Nonadditivities of the Particle Sizes Hidden in Model Pair Potentials and Their Effects on Physical Adsorptions.

It is important to understand the mechanism of colloidal particle assembly near a substrate for development of drug delivery systems, micro-/nanorobots, batteries, heterogeneous catalysts, paints, and cosmetics. Understanding the mechanism is also important for crystallization of the colloidal particles and proteins. In this study, we calculated the physical adsorption of colloidal particles on a flat wall mainly using the integral equation theory, wherein small and large colloidal particles were employed. In the calculation system, like-charged electric double-layer potentials were used as pair potentials. In some cases, it was found that the small particles are more easily adsorbed. This result is unusual from the viewpoint of the Asakura-Oosawa theory, and we call it a "reversal phenomenon". Theoretical analysis revealed that the reversal phenomenon originates from the nonadditivities of the particle sizes. Using the knowledge obtained from this study, we invented a method to analyze the size nonadditivity hidden in model pair potentials. The method will be useful for confirmation of various simulation results regarding the adsorption and development of force fields for colloidal particles, proteins, and solutes.

Physical pictures of rotation mechanisms of F1- and V1-ATPases: Leading roles of translational, configurational entropy of water.

We aim to develop a theory based on a concept other than the chemo-mechanical coupling (transduction of chemical free energy of ATP to mechanical work) for an ATP-driven protein complex. Experimental results conflicting with the chemo-mechanical coupling have recently emerged. We claim that the system comprises not only the protein complex but also the aqueous solution in which the protein complex is immersed and the system performs essentially no mechanical work. We perform statistical-mechanical analyses on V1-ATPase (the A3B3DF complex) for which crystal structures in more different states are experimentally known than for F1-ATPase (the α3ß3γ complex). Molecular and atomistic models are employed for water and the structure of V1-ATPase, respectively. The entropy originating from the translational displacement of water molecules in the system is treated as a pivotal factor. We find that the packing structure of the catalytic dwell state of V1-ATPase is constructed by the interplay of ATP bindings to two of the A subunits and incorporation of the DF subunit. The packing structure represents the nonuniformity with respect to the closeness of packing of the atoms in constituent proteins and protein interfaces. The physical picture of rotation mechanism of F1-ATPase recently constructed by Kinoshita is examined, and common points and differences between F1- and V1-ATPases are revealed. An ATP hydrolysis cycle comprises binding of ATP to the protein complex, hydrolysis of ATP into ADP and Pi in it, and dissociation of ADP and Pi from it. During each cycle, the chemical compounds bound to the three A or ß subunits and the packing structure of the A3B3 or α3ß3 complex are sequentially changed, which induces the unidirectional rotation of the central shaft for retaining the packing structure of the A3B3DF or α3ß3γ complex stabilized for almost maximizing the water entropy. The torque driving the rotation is generated by water with no input of chemical free energy. The presence of ATP is indispensable as a trigger of the torque generation. The ATP hydrolysis or synthesis reaction is tightly coupled to the rotation of the central shaft in the normal or inverse direction through the water-entropy effect.

A methodology for creating mutants of G-protein coupled receptors stabilized in active state by combining statistical thermodynamics and evolutionary molecular engineering.

We challenged the stabilization of a G-protein coupled receptor (GPCR) in the active state solely by multiple amino-acid mutations without the agonist binding. For many GPCRs, the free energy of the active state is higher than that of the inactive state. When the inactive state is stabilized through the lowering of its free energy, the apparent midpoint temperature of thermal denaturation Tm exhibits a significant increase. However, this is not always the case for the stabilization of the active state. We constructed a modified version of our methodology combining statistical thermodynamics and evolutionary molecular engineering, which was recently developed for the inactive state. First, several residues to be mutated are determined using our statistical-thermodynamics theory. Second, a gene (mutant) library is constructed using Escherichia coli cells to efficiently explore most of the mutational space. Third, for the mutant screening, the mutants prepared in accordance with the library are expressed in engineered Saccharomyces cerevisiae YB14 cells which can grow only when a GPCR mutant stabilized in the active state has signaling function. For the adenosine A2A receptor tested, the methodology enabled us to sort out two triple mutants and a double mutant. It was experimentally corroborated that all the mutants exhibit much higher binding affinity for G protein than the wild type. Analyses indicated that the mutations make the structural characteristics shift toward those of the active state. However, only slight increases in Tm resulted from the mutations, suggesting the unsuitability of Tm to the stability measure for the active state.

