Coupled Nosé-Hoover equations of motions without time scaling

The Nosé-Hoover (NH) equation of motion is widely used in molecular dynamics simulations. It enables us to set a constant temperature and produce the canonical distribution for a target physical system. For the purpose of investigating the physical system under fluctuating temperature, we have introduced a coupled Nosé-Hoover equation in our previous work [J. Phys. A 48 455001 (2015)]. The coupled NH equation implements a fluctuating heat-bath temperature in the NH equation of the physical system, and also keeps a statistically complete description via an invariant measure of the total system composed of the physical system and a "temperature system" . However, a difficulty lies in that the time development of the physical system may not correspond to the realistic physical process, because of the need of a scaled time average to compute thermodynamical quantities. The current work gives a solution by presenting a new scheme, which is free from the scaled time but retains the statistical description. By use of simple model systems, we validate the current scheme and compare with the original scheme. The sampling property of the current scheme is also clari fied to investigate the effect of function setting used for the distribution of the total system.This is an author-created, un-copyedited version of an article accepted for publication/published in Journal of Physics A : Mathematical and Theoretical. IOP Publishing Ltd is not responsible for any errors or omissions in this version of the manuscript or any version derived from it. The Version of Record is available online at http://dx.doi.org/10.1088/1751-8113/50/1/015002

Double density dynamics : realizing a joint distribution of a physical system and a parameter system

This is an author-created, un-copyedited version of an article accepted for publication/published in Journal of Physics A : Mathematical and Theoretical. IOP Publishing Ltd is not responsible for any errors or omissions in this version of the manuscript or any version derived from it. The Version of Record is available online at http://doi.org/10.1088/1751-8113/48/45/455001

Structures and mechanisms of actin ATP hydrolysis

The major cytoskeleton protein actin undergoes cyclic transitions between the monomeric G-form and the filamentous F-form, which drive organelle transport and cell motility. This mechanical work is driven by the ATPase activity at the catalytic site in the F-form. For deeper understanding of the actin cellular functions, the reaction mechanism must be elucidated. Here, we show that a single actin molecule is trapped in the F-form by fragmin domain-1 binding and present their crystal structures in the ATP analog-, ADP-Pi-, and ADP-bound forms, at 1.15-Å resolutions. The G-to-F conformational transition shifts the side chains of Gln137 and His161, which relocate four water molecules including W1 (attacking water) and W2 (helping water) to facilitate the hydrolysis. By applying quantum mechanics/molecular mechanics calculations to the structures, we have revealed a consistent and comprehensive reaction path of ATP hydrolysis by the F-form actin. The reaction path consists of four steps: 1) W1 and W2 rotations; 2) PG–O3B bond cleavage; 3) four concomitant events: W1–PO3− formation, OH− and proton cleavage, nucleophilic attack by the OH− against PG, and the abstracted proton transfer; and 4) proton relocation that stabilizes the ADP-Pi–bound F-form actin. The mechanism explains the slow rate of ATP hydrolysis by actin and the irreversibility of the hydrolysis reaction. While the catalytic strategy of actin ATP hydrolysis is essentially the same as those of motor proteins like myosin, the process after the hydrolysis is distinct and discussed in terms of Pi release, F-form destabilization, and global conformational changes

Influence of the combination of SGLT2 inhibitors and GLP-1 receptor agonists on eGFR decline in type 2 diabetes: post-hoc analysis of RECAP study

