Arijit Kumar Deabc & Debabrata Goswami
This account reviews some recent studies pursued in our group on several control experiments with important applications in (one-photon) confocal and two-photon fluorescence laser-scanning microscopy and optical trapping with laser tweezers. We explore the simultaneous control of internal and external (i.e. centre-of-mass motion) degrees of freedom, which require the coupling of various control parameters to result in the spatiotemporal control. Of particular interest to us is the implementation of such control schemes in living systems. A live cell is a system of a large number of different molecules which combine and interact to generate complex structures and functions. These combinations and interactions of molecules need to be choreographed perfectly in time and space to achieve intended intra-cellular functions. Spatiotemporal control promises to be a versatile tool for dynamical control of spatially manipulated bio-molecules.
DOI
S. Stallinga
A theory of optical trapping at low Numerical Aperture (NA) is presented. The theory offers an analytical description of the competition between the stabilizing gradient and destabilizing scattering force. The trade-off can be characterized by a single dimensionless trapping parameter, which increases with bead size to wavelength ratio $a/\lambda$ and refractive index contrast $m$ and decreases with NA. The gradient force dominates for small trapping parameters, the scattering force for large trapping parameters. The potential well depth, maximum forces and trap stiffness as a function of the three parameters ($a/\lambda$, $m$, NA) can be mapped onto universal functions of the trapping parameter. These functions do not depend on any free parameter. The universal well depth and maximum force curves match with numerical results based on the exact multipole expansion of the optical trapping force. The paraxial limit of low NA is relevant for compact optical tweezers based on Optical Pickup Units known from optical data storage.
DOI
Bob M. Lansdorp and Omar A. Saleh
Single-molecule manipulation instruments, such as optical traps and magnetic tweezers, frequently use video tracking to measure the position of a force-generating probe. The instruments are calibrated by comparing the measured probe motion to a model of Brownian motion in a harmonic potential well; the results of calibration are estimates of the probe drag, α, and spring constant, κ. Here, we present both time- and frequency-domain methods to accurately and precisely extract α and κ from the probe trajectory. In the frequency domain, we discuss methods to estimate the power spectral density (PSD) from data (including windowing and blocking), and we derive an analytical formula for the PSD which accounts both for aliasing and the filtering intrinsic to video tracking. In the time domain, we focus on the Allan variance (AV): we present a theoretical equation for the AV relevant to typical single-molecule setups and discuss the optimal manner for computing the AV from experimental data using octave-sampled overlapping bins. We show that, when using maximum-likelihood methods to fit to the data, both the PSD and AV approaches can extract α and κ in an unbiased and low-error manner, though the AV approach is simpler and more robust.
DOI
Hao Yu, Xia Liu, Krishna Neupane, Amar Nath Gupta, Angela M. Brigley, Allison Solanki, Iveta Sosova, and Michael T. Woodside
Protein misfolding is a ubiquitous phenomenon associated with a wide range of diseases. Single-molecule approaches offer a powerful tool for deciphering the mechanisms of misfolding by measuring the conformational fluctuations of a protein with high sensitivity. We applied single-molecule force spectroscopy to observe directly the misfolding of the prion protein PrP, a protein notable for having an infectious misfolded state that is able to propagate by recruiting natively folded PrP. By measuring folding trajectories of single PrP molecules held under tension in a high-resolution optical trap, we found that the native folding pathway involves only two states, without evidence for partially folded intermediates that have been proposed to mediate misfolding. Instead, frequent but fleeting transitions were observed into off-pathway intermediates. Three different misfolding pathways were detected, all starting from the unfolded state. Remarkably, the misfolding rate was even higher than the rate for native folding. A mutant PrP with higher aggregation propensity showed increased occupancy of some of the misfolded states, suggesting these states may act as intermediates during aggregation. These measurements of individual misfolding trajectories demonstrate the power of single-molecule approaches for characterizing misfolding directly by mapping out nonnative folding pathways.
DOI
Z.L. Zhou, B. Tang, A.H.W. Ngan, Z.N. Dong, and Y.S. Wu
The protein–protein interactions between hepatitis B surface antigen (HBsAg) and itsantibodies (anti-HBs) were studied by measuring the binding force between microspheres coated with such proteins using optical tweezers. The interaction force between the protein-coated microspheres was found to be strongly influenced by the acidity of the surrounding liquid medium, as well as the experimental temperature, and it reaches a maximum value at around pH 7.5 and temperature around 37°C. By measuring the protein distribution on the surfaces of the microspheres and their contact areas using scanning electron microscopy, the specific binding force between an HBsAg and anti-HBs protein pair is estimated to be around 4.8 pN at the optimum pH value and temperature at an applied loading rate of around 1 pN/s.
DOI
Jolly Xavier, Raktim Dasgupta, Sunita Ahlawat, Joby Joseph, and Pradeep Kumar Gupta
We demonstrate tunable helically stacked multi-layered microrotors realized in vortex-embedded three dimensional (3D) optical twister patterns. Intensity-tunable annular irradiance profiles with higher order vortex are generated as well as simultaneously unfolded by phase-engineered multiple plane wave interference. In the individually tunable 3D helical bright arms of these unfolded vortex structures, 2 μm silica beads are optically trapped as spiraling multilayered handles of multi-armed microrotors. Further, multiple rows of such microrotors are parallelly actuated with controllable sense of rotation. We also present our observation on helical 3D stacking of micro-particles in these longitudinally gyrating multi-armed rotor traps.
