System−Bath Correlation Function Probed by Conventional and Time-Gated Stimulated Photon Echo

Structure and Dynamics of Stacking Interactions in an Antibody Binding Site

For years, antibodies (Abs) have been used as a paradigm for understanding how protein structure contributes to molecular recognition. However, with the ability to evolve Abs that recognize specific chromophores, they also have great potential as models for how protein dynamics contribute to molecular recognition. We previously raised murine Abs to different chromophores and, with the use of three-pulse photon echo peak shift spectroscopy, demonstrated that the immune system is capable of producing Abs with widely varying flexibility. We now report the characterization of the complexes formed between two Abs, 5D11 and 10A6, and the chromophoric ligand that they were evolved to recognize, 8-methoxypyrene-1,3,6-trisulfonic acid (MPTS). The sequences of the Ab genes indicate that they evolved from a common precursor. We also used a variety of spectroscopic methods to probe the photophysics and dynamics of the Ab-MPTS complexes and found that they are similar to each other but distinct from previously characterized anti-MPTS Abs. Structural studies revealed that this difference likely results from a unique mode of binding in which MPTS is sandwiched between the side chain of Phe^H98, which interacts with the chromophore via T-stacking, and the side chain of Trp^L91, which interacts with the chromophore via parallel stacking. The T-stacking interaction appears to mediate relaxation on the picosecond time scale, while the parallel stacking appears to mediate relaxation on an ultrafast, femtosecond time scale, which dominates the response. The anti-MPTS Abs thus not only demonstrate the simultaneous use of the two limiting modes of stacking for molecular recognition, but also provide a unique opportunity to characterize how dynamics might contribute to molecular recognition. Both types of stacking are common in proteins and protein complexes where they may similarly contribute to dynamics and molecular recognition.

Ultrafast Vibrational Echo Spectroscopy of Liquid Water from First-Principles Simulations

Vibrational echo spectroscopy has become a powerful technique to study vibrational spectral diffusion in water and aqueous solutions. The dynamics of vibrational spectral diffusion is intimately related to the hydrogen bond fluctuations in liquid water and other hydrogen bonded liquids. Earlier theoretical calculations of vibrational echo spectroscopy of aqueous systems were based on classical molecular dynamics simulations involving empirical force fields of water. In the current work, we have employed the method of ab initio molecular dynamics simulation to calculate the spectral observables of vibrational echo and two-dimensional infrared (2D-IR) spectroscopy of liquid water at room temperature under Condon and cumulant approximations. The time scales extracted from the temporal decay of the frequency-time correlation function (FTCF), short-time slope of three pulse photon echo (SP3E), dynamic line width (DLW), and the slope of nodal line of 2D-IR spectra are found to be in reasonably close agreement with each other which reinforces the assertion that signatures of FTCF can be captured using three pulse photon echo and 2D-IR spectroscopy.

Adaptive mutations alter antibody structure and dynamics during affinity maturation

While adaptive mutations can bestow new functions on proteins via the introduction or optimization of reactive centers, or other structural changes, a role for the optimization of protein dynamics also seems likely but has been more difficult to evaluate. Antibody (Ab) affinity maturation is an example of adaptive evolution wherein the adaptive mutations may be identified and Abs may be raised to specific targets that facilitate the characterization of protein dynamics. Here, we report the characterization of three affinity matured Abs that evolved from a common germline precursor to bind the chromophoric antigen (Ag), 8-methoxypyrene-1,3,6-trisulfonate (MPTS). In addition to characterizing the sequence, molecular recognition, and structure of each Ab, we characterized the dynamics of each complex by determining their mechanical response to an applied force via three-pulse photon echo peak shift (3PEPS) spectroscopy and deconvoluting the response into elastic, anelastic, and plastic components. We find that for one Ab, affinity maturation was accomplished via the introduction of a single functional group that mediates a direct contact with MPTS and results in a complex with little anelasticity or plasticity. In the other two cases, more mutations were introduced but none directly contact MPTS, and while their effects on structure are subtle, their effects on anelasticity and plasticity are significant, with the level of plasticity correlated with specificity, suggesting that the optimization of protein dynamics may have contributed to affinity maturation. A similar optimization of structure and dynamics may contribute to the evolution of other proteins.

