Physical Activity Recognition Using a Single Tri-Axis Accelerometer

 0  3  4  2017-02-01 13:04:39 Report infringing document
Proceedings of the World Congress on Engineering and Computer Science 2009 Vol I WCECS 2009, October 20-22, 2009, San Francisco, USA Physical Activity Recognition Using a Single Tri-Axis Accelerometer Mi-hee Lee, Jungchae Kim, Kwangsoo Kim, Inho Lee, Sun Ha Jee, Sun Kook Yoo* ㅔ에 Abstract—Main objective of this pilot study was to present a method to convenient monitoring of detailed ambulatory movements in daily life, by use of a portable measurement device employing single tri-axial accelerometer. In particular, we implemented a small-size wearable data storing system in real time that we used Micro SD-Memory card for convenient and long period habitual physical activity monitoring during daily life. Mean & standard deviation of acceleration and correlation features were extracted from acceleration data. Activity recognition on these features was performed using Fuzzy c means classification algorithm recognized standing, sitting, lying, walking and running with 99.5% accuracy. This study was pilot test for our developed system’s feasibilities. Further application of the present technique may be helpful in the health promotion of both young and elderly, and in the management of obese, diabetic, hyperlipidemic and cardiac patients Index Terms— Physical Activity, Accelerometer, Micro SD-Memory I. INTRODUCTION O Ver the past two decades, a striking increase in the number of people with the metabolic syndrome worldwide has taken place. This increase is associated with the global epidemic of obesity and diabetes. With the elevated risk not only of diabetes but also of cardiovascular disease from the metabolic syndrome, there is urgent need for strategies to prevent the emerging global epidemic [1,2]. Although the metabolic syndrome appears to be more common in people who are genetically susceptible, acquired underlying risk factors-being overweight or obese, physical inactivity, and an atherogenic diet-commonly elicit clinical manifestations [3]. This study was supported by a grant of the Seoul R&BD Program, Republic of Korea (10526) and the Ministry of Knowledge Economy(MKE) and Korea Institute for Advancement in Technology (KIAT) through the Workforce Development Program in Strategic Technology. M.H.Lee is with the Graduate School of Biomedical Engineering, Univ. of Yonsei. Seoul. Korea. (Phone:82-2-2123-2865; fax:82-2-392-4358; e-mail: J.C. Kim is with the Graduate School of Biomedical Engineering, Univ. of Yonsei. Seoul. Korea. (e-mail: K.S. Kim is with the Brain Korea 21 Project for Medical Science, Univ. of Yonsei. Seoul. Korea. (e-mail: cartia82@ I.H Lee is with the Graduate School of Biomedical Engineering, Univ. of Yonsei. Seoul. Korea. (e-mail: ) S.H. Jee is a professor at the Institute for Health Promotion, Graduate school of Public Health, Univ. of Yonsei, Seoul, Korea (e-mail: *SunKook Yoo is a professor at the Dept. of Medical Engineering, Univ. of Yonsei, Seoul, Korea (e-mail: Current guidelines recommend practical, regular, and moderate regimens of physical activity (eq, 30 min moderate-intensity exercise daily)[4]. Regular and sustained physical activity will improve all risk factors of the metabolic syndrome. Sedentary activities in leisure time should be replaced by more active behavior such as brisk walking, jogging, swimming, biking, golfing, and team sports. Combination of weight loss and exercise to reduce the incidence of type 2 diabetes in patients with glucose intolerance should not be dismissed [5]. A practical and reliable method to investigate individual’s daily physical activity allows better assessment such as of outcomes of medical interventions. Information such as intensity of exercise, types of activities is also necessary to appropriately formulate safe and beneficial exercise program on individual basis [6]. Ambulatory movement is the most accessible type of exercise easy to perform that does not require any special equipment. Therefore, a reliable assessment of ambulatory movements in daily life, such as standing, walking, ascending stairs (Up), descending stairs (Down) and running, is essential for exercise