On the role of global flow instability analysis in closed loop flow control

Control of linear flow instabilities has been demonstrated to be an effective theoretical flow control methodology, capable of modifying transitional flow on canonical geometries such as the plane channel and the flat-plate boundary layer.

A management model for closed-loop supply chains of reusable articles

This PhD dissertation is framed in the emergent fields of Reverse Logistics and ClosedLoop Supply Chain (CLSC) management. This subarea of supply chain management has gained researchers and practitioners' attention over the last 15 years to become a fully recognized subdiscipline of the Operations Management field. More specifically, among all the activities that are included within the CLSC area, the focus of this dissertation is centered in direct reuse aspects. The main contribution of this dissertation to current knowledge is twofold. First, a framework for the so-called reuse CLSC is developed. This conceptual model is grounded in a set of six case studies conducted by the author in real industrial settings. The model has also been contrasted with existing literature and with academic and professional experts on the topic as well. The framework encompasses four building blocks. In the first block, a typology for reusable articles is put forward, distinguishing between Returnable Transport Items (RTI), Reusable Packaging Materials (RPM), and Reusable Products (RP). In the second block, the common characteristics that render reuse CLSC difficult to manage from a logistical standpoint are identified, namely: fleet shrinkage, significant investment and limited visibility. In the third block, the main problems arising in the management of reuse CLSC are analyzed, such as: (1) define fleet size dimension, (2) control cycle time and promote articles rotation, (3) control return rate and prevent shrinkage, (4) define purchase policies for new articles, (5) plan and control reconditioning activities, and (6) balance inventory between depots. Finally, in the fourth block some solutions to those issues are developed. Firstly, problems (2) and (3) are addressed through the comparative analysis of alternative strategies for controlling cycle time and return rate. Secondly, a methodology for calculating the required fleet size is elaborated (problem (1)). This methodology is valid for different configurations of the physical flows in the reuse CLSC. Likewise, some directions are pointed out for further development of a similar method for defining purchase policies for new articles (problem (4)). The second main contribution of this dissertation is embedded in the solutions part (block 4) of the conceptual framework and comprises a two-level decision problem integrating two mixed integer linear programming (MILP) models that have been formulated and solved to optimality using AIMMS as modeling language, CPLEX as solver and Excel spreadsheet for data introduction and output presentation. The results obtained are analyzed in order to measure in a client-supplier system the economic impact of two alternative control strategies (recovery policies) in the context of reuse. In addition, the models support decision-making regarding the selection of the appropriate recovery policy against the characteristics of demand pattern and the structure of the relevant costs in the system. The triangulation of methods used in this thesis has enabled to address the same research topic with different approaches and thus, the robustness of the results obtained is strengthened.

