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Minhaeng Cho

Publications and source records attributed to Minhaeng Cho.

At least 19 recordsLinked to original sources
PubMed2007

Thermal denaturation of polyalanine peptide in water by molecular dynamics simulations and theoretical prediction of infrared spectra: helix-coil transition kinetics.

Perspectives in the helix-coil transition kinetics of secondary structures are examined by temperature-jump molecular dynamics (T-jump MD) simulations and theoretically calculated infrared (IR) spectra. Homopolymeric polyalanine, Ac-(A)(21)-NHMe (A21), is unfolded in water by T-jumps from 273 to 300 K approximately 450 K using AMBER ff99 and ff03 force fields. MD simulation results provide in silico evidence that 3(10)-helix and type I beta-turn motifs are highly probable in both ff99 and ff03 results. Temperature-dependent difference IR spectra of A21 do not possess an isosbestic point in both results, and isotope-labeled difference IR spectra in ff03 results predict characteristic profiles observed in experiments. Unfolding rates obtained from simulated time-resoled IR spectra are in good agreement with those estimated by helical contents, but they are still an order of magnitude smaller than experimental values. We demonstrate that the conventional criteria such as single-exponential fit of transient amide I absorbance, sigmoidal fit of temperature-dependent amide I absorbance, and Arrhenius plot of relaxation rates cannot guarantee the validity of assuming a two-state mechanism. We suggest a way of determining T(m) by the temperature dependence of center frequency and full width at half-maximum of amide I band. Overall, both ff99 and ff03 force fields give consistent results in reproducing key aspects concerned experimentally, but are not predominantly satisfactory in quantitative aspects.

Algorithms↗
PubMed2006

Phenol-benzene complexation dynamics: quantum chemistry calculation, molecular dynamics simulations, and two dimensional IR spectroscopy.

Molecular dynamics (MD) simulations and quantum mechanical electronic structure calculations are used to investigate the nature and dynamics of the phenol-benzene complex in the mixed solvent, benzene/CCl4. Under thermal equilibrium conditions, the complexes are continuously dissociating and forming. The MD simulations are used to calculate the experimental observables related to the phenol hydroxyl stretching mode, i.e., the two dimensional infrared vibrational echo spectrum as a function of time, which directly displays the formation and dissociation of the complex through the growth of off-diagonal peaks, and the linear absorption spectrum, which displays two hydroxyl stretch peaks, one for the complex and one for the free phenol. The results of the simulations are compared to previously reported experimental data and are found to be in quite reasonable agreement. The electronic structure calculations show that the complex is T shaped. The classical potential used for the phenol-benzene interaction in the MD simulations is in good accord with the highest level of the electronic structure calculations. A variety of other features is extracted from the simulations including the relationship between the structure and the projection of the electric field on the hydroxyl group. The fluctuating electric field is used to determine the hydroxyl stretch frequency-frequency correlation function (FFCF). The simulations are also used to examine the number distribution of benzene and CCl4 molecules in the first solvent shell around the phenol. It is found that the distribution is not that of the solvent mole fraction of benzene. There are substantial probabilities of finding a phenol in either a pure benzene environment or a pure CCl4 environment. A conjecture is made that relates the FFCF to the local number of benzene molecules in phenol's first solvent shell.

Benzene↗
PubMed2006

Site-specific hydrogen-bonding interaction between N-acetylproline amide and protic solvent molecules: comparisons of IR and VCD measurements with MD simulations.

The effects of solute-solvent interactions on solution structures of small peptides have been paid a great deal of attention. To study the effect of hydrogen-bonding interactions on peptide solution structures, we measured the amide I IR and VCD spectra of N-acetylproline amide (AP) in various protic solvents, i.e., D2O, MeOD, EtOD, and PrOD, and directly compared them with theoretically simulated ones. The numbers of protic solvent molecules hydrogen-bonded to the two peptide bonds in the AP were quantitatively determined by carrying out the molecular dynamics (MD) simulations and then compared with the spectral analyses of the experimentally measured amide I bands. The two peptides in the AP have different propensities of forming H-bonds with protic solvent molecules, and the H-bond population distribution is found to be strongly site-specific and solvent-dependent. However, it is found that adoption of the polyproline II (PII) conformation by AP in protic solvents does not strongly depend on the hydrogen bond network-forming ability of protic solvents nor on the solvent polarity. We present a brief discussion on the validity as well as limitation of the currently available force field parameters used for the present MD simulation study.