prescription in the clinics as well as in health promotion programs. A variety of methods exist to quantify levels of habitual physical activity during daily life, including objective measures such as heart rate, one-and three dimensional accelerometer, and pedometer, as well as subjective recall questionnaires like the International Physical Activity Questionnaire and physical activity logbooks [7,8]. Yet all possess some important limitations. Heart rate monitors have been widely used to quantify physiological stress, but their efficacy at low intensities has been questioned due to the potential interference of environmental conditions and emotional stress [9]. A wide range of self-report activity questionnaires exist that are well suited to large surveillance studies but are limited due to their reliance on subjective recall. Pedometers are an inexpensive form of body motion sensor, yet many fail to measure slow walking speeds or upper body movements, and most are unable to log data to determine changes in exercise intensity [10]. The most common accelerometers used in human activity research measure accelerations either in a vertical plane (uni-axial), or in three planes (tri-axial), with excellent data-logging abilities [1, 10]. Main objective of this study was to present a method to convenient monitoring of detailed ambulatory movements in daily life, by use of a portable measurement device employing single tri-axial accelerometer. Specially, we implemented a small-size wearable data store system in real time that we used Micro SD-Memory card (Secure Digital memory card) ISBN:978-988-17012-6-8 WCECS 2009 Proceedings of the World Congress on Engineering and Computer Science 2009 Vol I WCECS 2009, October 20-22, 2009, San Francisco, USA for convenient and long period habitual physical activity monitoring during daily life. In this work, the performance of activity recognition algorithms under conditions akin to those found in real-world settings is assessed. Activity recognition results are based on acceleration data collected from single tri-axial accelerometer placed on subjects’ waist under semi-naturalistic conditions for pilot test. II. MATERIAL AND METHOD subject was repeating postures such as standing, sitting, lying, walking and running. A representatives set of routine data is shown in figure 2. While the movements and postures contained within the routine are by no means a complete set of all possible activities that a given person might perform, they do form a basic set of simple activities which form an underlying structure to a person’s daily life, and are likely to provide a great deal of information in terms of the person’s balance, gait and activity levels if they can be accurately identified. A. Wearable measurement device Our long-term aim in developing an accelerometry monitoring system was to develop a practical system that could be used to monitor and assess physical activities in free-living subjects. Therefore, we developed a wearable device consisted of Micro SD-Memory card connector (AUTF-08WP01, AUSTONE Electronics, Inc., USA) with mini USB socket (5P, SMT type, SHIH HAN CO., LTD., Russia). Measured acceleration signal was stored on micro SD-Memory card or transmitted wirelessly using Zigbee-compatible 2.4G bandwidth for wireless communication, and CC2420 (Chipcon Co. Ltd., Norway) with a simple interface circuit around the chip. In addition, a ceramic chip antenna TI-AN048 (SMD type, Texas Instruments Co. USA) was applied for stable wireless transmission. For this we used ADXL330 (Analog Devices, Inc., USA), an acceleration sensor that is composed of a single chip and can detect tri-axis acceleration information, and measured acceleration information of axis X, Y and Z according to the subject’s posture and activity. Using the implemented system, we measured change in acceleration signal according to the change of activity pattern. Li-Ionic batteries, micro processor units and micro SD memory card, as shown in Figure 1. This equipment was small (60 x 40 x 20 [mm]) and light enough to carry without and restriction. Sampling frequency was 100Hz. Data was downloaded via USB, and processed offline by a PC. The equipment was designed