Ying-Jen Shiu

Ab initio study of the n-pi(*) electronic transition in acetone: Symmetry-forbidden vibronic spectra

Ab initio calculations of geometry and vibrational frequencies of the first singlet excited 1A2(1A″) state of acetone corresponding to the n-π* electronic transition have been carried out at the CASSCF/6-311G** level. The major geometry changes in this state as compared to the ground state involve CO out-of-plane wagging, CO stretch and torsion of the methyl groups, and the molecular symmetry changes from C2v to Cs. The most pronounced frequency changes in the 1A″ state are the decrease of the CO stretch frequency v3 by almost 500 cm−1 and the increase of the CH3 torsion frequency v12 from 22 to 170 cm−1. The optimized geometries and normal modes are used to compute the normal mode displacements which are applied for calculations of Franck–Condon factors. Transition matrix elements over the one-electron electric field operator at various atomic centers calculated at the state-average CASSCF/6-311+G** level are used to compute vibronic couplings between the ground 1A1, 1A2, and Rydberg 1B2(n-3s), 2 1A1(n-3...

Computational formulas for symmetry-forbidden vibronic spectra and their application to n–π* transition in neat acetone

In this study theoretical expressions are derived to investigate the non-Condon effect for symmetry-forbidden optical transition using displaced–distorted harmonic potential energy surfaces. These expressions can efficiently cope with multipromoting modes and multielectronic states involved in the non-Condon effect at a finite temperature. Ab initio and molecular dynamics calculation results can be directly invoked into the formulas. Based on the proposed formulas, the temperature dependence of the interference effects of multipromoting modes on the non-Condon optical linear spectra is investigated. To demonstrate the computational formulas, the optical absorption and dispersion fluorescence spectra for the forbidden transition of neat acetone, 1A1–1A2(n–π*), are also studied. Simulation results indicate that the vibrational frequency of CH3 torsion mode of acetone plays an important role in the optical spectra. Moreover, the electronic energy gap (adiabatic transition), the Stokes shift caused by environ...

Charge interaction and temperature effects on the solution structure of lysozyme as revealed by small-angle X-ray scattering

We have studied the structure of lysozyme as influenced by solution environment using small-angle X-ray scattering (SAXS). With an ellipsoid form factor and a structure factor derived using the mean spherical approximation to account for the electrostatic repulsion of lysozyme, we have extracted detailed structural information about the protein in aqueous solutions, including the size, shape, and net charge number. The SAXS data analysis shows that lysozyme in pure water, expressing an averaged net charge number of ~6, folds to an ellipsoid-like shape with a radius of gyration Rg = 16.6 A. Temperature-dependent SAXS for lysozyme in a buffer solution in which charge repulsion has been eliminated suggests that the protein may thermally unfold gradually along a preferred direction from the ellipsoidal shape with an aspect ratio of p ≃ 2 at 303 K to an elongated shape with p ≃ 3 at 343 K. The structural parameters of the unfolded lysozyme obtained using model fitting are compared with the envelope morphology simulated using a dummy-residues model. From the evolution of the volume of lysozyme during the thermal unfolding process, we deduce a free-energy profile for the protein thermally unfolded in water using a modified Ising model on the basis of a mean field approximation.

Thermodynamics and kinetics of protein folding: A mean field theory

The kinetic Ising model in the mean field approximation is applied to study the equilibrium and kinetic behaviors of protein folding–unfolding. In our model, we regard a protein as a topological collection of interacting peptide bonds (or other protein units). According to this model, thermodynamics and kinetics of protein folding–unfolding are related to the elementary process of folding ↔ unfolding of such interacting units. We shall show that even for the so-called two-state case of protein folding–unfolding, the kinetic behaviors are predicted to be in general non-exponential and that universal curves exist separately for the thermodynamic behaviors and kinetics behaviors of protein folding–unfolding. Our model can treat the effect of temperature and denaturant concentration on the thermodynamics and kinetics of protein folding–unfolding and provide the chevron plot. Satisfactory demonstrations are presented for treating experimental observations on the thermodynamical and kinetic responses of protein folding–unfolding to the changes in temperature and denaturant concentration and for exhibiting universal plots of proteins.

Nonadditive Interactions in Protein Folding: The Zipper Model of Cytochrome c

Hydrogen exchange experiments (Krishna et al. in J. Mol. Biol. 359:1410, 2006) reveal that folding–unfolding of cytochrome c occurs along a defined pathway in a sequential, stepwise manner. The simplified zipper-like model involving nonadditive coupling is proposed to describe the classical “on pathway” folding–unfolding behavior of cytochrome c. Using free energy factors extracted from HX experiments, the model can predict and explain cytochrome c behavior in spectroscopy studies looking at folding equilibria and kinetics. The implications of the proposed model are discussed for such problems as classical pathway vs. energy landscape conceptions, structure and function of a native fold, and interplay of secondary and tertiary interactions.

Probing the Acid-Induced Packing Structure Changes of the Molten Globule Domains of a Protein near Equilibrium Unfolding

Using simultaneously scanning small-angle X-ray scattering (SAXS) and UV-vis absorption with integrated online size exclusion chromatography, supplemental with molecular dynamics simulations, we unveil the long-postulated global structure evolution of a model multidomain protein bovine serum albumin (BSA) during acid-induced unfolding. Our results differentiate three global packing structures of the three molten globule domains of BSA, forming three intermediates I1, I2, and E along the unfolding pathway. The I1-I2 transition, overlooked in all previous studies, involves mainly coordinated reorientations across interconnected molten globule subdomains, and the transition activates a critical pivot domain opening of the protein for entering into the E form, with an unexpectedly large unfolding free energy change of -9.5 kcal mol-1, extracted based on the observed packing structural changes. The revealed local packing flexibility and rigidity of the molten globule domains in the E form elucidate how collective motions of the molten globule domains profoundly influence the folding-unfolding pathway of a multidomain protein.

A modified Ising model for the thermodynamic properties of local and global protein folding- unfolding observed by circular dichroism and small-angle X-ray scattering

Based on the mean-field approximation, we have applied a modified Ising model to describe general protein unfolding behavior at thermodynamic equilibrium with the free energy contributed by the subgroup units (amino acids or peptide bonds) of the protein. With the thermodynamic properties of the protein, this model can associate the stepwise change of an unfolding fraction ratio profile with the local and global conformation unfolding. Taking cytochrome c (cyt c) as a model protein, we have observed, using small-angle X-ray scattering and circular dichroism (CD), the global and local structure changes for the protein in three kinds of denaturant environments: acid, urea and guanidine hydrochloride. The small-angle X-ray scattering and CD results are mapped to the unfolding fractions as a function of the pH value or denaturant concentration, from which we have extracted local and global unfolding free energies of cyt c in different denaturant environments using a modified Ising model. Based on the characteristics of the thermodynamic properties deduced from the local and global protein folding–unfolding, we discuss the thermodynamic stabilities of the protein in the three denaturant environments, and the possible correlation between the global conformation change of the protein and the local unfolding activities of the S—Fe bond in the Met80-heme and the α-helices.