Структура, стабильность и комплексообразование сахар-связывающих белков с лигандами.
Возможность их использования в качестве чувствительного элемента биосенсорных систем на глюкозу
Диссертация
В течение последнего десятилетия представления о том, как осуществляется фолдинг белков, и даже представления о нативном белке как о белке с жесткой, строго детерминированной структурой, претерпели существенное изменение. На рубеже столетий стали появляться работы, свидетельствующие о том, что полипептидные цепи многих белков в принципе не способны образовывать компактное глобулярное состояние… Читать ещё >
Содержание
- СПИСОК УСЛОВНЫХ СОКРАЩЕНИЙ
- Актуальность исследования
- Цели и задачи исследования
- Основные положения, выносимые на защиту
- Научная новизна работы
- Теоретическое и практическое значение работы
- ГЛАВА 1. ОБЗОР ЛИТЕРАТУРЫ
- 1. 1. Нативные частично неупорядоченные белки
- 1. 2. Лиганд-связывающие белки из периплазмы грам-отрицательных бактерий
- 1. 2. 1. О-глюкоза/О-галактоза-связывающий белок
- 1. 2. 2. Трегалоза/мальтоза — связывающий белок
- 1. 3. Методы мониторинга глюкозы
- ГЛАВА 2. МАТЕРИАЛЫ И МЕТОДЫ
- 2. 1. Материалы
- 2. 2. Методы
- 2. 2. 1. Анализ пространственной структуры белков
- 2. 2. 2. Флуоресцентные измерения
- 2. 2. 3. Регистрация и анализ кривых затухания флуоресценции
- 2. 2. 4. Измерение спектров кругового дихроизма
- 2. 2. 5. Тушение флуоресценции акриламидом
- 2. 2. 6. Определение параметров связывания лиганд-рецептор с помощью интенсивных флуоресцентных характеристик
- 2. 2. 7. Расчет термодинамических параметров
- 2. 2. 8. Дифференциальная сканирующая калориметрия
- 3. 1. Роль лигандов в стабилизации структуры GGBP
- 3. 1. 1. Сворачивание-разворачивание ano и холоформы GGBP под действием GdnHCl
- 3. 1. 2. Тепловая денатурация GGBP и GGBP/Glc
- 3. 2. Влияние аминокислотных замен в положение 16 и 183 на стабильность GGBP и комплексообразование этого белка с глюкозой
- 3. 2. 1. Устойчивость GGBP/W183A и GGBP/F16A к денатурирующему действию гуан идингидрохлор ида
- 3. 2. 2. Тепловая денатурация мутантных форм GGBP/W183A и GGBP/F16A, а также комплексов этих белков с глюкозой
- 3. 3. Структура и стабильность ТМВР
- 3. 4. Возможность использования сахар-связывающих белков GGBP и ТМВР в качестве чувствительного элемента биосенсорной системы на глюкозу
Список литературы
- Turoverov KK, Kuznetsova IM, Uversky VN (2010) The protein kingdom extended: ordered and intrinsically disordered proteins, their folding, supramolecular complex formation, and aggregation. Prog Biophys Mol Biol 102 (2−3):73−84.
- Dunker AK, Cortese MS, Romero P, Iakoucheva LM, Uversky VN (2005) Flexible nets. The roles of intrinsic disorder in protein interaction networks. FEBS J 272 (20):5129−5148.
- Uversky VN (2008) Alpha-synuclein misfolding and neurodegenerative diseases. Curr Protein Pept Sei 9 (5):507−540.
- Yesylevskyy SO, Kharkyanen VN, Demchenko AP (2006) The change of protein intradomain mobility on ligand binding: is it a commonly observed phenomenon? Biophys J 91 (8):3002−3013.
- Uversky VN, Gillespie JR, Fink AL (2000) Why are «natively unfolded» proteins unstructured under physiologic conditions? Proteins 41 (3):415−427.
- Uversky VN, Roman A, Oldfield CJ, Dunker AK (2006) Protein intrinsic disorder and human papillomaviruses: increased amount of disorder in E6 and E7 oncoproteins from high risk HP Vs. J Proteome Res 5 (8): 1829−1842.
- Romero P, Obradovic Z, Kissinger C, Villafranca JE, Dunker AK Identifying disordered regions in proteins from amino acid sequence. In: Neural Networks, 1997., International Conference on, 9−12 Jun 1997 1997. pp 90−95 vol.91.
- Dunker AK, Garner E, Guilliot S, Romero P, Albrecht K, Hart J, Obradovic Z, Kissinger C, Villafranca JE (1998) Protein disorder and the evolution of molecular recognition: theory, predictions and observations. Pac Symp Biocomput:473−484.
- Dunker AK, Obradovic Z, Romero P, Garner EC, Brown CJ (2000) Intrinsic protein disorder in complete genomes. Genome Inform Ser Workshop Genome Inform 11:161 171.
- Oldfield CJ, Cheng Y, Cortese MS, Romero P, Uversky VN, Dunker AK (2005) Coupled folding and binding with alpha-helix-forming molecular recognition elements. Biochemistry 44 (37): 12 454−12 470.
- Ward JJ, Sodhi JS, McGuffin LJ, Buxton BF, Jones DT (2004) Prediction and functional analysis of native disorder in proteins from the three kingdoms of life. J Mol Biol 337 (3):635−645.
- Uversky VN, Oldfield CJ, Dunker AK (2005) Showing your ID: intrinsic disorder as an ID for recognition, regulation and cell signaling. J Mol Recognit 18 (5):343−384.
- Dunker AK, Obradovic Z (2001) The protein trinity—linking function and disorder. Nat Biotechnol 19 (9):805−806.
- Uversky VN (2002) Natively unfolded proteins: a point where biology waits for physics. Protein Sei 11 (4):739−756.
- Uversky VN (2003) Protein folding revisited. A polypeptide chain at the folding-misfolding-nonfolding cross-roads: which way to go? Cell Mol Life Sei 60 (9): 18 521 871.
- Daughdrill GW, Narayanaswami P, Gilmore SH, Belczyk A, Brown CJ (2007) Dynamic behavior of an intrinsically unstructured linker domain is conserved in the face of negligible amino acid sequence conservation. J Mol Evol 65 (3):277−288.
- Holmes KC, Popp D, Gebhard W, Kabsch W (1990) Atomic model of the actin filament. Nature 347 (6288):44−49.
- Dwyer MA, Hellinga HW (2004) Periplasmic binding proteins: a versatile superfamily for protein engineering. Curr Opin Struct Biol 14 (4):495−504.
- Tam R, Saier MH, Jr. (1993) Structural, functional, and evolutionary relationships among extracellular solute-binding receptors of bacteria. Microbiol Rev 57 (2):320−346.
- Felder CB, Graul RC, Lee AY, Merkle HP, