Rational automatic search method for stable docking models of protein and ligand

An efficient automatic method has been developed for docking a ligand molecule to a protein molecule. The method can construct energetically favorable docking models, considering specific interactions between the two molecules and conformational flexibility in the ligand. In the first stage of docking, likely binding modes are searched and estimated effectively in terms of hydrogen bonds, together with conformations in part of the ligand structure that includes hydrogen bonding groups. After that part is placed in the protein cavity and is optimized, conformations in the remaining part are also examined systematically. Finally, several stable docking models are obtained after optimization of the position, orientation and conformation of the whole ligand molecule. In all the screening processes, the total potential energy including intra- and intermolecular interaction energy, consisting of van der Waals, electrostatic and hydrogen bonding energies, is used as the index. The characteristics of our docking method are high accuracy of the results, fully automatic generation of models and short computational time. The efficiency of the method was confirmed by four docking trials using two enzyme systems. In two attempts to dock methotrexate to dihydrofolate reductase and 2'-GMP to ribonuclease T1, the exact structures of complexes in crystals were reproduced as the most stable docking models, without any assumptions concerning the binding modes and ligand conformations. The most stable docking models of dihydrofolate and trimethoprim, respectively, to dihydrofolate reductase were also in good agreement with those suggested by experiment. In all test cases, it was shown that our method can accurately predict the correct docking structures, discriminating the correct model from incorrect ones. The efficiency of our method was further tested from the viewpoint of ability to predict the relative stability of the docking structures of two triazine derivatives to dihydrofolate reductase. Our docking method provides a useful tool for rational drug design and investigations of biochemical reaction mechanisms.     

Stability and characterization of phospholipid Langmuir-Blodgett films

The regularity of the bilayer structure was compared between dipalmitoylphosphatidic acid (DPPA) Langmuir-Blodgett (LB) films and “oriented multilayers” of DPPA, using X-ray diffraction and electron spectroscopy for chemical analysis (ESCA). The angular variation of the (001) Bragg spot due to the irregularity of the lamellar repeat was remarkable in the system of oriented multilayers. In contrast, the spot of DPPA LB films exhibited only a slight angular variation, suggesting a regular structure of this film. The take-off angle dependence of the phosphorus:carbon ratio obtained by ESCA indicates that the regular layered structure in DPPA LB film is maintained after 49 layers are deposited.     

A hierarchy of uniquely parsable grammar classes and deterministic acceptors

We introduce a new class of grammars called uniquely parsable grammars (UPGs). A UPG is a kind of phrase structure grammar having a restricted type of rewriting rules, where parsing can be performed without backtracking. We show that, in spite of such restriction to the rules, UPGs are universal in their generating ability. We then define three subclasses of UPGs. They are M-UPGs (monotonic UPGs), RC-UPGs (UPGs with right-terminating and context-free-like rules), and REG-UPGs (regular UPGs). It is proved that the generating abilities of the classes of M-UPGs, RC-UPGs, and REG-UPGs are exactly characterized by the classes of deterministic linear-bounded automata, deterministic pushdown automata, and deterministic finite automata, respectively. Especially, the class of RC-UPGs gives a very simple grammatical characterization of the class of deterministic context-free languages. Thus, these four classes form a deterministic counterpart of the classical Chomsky hierarchy. Received August 30, 1995 / May 13, 1996     

4 Pro-R hydrogen of NADPH was abstracted for enzymatic hydride transfer by N-ethylmaleimide-reductase of Yarrowia lipolytica

We studied the steric course of the reaction catalyzed by the N-ethylmaleimide (NEM) reductase of Yarrowia (Candida) lipolytica (Y. lipolytica), using 4R-[4-2H1]NADPH and 4S-[4-2H1]NADPH as cofactors and N-ethylcitraconimide as substrate. Active substrates and inhibitors of NEM reductase and its subcellular distribution were also investigated to clarify the biochemical properties of this enzyme. NEM reductase catalyzes the reduction of N-ethylmaleimide to N-ethylsuccinimide with NAD(P)H as the cofactor. Several maleimide and cyclopentenone derivatives tested were also active substrates for NEM reductase of Y. lipolytica. Some pyrazolone derivatives, particularly 1-phenyl-5-pyrazolone, were found to be effective inhibitors of NEM reductase. Subcellular localization of NEM reductase was carried out using protoplast formation and differential centrifugation. Ninety-eight percent of the NEM reductase activity was recovered in the cytosolic fraction, indicating that NEM reductase in Y. lipolytica was the cytosolic enzyme. We also determined the stereochemical specificity of the reduction of N-ethylcitraconimide by NEM reductase in Y. lipolytica, showing that 4 Pro-R hydrogen of NADPH was abstracted for enzymatic hydride transfer by NEM reductase, and two hydrogen atoms from NADPH and H2O added to opposite faces of the double bond of N-ethylcitraconimide.     

Binding-time analysis for both static and dynamic expressions

This paper presents a specializer and a binding-time analyzer for a functional language where expressions are allowed to be used as both static and dynamic. With both static and dynamic expressions, data structures can be statically accessed while they are residualized at the same time. Previously, such data structures were treated as completely dynamic, which prevented their components from being accessed statically. The technique presented in this paper effectively allows data structures to be lifted which was prohibited in the conventional partial evaluators. The binding-time analysis is formalized as a type system and the solution is obtained by solving constraints generated by the type system. We prove the correctness of the constraint solving algorithm and show that the algorithm runs efficiently in almost linear time. Kenichi Asai, Ph.D.: He is a research associate at the Department of Computer Science, Faculty of Science, the University of Tokyo. He obtained his bachelors degree, masters degree, and doctor of Science from the University of Tokyo in 1990, 1992, and 1997, respectively. His research interests are in Programming Languages in general, in Partial Evaluation and Reflection in particular. He is a member of ACM, IPSJ, and JSSST.     

