Principal components of the protein dynamical transition

Proteins exhibit a solvent-driven dynamical transition at 180-220 K, manifested by nonlinearity in the temperature dependence of the average mean-square displacement. Here, molecular dynamics simulations of hydrated myoglobin show that the onset of the transition at approximately 180 K is characterized by the appearance of a single double-well principal component mode involving a global motion of two groups of helices. As the temperature is raised a few more quasiharmonic and multiminimum components successively appear. The results indicate an underlying simplicity in the protein dynamical transition.     

Essential dynamics and sidechain hydrogen bond cluster studies on eosinophil cationic protein

Eosinophil Cationic Protein (ECP) is a member of RNase A superfamily which carries out the obligatory catalytic role of cleaving RNA. It is involved in a variety of biological functions. Molecular dynamics simulations followed by essential dynamics analysis on this protein are carried out with the goal of gaining insights into the dynamical properties at atomic level. The top essential modes contribute to subspaces and to the transition phase. Further, the sidechain-sidechain/sidechain-mainchain hydrogen bond clusters are analyzed in the top modes, and compared with those of crystal structure. The role of residues identified by these methods is discussed in the context of concerted motion, structure and stability of the protein. Received 16 January 2002 Published online 13 September 2002     

Role of hydrogen bond in self-diffusion process in liquid water

Comparing the self-diffusion coefficient between water and non associated liquids, we discuss the role of hydrogen bond in the diffusion process.     

Protein dynamical transition does not require protein structure

Terahertz time domain spectroscopy shows that the protein dynamical transition, the rapid increase in protein dynamics occurring at approximately 200 K, needs neither tertiary nor secondary structure. Further, short chain alanine studies find a dynamical transition down to penta-alanine, with no transition observed for di-alanine or tri-alanine. These results reveal the temperature dependence arises strictly from the side-chain interaction with the solvent. The lack of a transition for shorter chain peptides may indicate a qualitative change in this interaction occurs at a specific peptide chain length.     

Manipulation and control of hydrogen bond dynamics in absorbed ice nanoclusters

Inelastic electron tunneling is used to explore the dynamics of ice nanoclusters adsorbed on Ag(111). The diffusion of entire nanoclusters or internal hydrogen bond rearrangement can be selectively controlled by injecting electrons either directly into the clusters themselves or indirectly ("indirect inelastic electron tunneling") into the substrate at distances of up to 20 nm from them; a reaction probability that oscillates with the tip-cluster lateral distance presents evidence that surface state electrons mediate the excitation. Density functional theory calculations reveal a strong sensitivity of the computed activation energies of the individual processes to the applied electrical field.     

Hydration-dependent dynamical transition in protein: protein interactions at approximately 240 K

Interprotein motions in low and fully hydrated carboxymyoglobin crystals are investigated using molecular dynamics simulation. Below approximately 240 K, the calculated dynamic structure factor exhibits a peak arising from interprotein vibration. Above approximately 240 K, the intermolecular fluctuations of the fully hydrated crystal increase drastically, whereas the low-hydration model exhibits no transition. Autocorrelation function analysis shows the transition to be dominated by the activation of diffusive intermolecular motion. The potential of mean force for the interaction remains quasiharmonic. The results indicate useful experimental avenues on protein:protein interactions to be explored using next-generation neutron sources.     

First-order phase transition in protein dynamics of ferritin

Detailed Mössbauer spectra of⁵⁷Fe in the iron storage protein, ferritin, in the temperature range between 250 and 280 K reveal a first-order phase transition with a thermal hysteresis loop of 7 K width. While the temperature is raised from 90 K to 271 K, Mössbauer spectra composed of a narrow line quadrupole doublet, typical for solids, are observed. Above this temperature, each spectrum is composed of the narrow line subspectrum and a broad line subspectrum whose relative intensity increases with temperature. The intensity of the narrow line subspectrum decreases by a factor of five at the critical temperature and thus shows a large increase in the mean square displacements atT _up=271 K. While decreasing the temperature, the bounded diffusive motions, expressed in the spectra by the coexistence of the narrow and broad lines, survive down toT _down=264 K, where again the spectral shapes and areas undergo a discontinuous jump. The narrow line subspectrum increases in intensity and the broad line subspectrum disappears. These phenomena may be understood in terms of supercooling of the water in the free channels and in the cavity of the ferritin molecule.     