to be attached on the waist (see figure 1). Fig. 1 Architecture of the wearable measurement device B. Activity Data Collection Table 1. Participant characteristics. The data for these experiments were gathered in an unsupervised pilot study in which healthy young (age 24-33) Case Gender (M/F) Age (yr) subjects performed a variety of activities in the three times on outdoor conditions. Characteristics of the participants are A M 26 presented in Table 1. B M 28 We put the acceleration measuring sensor system on the C M 28 left waist of the subjects, and measured change in acceleration signal according to change in ambulatory movement and D F 24 physical activities. In the experiment performed in this E F 33 research, the change of acceleration was measured while the Height (cm) 182 179 177 167 160 Weight (kg) 76 85 69 55 55 BMI (kgm-2) 22.9 26.5 22.0 19.7 21.5 ISBN:978-988-17012-6-8 WCECS 2009 Proceedings of the World Congress on Engineering and Computer Science 2009 Vol I WCECS 2009, October 20-22, 2009, San Francisco, USA Fig. 2 Representative data from the daily routine for each of the three axes of the tri-axial device Fig. 3 Activity recognition result using Fuzzy c means classification algorithm C.Feature Extraction Features were computed on 512 sample windows of acceleration data with 256 samples overlapping between consecutive windows. At a sampling frequency of 100Hz, each window represents 5.2seconds. Maximum acceleration, mean and standard deviation of acceleration channels were computed over sliding windows with 50% overlap has demonstrated success in past works. The 512 sample window size enabled fast computation of FFTs used for some of the features. The DC feature for normalization is the mean acceleration value of the signal over the window. Use of mean of maximum acceleration features has been shown to result in accurate recognition of certain postures and activities III. RESULTS This section describes the experiments and experimental results of the human posture recognition system. In the pilot test, a subject continuous posture change including standing, sitting, lying, walking and running. In the experiment, each posture was recognized third. Mean & standard deviation of acceleration and correlation features were extracted from acceleration data. Activity recognition on these features was performed using Fuzzy c means classification algorithm recognized standing, sitting, lying, walking and running with 99.5% accuracy as shown Table 2 and Figure 3 Table 2. Clustering results of different posture in a continuous motion Parameters & Real posture Jaccard score Purity Efficiency Standing Sitting Lying Walking Running Average 0.99 0.99 1 111 111 0.99 1 0.99 111 0.98 0.99 0.99 IV. DISCUSSION & CONCLUSION This paper proposes an ambulatory movement’s recognition system in daily life. A portable acceleration sensor module has been designed and implemented to measure human body motion. A small portable device utilizing single tri-axis accelerometer was developed, which detects features of ambulatory movements including vertical position shifts. The classification method based on Fuzzy c means classification algorithm, recognition accuracy of over 99% on a five activities (standing, sitting, lying, walking and running). These results are competitive with prior activity recognition results that only used laboratory data. However, several limitations are also observed for the system. Firstly, collected data was from younger (age 24-33) subjects. Secondly, single accelerometer of placed on body waist typically do not measure ascending and descending stairs walking. Accelerometers are preferable to detect frequency and intensity of vibrational human motion. [11] Many studies have demonstrated the usefulness of accelerometer for the evaluation of physical activity, mostly focusing on the detection of level walking or active/rest discrimination. [12-14] This study was pilot test for our developed system’s feasibilities. Further application of the present technique may be helpful in the health promotion of both young and elderly, and in the management of obese, diabetic, hyperlipidemic and cardiac patients. Efforts are being directed to make the device smaller