FT-IR Study of the Nature of the Proton and Li+ Motions in Gramicidin A and C

Systematic study of anharmonic features in a principal component analysis of gramicidin A

We use principal component analysis (PCA) to detect functionally interesting collective motions in molecular-dynamics simulations of membrane-bound gramicidin A. We examine the statistical and structural properties of all PCA eigenvectors and eigenvalues for the backbone and side-chain atoms. All eigenvalue spectra show two distinct power-law scaling regimes, quantitatively separating large from small covariance motions. Time trajectories of the largest PCs converge to Gaussian distributions at long timescales, but groups of small-covariance PCs, which are usually ignored as noise, have subdiffusive distributions. These non-Gaussian distributions imply anharmonic motions on the free-energy surface. We characterize the anharmonic components of motion by analyzing the mean-square displacement for all PCs. The subdiffusive components reveal picosecond-scale oscillations in the mean-square displacement at frequencies consistent with infrared measurements. In this regime, the slowest backbone mode exhibits tilting of the peptide planes, which allows carbonyl oxygen atoms to provide surrogate solvation for water and cation transport in the channel lumen. Higher-frequency modes are also apparent, and we describe their vibrational spectra. Our findings expand the utility of PCA for quantifying the essential features of motion on the anharmonic free-energy surface made accessible by atomistic molecular-dynamics simulations.

Theoretical study of the structures and vibrational spectra of the hydrogen-bonded systems of 4-cyanophenol with N-bases

The structural and vibrational features of the hydrogen bonded complexes of 1,5,7-triazabicyclo [4.4.0] dec-5-ene (TBD) with one and two 4-CNPhOH molecules have been studied extensively by ab initio SCF/6-31G(d,p) and BLYP calculations with various basis sets: 6-31G(d,p), 6-31+G(d,p) and 6-31++G(d,p). Full geometry optimization was made for the complexes studied. The nature of the hydrogen bonding and the influence of the hydrogen bonding on the structural and vibrational characteristics of the monomers have been investigated. The corrected values of the dissociation energy for the hydrogen-bonded complexes have been calculated in order to estimate their stability. The calculated values of the dissociation energy per phenol molecule indicate that the complex: TBD: 4-CNPhOH (1:1) is more stable than the complex: TBD: 4-CNPhOH (1:2). The changes in the structural and vibrational characteristics upon hydrogen bonding depend on the strength of the hydrogen bonds. In agreement with the experiment, the calculations show that the complexation between TBD and 4-CNPhOH leads to considerably changes in the vibrational characteristics of the stretching O-H vibration. The vibrational frequency of the O-H stretching vibration is shifted to lower wave numbers upon hydrogen bonding. The predicted frequency shifts Deltanu(O-H) for the complexes--TBD: 4-CNPhOH (1:1) and TBD: 4-CNPhOH (1:2) are in the range from -190 cm(-1) to -586 cm(-1). In the same time the IR intensity of the O-H stretching vibration increases dramatically in the hydrogen-bonded complexes.

Spectroscopic and Semiempirical Studies of a Proton Channel Formed by the Methyl Ester of Monensin A

Monensin A is an ionophore able to carry protons and cations through the cell membrane. Its methyl ester (MON1) and its hydrates have been studied in acetonitrile, and its deuterated analogue by Fourier transform infrared (FTIR) and (1)H and (13)C NMR spectroscopies as well as by vapor pressure osmotic and PM5 semiempirical methods. Interestingly, these hydrates show new and unexpected biophysical and biochemical properties. The formation of the hydrates starts with a transfer of a proton from the O(IV)-H hydroxyl group of MON1 to an oxygen atom of a water molecule, which is subsequently hydrated by other water molecules forming the (MON1 + 3H(2)O) species. This hydrate exhibits a ringlike structure in which the water molecules form an almost linear hydrogen-bonded chain. Within this chain, the excess proton fluctuates very fast inside the water cluster as indicated by a continuous absorption in the FTIR spectra. The formation of the (MON1 + 3H(2)O) species is accompanied by a self-assembly process, leading to the formation of a proton channel made up of eight (MON1 + 3H(2)O) units with a length of 60 A, in which the proton can fluctuate over the whole distance. Semiempirical calculations suggest that due to the hydrophobic surface the channel can be incorporated readily in a lipid bilayer. This hypothetical new channel is thought to be able to transport protons through the cell membrane. Thus it is a suitable model for studying proton-transfer processes, and in addition, it may open interesting new fields of application.

Voltage-gated proton channels and other proton transfer pathways

Proton channels exist in a wide variety of membrane proteins where they transport protons rapidly and efficiently. Usually the proton pathway is formed mainly by water molecules present in the protein, but its function is regulated by titratable groups on critical amino acid residues in the pathway. All proton channels conduct protons by a hydrogen-bonded chain mechanism in which the proton hops from one water or titratable group to the next. Voltage-gated proton channels represent a specific subset of proton channels that have voltage- and time-dependent gating like other ion channels. However, they differ from most ion channels in their extraordinarily high selectivity, tiny conductance, strong temperature and deuterium isotope effects on conductance and gating kinetics, and insensitivity to block by steric occlusion. Gating of H(+) channels is regulated tightly by pH and voltage, ensuring that they open only when the electrochemical gradient is outward. Thus they function to extrude acid from cells. H(+) channels are expressed in many cells. During the respiratory burst in phagocytes, H(+) current compensates for electron extrusion by NADPH oxidase. Most evidence indicates that the H(+) channel is not part of the NADPH oxidase complex, but rather is a distinct and as yet unidentified molecule.

7Li-NMR and FTIR studies of lithium, potassium, rubidium, and cesium complexes with ionophore lasalocid in solution

Lasalocid metal salts were combined with 1 : 1 lithium and 2:2 potassium, rubidium, and cesium to form complexes. The nature of the lasolocid salt complexes was studied in a solid and chloroform by FTIR spectroscopy in the middle and far IR regions. The process of the complexation of lithium was also studied by (7)Li-NMR. In chloroform a 1 : 1 complex of lasalocid and Li(+) ions was formed. Continuous absorption was observed in the far FTIR spectrum of this complex. It indicated large Li(+) polarizability, which was due to fast fluctuations of the Li(+) ions in the multiminima potentials, in the monomeric structure. In the lasalocid salt with the other monovalent cations (K(+), Rb(+), Cs(+)) 2:2 complexes were formed in which the cations showed cation polarizability, which strongly depended on the mass and the radius of the cations.