Solvent Environment Revealed by Positively Chirped Pulses

The spectroscopy of large organic molecules and biomolecules in solution has been investigated using various time-resolved and frequency-resolved techniques. Of particular interest is the early response of the molecule and the solvent, which is difficult to study due to the ambiguity in assigning and differentiating inter- and intramolecular contributions to the electronic and vibrational populations and coherence. Our measurements compare the yield of fluorescence and stimulated emission for two laser dyes IR144 and IR125 as a function of chirp. While negatively chirped pulses are insensitive to solvent viscosity, positively chirped pulses are found to be uniquely sensitive probes of solvent viscosity. The fluorescence maximum for IR125 is observed near transform-limited pulses; however, for IR144, it is observed for positively chirped pulses once the pulses have been stretched to hundreds of femtoseconds. We conclude that chirped pulse spectroscopy is a simple one-beam method that is sensitive to early solvation dynamics.

Ultrafast solvation dynamics and charge transfer reactions in room temperature ionic liquids

In this perspective, we review the recent studies concerning the liquid structure and solvation dynamics of ionic liquids, and their influence upon electron transfer and charge transfer reactions.

Dynamics of water confined in reversed micelles: multidimensional vibrational spectroscopy study

Here we perform a comprehensive study of ultrafast molecular and vibrational dynamics of water confined in small reversed micelles (RMs). The molecular picture is elucidated with two-dimensional infrared (2D IR) spectroscopy of water OH stretch vibrations and molecular dynamics simulations, bridged by theoretical calculations of linear and 2D IR vibrational spectra. To investigate the effects of intermolecular coupling, experiments and modeling are performed for isotopically diluted (HDO in D2O) and undiluted (H2O) water. We put a separation of water inside RMs into two subensembles (water-bound and surfactant-bound molecules), observed by many before, on a solid theoretical basis. Water molecules fully attached to the lipid interface ("shell" water) are decoupled from one another and from the central water nanopool ("core" water). The environmental fluctuations are largely "frozen" for the shell water, while the core waters demonstrate much faster dynamics but still not as fast as in the bulk case. A substantial nanoconfinement effect on the dynamics of the core water is observed after disentanglement of the shell water contribution, which is fully confirmed by the simulations of 2D IR spectra. Current results provide new insights into interaction between biological objects like membranes or proteins with the surrounding aqueous bath, and highlight peculiarities in vibrational energy redistribution near the lipid surface.

Protein dynamics and the diversity of an antibody response

The immune system is remarkable in its ability to produce antibodies (Abs) with virtually any specificity from a limited repertoire of germ line precursors. Although the contribution of sequence diversity to this molecular recognition has been studied for decades, recent models suggest that protein dynamics may also broaden the range of targets recognized. To characterize the contribution of protein dynamics to immunological molecular recognition, we report the sequence, thermodynamic, and time-resolved spectroscopic characterization of a panel of eight Abs elicited to the chromophoric antigen 8-methoxypyrene-1,3,6-trisulfonate (MPTS). Based on the sequence data, three of the Abs arose from unique germ line Abs, whereas the remaining five comprise two sets of siblings that arose by somatic mutation of a common precursor. The thermodynamic data indicate that the Abs recognize MPTS via a variety of mechanisms. Although the spectroscopic data reveal small differences in protein dynamics, the anti-MPTS Abs generally show similar levels of flexibility and conformational heterogeneity, possibly representing the convergent evolution of the dynamics necessary for function. However, one Ab is significantly more rigid and conformationally homogeneous than the others, including a sibling Ab from which it differs by only five somatic mutations. This example of divergent evolution demonstrates that point mutations are capable of fixing significant differences in protein dynamics. The results provide unique insight into how high affinity Abs may be produced that bind virtually any target and possibly, from a more general perspective, how new protein functions are evolved.

