Masayoshi Takayanagi

Combined mechanism of conformational selection and induced fit in U1A-RNA molecular recognition.

In this study, we demonstrate that U1A-RNA molecular recognition is mediated by a combined mechanism of conformational selection and induced fit. The binding of U1A to RNA has been discussed in the context of induced fit that involves the reorientation of the α-helix in the C-terminal region (Helix-C) of U1A to permit RNA access only when U1A correctly recognizes RNA. However, according to our molecular dynamics simulations, even in the absence of RNA, Helix-C spontaneously reoriented to permit RNA access. Nonetheless, such a conformational change was still incomplete. Helix-C was often partially or even fully unfolded and in an infrequent RNA-accessible conformation, which can be detected using state-of-the-art nuclear magnetic resonance methodology. These results suggest that the formation of an energetically stabilized complex is promoted by specific interactions between U1A and RNA. In conclusion, in the recognition of RNA by U1A protein, we propose a combined mechanism that requires the reorientation of Helix-C and the subsequent contact with RNA through conformational selection, although the stabilization of the U1A-RNA complex is caused by induced fit. We further propose a modification to the conventional assumption regarding the mechanism of U1A-RNA molecular recognition.

Structural Dynamics of Clamshell Rotation during the Incipient Relaxation Process of Photodissociated Carbonmonoxy Myoglobin: Statistical Analysis by the Perturbation Ensemble Method

The structural dynamics of the clamshell rotation of photodissociated carbonmonoxy myoglobin, which is expected to be important for hemoglobin allostery, is investigated by the perturbation ensemble method. In this method, many pairs of perturbed and unperturbed molecular dynamics trajectories are ensemble-averaged to cancel out thermal noises and to detect subtle changes. The number of MD trajectory pairs, in this work 2000 pairs, should be determined to obtain physical properties of interest with statistically meaningful precisions. The calculated structural changes after 20 ps of the photodissociation are consistent with those by time-resolved X-ray diffraction at 100 ps delay time. In the heme proximal side region including the F and H helices, both helices displaced in the proximal direction. Meanwhile, in the heme distal side region including E and A helices, both helices moved toward the heme group after photodissociation. These proximal and distal side displacements occur on a fast time scale (almost complete within 3 ps) and are consistent with the clamshell rotation. Moreover, it was found that the ensemble-averaged structural dynamics of the photodissociated MbCO is independent of the amount of initial excess vibrational energy of the heme, or the difference of excitation photon wavelength. These results provide atomistic details on the functionally important dynamics of the clamshell rotation. Application of the present methodology to Hb will give new insight into the incipient stereochemical mechanism of hemoglobin allostery.

Oxygen Entry through Multiple Pathways in T-State Human Hemoglobin

The heme oxygen (O2) binding site of human hemoglobin (HbA) is buried in the interior of the protein, and there is a debate over the O2 entry pathways from solvent to the binding site. As a first step to understand HbA O2 binding process at the atomic level, we detected all significant multiple O2 entry pathways from solvent to the binding site in the α and β subunits of the T-state tetramer HbA by utilizing ensemble molecular dynamics (MD) simulation. By executing 128 independent 8 ns MD trajectories in O2-rich aqueous solvent, we simulated the O2 entry processes and obtained 141 and 425 O2 entry events in the α and β subunits of HbA, respectively. We developed the intrinsic pathway identification by clustering method to achieve a persuasive visualization of the multiple entry pathways including both the shapes and relative importance of each pathway. The rate constants of O2 entry estimated from the MD simulations correspond to the experimentally observed values, suggesting that O2 ligands enter the binding site through multiple pathways. The obtained multiple pathway map can be utilized for future detailed analysis of HbA O2 binding process.

