Kyung Koo Lee

Computational spectroscopy of ubiquitin: comparison between theory and experiments.

Using the constrained molecular dynamics simulation method in combination with quantum chemistry calculation, Hessian matrix reconstruction, and fragmentation approximation methods, the authors have established computational schemes for numerical simulations of amide I IR absorption, vibrational circular dichroism (VCD), and two-dimensional (2D) IR photon echo spectra of the protein ubiquitin in water. Vibrational characteristic features of these spectra in the amide I vibration region are discussed. From the semiempirical quantum chemistry calculation results on an isolated ubiquitin, amide I local mode frequencies and vibrational coupling constants were fully determined. It turns out that the amide I local mode frequencies of ubiquitin in both gas phase and aqueous solution are highly heterogeneous and site dependent. To directly test the quantitative validity of thus obtained spectroscopic properties, they compared the experimentally measured amide I IR, 2D IR, and electronic circular dichroism spectra with experiments, and found good agreements between theory and experiments. However, the simulated VCD spectrum is just qualitatively similar to the experimentally measured one. This indicates that, due to delicate cancellations between the positive and negative VCD contributions, the prediction of protein VCD spectrum is critically relied on quantitative accuracy of the theoretical model for predicting amide I local mode frequencies. On the basis of the present comparative investigations, they found that the site dependency of amide I local mode frequency, i.e., diagonal heterogeneity of the vibrational Hamiltonian matrix in the amide I local mode basis, is important. It is believed that the present computational methods for simulating various vibrational and electronic spectra of proteins will be of use in further refining classical force fields and in addressing the structure-spectra relationships of proteins in solution.

Classical and quantum mechanical/molecular mechanical molecular dynamics simulations of alanine dipeptide in water: comparisons with IR and vibrational circular dichroism spectra.

We have implemented the combined quantum mechanical (QM)/molecular mechanical (MM) molecular dynamics (MD) simulations of alanine dipeptide in water along with the polarizable and nonpolarizable classical MD simulations with different models of water. For the QM/MM MD simulation, the alanine dipeptide is treated with the AM1 or PM3 approximations and the fluctuating solute dipole moment is calculated by the Mulliken population analysis. For the classical MD simulations, the solute is treated with the polarizable or nonpolarizable AMBER and polarizable CHARMM force fields and water is treated with the TIP3P, TIP4P, or TIP5P model. It is found that the relative populations of right-handed alpha-helix and extended beta and P(II) conformations in the simulation trajectory strongly depend on the simulation method. For the QM/MM MD simulations, the PM3/MM shows that the P(II) conformation is dominant, whereas the AM1/MM predicts that the dominant conformation is alpha(R). Polarizable CHARMM force field gives almost exclusively P(II) conformation and other force fields predict that both alpha-helical and extended (beta and P(II)) conformations are populated with varying extents. Solvation environment around the dipeptide is investigated by examining the radial distribution functions and numbers and lifetimes of hydrogen bonds. Comparing the simulated IR and vibrational circular dichroism spectra with experimental results, we concluded that the dipeptide adopts the P(II) conformation and PM3/MM, AMBER03 with TIP4P water, and AMBER polarizable force fields are acceptable for structure determination of the dipeptide considered in this paper.

Circular dichroism eigenspectra of polyproline II and β-strand conformers of trialanine in water: Singular value decomposition analysis†

Despite that a number of experimental and theoretical investigations have been carried out to determine the structure of trialanine in water, the reported populations of polyproline II (PPII) and β-strand conformers vary and were found to be dependent on which spectroscopic method was used. Such discrepancies are due to limitations of different spectroscopic methods used. Here, the temperature- and pH-dependent circular dichroism (CD) and NMR experiments have been carried out to develop a self-consistent singular value decomposition procedure. The temperature-dependent CD spectra indicate the presence of two conformers, but due to the two peptide bonds in a trialanine, one should take into consideration of four different conformers to fully interpret the NMR results. From the pH-dependent NMR coupling constant measurements, the conformation of zwitterionic trialanine is little different from that of cationic one. The strong pH dependency of CD spectrum is likely due to charge transfer transitions between carboxylate and nearby peptide groups or internal field effects not to pH-dependent conformational change. To simultaneously analyze the temperature-dependent CD and NMR data, a self-consistent procedure was used to newly determine the reference NMR coupling constants required to estimate one of the peptide dihedral angles. From the estimated enthalpy and entropy changes associated with the transition from enthalpically favorable PPII conformer to entropically favorable β-strand conformer, the relative populations of the four possible conformers of trialanine were determined and compared with the previous experimental findings. We anticipate that the present experimental results and interpretation procedure would be of use in determining the solution structures of small oligopeptides in the future.