An implantable centrifugal blood pump for long term circulatory support

A compact centrifugal blood pump was developed as an implantable left ventricular assist system. The impeller diameter is 40 mm and the pump dimensions are 55 x 64 mm. This first prototype was fabricated from titanium alloy, resulting in a pump weight of 400 g including a brushless DC motor. Weight of the second prototype pump was reduced to 280 g. The entire blood contacting surface is coated with diamond like carbon to improve blood compatibility. Flow rates of over 7 L/min against 100 mmHg pressure at 2,500 rpm with 9 W total power consumption have been measured. A newly designed mechanical seal with a recirculating purge system ("Cool-Seal") is used as a shaft seal. In this seal system, seal temperature is kept under 40 degrees C to prevent heat denaturation of blood proteins. Purge fluid also cools the pump motor coil and journal bearing. The purge fluid is continuously purified and sterilized by an ultrafiltration filter incorporated into the paracorporeal drive console. In vitro experiments with bovine blood demonstrated an acceptably low hemolysis rate (normalized index of hemolysis = 0.005 +/- 0.002 g/100 L). In vivo experiments are currently ongoing using calves. Via left thoracotomy, left ventricular apex-descending aorta bypass was performed utilizing a PTFE (Polytetrafluoroethylene) vascular graft, with the pump placed in the left thoracic cavity. In two in vivo experiments, pump flow rate was maintained at 5-8 L/min, and pump power consumption remained stable at 9-10 W. All plasma free hemoglobin levels were measured at < 15 mg/dl. The seal system has demonstrated good seal capability with negligible purge fluid consumption (< 0.5 ml/ day). Both animals remain under observation after 162 and 91 days of continuous pump function.     

Pitch-based carbon fibres derived from thermoset fibres oxidized with Cl2 containing air

Mesophase pitch-based carbon fibres thermoset with Cl₂ containing air were studied for their microstructures and physical properties. Carbon fibres thermoset with Cl₂ containing air and heat-treated at 2000C (Cl₂2000) possessed slightly smaller mean sizes of crystallites L _c(0 0 2)s, lower densities, lower tensile moduli of elasticity, and higher tensile strengths than those thermoset with air. X-ray diffraction measurements revealed a somewhat lower degree of preferred orientation of a carbon fibre which was thermoset with Cl₂ containing air. The Cl₂ thermosetting partly disordered the periodic arrangement of crystallites and reduced the crystallite size L _c(0 0 2) of a carbon fibre heat-treated at a lower temperature. A strong temperature dependence of resistivity was shown for Cl₂800, suggesting much disorder in its microstructure due to the Cl₂ thermosetting, and Cl₂1000 and Cl₂1200, respectively showed specific temperature dependencies of resistivities.     

Flexible service consolidation with nested virtualization and library operating systems

In Infrastructure-as-a-service (IaaS) clouds, users can reduce costs by scale-in or scale-down when running services are underutilized. Since these optimizations of instance deployment require at least one minimum instance even for running an underutilized service, cost reduction is limited. For further optimization, multiple services can be consolidated into one instance. However, services have to be stopped temporarily at the consolidation time, and isolation between services becomes weaker after the consolidation. To solve these problems, this paper proposes FlexCapsule, which enables seamless and secure service consolidation in existing IaaS clouds. FlexCapsule runs each service in a lightweight virtual machine (VM) called an app VM, using a library operating system. An app VM runs inside an instance using a technique called nested virtualization. FlexCapsule can optimize instance deployment with negligible downtime by flexibly migrating app VMs. Due to strong isolation provided by app VMs, it can guarantee security between consolidated services. In addition, FlexCapsule provides multiprocess support using app VMs by emulating process fork and process pools. We have implemented FlexCapsule in Xen using both fully virtualized OS^v and paravirtualized MiniOS. Then, we examined the effectiveness of FlexCapsule using several applications. Due to the premature implementation of nested virtualization in Xen, the performance of app VMs largely degraded, but we believe that the performance could be improved using several existing optimizations.     

Enhanced Electroluminescence from Organic Light‐Emitting Diodes with an Organic–Inorganic Perovskite Host Layer

The development of host materials with high performance is essential for fabrication of efficient and stable organic light‐emitting diodes (OLEDs). Although host materials used in OLEDs are typically organics, in this study, it is shown that the organic–inorganic perovskite CH₃NH₃PbCl₃ (MAPbCl₃) can be used as a host layer for OLEDs. Vacuum‐evaporated MAPbCl₃ films have a wide band gap of about 3 eV and very high and relatively balanced hole and electron mobilities, which are suitable for the host material. Photoluminescence and electroluminescence take place through energy transfer from MAPbCl₃ to an organic emitter in films. Incorporation of an MAPbCl₃ host layer into OLEDs leads to a reduction of driving voltage and enhancement of external quantum efficiency as compared to devices with a conventional organic host layer. Additionally, OLEDs with an MAPbCl₃ host layer demonstrate very good operational stability under continuous current operation. These results can be extensively applied to organic‐ and perovskite‐based optoelectronics.