Controlling the Rigidity of Kinesin-Propelled Microtubules in an In Vitro Gliding Assay Using the Deep-Sea Osmolyte Trimethylamine N-Oxide.

The biomolecular motor protein kinesin and its associated filamentous protein microtubule have been finding important nanotechnological applications in the recent years. Rigidity of the microtubules, which are propelled by kinesin motors in an in vitro gliding assay, is an important metric that determines the success of utilization of microtubules and kinesins in various applications, such as transportation, sensing, sorting, molecular robotics, etc. Therefore, regulating the rigidity of kinesin-propelled microtubules has been critical. In this work, we report a simple strategy to regulate the rigidity of kinesin-propelled microtubules in an in vitro gliding assay. We demonstrate that rigidity of the microtubules, propelled by kinesins in an in vitro gliding assay, can be modulated simply by using the natural osmolyte trimethylamine N-oxide (TMAO). By varying the concentration of TMAO in the gliding assay, the rigidity of microtubules can be modulated over a wide range. Based on this strategy, we are able to reduce the persistence length of microtubules, a measure of microtubule rigidity, ∼8 fold by using TMAO at the concentration of 1.5 M. Furthermore, we found that the decreased rigidity of the kinesin-propelled microtubules can be restored upon elimination of TMAO from the in vitro gliding assay. Alteration in the rigidity of microtubules is accounted for by the non-uniformity of the force applied by kinesins along the microtubules in the presence of TMAO. This work offers a facile strategy to reversibly regulate the rigidity of kinesin-propelled microtubules in situ, which would widen the applications of the biomolecular motor kinesin and its associated protein microtubule in various fields.

Development of an Outward Proton Pumping Rhodopsin with a New Record in Thermostability by Means of Amino Acid Mutations.

We have developed a methodology for identifying further thermostabilizing mutations for an intrinsically thermostable membrane protein. The methodology comprises the following steps: (1) identifying thermostabilizing single mutations (TSSMs) for residues in the transmembrane region using our physics-based method; (2) identifying TSSMs for residues in the extracellular and intracellular regions, which are in aqueous environment, using an empirical force field FoldX; and (3) combining the TSSMs identified in steps (1) and (2) to construct multiple mutations. The methodology is illustrated for thermophilic rhodopsin whose apparent midpoint temperature of thermal denaturation Tm is ∼91.8 °C. The TSSMs previously identified in step (1) were F90K, F90R, and Y91I with ΔTm ∼5.6, ∼5.5, and ∼2.9 °C, respectively, and those in step (2) were V79K, T114D, A115P, and A116E with ΔTm ∼2.7, ∼4.2, ∼2.6, and ∼2.3 °C, respectively (ΔTm denotes the increase in Tm). In this study, we construct triple and quadruple mutants, F90K+Y91I+T114D and F90K+Y91I+V79K+T114D. The values of ΔTm for these multiple mutants are ∼11.4 and ∼13.5 °C, respectively. Tm of the quadruple mutant (∼105.3 °C) establishes a new record in a class of outward proton pumping rhodopsins. It is higher than Tm of Rubrobacter xylanophilus rhodopsin (∼100.8 °C) that was the most thermostable in the class before this study.

Peak deflection index as a predictor of a free-wall implantation of contemporary leadless pacemakers.