An ICT-based closed-loop model to improve care for heart failure patients

Durante las últimas décadas se ha producido un fenómeno global de envejecimiento en la población. Esta tendencia se puede observar prácticamente en todos los países del mundo y se debe principalmente a los avances en la medicina, y a los descensos en las tasas de fertilidad y mortalidad. El envejecimiento de la población tiene un gran impacto en la salud de los ciudadanos, y a menudo es la causa de aparición de enfermedades crónicas. Este tipo de enfermedades supone una amenaza y una carga importantes para la sociedad, especialmente en aspectos como la mortalidad o los gastos en los sistemas sanitarios. Entre las enfermedades cardiovasculares, la insuficiencia cardíaca es probablemente la condición con mayor prevalencia y afecta a 23-26 millones de personas en todo el mundo. Normalmente, la insuficiencia cardíaca presenta un mal pronóstico y una tasa de supervivencia bajas, en algunos casos peores que algún tipo de cáncer. Además, suele ser la causa de hospitalizaciones frecuentes y es una de las enfermedades más costosas para los sistemas sanitarios. La tendencia al envejecimiento de la población y la creciente incidencia de las enfermedades crónicas están llevando a una situación en la que los sistemas de salud no son capaces de hacer frente a la demanda de la sociedad. Los servicios de salud existentes tendrán que adaptarse para ser efectivos y sostenibles en el futuro. Es necesario identificar nuevos paradigmas de cuidado de pacientes, así como mecanismos para la provisión de servicios que ayuden a transformar estos sistemas sanitarios. En este contexto, esta tesis se plantea la búsqueda de soluciones, basadas en las Tecnologías de la Información y la Comunicación (TIC), que contribuyan a realizar la transformación en los sistemas sanitarios. En concreto, la tesis se centra en abordar los problemas de una de las enfermedades con mayor impacto en estos sistemas: la insuficiencia cardíaca. Las siguientes hipótesis constituyen la base para la realización de este trabajo de investigación: 1. Es posible definir un modelo basado en el paradigma de lazo cerrado y herramientas TIC que formalice el diseño de mejores servicios para pacientes con insuficiencia cardíaca. 2. El modelo de lazo cerrado definido se puede utilizar para definir un servicio real que ayude a gestionar la insuficiencia cardíaca crónica. 3. La introducción, la adopción y el uso de un servicio basado en el modelo definido se traducirá en mejoras en el estado de salud de los pacientes que sufren insuficiencia cardíaca. a. La utilización de un sistema basado en el modelo de lazo cerrado definido mejorará la experiencia del usuario de los pacientes. La definición del modelo planteado se ha basado en el estándar ISO / EN 13940- Sistema de conceptos para dar soporte a la continuidad de la asistencia. Comprende un conjunto de conceptos, procesos, flujos de trabajo, y servicios como componentes principales, y representa una formalización de los servicios para los pacientes con insuficiencia cardíaca. Para evaluar el modelo definido se ha definido un servicio real basado en el mismo, además de la implementación de un sistema de apoyo a dicho servicio. El diseño e implementación de dicho sistema se realizó siguiendo la metodología de Diseño Orientado a Objetivos. El objetivo de la evaluación consistía en investigar el efecto que tiene un servicio basado en el modelo de lazo cerrado sobre el estado de salud de los pacientes con insuficiencia cardíaca. La evaluación se realizó en el marco de un estudio clínico observacional. El análisis de los resultados ha comprendido métodos de análisis cuantitativos y cualitativos. El análisis cuantitativo se ha centrado en determinar el estado de salud de los pacientes en base a datos objetivos (obtenidos en pruebas de laboratorio o exámenes médicos). Para realizar este análisis se definieron dos índices específicos: el índice de estabilidad y el índice de la evolución del estado de salud. El análisis cualitativo ha evaluado la autopercepción del estado de salud de los pacientes en términos de calidad de vida, auto-cuidado, el conocimiento, la ansiedad y la depresión, así como niveles de conocimiento. Se ha basado en los datos recogidos mediante varios cuestionarios o instrumentos estándar (i.e. EQ-5D, la Escala de Ansiedad y Depresión (HADS), el Cuestionario de Cardiomiopatía de Kansas City (KCCQ), la Escala Holandesa de Conocimiento de Insuficiencia Cardíaca (DHFKS), y la Escala Europea de Autocuidado en Insuficiencia Cardíaca (EHFScBS), así como cuestionarios dedicados no estandarizados de experiencia de usuario. Los resultados obtenidos en ambos análisis, cuantitativo y cualitativo, se compararon con el fin de evaluar la correlación entre el estado de salud objetivo y subjetivo