and allow data collection for longer time periods. Implementation of real-time processing firmware and encapsulation of the hardware are our future studies. ACKNOWLEDGMENT This study was supported by a grant of the Seoul R&BD Program, Republic of Korea (10526) and the Ministry of Knowledge Economy(MKE) and Korea Institute for Advancement in Technology (KIAT) through the Workforce Development Program in Strategic Technology. ISBN:978-988-17012-6-8 WCECS 2009 Proceedings of the World Congress on Engineering and Computer Science 2009 Vol I WCECS 2009, October 20-22, 2009, San Francisco, USA REFERENCES [1] Zimmet P, Alberti KG, Shaw J. Global and societal implications of the diabetes epidemic. Nature 2001; 414: 782-787 [2] Grundy SM, Hansen B, Smith SC Jr, Cleeman JI, Kahn RA. Clinical management of metabolic syndrome: report of the American Heart Association/National Heart, Lung, and Blood Institute/American Diabetes Association conference on scientific issues related to management. Circulation 2004;109: 551-556 [3] R.H. Eckel, S.M. Grundy, P.Z. Zimmet, The metabolic syndrome. Lancet 2005; 365: 1415-28 [4] Thompson PD, Buchner D, Pina IL, et al. Exercise and physical activity in the prevention and treatment of atherosclerotic cardiovascular disease: a statement from the Council on Clinical Cardiology (Subcommittee on Exercise, Rehabilitation, and Prevention) and the Council on Nutrition, Physical Activity, and Metabolism (Subcommittee on Physical Activity). Circulation 2003; 107: 3109-3116 [5] Tuomilehto J, Lindstrom J, Eriksson JG, et al. Prevention of type 2 diabetes mellitus by changes in lifestyle among subjects with impaired glucose tolerance. N Engl J Med 2001; 344: 1343-1350 [6] Y. Ohtaki, M. Susumago, A. Suzuki et al. Automatic classification of ambulatory movements and evaluation of energy consumptions utilizing accelerometers and a barometer. Microsyst Technol 2005; 11: 1034-1040 [7] Bassett DR Jr. Validity and reliability issues in objective monitoring of physical activity. Res Q Exerc Sport 2000;71: S30–S36. [8] Craig CL, Marshall AL, Sjostrom M, Bauman AE, at al. International physical activity questionnaire: 12-country reliability and validity. Med Sci Sports Exerc 2003; 35: 1381–1395. [9] Allor KM and Pivarnik JM. Stability and convergent validity of three physical activity assessments. Med Sci Sports Exerc 2001; 33: 671–676. [10] LaMonte MJ, Ainsworth BE, and Tudor-Locke C. Assessment of physical activity and energy expenditure. In: Obesity: Etiology, Assessment, Treatment and Prevention, edited by Andersen RE. Champaign, IL:Human Kinetics, 2003; p. 111–117. [11] Bouten CVC, Koekkoek KTM, Verduin M, Kodde R, Janssen JD. A triaxial accelerometer and portable data processing unit for the assessment of daily physical activity. IEEE Transactions on Biomedical Engineering 1997;44(3):136–147 [12] Nakahara AK, Sabelman EE, Jaffe DL, Development of a second generation wearable accelerometric motion analysis system. Proceedings of the first joint EMBS/BMES conference, 1999; 630 [13] Aminian K, Robert P, Buchser EE, Rutschmann B, Hayoz D, Depairon M, Physical activity monitoring based on accelerometry. Medical and Biological Engineering and Computing 1999; 37:304–308 [14] Mathie MJ, Lovell NH, Coster CF, Celler BG, Determining activity using a triaxial accelerometer. In: Proceedings of the second joint EMBS/BMES conference, 2002; 2481–2482 ISBN:978-988-17012-6-8 WCECS 2009 enfocar la importancia de la producción mediática de los niños en su descubrimiento del mundo, sobre todo utilizando el periódico escolar y la imprenta. Asimismo las asociaciones de profesores trabajaron en esta línea e incluso la enseñanza católica se comprometió desde los años sesenta realizando trabajos originales en el marco de la corriente del Lenguaje Total. Páginas 43-48 45 Comunicar, 28, 2007 En el ámbito de los medios, también desde el principio del siglo XX hay ciertas corrientes de conexión. Pero es a lo largo de los años sesenta cuando se constituyeron asociaciones de periodistas apasionados por sus funciones de mediadores, que fomentaron la importancia ciudadana de los medios como algo cercano a los jóvenes, a los profesores y a las familias. Así se crearon la APIJ (Asociación de Prensa Información para la Juventud), la ARPEJ (Asociación Regional de Prensa y Enseñanza para la Juventud), el CIPE (Comité Interprofesional para la Prensa en la Escuela) o la APE (Asociación de Prensa y Enseñanza), todas ellas para la prensa escrita Estas asociaciones fueron precedidas por movimientos surgidos en mayo de 1968, como el CREPAC que, utilizando películas realizadas por periodistas conocidos, aclaraba temas que habían sido manipulados por una televisión demasiado próxima al poder político y realizaba encuentros con grupos de telespectadores. cipio del siglo XX, y nos han legado textos fundadores muy preciados, importantes trabajos de campo y muchos logros educativos y pedagógicos. La educación en medios ha tenido carácter de oficialidad de múltiples maneras, aunque nunca como una enseñanza global. Así la campaña «Operación Joven Telespectador Activo» (JTA), lanzada al final de los años setenta y financiada de manera interministerial para hacer reflexionar sobre las prácticas televisuales de los jóvenes, la creación del CLEMI (Centro de Educación y Medios de Comunicación) en el seno del Ministerio de Educación Nacional en 1983, la creación de la optativa «Cine-audiovisual» en los bachilleratos de humanidades de los institutos en 1984 (primer bachillerato en 1989) y múltiples referencias a la educación de la imagen, de la prensa, de Internet. La forma más visible y rápida de evaluar el lugar de la educación en medios es valorar el lugar que se le ha reservado en los libros de texto del sistema educa- 2. Construir la educación en los medios sin nombrarla El lugar que ocupa la edu- La denominación «educación en medios», que debería cación en los medios es muy ambiguo, aunque las cosas están cambiando recientemente. entenderse como un concepto integrador que reagrupase todos los medios presentes y futuros, es a menudo percibida En principio, en Francia, co- por los «tradicionalistas de la cultura» como una tendencia mo en muchos otros países, la educación en los medios no es hacia la masificación y la pérdida de la calidad. una disciplina escolar a tiempo completo, sino que se ha ido conformado progresivamente a través de experiencias y reflexiones teóricas que han tivo en Francia. Una inmersión sistemática nos permi- permitido implantar interesantes actividades de carác- te constatar que los textos oficiales acogen numerosos ter puntual. Se ha ganado poco a poco el reconoci- ejemplos, citas, sin delimitarla con precisión. miento de la institución educativa y la comunidad es- colar. Podemos decir que ha conquistado un «lugar», 3. ¿Por qué la escuela ha necesitado casi un siglo en el ámbito de la enseñanza transversal entre las dis- para oficilializar lo que cotidianamente se hacía en ciplinas existentes. ella? Sin embargo, la escuela no está sola en esta aspi- Primero, porque las prácticas de educación en me- ración, porque el trabajo en medios es valorado igual- dios han existido antes de ser nombradas así. Recor- mente por el Ministerio de Cultura (campañas de foto- demos que no fue hasta 1973 cuando aparece este grafía, la llamada «Operación Escuelas», presencia de término y que su definición se debe a los expertos del colegios e institutos en el cine ), así como el Minis- Consejo Internacional del Cine y de la Televisión, que terio de la Juventud y Deportes que ha emprendido en el seno de la UNESCO, definen de esta forma: numerosas iniciativas. «Por educación en medios conviene entender el estu- Así, esta presencia de la educación en los medios dio, la enseñanza, el aprendizaje de los medios moder- no ha sido oficial. ¡La educación de los medios no apa- nos de comunicación y de expresión que forman parte rece oficialmente como tal en los textos de la escuela de un dominio específico y autónomo de conocimien- francesa hasta 2006! tos en la teoría y la práctica pedagógicas, a diferencia Este hecho no nos puede dejar de sorprender ya de su utilización como auxiliar para la enseñanza y el que las experiencias se han multiplicado desde el prin- aprendizaje en otros dominios de conocimientos tales Páginas 43-48 46 Comunicar, 28, 2007 como los de matemáticas, ciencias y geografía». A pe- mente en todas las asignaturas. Incluso los nuevos cu- sar de que