Image time-correlation, dynamic light scattering, and birefringence for the study of the response of anisometric colloids to external fields

In this paper, a detailed description of equipment is given, specially designed to characterize the response of non-spherical colloids to external fields. To characterize slow structural changes on a large length scale we developed an image correlation method, fast dynamics on the colloidal-particle level is probed by means of a vertically mounted, small angle dynamic light scattering setup, while the orientational order (induced by the external field) is measured with a birefringence setup with off-normal incidence. The performance of this in situ set of instruments is illustrated by experiments on concentrated dispersions of very long and thin, charged colloidal rods (fd-virus particles) in external electric fields. Here, the frequency of the field is sufficiently low to polarize electrical double layers, leading to additional inter-colloidal interactions which are found to give rise to phase/state transitions and dynamical states (K. Kang and J. K. G. Dhont, Soft Matter 6, 273, 2010).

Molecular description of flexibility in an antibody combining site

Mature antibodies (Abs) that are exquisitely specific for virtually any foreign molecule may be produced by affinity maturation of naïve (or germline) Abs. However, the finite number of germline Abs available suggests that, in contrast to mature Abs, germline Abs must be broadly polyspecific so that they are able to recognize a wide range of ligands. Thus, affinity maturation must play a role in mediating Ab specificity. One biophysical property that distinguishes polyspecificity from specificity is protein flexibility; a flexible combining site is able to adopt different conformations that recognize different foreign molecules (or antigens), while a rigid combining site is locked into a conformation that is specific for a given antigen. Recent studies (Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 8821-8826) have examined, at the atomic level, the structural properties that mediate changes in flexibility at four stages of affinity maturation in the 4-4-20 Ab. These studies employed molecular dynamics simulations to reveal a network of residue interactions that mediate the flexibility changes accompanying maturation. The flexibility of the Ab combining sites in these molecular systems was originally measured using three-pulse photon echo spectroscopy (3PEPS). The present investigation extends this work by providing a concrete link between structural properties of the Ab molecules and features of the spectroscopic measurements used to characterize their flexibility. Results obtained from the simulations are in good qualitative agreement with the experimental measurements and indicate that the spectroscopic signal is sensitive to protein dynamics distributed throughout the entire combining site. Thus, the simulations provide a molecular-level interpretation of the changes induced by affinity maturation of the Ab. The results suggest that 3PEPS spectroscopy in combination with molecular dynamics simulations can provide a detailed description of protein dynamics and, in this case, how it is evolved for biological function.

Two-dimensional electronic spectroscopy of molecular excitons

Understanding of the nuclear and electronic structure and dynamics of molecular systems has advanced considerably through probing the nonlinear response of molecules to sequences of pulsed electromagnetic fields. The ability to control various degrees of freedom of the excitation pulses-such as duration, sequence, frequency, polarization, and shape-has led to a variety of time-resolved spectroscopic methods. The various techniques that researchers use are commonly classified by their dimensionality, which refers to the number of independently variable time delays between the pulsed fields that induce the signal. Though pico- and femtosecond time-resolved spectroscopies of electronic transitions have come of age, only recently have researchers been able to perform two-dimensional electronic spectroscopy (2D-ES) in the visible frequency regime and correlate transition frequencies that evolve in different time intervals. The two-dimensional correlation plots and their temporal evolution allow one to access spectral information that is not exposed directly in other one-dimensional nonlinear methods. In this Account, we summarize our studies of a series of increasingly complex molecular chromophores. We examine noninteracting dye molecules, a monomer-dimer equilibrium of a prototypical dye molecule, and finally a supramolecular assembly of electronically coupled absorbers. By tracing vibronic signal modulations, differentiating line-broadening mechanisms, analyzing distinctly different relaxation dynamics, determining electronic coupling strengths, and directly following excitation energy transfer pathways, we illustrate how two-dimensional electronic spectroscopy can image physical phenomena that underlie the optical response of a particular system. Although 2D-ES is far from being a "turn-key" method, we expect that experimental progress and potential commercialization of instrumentation will make 2D-ES accessible to a much broader scientific audience, analogous to the development of multidimensional NMR and 2D-IR.