BACKGROUND: Leadless pacemakers are an effective treatment for bradycardia. However, some cases exhibit pericardial effusions, presumably associated with device implantations on the right ventricular free-wall. The present study was carried out to find the ECG features during ventricular pacing with a Micra, which enabled distinguishing free-wall implantations from septal implantations without using imaging modalities. METHODS: Thirty-one consecutive patients who received Micra implantations in our facility were enrolled. The location of the device in the right ventricle was evaluated using echocardiography or computed tomography in order to determine whether the device was implanted on the septum (Sep group), apex (Apex group), or free-wall (FW group). The differences in the 12-lead ECG during ventricular pacing by the Micra were analyzed between the Sep and FW groups. RESULTS: The body of the Micra was clearly identifiable in 22 patients. The location of the device was classified into Sep in 12 patients, Apex in 4, and FW in 6. The mean age was highest in the FW and lowest in the Sep group (82.7 ± 6.6 vs. 72.8 ± 8.7 years, p = 0.027). The peak deflection index (PDI) was significantly larger in the FW group than Sep/Apex group in lead V1 (Sep: 0.505 ± 0.010, Apex: 0.402 ± 0.052, FW: 0.617 ± 0.043, p = 0.004) and lead V2 (Sep: 0.450 ± 0.066, Apex: 0.409 ± 0.037, FW: 0.521 ± 0.030, p = 0.011), whereas there was no difference in the QRS duration, transitional zone, and QRS notching. CONCLUSION: The PDI in V1 could be useful for predicting implantations of Micra devices on the free-wall and may potentially stratify the risk of postprocedural pericardial effusions.

Predicting therapies in Japanese hypertrophic cardiomyopathy patients with an implantable cardioverter-defibrillator using the 2014 European Society of Cardiology guidelines.

Previous studies have shown that the sudden cardiac death (SCD) prediction model proposed by the 2014 European Society of Cardiology (ESC) guideline (5-Year Risk-SCD) was validated in European patients with hypertrophic cardiomyopathy (HCM). However, there are limited data on Asian patients with HCM. We assessed the validity of the estimated 5-Year Risk-SCD in Japanese HCM patients with an implantable cardioverter-defibrillator (ICD) using the2014 ESC guidelines. We retrospectively examined data of 492 consecutive Japanese patients with an ICD. Sixty-two Japanese HCM patients with an ICD were enrolled in this study, and 50 patients (81%) were followed up for ≥ 5 years. We analyzed the characteristics and outcomes of these 50 patients. We investigated the incidence of appropriate ICD therapy as categorized by the ESC guideline and compared the 5-Year Risk-SCD with the 5-year rate of appropriate shock therapies. Based on the 2012 Japanese Circulation Society guideline and the 2011guidelines of the American Heart Association and American College of Cardiology Foundation, 10 and 40 patients met classes I and IIa of the ICD recommendation, respectively. However, only 18 (36%) patients were classified into class I or IIa of the ESC guideline. Among 50 patients followed up for ≥ 5 years after ICD implantation, the incidences of appropriate ICD therapies for classes I, IIa, IIb, and III indications based on the 2014 ESC guideline were 50%, 38%, 17%, and 0%, respectively. Risk stratification for SCD using 5-Year Risk-SCD is valid in Japanese HCM patients with an ICD, and the 2014 ESC guideline might be useful for the indication of ICD implantation in Japan.

Successful cryoablation of ventricular extrasystoles originating from the vicinity of the left anterior fascicle.

A 32-year-old male received catheter ablation of frequent ventricular extrasystoles (VEs). His electrocardiogram showed monomorphic VEs with an inferior axis and early precordial transitional zone. During electrophysiological testing, a 10-pole catheter positioned in the left ventricular outflow tract recorded sharp pre-potentials just before the ventricular activation during VEs as well as sinus beats. Three-dimensional mapping was performed by annotating the sharp pre-potentials to reveal that the earliest activation site was deemed to be close to the left anterior fascicle. A cryoablation catheter was introduced into the left ventricle and freezing for 240 seconds successfully eliminated the clinical VEs without any complications.

Theoretical identification of thermostabilizing amino acid mutations for G-protein-coupled receptors.

Thermostabilization of a membrane proteins, especially G-protein-coupled receptors (GPCRs), is often necessary for biochemical applications and pharmaceutical studies involving structure-based drug design. Here we review our theoretical, physics-based method for identifying thermostabilizing amino acid mutations. Its novel aspects are the following: The entropic effect originating from the translational displacement of hydrocarbon groups within the lipid bilayer is treated as a pivotal factor; a reliable measure of thermostability is introduced and a mutation which enlarges the measure to a significant extent is chosen; and all the possible mutations can be examined with moderate computational effort. It was shown that mutating the residue at a position of NBW = 3.39 (NBW is the Ballesteros-Weinstein number) to Arg or Lys leads to the stabilization of significantly many different GPCRs of class A in the inactive state. Up to now, we have been successful in stabilizing several GPCRs and newly solving three-dimensional structures for the muscarinic acetylcholine receptor 2 (M2R), prostaglandin E receptor 4 (EP4), and serotonin 2A receptor (5-HT2AR) using X-ray crystallography. The subjects to be pursued in future studies are also discussed.