DOI
Rahul P. Trivedi, Ivan I. Klevets, Bohdan Senyuk, Taewoo Lee, and Ivan I. Smalyukh
Colloidal systems find important applications ranging from fabrication of photonic crystals to direct probing of phenomena typically encountered in atomic crystals and glasses. New applications—such as nanoantennas, plasmonic sensors, and nanocircuits—pose a challenge of achieving sparse colloidal assemblies with tunable interparticle separations that can be controlled at will. We demonstrate reconfigurable multiscale interactions and assembly of colloids mediated by defects in cholesteric liquid crystals that are probed by means of laser manipulation and three-dimensional imaging. We find that colloids attract via distance-independent elastic interactions when pinned to the ends of cholesteric oily streaks, line defects at which one or more layers are interrupted. However, dislocations and oily streaks can also be optically manipulated to induce kinks, allowing one to lock them into the desired configurations that are stabilized by elastic energy barriers for structural transformation of the particle-connecting defects. Under the influence of elastic energy landscape due to these defects, sublamellar-sized colloids self-assemble into structures mimicking the cores of dislocations and oily streaks. Interactions between these defect-embedded colloids can be varied from attractive to repulsive by optically introducing dislocation kinks. The reconfigurable nature of defect–particle interactions allows for patterning of defects by manipulation of colloids and, in turn, patterning of particles by these defects, thus achieving desired colloidal configurations on scales ranging from the size of defect core to the sample size. This defect-colloidal sculpturing may be extended to other lamellar media, providing the means for optically guided self-assembly of mesoscopic composites with predesigned properties.
DOI
Tomoaki Masuda, Alexey N. Petrov, Ryo Iizuka, Takashi Funatsu, Joseph D. Puglisi, and Sotaro Uemura
Initiation factor 2 (IF2) is a key factor in initiation of bacterial protein synthesis. It recruits initiator tRNA to the small ribosomal subunit and facilitates joining of the large ribosomal subunit. Using reconstituted translation system of Escherichia coli and optical tweezers, we directly measure the rupture force between single ribosomal complexes and mRNAs for initiation complexes in the presence and the absence of IF2. We demonstrate that IF2 together with codon recognition by initiator tRNA increases the force required to dislocate mRNA from the ribosome complexes; mRNA stabilization by IF2 required the presence of a joined 50S subunit, and was independent of bound guanine nucleotide. IF2 thus helps lock the 70S ribosome over the start codon during initiation, thus maintaining reading frame. Our results show how mRNA is progressively stabilized on the ribosome through distinct steps of initiation.
DOI
Wilhelm J. Walter, Michael P. Koonce, Bernhard Brenner, and Walter Steffen
Cytoplasmic dynein is a microtubule-based molecular motor that participates in a multitude of cell activities, from cell division to organelle transport. Unlike kinesin and myosin, where different tasks are performed by highly specialized members of these superfamilies, a single form of the dynein heavy chain is utilized for different functions. This versatility demands an extensive regulation of motor function. Using an improved application of an optical trap, we were now able to demonstrate that cytoplasmic dynein can generate a discrete power stroke as well as a processive walk in either direction; i.e., towards the plus- or towards the minus-end of a microtubule. Thus, dynein’s motor functions can be described by four basic modes of motion: processive and nonprocessive movement, and movement in the forward and reverse directions. Importantly, these four modes of movement can be controlled by two switches. One switch, based on phosphate, determines the directionality of movement. The second switch, depending on magnesium, converts cytoplasmic dynein from a nonprocessive to a processive motor. The two switches can be triggered separately or jointly by changing concentrations of phosphate and magnesium in the local environment. The control of four modes of movement by two switches has major implications for our understanding of the cellular functions and regulation of cytoplasmic dynein. Based on recent studies of dynein’s structure we are able to draw new conclusions on cytoplasmic dynein’s stepping mechanism.
DOI
Nicholas Hyun, Charlie Chandsawangbhuwana, Collin Yang-Wong, Michael W. Berns, Qingyuan Zhu, Linda Z. Shi
The purpose of this study is to analyze human sperm motility and energetics in media with different viscosities. Multiple experiments were performed to collect motility parameters using customized computer tracking software that measures the curvilinear velocity (VCL) and the minimum laser power (Pesc) necessary to hold an individual sperm in an optical trap. The Pesc was measured by using a 1064 nm Nd:YVO4continuous wave laser that optically traps motile sperm at a power of 450 mW in the focused trap spot. The VCL was measured frame by frame before trapping. In order to study sperm energetics under different viscous conditions sperm were labeled with the fluorescent dye DiOC6(3) to measure membrane potentials of mitochondria in the sperm midpiece. Fluorescence intensity was measured before and during trapping. The results demonstrate a decrease in VCL but an increase in Pesc with increasing viscosity. Fluorescent intensity is the same regardless of the viscosity level indicating no change in sperm energetics. The results suggest that, under the conditions tested, viscosity physically affects the mechanical properties of sperm motility rather than the chemical pathways associated with energetics.
DOI