Journal Article↗
PubMed2006

Vibrational spectroscopic characteristics of secondary structure polypeptides in liquid water: constrained MD simulation studies.

Using the constrained MD simulation method in combination with quantum chemistry calculation, Hessian matrix reconstruction, and fragmentation approximation methods, we established a computational scheme for numerical simulations of amide I IR absorption, vibrational circular dichroism (VCD), and 2D IR photon echo spectra of peptides in solution. Six different secondary structure peptides, i.e., alpha-helix, 3(10)-helix, pi-helix, antiparallel and parallel beta-sheets, and polyproline II (P(II)), are considered, and the vibrational characteristic features in their linear and nonlinear spectra in the amide I band region are discussed. Isotope-labeling effects on IR and VCD spectra are notable only for alpha- and pi-helical peptides due to the strong vibrational couplings between two nearest neighboring amide I local oscillators. The amplitudes of difference 2D IR spectra are shown to be strongly dependent on both the extent of mode delocalization and the relative orientation of local mode transition dipoles determined by secondary structure.

Alanine↗
PubMed2006

Structure of N-acetylproline amide in liquid water: experimentally measured and numerically simulated infrared and vibrational circular dichroism spectra.

A few experimental and theoretical studies on the molecular structure of N-acetylproline amide (AP) in D2O solution have been reported recently. However, there is no consensus of the precise structure of AP in D2O because spectroscopically determined structures and a theoretically simulated one have been found to be different from one another. To determine its aqueous solution structure, IR and vibrational circular dichroism spectra of both L- and D-form AP solutions were measured. Molecular dynamics simulations with two different force fields and density functional theory calculations for the trans and cis rotamers of AP were performed to numerically simulate those spectra. Comparisons between experimentally measured and computationally simulated spectra directly suggest that the AP in water adopts a polyproline II-like conformation and that the force field parameter ff03 in the AMBER 8 suite of programs is more realistic and reliable in predicting molecular structure of AP in water than the ff99 in AMBER 7.

Amides↗
PubMed2006

Vibrational dynamics of DNA. I. Vibrational basis modes and couplings.

Carrying out density functional theory calculations of four DNA bases, base derivatives, Watson-Crick (WC) base pairs, and multiple-layer base pair stacks, we studied vibrational dynamics of delocalized modes with frequency ranging from 1400 to 1800 cm(-1). These modes have been found to be highly sensitive to structure fluctuation and base pair conformation of DNA. By identifying eight fundamental basis modes, it is shown that the normal modes of base pairs and multilayer base pair stacks can be described by linear combinations of these vibrational basis modes. By using the Hessian matrix reconstruction method, vibrational coupling constants between the basis modes are determined for WC base pairs and multilayer systems and are found to be most strongly affected by the hydrogen bonding interaction between bases. It is also found that the propeller twist and buckle motions do not strongly affect vibrational couplings and basis mode frequencies. Numerically simulated IR spectra of guanine-cytosine and adenine-thymine bases pairs as well as of multilayer base pair stacks are presented and described in terms of coupled basis modes. It turns out that, due to the small interlayer base-base vibrational interactions, the IR absorption spectrum of multilayer base pair system does not strongly depend on the number of base pairs.

Base Pairing↗
PubMed2006

Vibrational dynamics of DNA. II. Deuterium exchange effects and simulated IR absorption spectra.

In Paper I, we studied vibrational properties of normal bases, base derivatives, Watson-Crick base pairs, and multiple layer base pair stacks in the frequency range of 1400-1800 cm(-1). However, typical IR absorption spectra of single- and double-stranded DNA have been measured in D(2)O solution. Consequently, the more relevant bases and base pairs are those with deuterium atoms in replacement with labile amino hydrogen atoms. Thus, we have carried out density functional theory vibrational analyses of properly deuterated bases, base pairs, and stacked base pair systems. In the frequency range of interest, both aromatic ring deformation modes and carbonyl stretching modes appear to be strongly IR active. Basis mode frequencies and vibrational coupling constants are newly determined and used to numerically simulate IR absorption spectra. It turns out that the hydration effects on vibrational spectra are important. The numerically simulated vibrational spectra are directly compared with experiments. Also, the (18)O-isotope exchange effect on the poly(dG):poly(dC) spectrum is quantitatively described. The present calculation results will be used to further simulate two-dimensional IR photon echo spectra of DNA oligomers in the companion Paper III.

Base Pairing↗
PubMed2006

Vibrational dynamics of DNA. III. Molecular dynamics simulations of DNA in water and theoretical calculations of the two-dimensional vibrational spectra.

A theoretical description of the vibrational excitons in DNA is presented by using the vibrational basis mode theory developed in Papers I and II. The parameters obtained from the density functional theory calculations, such as vibrational coupling constants and basis mode frequencies, are used to numerically simulate two-dimensional (2D) IR spectra of dG(n):dC(n) and dA(n):dT(n) double helices with n varying from 1 to 10. From the molecular dynamics simulations of dG(5)C(5) and dA(5)T(5) double helices in D(2)O solution, it is found that the thermally driven internal motions of these systems in an aqueous solution do not induce strong fluctuations of basis mode frequencies nor vibrational couplings. In order to construct the two-exciton Hamiltonian, the vibrational anharmonicities of eight basis modes are obtained by carrying out B3LYP6-31G(*) calculations for the nine basis modes. The simulated 2D IR spectra of dG(n):dC(n) double helix in D(2)O solution are directly compared with closely related experimental results. The 2D IR spectra of dG(n):dC(n) and dA(n):dT(n) are found to be weakly dependent on the number of base pairs. The present work demonstrates that the computational procedure combining quantum chemistry calculation and molecular dynamics simulation methods can be of use to predict 2D IR spectra of nucleic acids in solutions.

Base Pairing↗
PubMed2005

IR spectra of N-methylacetamide in water predicted by combined quantum mechanical/molecular mechanical molecular dynamics simulations.

We applied the combined quantum mechanical (QM)/molecular mechanical (MM) molecular dynamics (MD) simulation method in assessing IR spectra of N-methylacetamide and its deuterated form in aqueous solutions. The model peptide is treated at the Austin Model 1 (AM1) level and the induced dipole effects by the solvent are incorporated in fluctuating solute dipole moments, which are calculated using partial charges from Mulliken population analyses without resorting to any available high-level ab initio dipole moment data. Fourier transform of the solute dipole autocorrelation function produces in silico IR spectra, in which the relative peak intensities and bandwidths of major amide bands are quantitatively compatible with experimental results only when both geometric and electronic polarizations of the peptide by the solvent are dealt with at the same quantum-mechanical level. We cast light on the importance of addressing dynamic charge fluctuations of the solute in calculating IR spectra by comparing classical and QM/MM MD simulation results. We propose the adjustable scaling factors for each amide mode to be directly compared with experimental data.

Acetamides↗
PubMed2005

The integrated photon echo and solvation dynamics. II. Peak shifts and two-dimensional photon echo of a coupled chromophore system.

A theoretical description of one- and two-color photon echo peak shifts (PEPS) and two-dimensional (2D) photon echo spectrum (PES) of a coupled chromophore system are presented. The effects of population relaxation in the one-exciton states on both the PEPS and the 2D PES are investigated. For values of time T shorter than the population relaxation time, a finite two-color peak shift magnitude and nonzero cross peaks in the 2D PES provide evidence of electronic coupling between the chromophores. These two distinct observables, i.e., PEPS and off-diagonal peaks, both originate from the electronic coupling. However, it is shown that the PEPS and 2D PES methods can provide complementary information on the structure-dependent nonlinear optical responses of coupled chromophore systems.