de los pacientes. Los resultados de la validación demostraron que el modelo propuesto tiene efectos positivos en el cuidado de los pacientes con insuficiencia cardíaca y contribuye a mejorar su estado de salud. Asimismo, ratificaron al modelo como instrumento válido para la definición de servicios mejorados para la gestión de esta enfermedad. ABSTRACT During the last decades we have witnessed a global aging phenomenon in the population. This can be observed in practically every country in the world, and it is mainly caused by the advances in medicine, and the decrease of mortality and fertility rates. Population aging has an important impact on citizens’ health and it is often the cause for chronic diseases, which constitute global burden and threat to the society in terms of mortality and healthcare expenditure. Among chronic diseases, Chronic Heart Failure (CHF) or Heart Failure (HF) is probably the one with highest prevalence, affecting between 23 and 26 million people worldwide. Heart failure is a chronic, long-term and serious condition with very poor prognosis and worse survival rates than some type of cancers. Additionally, it is often the cause of frequent hospitalizations and one of the most expensive conditions for the healthcare systems. The aging trends in the population and the increasing incidence of chronic diseases are leading to a situation where healthcare systems are not able to cope with the society demand. Current healthcare services will have to be adapted and redefined in order to be effective and sustainable in the future. There is a need to find new paradigms for patients’ care, and to identify new mechanisms for services’ provision that help to transform the healthcare systems. In this context, this thesis aims to explore new solutions, based on ICT, that contribute to achieve the needed transformation within the healthcare systems. In particular, it focuses on addressing the problems of one of the diseases with higher impact within these systems: Heart Failure. The following hypotheses represent the basis to the elaboration of this research: 1. It is possible to define a model based on a closed-loop paradigm and ICT tools that formalises the design of enhanced healthcare services for chronic heart failure patients. 2. The described closed-loop model can be exemplified in a real service that supports the management of chronic heart failure disease. 3. The introduction, adoption and use of a service based on the outlined model will result in improvements in the health status of patients suffering heart failure. 4. The user experience of patients when utilizing a system based on the defined closed-loop model will be enhanced. The definition of the closed-loop model for health care support of heart failure patients have been based on the standard ISO/EN 13940 System of concepts to support continuity of care. It includes a set of concept, processes and workflows, and services as main components, and it represent a formalization of services for heart failure patients. In order to be validated, the proposed closed-loop model has been instantiated into a real service and a supporting IT system. The design and implementation of the system followed the user centred design methodology Goal Oriented Design. The validation, that included an observational clinical study, aimed to investigate the effect that a service based on the closed-loop model had on heart failure patients’ health status. The analysis of results comprised quantitative and qualitative analysis methods. The quantitative analysis was focused on determining the health status of patients based on objective data (obtained in lab tests or physical examinations). Two specific indexes where defined and considered in this analysis: the stability index and the health status evolution index. The qualitative analysis assessed the self-perception of patients’ health status in terms of quality of life, self-care, knowledge, anxiety and depression, as well as knowledge levels. It was based on the data gathered through several standard instruments (i.e. EQ-5D, the Hospital Anxiety and Depression Scale, the Kansas City Cardiomyopathy Questionnaire, the Dutch Heart Failure Knowledge Scale, and the European Heart Failure Self-care Behaviour Scale) as well as dedicated non-standardized user experience questionnaires. The results obtained in both analyses, quantitative and qualitative, were compared in order to assess the correlation between the objective and subjective health status of patients. The results of the validation showed that the proposed model contributed to improve the health status of the patients and had a positive effect on the patients’ care. It also proved that the model is a valid instrument for designing enhanced healthcare services for heart failure patients.