Toward Understanding Allosteric Activation of Thrombin: A Conjecture for Important Roles of Unbound Na+ Molecules around Thrombin

We shed light on important roles of unbound Na(+) molecules in enzymatic activation of thrombin. Molecular mechanism of Na(+)-activation of thrombin has been discussed in the context of allostery. However, the recent challenge to redesign K(+)-activated thrombin revealed that the allosteric interaction is insufficient to explain the mechanism. Under these circumstances, we have examined the roles of unbound Na(+) molecule in maximization of thrombin-substrate association reaction rate. We performed all-atomic molecular dynamics (MD) simulations of thrombin in the presence of three different cations; Li(+), Na(+), and Cs(+). Although these cations are commonly observed in the vicinity of the S1-pocket of thrombin, smaller cations are distributed more densely and extensively than larger ones. This suggests the two observation rules: (i) thrombin surrounded by Na(+) is at an advantage in the initial step of association reaction, namely, the formation of an encounter complex ensemble, and (ii) the presence of Na(+) molecules does not necessarily have an advantage in the final step of association reaction, namely, the formation of the stereospecific complex. In conclusion, we propose a conjecture that unbound Na(+) molecules also affect the maximization of rate constant of thrombin-substrate association reaction through optimally forming an encounter complex ensemble.

Dewetting of S1-Pocket via Water Channel upon Thrombin-Substrate Association Reaction.

Upon protein-substrate association reaction, dewetting of the substrate-binding pocket is one of the rate-limiting processes. However, understanding the microscopic mechanism still remains challenging because of practical limitations of experimental methodologies. We have addressed the problem here by using molecular dynamics (MD) simulation of the thrombin-substrate association reaction. During the MD simulation, ArgP1 in a substrate accessed thrombins substrate-binding pocket and formed specific hydrogen bonds (H-bonds) with Asp189 in thrombin, while the catalytic serine of thrombin was still away from the substrates active site. It is assumed that the thrombin-substrate association reaction is regulated by a stepwise mechanism. Furthermore, in the earlier stage of ArgP1 access to the pocket, we observed that ArgP1 was spatially separated from Asp189 by two water molecules in the pocket. These water molecules transferred from the pocket, followed by the specific H-bond formation between thrombin and the substrate. Interestingly, they were not evacuated directly from the pocket to the bulk solvent, but moved to the water channel of thrombin. This observation indicates that the channel plays functional roles in dewetting upon the association reaction.

Intrinsic Alterations in the Partial Molar Volume on the Protein Denaturation: Surficial Kirkwood−Buff Approach

The partial molar volume (PMV) of the protein chymotrypsin inhibitor 2 (CI2) was calculated by all-atom MD simulation. Denatured CI2 showed almost the same average PMV value as that of native CI2. This is consistent with the phenomenological question of the protein volume paradox. Furthermore, using the surficial Kirkwood-Buff approach, spatial distributions of PMV were analyzed as a function of the distance from the CI2 surface. The profiles of the new R-dependent PMV indicate that, in denatured CI2, the reduction in the solvent electrostatic interaction volume is canceled out mainly by an increment in thermal volume in the vicinity of its surface. In addition, the PMV of the denatured CI2 was found to increase in the region in which the number density of water atoms is minimum. These results provide a direct and detailed picture of the mechanism of the protein volume paradox suggested by Chalikian et al.

Formation of Reactant Complex Structure for Initiation Reaction of Lactone Ring-Opening Polymerization by Cooperation of Multiple Cyclodextrin

Ring-opening polymerization of lactones initiated by cyclodextrins has been reported as a promising polymer synthetic method. To investigate the unknown molecular level mechanism of the initiation reaction, we executed molecular dynamics simulations of model systems composed of single or multiple β-cyclodextrin (β-CD) molecules in δ-valerolactone (VL) solvent and explored the reactant complex structures satisfying three conditions (VL inclusion in the β-CD cavity, hydrogen bonding, and nucleophilic attack) at the same time. As a result, we confirmed the formation of the reactant complex structure. Comparison between the single and multiple β-CD models revealed that the formation is more frequent and the distance for the nucleophilic attack is shorter in the multiple model. Therefore, we anticipate that the reaction proceeds more efficiently by the cooperation of multiple β-CDs. This finding will contribute to understanding the reaction mechanism from the atomistic point of view.