Role of geometrical prodan structures in the determination of possible centers of hydrogen bond formation

Using the method of intermediate neglect of differential overlap (INDO), quantum-chemical investigations of geometrical prodan structures with different rotation and deflection angles of methyl groups in the dimethylaminogroup of the molecule are performed. The charge distribution is studied for different conformations of the molecule. The possible centers of prodan interaction with proton-donor solvents are estimated. It is demonstrated that in addition to the oxygen and nitrogen atoms, the carbon atoms of the hydrocarbon chain and the aromatic prodan ring can interact with the solvent. __________ Translated from Izvestiya Vysshikh Uchebnykh Zavedenii, Fizika, No. 1, pp. 10–16, January, 2008.     

Fluid dynamical description of the chiral transition

We investigate the dynamics of the chiral transition in an expanding quark-antiquark plasma. The calculations are made within a linear σ-model with explicit quark and antiquark degrees of freedom. We solve numerically the classical equations of motion for chiral fields coupled to the fluid dynamical equations for the plasma. Fast initial growth and strong oscillations of the chiral field and strong amplification of long wavelength modes of the pion field are observed in the course of the chiral transition.     

Dynamic model of the hydrogen bond

A new approach to the theory of the hydrogen bond is attempted which is based on the idea of the indirect interaction between the non-bonding electrons via the chemical bond. This indirect mechanism leads to an effective interaction between the non-bonding electrons and to the formation of correlated electron pairs from the non-bonding electrons with opposite spins from opposite sides of the chemical bond. The ground-state energy of the correlated pairs is lowered and the excited-state energy is raised, the three-centre asymmetric arrangement favoured and the dipole moment of the system increased.     

乙二醇分子间氢键结构与溶剂效应

采用密度泛函理论在B3LYP/6-311++G** (范德华校正)水平上研究乙二醇在气相中分别与乙腈、丙酮、四氢呋喃、水、乙二醇形成氢键二聚体的结构性质,根据PCM 极化统一场模型讨论氢键溶剂效应。结果表明,五种氢键二聚体分子中的氢键属于红移氢键,溶剂使氢键二聚体分子的偶极矩变大,并对OH振动频率的影响不大。     

乙二醇分子间氢键结构与溶剂效应

采用密度泛函理论在B3LYP/6-311++G~(**)水平上研究乙二醇在气相中分别与乙腈、丙酮、四氢呋喃、水、乙二醇形成氢键二聚体的结构性质,根据PCM(polarized continuum model)极化统一场模型讨论氢键溶剂效应.结果表明,五种氢键二聚体分子中的氢键属于红移氢键,溶剂使氢键二聚体分子的偶极矩变大,并对OH振动频率的影响不大.     

Second-order phase transition in causal dynamical triangulations

Causal dynamical triangulations are a concrete attempt to define a nonperturbative path integral for quantum gravity. We present strong evidence that the lattice theory has a second-order phase transition line, which can potentially be used to define a continuum limit in the conventional sense of nongravitational lattice theories.     

Dispersion-induced dynamical transition in parametric solitary waves

We investigate the influence of dispersion on parametric solitary waves. We show that dispersion is responsible for a transition towards a new type of dynamical solitary wave characterized by the presence of traveling phase defect arrays within their envelopes. The transition is described analytically through an original extension of the Kolmogorov-Petrovskii-Piskunov approach to front propagation into unstable states.     

2H NMR study of phase transition and hydrogen dynamics in hydrogen bonded organic antiferroelectric 55DMBP-H2ca

Hydrogen dynamics in one-dimensional hydrogen bonded organic antiferroelectric, co-crystal of 5,5’-dimethyl-2,2’-bipyridine (55DMBP) and chloranilic acid (H₂ca), was investigated by use of ²H high resolution solid-state NMR. The two types of hydrogen bonds O-H …N and N⁺-H …O^? in the antiferroelectric phase were clearly observed as the splitting of the side band of the ²H MAS NMR spectra of the acid-proton deuterated compound 55DMBP-D ₂ca. The temperature dependence of the spin-lattice relaxation time was measured of the N⁺-H and O-H deuterons, respectively. It was suggested that the motion of the O-H deuteron is already in the antiferroelectric phase in the fast-motion regime in the NMR time scale, while that of the N⁺-H deuteron is a slow motion. In the high-temperature paraelectric phase, the both deuterons become equivalent and the fast motion of the deuterons in the NMR time scale is taking place with the activation energy of 7.9 kJ mol^?1.