esta definición ha servido para otorgarle un rrículos de materias científicas en 2006 para los alum- reconocimiento real, los debates sobre lo que abarca y nos de 11 a 18 años hacen referencia a la necesidad no, no están totalmente extinguidos. de trabajar sobre la información científica y técnica y En segundo lugar, porque si bien a la escuela fran- el uso de las imágenes que nacen de ella. cesa le gusta la innovación, después duda mucho en Desde junio de 2006, aparece oficialmente el tér- reflejar y sancionar estas prácticas innovadoras en sus mino «educación en medios» al publicar el Ministerio textos oficiales. Nos encontramos con una tradición de Educación los nuevos contenidos mínimos y las sólidamente fundada sobre una transmisión de conoci- competencias que deben adquirir los jóvenes al salir mientos muy estructurados, organizados en disciplinas del sistema educativo. escolares que se dedican la mayor parte a transmitir Este documento pretende averiguar cuáles son los conocimientos teóricos. La pedagogía es a menudo se- conocimientos y las competencias indispensables que cundaria, aunque los profesores disfrutan de una ver- deben dominar para terminar con éxito su escolaridad, dadera libertad pedagógica en sus clases. El trabajo seguir su formación y construir su futuro personal y crítico sobre los medios que estaba aún en elaboración profesional. Siete competencias diferentes han sido te- necesitaba este empuje para hacerse oficial. nidas en cuenta y en cada una de ellas, el trabajo con Aunque el trabajo de educación en los medios no los medios es reconocido frecuentemente. Para citar esté reconocido como disciplina, no está ausente de un ejemplo, la competencia sobre el dominio de la len- gua francesa definen las capa- cidades para expresarse oral- La metodología elaborada en el marco de la educación en mente que pueden adquirirse con la utilización de la radio e, medios parece incluso permitir la inclinación de la sociedad incluso, se propone fomentar de la información hacia una sociedad del conocimiento, como defiende la UNESCO. En Francia, se necesitaría unir el interés por la lectura a través de la lectura de la prensa. La educación en los medios las fuerzas dispersas en función de los soportes mediáticos y orientarse más hacia la educación en medios que al dominio adquiere pleno derecho y entidad en la sección sexta titulada «competencias sociales y cívi- técnico de los aparatos. cas» que indica que «los alum- nos deberán ser capaces de juz- gar y tendrán espíritu crítico, lo que supone ser educados en los las programaciones oficiales, ya que, a lo largo de un medios y tener conciencia de su lugar y de su influencia estudio de los textos, los documentalistas del CLEMI en la sociedad». han podido señalar más de una centena de referencias a la educación de los medios en el seno de disciplinas 4. Un entorno positivo como el francés, la historia, la geografía, las lenguas, Si nos atenemos a las cifras, el panorama de la las artes plásticas : trabajos sobre las portadas de educación en medios es muy positivo. Una gran ope- prensa, reflexiones sobre temas mediáticos, análisis de ración de visibilidad como la «Semana de la prensa y publicidad, análisis de imágenes desde todos los ángu- de los medios en la escuela», coordinada por el CLE- los, reflexión sobre las noticias en los países europeos, MI, confirma año tras año, después de 17 convocato- información y opinión rias, el atractivo que ejerce sobre los profesores y los Esta presencia se constata desde la escuela mater- alumnos. Concebida como una gran operación de nal (2 a 6 años) donde, por ejemplo, se le pregunta a complementariedad (2000) Structure and mechanism of the aberrant ba3-cytochrome c oxidase from Thermus thermophilus. EMBO J 19: 1766–1776. 9. Hunsicker-Wang LM, Pacoma RL, Chen Y, Fee JA, Stout CD (2005) A novel cryoprotection scheme for enhancing the diffraction of crystals of recombinant cytochrome ba3 oxidase from Thermus thermophilus. Acta Crystallogr D Biol Crystallogr 61: 340–343. 10. Buschmann S, Warkentin E, Xie H, Langer JD, Ermler U, et al. (2010) The structure of cbb3 cytochrome oxidase provides insights into proton pumping. Science 329: 327–330. 