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Nicotinic acetylcholine receptors (nAChRs) are a diverse familyof homo- or heteropentameric ligand-gated ion channels.Understanding the physiological role of each nAChR subtypeand the key residues responsible for normal and pathologicalstates is important. α-Conotoxin neuropeptides are highly selectiveprobes capable of discriminating different subtypes ofnAChRs. In this study, we performed homology modeling togenerate the neuronal α3, β2 and β4 subunits using the x-raystructure of the α1 subunit as a template. The structures of theextracellular domains containing ligand binding sites in theα3β2 and α3β4 nAChR subtypes were constructed using MDsimulations and ligand docking processes in their free and ligand-bound states using α-conotoxin GIC, which exhibited thehighest α3β2 vs. α3β4 discrimination ratio. The results providea reasonable structural basis for such a discriminatoryability, supporting the idea that the present strategy can beused for future investigations on nAChR-ligand complexes.[BMB reports 2012; 45(5): 275-280]

Amide I local mode frequencies and vibrational coupling constants in various multiple-stranded antiparallel beta-sheet polyalanines are calculated using the semiempirical calculation method and Hessian matrix reconstruction methods. The intrastrand interaction-induced amide I local mode frequency shifts and their site dependencies are determined and various vibrational coupling constants are investigated.

Hydration effects on the C=N stretching mode frequencies of MeCN and MeSCN are investigated by carrying out ab initio calculations for a number of MeCN-water and MeSCN-water complexes with varying number of water molecules. It is found that the CN frequency shift induced by the hydrogen-bonding interactions with water molecules originate from two different ways to form hydrogen bonds with the nitrogen atom of the CN group. Considering the MeCN- and MeSCN-water cluster calculation results as databases, we first examined the validity of vibrational Stark effect relationship between the CN frequency and the electric field component parallel to the CN bond and found no strong correlation between the two. However, taking into account of additional electric field vector components is a simple way to generalize the vibrational Stark theory for the nitrile chromophore. Also, the electrostatic potential calculation method has been proposed and examined in detail. It turned out that the interactions of water molecules with nitrogen atom’s lone pair orbital and with nitrile π orbitals can be well described by the electrostatic potential calculation method. The present computational results will be of use to quantitatively simulate various linear and nonlinear vibrational spectra of nitrile compounds in solutions. [ABSTRACT FROM AUTHOR]

Linear and nonlinear IR spectroscopic studies of nucleic acids can provide crucial information on solution conformations of DNA double helix and its complex with other molecules. Carrying out density functional theory calculations of A-, B-, and Z-form DNA’s, the authors obtained vibrational spectroscopic properties as well as coupling constants between different basis modes. The vibrational couplings that determine the extent of exciton delocalization are strongly dependent on DNA conformation mainly because the interlayer distance between two neighboring base pairs changes with respect to the DNA conformation. The Z-DNA has comparatively small interlayer vibrational coupling constants so that its vibrational spectrum depends little on the number of base pairs, whereas the A-DNA shows a notable dependency on the size. Furthermore, it is shown that a few distinctively different line shape changes in both IR and two-dimensional IR spectra as the DNA conformation changes from B to A or from B to Z can be used as marker bands and characteristic features distinguishing different DNA conformations. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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 dGn:dCn and dAn:dTn double helices with n varying from 1 to 10. From the molecular dynamics simulations of dG5C5 and dA5T5 double helices in D2O 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 B3LYP/6-31G* calculations for the nine basis modes. The simulated 2D IR spectra of dGn:dCn double helix in D2O solution are directly compared with closely related experimental results. The 2D IR spectra of dGn:dCn and dAn:dTn 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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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 D2O 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 18O-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. [ABSTRACT FROM AUTHOR]

The antiparallel and parallel β 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 β sheet from a parallel β 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 β 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 β sheet are significantly larger than those of the diagonal peaks, whereas the cross-peak amplitudes in the 2D difference spectrum of a parallel β 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 β 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. [ABSTRACT FROM AUTHOR]

A theoretical study is performed on chain length and site dependencies of amide I local mode frequencies of alpha-helical polyalanines by carrying out semiemphirical quantum chemistry calculations. A theoretical model that could be used to quantatively predict both the local amide I mode frequencies and coupling constants between two different local amide I modes is developed.

Background: A candidate oncogene GIG47, previously known as a neudesin with a neurotrophic activity, was identified by applying the differential expression analysis method. Methods: As a first step to understand the molecular role of GIG47, we analyzed the expression profile of GIG47 in multiple human cancers including the breast cancer and characterized its function related to human carcinogenesis. Based on this oncogenic role of GIG47, we then embarked on determining the high-resolution structure of GIG47. We have applied multidimensional heteronuclear NMR methods to GIG47. Results: GIG47 was over-expressed in primary breast tumors as well as other human tumors including carcinomas of the uterine cervix, malignant lymphoma, colon, lung, skin, and leukemia. To establish its role in the pathogenesis of breast cancer in humans, we generated stable transfectants of MCF7 cells. The ectopic expression of GIG47 in MCF7 cells promoted the invasiveness in the presence of 50% serum. In addition, it also resulted in the increased tumorigenicity in in vivo tumor formation assay. The tumorigenesis mechanism involving GIG47 might be mediated by the activation of MAPK and PI3K pathways. These results indicate that GIG47 plays a role in the breast tumorigenesis, thus representing a novel target for the treatment of breast cancer. To facilitate the development of GIG47-targeted therapeutics, we determined the structural configuration of GIG47. The high-resolution structure of GIG47 was obtained by combination of NMR and homology modeling. The overall structure of GIG47 has four α-helices and 6 β-strands, arranged in a β1-α1- beta;2-β3-α2-β4-α3-α4-β5-β6 topology. There is a potential heme/steroid binding pocket formed between two helices α2 and α3. Conclusion: The determined three-dimensional structure of GIG47 may facilitate the development of potential anti-cancer agents. [ABSTRACT FROM AUTHOR]

Protein engineering method to study the mutation effects on muscle acyiphosphatase (AcP) has been actively applied to describe kinetics and thermodynamics associated with AcP aggregation as well as folding processes. Despite the extensive mutation experiments, the molecular origin and the structural motifs for aggregation and folding kinetics as well as thermodynamics of AcP have not been rationalized at the atomic resolution. To this end, we have investigated the mutation effects on the structures and thermodynamics for the aggregation and folding of AcP by using the combination of fully atomistic, explicit.water molecular dynamics simulations, and three-dimensional reference interaction site model theory. The results indicate that the A3OG mutant with the fastest experimental aggregation rate displays considerably decreased αl-helical contents as well as disrupted hydrophobic core compared to the wild-type AcP. Increased solvation free energy as well as hydrophobicity upon A3OG mutation is achieved due to the dehydration of hydrophilic side chains in the disrupted αl-helix region, of A30G. In contrast, the Y91Q mutant with the slowest aggregation rate shows a non-native H-bonding network spanning the mutation site to hydrophobic core and αl-helix region, which rigidifies the native state protein conformation with the enhanced CU -helicity. Furthermore, Y91Q exhibits decreased solvation free energy and hydrophobicity compared to wild type due to more exposed and solvated hydrophilic side chains in the α1-region. On the other hand, the experimentally observed slower folding rates in both mutants are accompanied by decreased helicity in α2-helix upon mutation. We here provide the atomic-level structures and thermodynamic quantities of AcP mutants and rationalize the structural origin for the changes that occur upon introduction of those mutations along the AcP aggregation and folding processes. [ABSTRACT FROM AUTHOR]