Dissimilar dynamics of coupled water vibrations

Dissimilar dynamics of coupled stretch vibrations of a water molecule are revealed by two-dimensional IR correlation spectroscopy. These are caused by essentially non-Gaussian fluctuations of the electric field exerted by the environment on the individual OH stretch vibrations. Non-Gaussian statistics of the individual site frequency fluctuations results in distinctively different dephasing of the symmetric and asymmetric eigenmodes. This phenomenon can only be described if the assumption of Gaussian dynamics in the traditional theories is abandoned.

Ultrafast dynamics in reverse micelles

Recent advances in ultrafast laser technology have spurred investigations of microheterogeneous solutions. In particular, researchers have explored details of reverse micelles (RMs), which present isolated droplets of polar solvent sequestered from a continuous nonpolar phase by a surfactant layer. This review explores recent studies utilizing a variety of ultrafast laser techniques to uncover details about structure and dynamics in various RMs. Using ultrafast vibrational spectroscopy, researchers have probed hydrogen-bond dynamics and vibrational energy relaxation in RMs. These studies have developed our understanding of reverse micellar structure, identifying varying water environments in the RMs. In a plethora of experiments employing probe molecules, researchers have explored the confined environment presented by RMs and their impact on a range of chemical reactions. These studies have shown that confinement, rather than the specific interactions with surfactants, is an important factor determining the impact of the reverse micellar environment on the chemistry.

Three-pulse photon echo peak shift spectroscopy as a probe of flexibility and conformational heterogeneity in protein folding

We investigate the equilibrium unfolding of Zn-cytochrome c in guanidine hydrochloride by three-pulse photon echo peak shift (3PEPS) spectroscopy. Unexpectedly, the measurements reveal that inhomogeneous broadening of the sample at the midpoint of the denaturation is larger than that of either native or unfolded states. To interpret this finding, we present simulations of the peak shift for both two-state and three-state unfolding models. Both the denaturant concentration dependence of the asymptotic peak shift (APS) and the wavelength dependence of the APS at the midpoint of the denaturation are different for the two models. Our data are consistent with two-state unfolding.

Exploring the energy landscape of antibody-antigen complexes: protein dynamics, flexibility, and molecular recognition

The production of antibodies that selectively bind virtually any foreign compound is the hallmark of the immune system. While much is understood about how sequence diversity contributes to this remarkable feat of molecular recognition, little is known about how sequence diversity impacts antibody dynamics, which is also expected to contribute to molecular recognition. Toward this goal, we examined a panel of antibodies elicited to the chromophoric antigen fluorescein. On the basis of isothermal titration calorimetry, we selected six antibodies that bind fluorescein with diverse binding entropies, suggestive of varying contributions of dynamics to molecular recognition. Sequencing revealed that two pairs of antibodies employ homologous heavy chains that were derived from common germline genes, while the other two heavy chains and all six of the light chains were derived from different germline genes and are not homologous. Interestingly, more than half of all the somatic mutations acquired during affinity maturation among the six antibodies are located in positions unlikely to contact fluorescein directly. To quantify and compare the dynamics of the antibody-fluorescein complexes, three-pulse photon echo peak shift and transient grating spectroscopy were employed. All of the antibodies exhibited motions on three distinct time scales, ultrafast motions on the <100 fs time scale, diffusive motions on the picosecond time scale, and motions that occur on time scales longer than nanoseconds and thus appear static. However, the exact frequency of the picosecond time scale motion and the relative contribution of the different motions vary significantly among the antibody-chromophore complexes, revealing a high level of dynamic diversity. Using a hierarchical model, we relate the data to features of the antibodies' energy landscapes as well as their flexibility in terms of elasticity and plasticity. In all, the data provide a consistent picture of antibody flexibility, which interestingly appears to be correlated with binding entropy as well as with germline gene use and the mutations introduced during affinity maturation. The data also provide a gauge of the dynamic diversity of the antibody repertoire and suggest that this diversity might contribute to molecular recognition by facilitating the recognition of the broadest range of foreign molecules.