11. Fee JA, Case DA, Noodleman L (2008) Toward a chemical mechanism of proton pumping by the B-type cytochrome c oxidases: application of density functional theory to cytochrome ba3 of Thermus thermophilus. J Am Chem Soc 130: 15002–15021. 12. Chang HY, Hemp J, Chen Y, Fee JA, Gennis RB (2009) The cytochrome ba3 oxygen reductase from Thermus thermophilus uses a single input channel for proton delivery to the active site and for proton pumping. Proc Natl Acad Sci U S A 106: 16169–16173. 13. Luna VM, Chen Y, Fee JA, Stout CD (2008) Crystallographic studies of Xe and Kr binding within the large internal cavity of cytochrome ba3 from Thermus thermophilus: structural analysis and role of oxygen transport channels in the heme-Cu oxidases. Biochemistry 47: 4657–4665. PLoS ONE | 11 July 2011 | Volume 6 | Issue 7 | e22348 The 1.8 Å Structure of ba3Oxidase 27. Vogeley L, Sineshchekov OA, Trivedi VD, Sasaki J, Spudich JL, et al. (2004) Anabaena sensory rhodopsin: a photochromic color sensor at 2.0 A. Science 306: 1390–1393. 28. Cherezov V, Rosenbaum DM, Hanson MA, Rasmussen SG, Thian FS, et al. (2007) High-resolution crystal structure of an engineered human beta2adrenergic G protein-coupled receptor. Science 318: 1258–1265. 29. Jaakola VP, Griffith MT, Hanson MA, Cherezov V, Chien EY, et al. (2008) The 2.6 angstrom crystal structure of a human A2A adenosine receptor bound to an antagonist. Science 322: 1211–1217. 30. Wu B, Chien EY, Mol CD, Fenalti G, Liu W, et al. (2010) Structures of the CXCR4 chemokine GPCR with small-molecule and cyclic peptide antagonists. Science 330: 1066–1071. 31. Chien EY, Liu W, Zhao Q, Katritch V, Han GW, et al. (2010) Structure of the Human Dopamine D3 Receptor in Complex with a D2/D3 Selective Antagonist. Science 330: 1091–1095. 32. Hanson MA, Cherezov V, Griffith MT, Roth CB, Jaakola VP, et al. (2008) A specific cholesterol binding site is established by the 2.8 A structure of the human beta2-adrenergic receptor. Structure 16: 897–905. 33. Cherezov V, Liu W, Derrick JP, Luan B, Aksimentiev A, et al. (2008) In meso crystal structure and docking simulations suggest an alternative proteoglycan binding site in the OpcA outer membrane adhesin. Proteins 71: 24–34. 34. Cherezov V, Clogston J, Papiz MZ, Caffrey M (2006) Room to move: crystallizing membrane proteins in swollen lipidic mesophases. J Mol Biol 357: 1605–1618. 35. Caffrey M (2009) Crystallizing membrane proteins for structure determination: use of lipidic mesophases. Annu Rev Biophys 38: 29–51. 36. Loh HH, Law PY (1980) The role of membrane lipids in receptor mechanisms. Annu Rev Pharmacol Toxicol 20: 201–234. 37. Lee AG (2004) How lipids affect the activities of integral membrane proteins. Biochim Biophys Acta 1666: 62–87. 38. Robinson NC (1993) Functional binding of cardiolipin to cytochrome c oxidase. J Bioenerg Biomembr 25: 153–163. 39. Qin L, Sharpe MA, Garavito RM, Ferguson-Miller S (2007) Conserved lipidbinding sites in membrane proteins: a focus on cytochrome c oxidase. Curr Opin Struct Biol 17: 444–450. 40. Sedlak E, Panda M, Dale MP, Weintraub ST, Robinson NC (2006) Photolabeling of cardiolipin binding subunits within bovine heart cytochrome c oxidase. Biochemistry 45: 746–754. 41. Hunte C, Richers S (2008) Lipids and membrane protein structures. Curr Opin Struct Biol 18: 406–411. 42. Reichow SL, Gonen T (2009) Lipid-protein interactions probed by electron crystallography. Curr Opin Struct Biol 19: 560–565. 43. Yang YL, Yang FL, Jao SC, Chen MY, Tsay SS, et al. (2006) Structural elucidation of phosphoglycolipids from strains of the bacterial thermophiles Thermus and Meiothermus. J Lipid Res 47: 1823–1832. 44. Belrhali H, Nollert P, Royant A, Menzel C, Rosenbusch JP, et al. (1999) Protein, lipid and water organization in bacteriorhodopsin crystals: a molecular view of the purple membrane at 1.9 A resolution. Structure 7: 909–917. 45. Long SB, Tao X, Campbell EB, MacKinnon R (2007) Atomic structure of a voltage-dependent K+ channel in a lipid membrane-like environment. Nature 450: 376–382. 46. Gonen T, Cheng Y, Sliz P, Hiroaki Y, Fujiyoshi Y, et al. (2005) Lipid-protein interactions in double-layered two-dimensional AQP0 crystals. Nature 438: 633–638. 