Accurate and rapid calculation of hydration free energy and its physical implication for biomolecular functions.

Here we review a new method for calculating a hydration free energy (HFE) of a solute and discuss its physical implication for biomolecular functions in aqueous environments. The solute hydration is decomposed into processes 1 and 2. A cavity matching the geometric characteristics of the solute at the atomic level is created in process 1. Solute-water van der Waals and electrostatic interaction potentials are incorporated in process 2. The angle-dependent integral equation theory combined with our morphometric approach is applied to process 1, and the three-dimensional reference interaction site model theory is employed for process 2. Molecular models are adopted for water. The new method is characterized by the following. Solutes with various sizes including proteins can be treated in the same manner. It is almost as accurate as the molecular dynamics simulation despite its far smaller computational burden. It enables us to handle a solute possessing a significantly large total charge without difficulty. The HFE can be decomposed into a variety of physically insightful, energetic, and entropic components. It is best suited to the elucidation of mechanisms of protein folding, pressure and cold denaturation of a protein, and different types of molecular recognition.

Development and structural determination of an anti-PrPC aptamer that blocks pathological conformational conversion of prion protein.

Prion diseases comprise a fatal neuropathy caused by the conversion of prion protein from a cellular (PrPC) to a pathological (PrPSc) isoform. Previously, we obtained an RNA aptamer, r(GGAGGAGGAGGA) (R12), that folds into a unique G-quadruplex. The R12 homodimer binds to a PrPC molecule, inhibiting PrPC-to-PrPSc conversion. Here, we developed a new RNA aptamer, r(GGAGGAGGAGGAGGAGGAGGAGGA) (R24), where two R12s are tandemly connected. The 50% inhibitory concentration for the formation of PrPSc (IC50) of R24 in scrapie-infected cell lines was ca. 100 nM, i.e., much lower than that of R12 by two orders. Except for some antibodies, R24 exhibited the lowest recorded IC50 and the highest anti-prion activity. We also developed a related aptamer, r(GGAGGAGGAGGA-A-GGAGGAGGAGGA) (R12-A-R12), IC50 being ca. 500 nM. The structure of a single R12-A-R12 molecule determined by NMR resembled that of the R12 homodimer. The quadruplex structure of either R24 or R12-A-R12 is unimolecular, and therefore the structure could be stably formed when they are administered to a prion-infected cell culture. This may be the reason they can exert high anti-prion activity.

Methodology for Further Thermostabilization of an Intrinsically Thermostable Membrane Protein Using Amino Acid Mutations with Its Original Function Being Retained.

We develop a new methodology best suited to the identification of thermostabilizing mutations for an intrinsically stable membrane protein. The recently discovered thermophilic rhodopsin, whose apparent midpoint temperature of thermal denaturation Tm is measured to be ∼91.8 °C, is chosen as a paradigmatic target. In the methodology, we first regard the residues whose side chains are missing in the crystal structure of the wild type (WT) as the "residues with disordered side chains," which make no significant contributions to the stability, unlike the other essential residues. We then undertake mutating each of the residues with disordered side chains to another residue except Ala and Pro, and the resultant mutant structure is constructed by modifying only the local structure around the mutated residue. This construction is based on the postulation that the structure formed by the other essential residues, which is nearly optimized in such a highly stable protein, should not be modified. The stability changes arising from the mutations are then evaluated using our physics-based free-energy function (FEF). We choose the mutations for which the FEF is much lower than for the WT and test them by experiments. We successfully find three mutants that are significantly more stable than the WT. A double mutant whose Tm reaches ∼100 °C is also discovered.

Hydration properties of a protein at low and high pressures: Physics of pressure denaturation.