Accumulating evidence has demonstrated that both SGLT2 inhibitors (SGLT2i) and GLP-1 receptor agonists (GLP1Ra) have protective effects in patients with diabetic kidney disease. Combination therapy with SGLT2i and GLP1Ra is commonly used in patients with type 2 diabetes (T2D). We previously reported that in combination therapy of SGLT2i and GLP1Ra, the effect on the renal composite outcome did not differ according to the preceding drug. However, it remains unclear how the initiation of combination therapy is associated with the renal function depending on the preceding drug. In this post hoc analysis, we analyzed a total of 643 T2D patients (GLP1Ra-preceding group, n = 331; SGLT2i-preceding group, n = 312) and investigated the differences in annual eGFR decline. Multiple imputation and propensity score matching were performed to compare the annual eGFR decline. The reduction in annual eGFR decline in the SGLT2i-preceding group (pre: −3.5 ± 9.4 mL/min/1.73 m2/year, post: −0.4 ± 6.3 mL/min/1.73 m2/year, p < 0.001), was significantly smaller after the initiation of GLP1Ra, whereas the GLP1Ra-preceding group tended to slow the eGFR decline but not to a statistically significant extent (pre: −2.0 ± 10.9 mL/min/1.73 m2/year, post: −1.8 ± 5.4 mL/min/1.73 m2/year, p = 0.83) after the initiation of SGLT2i. After the addition of GLP1Ra to SGLT2i-treated patients, slower annual eGFR decline was observed. Our data raise the possibility that the renal benefits—especially annual eGFR decline—of combination therapy with SGLT2i and GLP1Ra may be affected by the preceding drug

Minimum Free Energy Path of Ligand-Induced Transition in Adenylate Kinase

Large-scale conformational changes in proteins involve barrier-crossing transitions on the complex free energy surfaces of high-dimensional space. Such rare events cannot be efficiently captured by conventional molecular dynamics simulations. Here we show that, by combining the on-the-fly string method and the multi-state Bennett acceptance ratio (MBAR) method, the free energy profile of a conformational transition pathway in Escherichia coli adenylate kinase can be characterized in a high-dimensional space. The minimum free energy paths of the conformational transitions in adenylate kinase were explored by the on-the-fly string method in 20-dimensional space spanned by the 20 largest-amplitude principal modes, and the free energy and various kinds of average physical quantities along the pathways were successfully evaluated by the MBAR method. The influence of ligand binding on the pathways was characterized in terms of rigid-body motions of the lid-shaped ATP-binding domain (LID) and the AMP-binding (AMPbd) domains. It was found that the LID domain was able to partially close without the ligand, while the closure of the AMPbd domain required the ligand binding. The transition state ensemble of the ligand bound form was identified as those structures characterized by highly specific binding of the ligand to the AMPbd domain, and was validated by unrestrained MD simulations. It was also found that complete closure of the LID domain required the dehydration of solvents around the P-loop. These findings suggest that the interplay of the two different types of domain motion is an essential feature in the conformational transition of the enzyme

Multiscale Enhanced Sampling Using Machine Learning

Multiscale enhanced sampling (MSES) allows for an enhanced sampling of all-atom protein structures by coupling with the accelerated dynamics of the associated coarse-grained (CG) model. In this paper, we propose an MSES extension to replace the CG model with the dynamics on the reduced subspace generated by a machine learning approach, the variational autoencoder (VAE). The molecular dynamic (MD) trajectories of the ribose-binding protein (RBP) in both the closed and open forms were used as the input by extracting the inter-residue distances as the structural features in order to train the VAE model, allowing the encoded latent layer to characterize the difference in the structural dynamics of the closed and open forms. The interpolated data characterizing the RBP structural change in between the closed and open forms were thus efficiently generated in the low-dimensional latent space of the VAE, which was then decoded into the time-series data of the inter-residue distances and was useful for driving the structural sampling at an atomistic resolution via the MSES scheme. The free energy surfaces on the latent space demonstrated the refinement of the generated data that had a single basin into the simulated data containing two closed and open basins, thus illustrating the usefulness of the MD simulation together with the molecular mechanics force field in recovering the correct structural ensemble

チョウワ キンジ モデル ノ カクチョウ ニ ヨル タンパクシツ ブンシ ノ ヒセンケイ ダイナミクス ノ カイセキ

京都大学0048新制・課程博士博士(理学)甲第9983号理博第2644号新制||理||1346(附属図書館)UT51-2003-H404京都大学大学院理学研究科化学専攻(主査)教授 加藤 重樹, 教授 梶本 興亜, 教授 三木 邦夫学位規則第4条第1項該当Doctor of ScienceKyoto UniversityDA