VHDL-based system design of a cognitive sensorimotor loop (CSL) for haptic Human-Machine Interaction (HMI)

This document is a summary of the Bachelor thesis titled “VHDL-Based System Design of a Cognitive Sensorimotor Loop (CSL) for Haptic Human-Machine Interaction (HMI)” written by Pablo de Miguel Morales, Electronics Engineering student at the Universidad Politécnica de Madrid (UPM Madrid, Spain) during an Erasmus+ Exchange Program at the Beuth Hochschule für Technik (BHT Berlin, Germany). The tutor of this project is Dr. Prof. Hild. This project has been developed inside the Neurobotics Research Laboratory (NRL) in close collaboration with Benjamin Panreck, a member of the NRL, and another exchange student from the UPM Pablo Gabriel Lezcano. For a deeper comprehension of the content of the thesis, a deeper look in the document is needed as well as the viewing of the videos and the VHDL design. In the growing field of automation, a large amount of workforce is dedicated to improve, adapt and design motor controllers for a wide variety of applications. In the specific field of robotics or other machinery designed to interact with humans or their environment, new needs and technological solutions are often being discovered due to the existing, relatively unexplored new scenario it is. The project consisted of three main parts: Two VHDL-based systems and one short experiment on the haptic perception. Both VHDL systems are based on a Cognitive Sensorimotor Loop (CSL) which is a control loop designed by the NRL and mainly developed by Dr. Prof. Hild. The CSL is a control loop whose main characteristic is the fact that it does not use any external sensor to measure the speed or position of the motor but the motor itself. The motor always generates a voltage that is proportional to its angular speed so it does not need calibration. This method is energy efficient and simplifies control loops in complex systems. The first system, named CSL Stay In Touch (SIT), consists in a one DC motor system controller by a FPGA Board (Zynq ZYBO 7000) whose aim is to keep contact with any external object that touches its Sensing Platform in both directions. Apart from the main behavior, three features (Search Mode, Inertia Mode and Return Mode) have been designed to enhance the haptic interaction experience. Additionally, a VGA-Screen is also controlled by the FPGA Board for the monitoring of the whole system. This system has been completely developed, tested and improved; analyzing its timing and consumption properties. The second system, named CSL Fingerlike Mechanism (FM), consists in a fingerlike mechanical system controlled by two DC motors (Each controlling one part of the finger). The behavior is similar to the first system but in a more complex structure. This system was optional and not part of the original objectives of the thesis and it could not be properly finished and tested due to the lack of time. The haptic perception experiment was an experiment conducted to have an insight into the complexity of human haptic perception in order to implement this knowledge into technological applications. The experiment consisted in testing the capability of the subjects to recognize different objects and shapes while being blindfolded and with their ears covered. Two groups were done, one had full haptic perception while the other had to explore the environment with a plastic piece attached to their finger to create a haptic handicap. The conclusion of the thesis was that a haptic system based only on a CSL-based system is not enough to retrieve valuable information from the environment and that other sensors are needed (temperature, pressure, etc.) but that a CSL-based system is very useful to control the force applied by the system to interact with haptic sensible surfaces such as skin or tactile screens. RESUMEN. Este documento es un resumen del proyecto fin de grado titulado “VHDL-Based System Design of a Cognitive Sensorimotor Loop (CSL) for Haptic Human-Machine Interaction (HMI)” escrito por Pablo de Miguel, estudiante de Ingeniería Electrónica de Comunicaciones en la Universidad Politécnica de Madrid (UPM Madrid, España) durante un programa de intercambio Erasmus+ en la Beuth Hochschule für Technik (BHT Berlin, Alemania). El tutor de este proyecto ha sido Dr. Prof. Hild. Este proyecto se ha desarrollado dentro del Neurorobotics Research Laboratory (NRL) en estrecha colaboración con Benjamin Panreck (un miembro del NRL) y con Pablo Lezcano (Otro estudiante de intercambio de la UPM). Para una comprensión completa del trabajo es necesaria una lectura detenida de todo el documento y el visionado de los videos y análisis del diseño VHDL incluidos en el CD adjunto. En el creciente sector de la automatización, una gran cantidad de esfuerzo está dedicada a mejorar, adaptar y diseñar controladores de motor para un gran rango de aplicaciones. En el campo específico de la robótica u otra maquinaria diseñada para interactuar con los humanos o con su entorno, nuevas necesidades y soluciones tecnológicas se siguen desarrollado debido al relativamente inexplorado y nuevo escenario que supone. El proyecto consta de tres partes principales: Dos sistemas basados en VHDL y un pequeño experimento sobre la percepción háptica. Ambos sistemas VHDL están basados en el Cognitive Sesnorimotor Loop (CSL) que es un lazo de control creado por el NRL y cuyo desarrollador principal ha sido Dr. Prof. Hild. El CSL es un lazo de control cuya principal característica es la ausencia de sensores externos para medir la velocidad o la posición del motor, usando el propio motor como sensor. El motor siempre genera un voltaje proporcional a su velocidad angular de modo que no es necesaria calibración. Este método es eficiente en términos energéticos y simplifica los lazos de control en sistemas complejos. El primer sistema, llamado CSL Stay In Touch (SIT), consiste en un sistema formado por un motor DC controlado por una FPGA Board (Zynq ZYBO 7000) cuyo objetivo es mantener contacto con cualquier objeto externo que toque su plataforma sensible en ambas direcciones. Aparte del funcionamiento básico, tres modos (Search Mode, Inertia Mode y Return Mode) han sido diseñados para mejorar la interacción. Adicionalmente, se ha diseñado el control a través de la FPGA Board de una pantalla VGA para la monitorización de todo el sistema. El sistema ha sido totalmente desarrollado, testeado y mejorado; analizando su propiedades de timing y consumo energético. El segundo sistema, llamado CSL Fingerlike Mechanism (FM), consiste en un mecanismo similar a un dedo controlado por dos motores DC (Cada uno controlando una falange). Su comportamiento es similar al del primer sistema pero con una estructura más compleja. Este sistema no formaba parte de los objetivos iniciales del proyecto y por lo tanto era opcional. No pudo ser plenamente desarrollado debido a la falta de tiempo. El experimento de percepción háptica fue diseñado para profundizar en la percepción háptica humana con el objetivo de aplicar este conocimiento en aplicaciones tecnológicas. El experimento consistía en testear la capacidad de los sujetos para reconocer diferentes objetos, formas y texturas en condiciones de privación del sentido del oído y la vista. Se crearon dos grupos, en uno los sujetos tenían plena percepción háptica mientras que en el otro debían interactuar con los objetos a través de una pieza de plástico para generar un hándicap háptico. La conclusión del proyecto fue que un sistema háptico basado solo en sistemas CSL no es suficiente para recopilar información valiosa del entorno y que debe hacer uso de otros sensores (temperatura, presión, etc.). En cambio, un sistema basado en CSL es idóneo para el control de la fuerza aplicada por el sistema durante la interacción con superficies hápticas sensibles tales como la piel o pantallas táctiles.