Using experimentally determined structures of ubiquitin at 1 and 3000 bar, we generate sufficiently large ensembles of model structures in the native and pressure-induced (denatured) states by means of molecular dynamics simulations with explicit water. We calculate the values of a free-energy function (FEF), which comprises the hydration free energy (HFE) and the intramolecular (conformational) energy and entropy, for the two states at 1 and 3000 bar. The HFE and the conformational entropy, respectively, are calculated using our statistical-mechanical method, which has recently been shown to be accurate, and the Boltzmann-quasi-harmonic method. The HFE is decomposed into a variety of physically insightful components. We show that the FEF of the native state is lower than that of the denatured state at 1 bar, whereas the opposite is true at 3000 bar, thus being successful in reproducing the pressure denaturation. We argue that the following two quantities of hydration play essential roles in the denaturation: the WASA-dependent term in the water-entropy loss upon cavity creation for accommodating the protein (WASA is the water-accessible surface area of the cavity) and the protein-water Lennard-Jones interaction energy. At a high pressure, the mitigation of the serious water crowding in the system is the most important, and the WASA needs to be sufficiently enlarged with the increase in the excluded-volume being kept as small as possible. The denatured structure thus induced is characterized by the water penetration into the protein interior. The pressure denaturation is accompanied by a significantly large gain of water entropy.

How Does a Microbial Rhodopsin RxR Realize Its Exceptionally High Thermostability with the Proton-Pumping Function Being Retained?

We often encounter a case where two proteins, whose amino-acid sequences are similar, are quite different with regard to the thermostability. As a striking example, we consider the two seven-transmembrane proteins: recently discovered Rubrobacter xylanophilus rhodopsin (RxR) and long-known bacteriorhodopsin from Halobacterium salinarum (HsBR). They commonly function as a light-driven proton pump across the membrane. Though their sequence similarity and identity are ∼71 and ∼45%, respectively, RxR is much more thermostable than HsBR. In this study, we solve the three-dimensional structure of RxR using X-ray crystallography and find that the backbone structures of RxR and HsBR are surprisingly similar to each other: The root-mean-square deviation for the two structures calculated using the backbone Cα atoms of the seven helices is only 0.86 Å, which makes the large stability difference more puzzling. We calculate the thermostability measure and its energetic and entropic components for RxR and HsBR using our recently developed statistical-mechanical theory. The same type of calculation is independently performed for the portions playing essential roles in the proton-pumping function, helices 3 and 7, and their structural properties are related to the probable roles of water molecules in the proton-transporting mechanism. We succeed in elucidating how RxR realizes its exceptionally high stability with the original function being retained. This study provides an important first step toward the establishment of a method correlating microscopic, geometric characteristics of a protein with its thermodynamic properties and enhancing the thermostability through amino-acid mutations without vitiating the original function.

Percutaneous Transluminal Septal Myocardial Ablation for Hypertrophic Obstructive Cardiomyopathy Under Extracorporeal Membrane Oxygenation Support.

We report the case of a 70-year-old woman with hypertrophic obstructive cardiomyopathy, who was admitted because of severe heart failure and cardiogenic shock and mechanical support requiring extracorporeal membrane oxygenation. She recovered well by percutaneous transluminal septal myocardial ablation under the extracorporeal membrane oxygenation support and was discharged without complications. (Level of Difficulty: Advanced.).

Estimation of the accessory pathway location of the manifest Wolf-Parkinson-White syndrome using synthesized right-sided chest leads.

PURPOSE: The classification using QRS morphology of V1 lead is a useful simple predictor of accessory pathway location (type A, R or Rs pattern; type B, rS pattern; type C, QS or Qr pattern), but often leads to misdiagnosis of accessory pathway location, especially in types B and C. The synthesized 18-lead electrocardiography (ECG) derived from standard 12-lead ECG can provide virtual waveforms of right-sided chest leads. This study aimed to evaluate the usefulness of the right-sided chest lead ECG for prediction of accessory pathway location. METHODS: This retrospective study included 44 patients in whom successful ablation of manifest Wolff-Parkinson-White (WPW) syndrome was performed. Synthesized ECG waveforms were automatically generated, and ECG data obtained before the procedure. RESULTS: There were 26, 4, and 14 patients with left, right, and septal accessory pathways, respectively. All left accessory pathway cases have type A in V1 and syn-V4R leads. Of the 4 right accessory pathway cases, 2 have type B in V1 and syn-V4R leads. Other 2 of 4 cases have type C. In V1 lead, 5 of 14 septal accessory pathway cases have type C, 7 of 14 cases have type B, and 2 of 14cases have type A. In syn-V4R lead, all 14 septal accessory pathway cases have type C. The QRS morphology of V1 and syn-V4 leads could predict the site of accessory pathway with overall accuracy of 79% and 95%, respectively. CONCLUSIONS: QRS morphology of syn-V4R lead may be useful for predicting accessory pathway location of manifest WPW syndrome.

