Computational Analysis Reveals a Critical Point Mutation in the N-Terminal Region of the Signaling Lymphocytic Activation Molecule Responsible for the Cross-Species Infection with Canine Distemper Virus

Infection of hosts by morbilliviruses is facilitated by the interaction between viral hemagglutinin (H-protein) and the signaling lymphocytic activation molecule (SLAM). Recently, the functional importance of the n-terminal region of human SLAM as a measles virus receptor was demonstrated. However, the functional roles of this region in the infection process by other morbilliviruses and host range determination remain unknown, partly because this region is highly flexible, which has hampered accurate structure determination of this region by X-ray crystallography. In this study, we analyzed the interaction between the H-protein from canine distemper virus (CDV-H) and SLAMs by a computational chemistry approach. Molecular dynamics simulations and fragment molecular orbital analysis demonstrated that the unique His28 in the N-terminal region of SLAM from Macaca is a key determinant that enables the formation of a stable interaction with CDV-H, providing a basis for CDV infection in Macaca. The computational chemistry approach presented should enable the determination of molecular interactions involving regions of proteins that are difficult to predict from crystal structures because of their high flexibility.     

Enhanced conformational sampling method for proteins based on the TaBoo SeArch algorithm: Application to the folding of a mini‐protein,chignolin

The conformational samplings are indispensible for obtaining reliable canonical ensembles, which provide statistical averages of physical quantities such as free energies. However, the samplings of vast conformational space of biomacromolecules by conventional molecular dynamics (MD) simulations might be insufficient, due to their inadequate accessible time‐scales for investigating biological functions. Therefore, the development of methodologies for enhancing the conformational sampling of biomacromolecules still remains as a challenging issue in computational biology. To tackle this problem, we newly propose an efficient conformational search method, which is referred as TaBoo SeArch (TBSA) algorithm. In TBSA, an inverse energy histogram is used to select seeds for the conformational resampling so that states with high frequencies are inhibited, while states with low frequencies are efficiently sampled to explore the unvisited conformational space. As a demonstration, TBSA was applied to the folding of a mini‐protein, chignolin, and automatically sampled the native structure (C_α root mean square deviation < 1.0 Å) with nanosecond order computational costs started from a completely extended structure, although a long‐time 1‐µs normal MD simulation failed to sample the native structure. Furthermore, a multiscale free energy landscape method based on the conformational sampling of TBSA were quantitatively evaluated through free energy calculations with both implicit and explicit solvent models, which enable us to find several metastable states on the folding landscape. © 2015 Wiley Periodicals, Inc.     

Irreversible helix rearrangement from Cis‐transoid to Cis‐cisoid in poly(p‐n‐hexyloxyphenylacetylene) induced by heat‐treatment in solid phase

Polymerization of p‐n‐hexyloxyphenylacetylene (pHPA) by using a [Rh(norbornadine)Cl]₂‐triethylamine catalyst was carried out at room temperature to afford stereoregular helical poly(p‐n‐hexyloxyphenylacetylene)s (PpHPAs). When ethanol and n‐hexane were used as polymerization solvents, a bright yellow PpHPAs, poly( Y ) with M_n = 8.5 × 10⁴ and its purple red polymer, poly( R ) with M_n = 5.3 × 10⁴ were obtained in 95% yields and 84% yields, respectively. Diffuse reflective UV–vis spectra of poly( Y ) and poly( R ) in solid phase showed different broad absorption peaks at 445 and 575 nm, respectively. X‐Ray diffraction patterns of poly( Y ) and poly( R ) showed typical columnar structures assignable to cis‐transoid and cis‐cisoid structures, respectively, which were also supported by molecule mechanics calculation. Poly( Y ) was irreversibly transformed to a reddish‐black polymer, poly( Y‐B ), which columnar diameter was nearly the same as that of poly( R ). Further, poly( Y ) showed an exothermic peak in the differential scanning calorimetry trace at 80 °C for 1 h in N₂ gas. Thus, these findings suggest a thermally irreversible rearrangement from an unstable cis‐transoid form, poly( Y ) with a stretched cis‐transoid helix to a stable cis‐cisoid form, poly( R ), with a contracted cis‐cisoid helix in the solid phase to give poly( Y → B ) with the cis‐cisoid form. © 2012 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2012     

Synthesis and properties of thermotropic liquid-crystalline polyesters containing 9,10-diphenylanthracene moiety in the main chain