Deletion of the loop region of Bcl-2 completely blocks paclitaxel-induced apoptosis

At high concentrations, the tubule poison paclitaxel is able to kill cancer cells that express Bcl-2; it inhibits the antiapoptotic activity of Bcl-2 by inducing its phosphorylation. To localize the site on Bcl-2 regulated by phosphorylation, mutant forms of Bcl-2 were constructed. Mutant forms of Bcl-2 with an alteration in serine at amino acid 70 (S70A) or with deletion of a 60-aa loop region between the α1 and α2 helices (Δloop Bcl-2, which also deletes amino acid 70) were unable to be phosphorylated by paclitaxel treatment of MDA-MB-231 cells into which the genes for the mutant proteins were transfected. The Δloop mutant completely inhibited paclitaxel-induced apoptosis. In cells expressing the S70A mutant, paclitaxel induced about one-third the level of apoptosis seen with wild-type Bcl-2. To evaluate the role of mitogen-activated protein kinases (MAPKs) in Bcl-2 phosphorylation, the activation of c-Jun N-terminal kinase (JNK), extracellular signal-regulated kinase (ERK), and p38 was examined. Paclitaxel-induced apoptosis was associated with phosphorylation of Bcl-2 and activation of ERK and JNK MAPKs. If JNK activation was blocked by transfections with either a stress-activated protein kinase kinase dominant-negative (K→R) gene (which prevents the activation of a kinase upstream of JNK) or MAPK phosphatase-1 gene (which dephosphorylates and inactivates JNK), Bcl-2 phosphorylation did not occur, and the cells were not killed by paclitaxel. By contrast, neither an ERK inhibitor (PD098059) nor p38 inhibitors (SB203580 and SB202190) had an effect on Bcl-2 phosphorylation. Thus, our data show that the antiapoptotic effects of Bcl-2 can be overcome by phosphorylation of Ser-70; forms of Bcl-2 lacking the loop region are much more effective at preventing apoptosis than wild-type Bcl-2 because they cannot be phosphorylated. JNK, but not ERK or p38 MAPK, appear to be involved in the phosphorylation of Bcl-2 induced by paclitaxel.