Comparison of the performance of implantable cardioverter-defibrillator leads among manufacturers.

BACKGROUND: Leads are often considered the weakest link in implantable cardioverter-defibrillator (ICD) systems, and lead dysfunction is a major concern for ICD recipients. The aim of this study was to compare the lead performance from three different manufacturers. METHODS: We retrospectively reviewed consecutive patients who underwent ICD system implantation at Chiba University Hospital, Japan, between March 2008 and September 2017. The following leads were implanted in our center: Durata (St. Jude Medical, St. Paul, MN, USA, now Abbott) (n = 105), Linox and LinoxSmart (Biotronik, Berlin, Germany) (n = 66), and Sprint Quattro (Medtronic, Minneapolis, MN, USA) (n = 126). RESULTS: A total of 297 ICD leads were analyzed. Failure rates for Durata, Linox/LinoxSmart, and Sprint Quattro were 0.20%/patient year, 0.95%/patient year, and 1.84%/patient year, respectively, during a mean follow-up of 4.8, 6.4, and 3.0 years, respectively. The cumulative ICD lead survival probability was 98.9%, 100%, and 87.5%, after 5 years, respectively. The survival probability over the entire follow-up time as measured by the log-rank test was lower for Sprint Quattro leads than for either Durata (p = 0.011) or Linox/LinoxSmart (p = 0.028). The difference between Durata and Linox/LinoxSmart was not significant (p = 0.393). CONCLUSIONS: In this single-center retrospective study, the performance of Sprint Quattro was lower than the performance of Linox/LinoxSmart and Durata leads. Large-scale, multi-center studies or manufacturer-independent registries may be necessary to confirm or reject self-reported survival probabilities from manufacturers' product performance reports.

How Does the Recently Discovered Peptide MIP Exhibit Much Higher Binding Affinity than an Anticancer Protein p53 for an Oncoprotein MDM2?

An oncoprotein MDM2 binds to the extreme N-terminal peptide region of a tumor suppressor protein p53 (p53NTD) and inhibits its anticancer activity. We recently discovered a peptide named MIP which exhibits much higher binding affinity for MDM2 than p53NTD. Experiments showed that the binding free energy (BFE) of MDM2-MIP is lower than that of MDM2-p53NTD by approximately -4 kcal/mol. Here, we develop a theoretical method which is successful in reproducing this quantitative difference and elucidating its physical origins. It enables us to decompose the BFE into a variety of energetic and entropic components, evaluate their relative magnitudes, and identify the physical factors driving or opposing the binding. It should be applicable also to the assessment of differences among ligands in the binding affinity for a particular receptor, which is a central issue in modern chemistry. In the MDM2 case, the higher affinity of MIP is ascribed to a larger gain of translational, configurational entropy of water upon binding. This result is useful to the design of a peptide possessing even higher affinity for MDM2 as a reliable drug against a cancer.

An accurate and rapid method for calculating hydration free energies of a variety of solutes including proteins.

A new method is developed for calculating hydration free energies (HFEs) of polyatomic solutes. The solute insertion is decomposed into the creation of a cavity in water matching the geometric characteristics of the solute at the atomic level (process 1) and the incorporation of solute-water van der Waals and electrostatic interactions (process 2). The angle-dependent integral equation theory combined with our morphometric approach and the three-dimensional interaction site model theory are applied to processes 1 and 2, respectively. Neither a stage of training nor parameterization is necessitated. For solutes with various sizes including proteins, the HFEs calculated by the new method are compared to those obtained using a molecular dynamics simulation based on solution theory in energy representation (the ER method developed by Matubayasi and co-workers), currently the most reliable tool. The agreement is very good especially for proteins. The new method is characterized by the following: The calculation can rapidly be finished; a solute possessing a significantly large total charge can be handled without difficulty; and since it yields not only the HFE but also its many physically insightful energetic and entropic components, it is best suited to the elucidation of mechanisms of diverse phenomena such as the receptor-ligand binding, different types of molecular recognition, and protein folding, denaturation, and association.