We synthesized thermotropic liquid-crystalline polyesters in which 9,10-diphenylanthracene moieties are incorporated into the main chain type of polyester forming the chiral smectic C (Sm C*). The polymers were prepared by the isopropyltitanate-catalyzed reaction of biphenyldicarboxylic acid and the corresponding diols, with different ratios of diol of 9,10-diphenylanthracene moiety to the alkane diols (1, 5, and 10 mol %) under nitrogen atmosphere. The polymers exhibited thermotropic liquid crystals despite the presence of a bulky diphenylanthracene moiety in the main chain. The circular dichroism spectra revealed that a Sm C* phase was formed in the polymer with 1 mol % of anthracene moiety, although only an Sm A phase was formed in the other polymers. This is the first example of a Sm C* polyester containing a diphenylanthracene moiety in the main chain. Furthermore, we measured the optical properties of the polymers and found that they exhibited very high fluorescent efficiency. The fluorescence spectra of the thin film differed from that of a CH₂Cl₂ solution.     

On the induced‐fit mechanism of substrate‐enzyme binding structures of nylon‐oligomer hydrolase

We present a detailed computational investigation of the induced‐fit motion in a nylon‐oligomer hydrolase (NylB) upon substrate binding. To this aim, we resort on the recently introduced parallel cascade selection molecular dynamics approach, allowing for an accelerated access to the set of conformational changes from an open‐ to a closed‐state structure to form the enzyme‐substrate complex in a specific induce‐fit mechanism. The structural investigation is quantitatively complemented by free energy analyses within the umbrella sampling algorithm accompanied by weighted histogram analysis. We find that the stabilization free energy is about 1.4 kcal/mol, whereas the highest free energy barrier to be overcome is about 2.3 kcal/mol. Conversely, the energetic contribution for the substrate binding is about 20 kcal/mol, as estimated from Generalized Born/Surface Area. This means that the open‐close induced‐fit motion could occur frequently once the substrate binds to the open state of NylB. © 2014 Wiley Periodicals, Inc.     

Design of Photostable,Activatable Near‐Infrared Photoacoustic Probes Using Tautomeric Benziphthalocyanine as a Platform

Near‐infrared (NIR) imaging techniques have attracted significant attention for biological and medicinal applications due to the ability of NIR to penetrate deeply into tissues. However, there are very few stable, activatable molecular probes that can utilize NIR light in the wavelength range beyond 800 nm. Herein, we report a new activatable NIR system for photoacoustic imaging based on tautomeric benziphthalocyanines (BPcs). We found that the existence of a free hydroxyl group is crucial for NIR absorption of BPcs. Synthesized water‐soluble hydroxy BPcs exhibited high photostability and no fluorescence, which are desirable features for photoacoustic imaging. We synthesized BPcs in which the free hydroxyl group was masked by an esterase‐labile or an H₂O₂‐labile group. The photoacoustic signals of these hydroxy‐masked BPcs were increased upon NIR excitation at 880 nm in the presence of esterase or H₂O₂, respectively. These are rare examples of activatable probes utilizing NIR light at around 900 nm.     

Theoretical studies on magnetic interactions between Cu(II) ions in hydroxypyridone nucleobases

The origin of a ferromagnetic interaction between Cu²⁺ ions in the Cu²⁺–DNA system which reported by Tanaka et al. is examined by using DFT calculations. In order to consider effects of an entanglement and a dis-entanglement of the double helix chain, three types of structural disorders i.e. distance, rotation angle and discrepancy in XY-plane, are considered in the model dimer structure. All calculated results show that J_ab values are weak anti-ferromagnetic couplings. Boltzmann distribution simulation indicates that the high spin (HS) species exist 21% at 1.5 K by thermal excitation within the model structure.     

Acidic‐pH‐Activatable Fluorescence Probes for Visualizing Exocytosis Dynamics

Live imaging of exocytosis dynamics is crucial for a precise spatiotemporal understanding of secretion phenomena, but current approaches have serious limitations. We designed and synthesized small‐molecular fluorescent probes that were chemically optimized for sensing acidic intravesicular pH values, and established that they can be used to sensitively and reliably visualize vesicular dynamics following stimulation. This straightforward technique for the visualization of exocytosis as well as endocytosis/reacidification processes with high spatiotemporal precision is expected to be a powerful tool for investigating dynamic cellular phenomena involving changes in the pH value.