The ability of HIV type 1 to use CCR-3 as a coreceptor is controlled by envelope V1/V2 sequences acting in conjunction with a CCR-5 tropic V3 loop

Although infection by primary HIV type 1 (HIV-1) isolates normally requires the functional interaction of the viral envelope protein with both CD4 and the CCR-5 coreceptor, a subset of such isolates also are able to use the distinct CCR-3 receptor. By analyzing the ability of a series of wild-type and chimeric HIV-1 envelope proteins to mediate CCR-3-dependent infection, we have determined that CCR-3 tropism maps to the V1 and V2 variable region of envelope. Although substitution of the V1/V2 region of a CCR-3 tropic envelope into the context of a CCR-5 tropic envelope is both necessary and sufficient to confer CCR-3 tropism, this same substitution has no phenotypic effect when inserted into a CXCR-4 tropic HIV-1 envelope context. However, this latter chimera acquires both CCR-3 and CCR-5 tropism when a CCR-5 tropic V3 loop sequence also is introduced. These data demonstrate that the V1/2 region of envelope can, like the V3 loop region, encode a particular coreceptor requirement and suggest that a functional envelope:CCR-3 interaction may depend on the cooperative interaction of CCR-3 with both the V1/V2 and the V3 region of envelope.

AtGRP7, a nuclear RNA-binding protein as a component of a circadian-regulated negative feedback loop in Arabidopsis thaliana

The endogenous clock that drives circadian rhythms is thought to communicate temporal information within the cell via cycling downstream transcripts. A transcript encoding a glycine-rich RNA-binding protein, Atgrp7, in Arabidopsis thaliana undergoes circadian oscillations with peak levels in the evening. The AtGRP7 protein also cycles with a time delay so that Atgrp7 transcript levels decline when the AtGRP7 protein accumulates to high levels. After AtGRP7 protein concentration has fallen to trough levels, Atgrp7 transcript starts to reaccumulate. Overexpression of AtGRP7 in transgenic Arabidopsis plants severely depresses cycling of the endogenous Atgrp7 transcript. These data establish both transcript and protein as components of a negative feedback circuit capable of generating a stable oscillation. AtGRP7 overexpression also depresses the oscillation of the circadian-regulated transcript encoding the related RNA-binding protein AtGRP8 but does not affect the oscillation of transcripts such as cab or catalase mRNAs. We propose that the AtGRP7 autoregulatory loop represents a “slave” oscillator in Arabidopsis that receives temporal information from a central “master” oscillator, conserves the rhythmicity by negative feedback, and transduces it to the output pathway by regulating a subset of clock-controlled transcripts.

The structure of the acto-myosin subfragment 1 complex: Results of searches using data from electron microscopy and x-ray crystallography

Surmises of how myosin subfragment 1 (S1) interacts with actin filaments in muscle contraction rest upon knowing the relative arrangement of the two proteins. Although there exist crystallographic structures for both S1 and actin, as well as electron microscopy data for the acto–S1 complex (AS1), modeling of this arrangement has so far only been done “by eye.” Here we report fitted AS1 structures obtained using a quantitative method that is both more objective and makes more complete use of the data. Using undistorted crystallographic results, the best-fit AS1 structure shows significant differences from that obtained by visual fitting. The best fit is produced using the F-actin model of Holmes et al. [Holmes, K. C., Popp, D., Gebhard, W. & Kabsch, W. (1990) Nature (London) 347, 44–49]. S1 residues at the AS1 interface are now found at a higher radius as well as being translated axially and rotated azimuthally. Fits using S1 plus loops missing from the crystal structure were achieved using a homology search method to predict loop structures. These improved fits favor an arrangement in which the loop at the 50- to 20-kDa domain junction of S1 is located near the N terminus of actin. Rigid-body movements of the lower 50-kDa domain, which further improve the fit, produce closure of the large 50-kDa domain cleft and bring conserved residues in the lower 50-kDa domain into an apparently appropriate orientation for close interaction with actin. This finding supports the idea that binding of ATP to AS1 at the end of the ATPase cycle disrupts the actin binding site by changing the conformation of the 50-kDa cleft of S1.