Algorithms↗
PubMed2005

Characteristic two-dimensional IR spectroscopic features of antiparallel and parallel beta-sheet polypeptides: simulation studies.

The antiparallel and parallel beta sheets are two of the most abundant secondary structures found in proteins. Although various spectroscopic methods have been used to distinguish these two different structures, the linear spectroscopic measurements could not provide incisive information for distinguishing an antiparallel beta sheet from a parallel beta sheet. After carrying out quantum-chemistry calculations and model simulations, we show that the polarization-controlled two-dimensional (2D) IR photon echo spectroscopy can be of critical use in distinguishing these two different beta sheets. Particularly, the ratio between the diagonal peak and the cross peak is found to be strongly dependent on the quasi-2D array of the amide I local-mode transition dipole vectors. The relative intensities of the cross peaks in the 2D difference spectrum of an antiparallel beta sheet are significantly larger than those of the diagonal peaks, whereas the cross-peak amplitudes in the 2D difference spectrum of a parallel beta sheet are much weaker than the main diagonal-peak amplitudes. A detailed discussion on the origin of the diagonal- and cross-peak intensity distributions of both the antiparallel and parallel beta sheets is presented by examining vibrational exciton delocalization, relative angles between two different normal-mode transition dipoles, and natures of the cross peaks in the 2D difference spectrum.

Computer Simulation↗
PubMed2005

Simulation studies of amide I IR absorption and two-dimensional IR spectra of beta hairpins in liquid water.

Amide I IR absorption and two-dimensional (2D) IR photon echo spectra of a model beta hairpin in aqueous solution are theoretically studied and simulated by combining semiempirical quantum chemistry calculations and molecular dynamics simulation methods. The instantaneous normal-mode analysis of the beta hairpin in solution is performed to obtain the density of states and the inverse participation ratios of the one-exciton states. The motional and exchange narrowing processes are taken into account by employing the time-correlation function theory for the linear and nonlinear response functions. Numerically simulated IR absorption and 2D spectra are then found to be determined largely by the amide I normal modes delocalized on the peptides in the two strands. The site-specific isotope-labeling effects on the IR and 2D IR spectra are discussed. The simulation results for the ideal (A17) beta hairpin are directly compared with those of the realistic 16-residue (GB1) beta hairpin from an immunoglobulin G-binding protein. It was found that the characteristic features in IR and 2D spectra of both the ideal (A17) beta hairpin and the GB1 beta hairpin are the same. The simulated IR spectrum of the GB1 beta hairpin is found to be in good agreement with experiment, which demonstrates that the present computational method is quantitatively reliable.

Absorption↗
PubMed2005

Exciton analysis in 2D electronic spectroscopy.

A theoretical description of femtosecond two-dimensional electronic spectroscopy of multichromophoric systems is presented. Applying the stationary phase approximation to the calculation of photon echo spectra and taking into account exciton relaxation processes, we obtain an analytic expression for numerical simulations of time- and frequency-resolved 2D photon echo signals. The delocalization of one-exciton states, spatial overlaps between the probability densities of different excitonic states, and their influences on both one- and two-dimensional electronic spectra are studied. The nature of the off-diagonal cross-peaks and the time evolution of both diagonal and off-diagonal peak amplitudes are discussed in detail by comparing experimentally measured and theoretically simulated 2D spectra of the natural Fenna-Matthews-Olson (FMO) photosynthetic light-harvesting complex. We find that there are two noncascading exciton energy relaxation pathways.

Algorithms↗
PubMed2005

Amide I vibrational circular dichroism of polypeptides: generalized fragmentation approximation method.