Non-site-specific allosteric effect of oxygen on human hemoglobin under high oxygen partial pressure.

Protein allostery is essential for vital activities. Allosteric regulation of human hemoglobin (HbA) with two quaternary states T and R has been a paradigm of allosteric structural regulation of proteins. It is widely accepted that oxygen molecules (O2) act as a “site-specific” homotropic effector, or the successive O2 binding to the heme brings about the quaternary regulation. However, here we show that the site-specific allosteric effect is not necessarily only a unique mechanism of O2 allostery. Our simulation results revealed that the solution environment of high O2 partial pressure enhances the quaternary change from T to R without binding to the heme, suggesting an additional “non-site-specific” allosteric effect of O2. The latter effect should play a complementary role in the quaternary change by affecting the intersubunit contacts. This analysis must become a milestone in comprehensive understanding of the allosteric regulation of HbA from the molecular point of view.

Sequence-regulated copolymerization based on periodic covalent positioning of monomers along one-dimensional nanochannels

The design of monomer sequences in polymers has been a challenging research subject, especially in making vinyl copolymers by free-radical polymerization. Here, we report a strategy to obtain sequence-regulated vinyl copolymers, utilizing the periodic structure of a porous coordination polymer (PCP) as a template. Mixing of Cu2+ ion and styrene-3,5-dicarboxylic acid (S) produces a PCP, [Cu(styrene-3,5-dicarboxylate)]n, with the styryl groups periodically immobilized along the one-dimensional channels. After the introduction of acrylonitrile (A) into the host PCP, radical copolymerization between A and the immobilized S is performed inside the channel, followed by decomposing the PCP to isolate the resulting copolymer. The predominant repetitive SAAA sequence in the copolymer is confirmed by monomer composition, NMR spectroscopy and theoretical calculations. Copolymerization using methyl vinyl ketone also provides the same type of sequence-regulated copolymer, showing that this methodology has a versatility to control the copolymer sequence via transcription of PCP periodicity at the molecular level.Achieving sequence control in polymers is limited by the relative monomer reactivity and thus often statistically random copolymers are obtained. Here the authors show sequence control in radical polymerizations by immobilising the monomer on a porous coordination polymer and subsequent polymerization with a second free monomer.

Bound Na(+) is a Negative Effecter for Thrombin-Substrate Stereospecific Complex Formation.

Thrombin has been studied as a paradigmatic protein of Na(+)-activated allosteric enzymes. Earlier structural studies suggest that Na(+)-binding promotes the thrombin-substrate association reaction. However, it is still elusive because (1) the structural change, driven by Na(+)-binding, is as small as the thermal fluctuation, and (2) the bound Na(+) is close to Asp189 in the primary substrate binding pocket (S1-pocket), possibly preventing substrate access via repulsive interaction. It still remains a matter of debate whether Na(+)-binding actually promotes the reaction. To solve this problem, we examined the effect of Na(+) on the reaction by employing molecular dynamics (MD) simulations. By executing independent 210 MD simulations of apo and holo systems, we obtained 80 and 26 trajectories undergoing substrate access to S1-pocket, respectively. Interestingly, Na(+)-binding results in a 3-fold reduction of the substrate access. Furthermore, we examined works for the substrate access and release, and found that Na(+)-binding is disadvantageous for the presence of the substrate in the S1-pocket. These observations provide the insight that the bound Na(+) is essentially a negative effecter in thrombin-substrate stereospecific complex formation. The insight rationalizes an enigmatic feature of thrombin, relatively low Na(+)-binding affinity. This is essential to reduce the disadvantage of Na(+)-binding in the substrate-binding.