Substrate-induced conformational change in a trimeric ornithine transcarbamoylase

The crystal structure of Escherichia coli ornithine transcarbamoylase (OTCase, EC 2.1.3.3) complexed with the bisubstrate analog N-(phosphonacetyl)-l-ornithine (PALO) has been determined at 2.8-Å resolution. This research on the structure of a transcarbamoylase catalytic trimer with a substrate analog bound provides new insights into the linkages between substrate binding, protein–protein interactions, and conformational change. The structure was solved by molecular replacement with the Pseudomonas aeruginosa catabolic OTCase catalytic trimer (Villeret, V., Tricot, C., Stalon, V. & Dideberg, O. (1995) Proc. Natl. Acad. Sci. USA 92, 10762–10766; Protein Data Bank reference pdb 1otc) as the model and refined to a crystallographic R value of 21.3%. Each polypeptide chain folds into two domains, a carbamoyl phosphate binding domain and an l-ornithine binding domain. The bound inhibitor interacts with the side chains and/or backbone atoms of Lys-53, Ser-55, Thr-56, Arg-57, Thr-58, Arg-106, His-133, Asn-167, Asp-231, Met-236, Leu-274, Arg-319 as well as Gln-82 and Lys-86 from an adjacent chain. Comparison with the unligated P. aeruginosa catabolic OTCase structure indicates that binding of the substrate analog results in closure of the two domains of each chain. As in E. coli aspartate transcarbamoylase, the 240s loop undergoes the largest conformational change upon substrate binding. The clinical implications for human OTCase deficiency are discussed.

Structural Characterization of the Loop at the Alpha-Subunit C-Terminus of the Mixed Lineage Leukemia Protein Activating Protease Taspase1.

Funding: The authors acknowledge the Fonds of Chemical Industry for funding JvdB by their Chemiefonds grant and the DFG for funding PB and CB (CRC 1093).

Multiple loop structures critical for ligand binding of the integrin α4 subunit in the upper face of the β-propeller mode 1

A non-I-domain integrin, α4β1, recognizes vascular cell adhesion molecule 1 (VCAM-1) and the IIICS portion of fibronectin. To localize regions of α4 critical for ligand binding, we swapped several predicted loops within or near the putative ligand-binding site of α4 (which spans repeats 2–5 of the seven N-terminal repeats) with the corresponding regions of α5. Swapping residues 112–131 in repeat 2, or residues 237–247 in repeat 4, completely blocked adhesion to immobilized VCAM-1 and connecting segment 1 (CS-1) peptide. However, swapping residues 40–52 in repeat 1, residues 151–164 in repeat 3, or residues 282–288 (which contain a putative cation binding motif) in repeat 5 did not affect or only slightly reduced adhesion to these ligands. The binding of several function-blocking antibodies is blocked by swapping residues 112–131, 151–164, and 186–191 (which contain previously identified residues critical for ligand binding, Tyr-187 and Gly-190). These results are consistent with the recently published β-propeller folding model of the integrin α4 subunit [Springer, T. A. (1997) Proc. Natl. Acad. Sci. USA 94, 65–72], in which seven four-stranded β-sheets are arranged in a torus around a pseudosymmetric axis. The regions of α4 critical for ligand binding are adjacent to each other and are located in the upper face, the predicted ligand-binding site, of the β-propeller model, although they are not adjacent in the primary structure.

A curved RNA helix incorporating an internal loop with G·A and A·A non-Watson–Crick base pairing

The crystal structure of the RNA dodecamer 5′-GGCC(GAAA)GGCC-3′ has been determined from x-ray diffraction data to 2.3-Å resolution. In the crystal, these oligomers form double helices around twofold symmetry axes. Four consecutive non-Watson–Crick base pairs make up an internal loop in the middle of the duplex, including sheared G·A pairs and novel asymmetric A·A pairs. This internal loop sequence produces a significant curvature and narrowing of the double helix. The helix is curved by 34° from end to end and the diameter is narrowed by 24% in the internal loop. A Mn2+ ion is bound directly to the N7 of the first guanine in the Watson–Crick region following the internal loop and the phosphate of the preceding residue. This Mn2+ location corresponds to a metal binding site observed in the hammerhead catalytic RNA.