Ion-pairing dynamics of Li + and SCN − in dimethylformamide solution: Chemical exchange two-dimensional infrared spectroscopy

Ultrafast two-dimensional infrared (2DIR) spectroscopy has been proven to be an exceptionally useful method to study chemical exchange processes between different vibrational chromophores under thermal equilibria. Here, we present experimental results on the thermal equilibrium ion pairing dynamics of Li(+) and SCN(-) ions in N,N-dimethylformamide. Li(+) and SCN(-) ions can form a contact ion pair (CIP). Varying the relative concentration of Li(+) in solution, we could control the equilibrium CIP and free SCN(-) concentrations. Since the CN stretch frequency of Li-SCN CIP is blue-shifted by about 16 cm(-1) from that of free SCN(-) ion, the CN stretch IR spectrum is a doublet. The temperature-dependent IR absorption spectra reveal that the CIP formation is an endothermic (0.57 kJ∕mol) process and the CIP state has larger entropy by 3.12 J∕(K mol) than the free ion states. Since the two ionic configurations are spectrally distinguishable, this salt solution is ideally suited for nonlinear IR spectroscopic investigations to study ion pair association and dissociation dynamics. Using polarization-controlled IR pump-probe methods, we first measured the lifetimes and orientational relaxation times of these two forms of ionic configurations. The vibrational population relaxation times of both the free ion and CIP are about 32 ps. However, the orientational relaxation time of the CIP, which is ∼47 ps, is significantly longer than that of the free SCN(-), which is ∼7.7 ps. This clearly indicates that the effective moment of inertia of the CIP is much larger than that of the free SCN(-). Then, using chemical exchange 2DIR spectroscopy and analyzing the diagonal peak and cross-peak amplitude changes with increasing the waiting time, we determined the contact ion pair association and dissociation time constants that are found to be 165 and 190 ps, respectively. The results presented and discussed in this paper are believed to be important, not only because the ion-pairing dynamics is one of the most fundamental physical chemistry problems but also because such molecular ion-ion interactions are of critical importance in understanding Hofmeister effects on protein stability.

A comprehensive library of blocked dipeptides reveals intrinsic backbone conformational propensities of unfolded proteins

Despite prolonged scientific efforts to elucidate the intrinsic peptide backbone preferences of amino‐acids based on understanding of intermolecular forces, many open questions remain, particularly concerning neighboring peptide interaction effects on the backbone conformational distribution of short peptides and unfolded proteins. Here, we show that spectroscopic studies of a complete library of 400 dipeptides reveal that, irrespective of side‐chain properties, the backbone conformation distribution is narrow and they adopt polyproline II and β‐strand, indicating the importance of backbone peptide solvation and electronic effects. By directly comparing the dipeptide circular dichroism and NMR results with those of unfolded proteins, the comprehensive dipeptides form a complete set of structural motifs of unfolded proteins. We thus anticipate that the present dipeptide library with spectroscopic data can serve as a useful database for understanding the nature of unfolded protein structures and for further refinements of molecular mechanical parameters. Proteins 2011;

Ultrafast vibrational spectroscopy of cyanophenols.

Aromatic compounds with electron-donating or -accepting substituents exhibit interesting resonance effects on a variety of chemical reactivities and optical properties. To understand such effects and the possible relationship between vibrational energy dissipation pathways and resonance structures of aromatic compounds, we studied ortho-, meta-, and para-substituted cyanophenols and their anionic forms in methanol by using time- and frequency-resolved pump-probe and two-dimensional IR spectroscopy, where the nitrile group acts as an IR probe. From the measured transient spectra and singular-value decomposition analyses, we found that there is a combination band whose frequency is very close to that of the nitrile stretch mode. Due to the difference in the lifetimes of these two mode excited states, the transient pump-probe spectra commonly show notable blue-shifting behaviors in time. Comparing the vibrational lifetimes of neutral cyanophenols and cyanophenoxide anions in methanol and carrying out quantum mechanical/molecular mechanical molecular dynamics simulations to study hydrogen-bonding dynamics, we found that the vibrational energy of the nitrile stretch mode initially relaxes to intramolecular degrees of freedom instead of solvent modes. Also, the vibrational anharmonic frequency shifts, intrinsic lifetimes, and bandwidths of the nitrile stretch mode and the combination mode in these molecular systems are fully characterized, and their relationships with resonance structures are discussed. It is believed that the present work sheds light on the intrinsic vibrational relaxation process of the nitrile stretch mode in cyanophenols, even in the case when their IR spectra are congested by the spectrally overlapping combination bands, and the resonance effects of aromatic compounds on vibrational dynamics and relaxation processes.