Fragment analyses of vibrational circular dichroic response of dipeptides were carried out recently [Choi and Cho, J. Chem. Phys. 120, 4383 (2004)]. In the present paper, by using a minimal size unit peptide containing two chiral carbons covalently bonded to the peptide group, a generalized fragmentation approximation method is discussed and applied to the calculations of infrared-absorption and vibrational circular dichroism (VCD) intensities of amide I vibrations in various secondary structure polypeptides. Unlike the dipole strength determining IR-absorption intensity, the rotational strength is largely determined by the cross terms that are given by the inner product between the transition electric dipole and the transition magnetic dipole of two different peptides. This explains why the signs and magnitudes of VCD peaks are far more sensitive to the relative orientation and distance between different peptide bonds in a given protein. In order to test the validity of fragmentation approximation, three different segments in a globular protein ubiquitin, i.e., right-handed alpha-helix, beta-sheet, and beta-turn regions, were chosen for density-functional theory (DFT) calculations of amide I vibrational properties and the numerically simulated IR-absorption and VCD spectra by using the fragmentation method are directly compared with DFT results. It is believed that the fragmentation approximation method will be of use in numerically simulating vibrational spectra of proteins in solutions.

Journal Article↗
PubMed2005

Two-dimensional spectroscopy of electronic couplings in photosynthesis.

Time-resolved optical spectroscopy is widely used to study vibrational and electronic dynamics by monitoring transient changes in excited state populations on a femtosecond timescale. Yet the fundamental cause of electronic and vibrational dynamics--the coupling between the different energy levels involved--is usually inferred only indirectly. Two-dimensional femtosecond infrared spectroscopy based on the heterodyne detection of three-pulse photon echoes has recently allowed the direct mapping of vibrational couplings, yielding transient structural information. Here we extend the approach to the visible range and directly measure electronic couplings in a molecular complex, the Fenna-Matthews-Olson photosynthetic light-harvesting protein. As in all photosynthetic systems, the conversion of light into chemical energy is driven by electronic couplings that ensure the efficient transport of energy from light-capturing antenna pigments to the reaction centre. We monitor this process as a function of time and frequency and show that excitation energy does not simply cascade stepwise down the energy ladder. We find instead distinct energy transport pathways that depend sensitively on the detailed spatial properties of the delocalized excited-state wavefunctions of the whole pigment-protein complex.

Bacterial Proteins↗
PubMed2005

Theoretical study of internal field effects on peptide amide I modes.

Charged terminal groups or polar side chains of amino acids create spatially nonuniform electrostatic potential around intramolecular peptide bonds and induce amide I mode frequency shifts in polypeptides. By carrying out a series of quantum chemistry calculation studies of various ionic di- and tripeptides as well as dipeptides of 20 different amino acids, these internal field effects on vibrational properties are theoretically investigated. The amide I local and normal mode frequencies and dipole and rotational strengths determining IR and vibrational circular dichroism intensities, respectively, are found to depend on the polar nature of side chains, whereas the vibrational coupling strength weakly does so. The empirical correction and fragment analysis methods were used to theoretically calculate the amide I local mode frequencies and dipole and rotational strengths. These values were directly compared with ab initio and density functional theory calculation results, and the agreements were found to be quantitative.

Amides↗
PubMed2004

Theoretical calculations of infrared absorption, vibrational circular dichroism, and two-dimensional vibrational spectra of acetylproline in liquids water and chloroform.

Infrared absorption, vibrational circular dichroism, and two-dimensional infrared pump-probe and photon echo spectra of acetylproline solutions are theoretically calculated and directly compared with experiments. In order to quantitatively determine interpeptide interaction-induced amide I mode frequency shifts, high-level quantum chemistry calculations were performed. The solvatochromic amide I mode frequency shift and fluctuation were taken into account by carrying out molecular dynamics simulations of acetylproline dissolved in liquids water and chloroform and by using the extrapolation method developed recently. We first studied correlation time scales of the two amide I vibrational frequency fluctuations, cross correlation between the two fluctuating local mode frequencies, ensemble averaged conformations of the acetylproline molecule in liquids water and chloroform. The corresponding conformations of the acetylproline in liquids water and chloroform are close to the ideal 3(10) helix and the C(7) structure, respectively. A few methods proposed to determine the angle between the two transition dipoles associated with the amide I vibrations were tested and their limitations are discussed.

Journal Article↗