological processes in biological cells. One of these methods allows the action potential (AP) in cardiomyocytes or neurons to be monitored by means of second-harmonic generation (SHG). We now present the first, to our knowledge, simulations of the dependency of the intensity of the second harmonic (I(SHG)) on variations of the transmembrane potential (TMP) in a cardiomyocyte during an action potential (AP). For this, an amphiphilic potential-sensitive styryl dye molecule with nonlinear optical properties was embedded in a dipalmitoylphosphatidylcholine (DPPC) bilayer, replacing one of the phospholipid molecules. External electrical fields with different strengths were applied across the membrane to simulate the AP of a heart-muscle cell. We used a combined classical/quantum mechanical approach to model the structure and the spectroscopic properties of the embedded chromophore. Two 10 ns molecular dynamics (MD) simulations provided input geometries for semiempirical molecular orbital (QM/MM) single-point configuration interaction (CI) calculations, which were used to calculate the wavelengths and oscillator strengths of electronic transitions in the di-8-ANEPPS dye molecule. The results were then used in a sum-over-states treatment to calculate the second-order hyperpolarizability. The square of the hyperpolarizability scales with the intensity of the second harmonic, which is used to monitor the action potentials of cardiomyocytes experimentally. Thus, we computed changes in the intensity of the second harmonic (DeltaI(SHG)) as function of TMP changes. Our results agree well with experimental measurements.     

Protein conformational switches: from nature to design

Protein conformational switches alter their shape upon receiving an input signal, such as ligand binding, chemical modification, or change in environment. The apparent simplicity of this transformation--which can be carried out by a molecule as small as a thousand atoms or so--belies its critical importance to the life of the cell as well as its capacity for engineering by humans. In the realm of molecular switches, proteins are unique because they are capable of performing a variety of biological functions. Switchable proteins are therefore of high interest to the fields of biology, biotechnology, and medicine. These molecules are beginning to be exploited as the core machinery behind a new generation of biosensors, functionally regulated enzymes, and "smart" biomaterials that react to their surroundings. As inspirations for these designs, researchers continue to analyze existing examples of allosteric proteins. Recent years have also witnessed the development of new methodologies for introducing conformational change into proteins that previously had none. Herein we review examples of both natural and engineered protein switches in the context of four basic modes of conformational change: rigid-body domain movement, limited structural rearrangement, global fold switching, and folding-unfolding. Our purpose is to highlight examples that can potentially serve as platforms for the design of custom switches. Accordingly, we focus on inducible conformational changes that are substantial enough to produce a functional response (e.g., in a second protein to which it is fused), yet are relatively simple, structurally well-characterized, and amenable to protein engineering efforts.     

Molecular biosensing system based on intrinsically disordered proteins

Intrinsically disordered proteins (IDPs) that undergo structural transition upon binding their target molecules are becoming increasingly known. IDPs, because of their binding specificity and induced folding properties, can serve as biological recognition elements for sensing applications. In this paper, BRCA1, an IDP, was utilized as the biological recognition element to detect tumor suppressor protein p53 through the BRCA1/p53 binding interaction to serve as a proof-of-concept for the use of IDPs as recognition elements. The binding resulted in a disordered-to-ordered BRCA1 conformational change, as seen in our circular dichroism (CD) measurements. This conformational change in BRCA1 (residues 219-498) was utilized in the detection of p53 (residues 311-393) via both intrinsic and extrinsic fluorescent probes. Intrinsic tryptophan residues within the BRCA1 sequence detected p53 (311-393) with a detection limit of 0.559 nM (0.112 pmol). Two environmentally sensitive fluorophores, tetramethylrhodamine-5-maleimide (TMR) and 6-((5-dimethylaminonaphthalene-1-sulfonyl)amino)hexanoic acid, succinimidyl ester (dansyl-X, SE) were conjugated to BRCA1 (219-498). Dansyl-X, SE-conjugated BRCA1 (219-498) detected p53 (311-393) with a detection limit of 1.50 nM (0.300 pmol). The sensitivities for TMR and dansyl-X, SE-conjugated BRCA1 for the detection of p53 were nearly threefold and twofold higher, respectively, than the sensitivity reported using intrinsic BRCA1 tryptophan fluorescence. CD measurements did not reveal a disruption of p53/dye-conjugated BRCA1 binding, thus validating the applicability of environmentally sensitive fluorophores as transduction moieties to detect molecules which bind to IDPs and induce a structural change.     

Longitudinal diffusion behavior of hemicyanine dyes across phospholipid vesicle membranes as studied by second-harmonic generation and fluorescence spectroscopies

The adsorption and longitudinal diffusion behaviors of a series of hemicyanine dyes to phospholipid vesicle membranes were studied by second-harmonic generation (SHG) and fluorescence spectroscopies. It was observed that the longitudinal diffusion of cationic hemicyanine dyes takes place immediately after the initial adsorption of these dyes to the outer surface of the vesicle membrane. In contrast, hardly any amount of a zwitterionic hemicyanine dye with a sulfonate group diffused across the vesicle membrane within the measurement time (<2000 s). Based on the difference in the time-course responses of SHG and fluorescence spectroscopies for all of the hemicyanine dyes tested, we propose that hydration of the sulfonate group is mainly responsible for the low diffusivity of the zwitterionic hemicyanine dye.     

Reversible two-photon optical data storage in coumarin-based copolymers

A functionalized polymer film allowing for a complete and straightforward second-harmonic generation (SHG)-assisted high-contrast writing-reading-erasing-writing sequence is proposed. The whole process is supported by the reversible photoinduced dimerization of a coumarin chromophore and enables efficient optical data storage that can be detected only by SHG imaging.     

The effects of denaturants on protein conformation and behavior at air/solution interface

In this study, we discuss the interfacial behavior of five proteins with different conformational character, and each is investigated in native and denatured states. The protein molecules are layered and spread onto the air/solution interfaces to form protein monolayer. The surface pressure-time (Pi(t)) and surface pressure-area per molecule (Pi-A) isotherms were measured by using the Langmuir-Blodgett (LB) balance consisted of a Nima trough system. The differences between monolayered protein's behaviors at air/solution interface indicate that denaturants, such as urea, guanidinium chloride and dithiothreitol, have different effects on conformational changes of proteins. Additionally, the interfacial behavior of the proteins in our study provides a fundamental profile about the protein structural stability and implies industrial applications in protein refolding process.