Fluctuations Of Water Molecules Research Articles

Mechanistic Insights into the Halophilic Xylosidase Xylo-1 and Its Role in Xylose Production.

The Xylo-1 xylosidase, which belongs to the GH43 family, exhibits a high salt tolerance. The present study demonstrated that the catalytic activity of Xylo-1 increased by 195% in the presence of 5 M NaCl. Additionally, the half-life of Xylo-1 increased 25.9-fold in the presence of 1 M NaCl. Through comprehensive analysis including circular dichroism, fluorescence spectroscopy, and molecular dynamics simulations, we elucidated that the presence of Na+ ions increased the contact frequency between the surface acidic amino acids and the surrounding water molecules. This resulted in the stabilization of the surrounding hydration layer of Xylo-1. Additionally, Na+ ions also stabilized the substrate-binding conformation and the fluctuation of water molecules within the active site, which enhanced the catalytic activity of Xylo-1 by increasing the nucleophilic attack by the water molecules. Ultimately, the optimal reaction conditions for the production of xylose by synergistic catalysis with Xylo-1 and xylanase were determined. The results demonstrated that the conversion yield of the method was high for various sources of xylan, indicating the method could have potential industrial applications. This study explored the structure-activity relationship of catalysis in Xylo-1 under high-salt conditions, provides novel insights into the mechanism of halophilic enzymes, and serves as a reference for the industrial application of Xylo-1.

Structure of the Chromophore Binding Pocket in the Pr State of Plant Phytochrome phyA

A homology structural model was generated for plant phytochrome phyA utilizing the crystal structure of the sensory module of cyanobacterial phytochrome Cph1 (Cph1Δ2). As chromophores, either the native phytochromobilin cofactor (PΦB) or phycocyanobilin (PCB), the natural cofactor in Cph1, was incorporated. These homology models were further optimized by molecular dynamics (MD) simulations revealing a satisfying overall agreement with the crystal structure of Cph1Δ2. Notable differences in the PΦB adduct of phyA result from a restructuring of the small helical segment α(7) that leads to displacements of a few amino acids away from the cofactor. This repositioning of residues also include aspartate 218 such that, instead of its carbonyl function as in Cph1Δ2, an additional water molecule forms hydrogen bonds with the ring B and C NH groups. To validate the phyA structural model in the chromophore binding pocket, Raman spectra of the cofactor were calculated by means of the quantum mechanics/molecular mechanics (QM/MM) hybrid methodology and compared with the experimental resonance Raman (RR) spectra. The satisfactory overall agreement between calculated and experimental spectra is taken as an indication for the good quality of the structural model. Moreover, the methine bridge stretching modes and the effects of isotopic labeling at selected positions of the chromophore are very well reproduced to allow confirming even details of the methine bridge geometry as predicted by the homology model. Specifically, it is demonstrated that the experimental RR spectra are consistent with a torsional angle of ring D with respect to ring C that is distinctly higher for phyA-PCB (45°) and phyA-PΦB (42°) than for Cph1Δ2 (30°). Raman spectra calculated from different points of the MD trajectory display variations of the mode frequencies and intensities reflecting the structural fluctuations from snapshot to snapshot. The snapshot spectrum of the lowest energy structure and the sum of all snapshot spectra afford an equally good description of the experimental data. Particularly large variations between the snapshots are noted for the N-H in-plane bending mode of the pyrrole rings B and C, which reflect alterations of the hydrogen bond interactions brought about by fluctuations of water molecules in the cofactor cavity. This overestimation of the water molecule mobility is a consequence of the deficiency of the current QM/MM methodology that, due to the lack of appropriate protein force fields, cannot adequately account for the electrostatics in the cofactor pocket.

(Applications 3)Neutron Crystal Structure Analysis of Hydrogen-bonding Networks and Fluctuation of Water Molecules in Nucleotide Hydrates

核酸の構成単位であるヌクレオチドやヌクレオシドは水和物として結晶化するが，結晶周りの相対湿度に依存して結晶水数が変化し，相転移が誘起される。また，一部の系では，室温において結晶水の位置に顕著な乱れが存在し，その秩序化と相関した相転移が200K近傍で観測される。中性子結晶構造解析により，ヌクレオチド水和物に共通する水和構造，水素結合網の長距離の相関を持った切り替え，水素結合をアンカーとする結晶水の揺らぎなどの描像などが明らかになった。

The Key Event in Force-Induced Unfolding of Titin’s Immunoglobulin Domains

Steered molecular dynamics simulation of force-induced titin immunoglobulin domain I27 unfolding led to the discovery of a significant potential energy barrier at an extension of ∼14 Å on the unfolding pathway that protects the domain against stretching. Previous simulations showed that this barrier is due to the concurrent breaking of six interstrand hydrogen bonds (H-bonds) between β-strands A′ and G that is preceded by the breaking of two to three hydrogen bonds between strands A and B, the latter leading to an unfolding intermediate. The simulation results are supported by Ångstrom-resolution atomic force microscopy data. Here we perform a structural and energetic analysis of the H-bonds breaking. It is confirmed that H-bonds between strands A and B break rapidly. However, the breaking of the H-bond between strands A′ and G needs to be assisted by fluctuations of water molecules. In nanosecond simulations, water molecules are found to repeatedly interact with the protein backbone atoms, weakening individual interstrand H-bonds until all six A′–G H-bonds break simultaneously under the influence of external stretching forces. Only when those bonds are broken can the generic unfolding take place, which involves hydrophobic interactions of the protein core and exerts weaker resistance against stretching than the key event.