Integrated and dispersed photon echo studies of nitrile stretching vibration of 4-cyanophenol in methanol

By means of integrated and dispersed IR photon echo measurement methods, the vibrational dynamics of C-N stretch modes in 4-cyanophenol and 4-cyanophenoxide in methanol is investigated. The vibrational frequency-frequency correlation function (FFCF) is retrieved from the integrated photon echo signals by assuming that the FFCF is described by two exponential functions with about 400 fs and a few picosecond components. The excited state lifetimes of the C-N stretch modes of neutral and anionic 4-cyanophenols are 1.45 and 0.91 ps, respectively, and the overtone anharmonic frequency shifts are 25 and 28 cm(-1). At short waiting times, a notable underdamped oscillation, which is attributed to a low-frequency intramolecular vibration coupled to the CN stretch, in the integrated and dispersed vibrational echo as well as transient grating signals was observed. The spectral bandwidths of IR absorption and dispersed vibrational echo spectra of the 4-cyanophenoxide are significantly larger than those of its neutral form, indicating that the strong interaction between phenoxide and methanol causes large frequency fluctuation and rapid population relaxation. The resonance effects in a paradisubstituted aromatic compound would be of interest in understanding the conjugation effects and their influences on chemical reactivity of various aromatic compounds in organic solvents.

Phosphorylation effect on the GSSS peptide conformation in water: Infrared, vibrational circular dichroism, and circular dichroism experiments and comparisons with molecular dynamics simulations

The phosphorylation effect on the small peptide conformation in water has not been clearly understood yet, despite the widely acknowledged notion that control of protein activity by phosphorylation works mainly by inducing conformational change. To elucidate the detailed mechanism, we performed infrared (IR) absorption and vibrational and electronic circular dichroism studies of both unphosphorylated and phosphorylated tetrapeptides, GSSS 1 and GSSpS 2. The solution structure of the tetrapeptide is found to be little dependent on the presence of the neutral or negatively charged phosphoryl group, and to be a mixture of extended structures including polyproline II (PII) and beta-sheet conformations. The additional band at 1598 cm(-1) in the amide I IR spectrum of the phosphorylated peptide GSSpS at neutral pD appears to be clear spectroscopic evidence for direct intramolecular hydrogen-bonding interaction between the side chain dianionic phosphoryl group and the backbone amide proton. On the basis of amide I IR band analyses, the authors found that the probability of finding the phosphoryl group strongly H bonded to the backbone proton in GSSpS is about 43% at pD 7.0 and 37 degrees C. Such a H-bonding interaction in GSSpS has the biological standard enthalpy and entropy of -15.1 kJ/mol and -51.2 J/K mol, respectively. Comparisons between the experimentally measured IR and VCD spectra and the numerically simulated ones suggested that the currently available force field parameters need to be properly modified. The results in this paper may shed light on an unknown mechanism of controlling the peptide conformation by phosphorylation.

Infrared Probing of 4-Azidoproline Conformations Modulated by Azido Configurations

4-Azidoproline (Azp) can tune the stability of the polyproline II (P(II)) conformation in collagen. The azido group in the 4R and 4S configurations stabilizes and destabilizes the P(II) conformation, respectively. To obtain insights into the dependence of the conformational stability on the azido configuration, we carried out Fourier transform (FT) IR experiments with four 4-azidoproline derivatives, Ac-(4R/S)-Azp-(NH/O)Me. We found that the amide I and azido IR spectra are different depending on the azido configuration and C-terminal structure. The origin of such spectral differences between 4R and 4S configurations and between C-terminal methylamide and ester ends was elucidated by quantum chemistry calculations in combination with (1)H NMR and time- and frequency-resolved IR pump-probe spectroscopy. We found that the azido configurations and C-terminal structures affect intramolecular interactions, which are responsible for the ensuing conformational and thereby IR spectral differences. Consequently, 4-azidoproline conformations modulated by azido configurations can be probed by IR spectroscopy. These findings suggest that 4-azidoproline can be both a structure-control and -probing element, which enables the infrared tracking of proline roles in protein structure, function, and dynamics.

Polarization-Angle-Scanning 2DIR Spectroscopy of Coupled Anharmonic Oscillators: A Polarization Null Angle Method

Two-dimensional (2D) optical spectroscopy based on stimulated photon echo geometry requires multiple ultrashort pulses of which spatiotemporal properties and optical phases can be precisely controlled. Also, it is possible to change the incident beam polarization directions defined in a laboratory frame. Here, we introduce the polarization-angle-scanning (PAS) 2D spectroscopy and show that the diagonal and cross-peak amplitudes in the 2D spectrum can be arbitrarily modulated by spatially controlling the beam polarization directions. For a coupled anharmonic oscillator system, we specifically demonstrate that either diagonal or cross-peaks in the measured 2DIR spectra can be selectively eliminated and show that such polarization angles provide direct information on the relative angles between coupled transition dipoles and thereby on intricate details of molecular structures. We thus anticipate that the present PAS 2D optical spectroscopy can be a useful experimental method enabling us to probe structural evolutions of nonequilibrium state molecules by monitoring the time-dependent changes of the relative transition dipole directions.