Identification of specific Rp-phosphate oxygens in the tRNA anticodon loop required for ribosomal P-site binding

tRNA binding to the ribosomal P site is dependent not only on correct codon–anticodon interaction but also involves identification of structural elements of tRNA by the ribosome. By using a phosphorothioate substitution–interference approach, we identified specific nonbridging Rp-phosphate oxygens in the anticodon loop of tRNAPhe from Escherichia coli which are required for P-site binding. Stereo-specific involvement of phosphate oxygens at these positions was confirmed by using synthetic anticodon arm analogues at which single Rp- or Sp-phosphorothioates were incorporated. Identical interference results with yeast tRNAPhe and E. coli tRNAfMet indicate a common backbone conformation or common recognition elements in the anticodon loop of tRNAs. N-ethyl-N-nitrosourea modification–interference experiments with natural tRNAs point to the importance of the same phosphates in the loop. Guided by the crystal structure of tRNAPhe, we propose that specific Rp-phosphate oxygens are required for anticodon loop (“U-turn”) stabilization or are involved in interactions with the ribosome on correct tRNA–mRNA complex formation.

A conserved serine-rich stretch in the glutamate transporter family forms a substrate-sensitive reentrant loop

Neuronal and glial glutamate transporters remove the excitatory neurotransmitter glutamate from the synaptic cleft. The proteins belong to a large family of secondary transporters, which includes bacterial glutamate transporters. The C-terminal half of the glutamate transporters is well conserved and thought to contain the translocation path and the binding sites for substrate and coupling ions. A serine-rich sequence motif in this part of the proteins is located in a putative intracellular loop. Cysteine-scanning mutagenesis was applied to this loop in the glutamate transporter GltT of Bacillus stearothermophilus. The loop was found to be largely intracellular, but three consecutive positions in the conserved serine-rich motif (S269, S270, and E271) are accessible from both sides of the membrane. Single-cysteine mutants in the serine-rich motif were still capable of glutamate transport, but modification with N-ethylmaleimide blocked the transport activity in six mutants (T267C, A268C, S269C, S270C, E271C, and T272C). Two milimolars l-glutamate effectively protected against the modification of the cysteines at position 269–271 from the periplasmic side of the membrane but was unable to protect cysteine modification from the cytoplasmic side of the membrane. The results indicate that the conserved serine-rich motif in the glutamate transporter forms a reentrant loop, a structure that is found in several ion channels but is unusual for transporter proteins. The reentrant loop is of crucial importance for the function of the glutamate transporter.

The reactive site loop of the serpin SCCA1 is essential for cysteine proteinase inhibition

The high-molecular-weight serine proteinase inhibitors (serpins) are restricted, generally, to inhibiting proteinases of the serine mechanistic class. However, the viral serpin, cytokine response modifier A, and the human serpins, antichymotrypsin and squamous cell carcinoma antigen 1 (SCCA1), inhibit different members of the cysteine proteinase class. Although serpins employ a mobile reactive site loop (RSL) to bait and trap their target serine proteinases, the mechanism by which they inactivate cysteine proteinases is unknown. Our previous studies suggest that SCCA1 inhibits papain-like cysteine proteinases in a manner similar to that observed for serpin–serine proteinase interactions. However, we could not preclude the possibility of an inhibitory mechanism that did not require the serpin RSL. To test this possibility, we employed site-directed mutagenesis to alter the different residues within the RSL. Mutations to either the hinge or the variable region of the RSL abolished inhibitory activity. Moreover, RSL swaps between SCCA1 and the nearly identical serpin, SCCA2 (an inhibitor of chymotrypsin-like serine proteinases), reversed their target specificities. Thus, there were no unique motifs within the framework of SCCA1 that independently accounted for cysteine proteinase inhibitory activity. Collectively, these data suggested that the sequence and mobility of the RSL of SCCA1 are essential for cysteine proteinase inhibition and that serpins are likely to utilize a common RSL-dependent mechanism to inhibit both serine and cysteine proteinases.