47. Seelig A, Seelig J (1977) Effect of single cis double bound on the structure of a phospholipid bilayer. Biochemistry 16: 45–50. 48. Lomize MA, Lomize AL, Pogozheva ID, Mosberg HI (2006) OPM: orientations of proteins in membranes database. Bioinformatics 22: 623–625. 49. Hoyrup P, Callisen TH, Jensen MO, Halperin A, Mouritsen OG (2004) Lipid protrusions, membrane softness, and enzymatic activity. Phys Chem Chem Phys 6: 1608–1615. PLoS ONE | 50. Lee HJ, Svahn E, Swanson JM, Lepp H, Voth GA et al (2010) Intricate Role of Water in Proton Transport through Cytochrome c Oxidase. J Am Chem Soc 132: 16225–16239. 51. Aoyama H, Muramoto K, Shinzawa-Itoh K, Hirata K, Yamashita E, et al. (2009) A peroxide bridge between Fe and Cu ions in the O2 reduction site of fully oxidized cytochrome c oxidase could suppress the proton pump. Proc Natl Acad Sci U S A 106: 2165–2169. 52. Schmidt B, McCracken J, Ferguson-Miller S (2003) A discrete water exit pathway in the membrane protein cytochrome c oxidase, Proc Natl Acad Sci U S A 100: 15539–15542. 53. Einarsdottir O, Choc MG, Weldon S, Caughey WS (1988) The site and mechanism of dioxygen reduction in bovine heart cytochrome c oxidase. J Biol Chem 263: 13641–13654. 54. Agmon N (1995) The Grotthuss mechanism. Chem Phys Lett 244: 456– 462. 55. Salomonsson L, Lee A, Gennis RB, Brzezinski P (2004) A single amino-acid lid renders a gas-tight compartment within a membrane-bound transporter. Proc Natl Acad Sci U S A 101: 11617–11621. 56. Yin H, Feng G, Clore GM, Hummer G, Rasaiah JC (2010) Water in the polar and nonpolar cavities of the protein Interleukin-1-beta. J Phys Chem B 114: 16290–16297. 57. Eisenberger P, Shulman RG, Brown GS, Ogawa S (1976) Structure-function relations in hemoglobin as determined by x-ray absorption spectroscopy. Proc Natl Acad Sci U S A 73: 491–495. 58. Chishiro T, Shimazaki Y, Tani F, Tachi Y, Naruta Y, et al. (2003) Isolation and crystal structure of a peroxo-brodged heme-copper complex. Ang Chem Int Ed 42: 2788– 2791. 59. Ostermeier C, Harrenga A, Ermler U, Michel H (1997) Structure at 2.7 A resolution of the Paracoccus denitrificans two-subunit cytochrome c oxidase complexed with an antibody FV fragment. Proc Natl Acad Sci U S A 94: 10547–10553. 60. Kaila VRI, Oksanen E, Goldman A, Bloch D, Verkhovsky MI, et al. (2011) A combined quantum chemical and crystallographic study on the oxidized binuclear center of cytochrome c oxidase. Biochim Biophys Acta 1807: 769–778. 61. Sakaguchi M, Shinzawa-Itoh K, Yoshikawa S, Ogura T (2010) A resonance Raman band assignable to the O-O stretching mode in the resting oxidized state of bovine heart cytochrome c oxidise. J Bioenerg Biomembr 42: 241–243. 62. Chance B, Saronio C, Waring A, Leigh Jr. JS (1978) Cytochrome c-cytochrome oxidase interactions at subzero temperatures. Biochim. Biophys. Acta 503: 37–55. 63. Cheng A, Hummel B, Qiu H, Caffrey M (1998) A simple mechanical mixer for small viscous lipid-containing samples. Chem Phys Lipids 95: 11–21. 64. Cherezov V, Peddi A, Muthusubramaniam L, Zheng YF, Caffrey M (2004) A robotic system for crystallizing membrane and soluble proteins in lipidic mesophases. Acta Crystallogr D Biol Crystallogr 60: 1795–1807. 65. Minor W, Cymborowski M, Otwinowski Z, Chruszcz M (2006) HKL-3000: the integration of data reduction and structure solution - from diffraction images to an initial model in minutes. Acta Crystallogr D Biol Crystallogr 62: 859–866. 66. McCoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC, et al. (2007) Phaser crystallographic software. J Appl Crystallogr 40: 658–674. 67. McRee DE (2004) Differential evolution for protein crystallographic optimizations. Acta Crystallogr D Biol Crystallogr 60: 2276–2279. 68. Unno M, Chen H, Kusama S, Shaik S, Ikeda-Saito M (2007) Structural characterization of the fleeting ferric peroxo species in myoglobin, Experiment and theory. J Am Chem Soc 129: 13394–13395. 69. Kuhnel K, Derat E, Terner J, Shaik S, Schlicting I (2007) Structure and quantum chemical characterization of chloroperoxidase compound 0, a common reaction intermediate of diverse heme enzymes. Proc Natl Acad Sci U S A 104: 99–104. 12 July 2011 | Volume 6 | Issue 7 | e22348
123dok avatar

Ingressou : 2016-12-29

Documento similar

Physical Activity Recognition Using a Single..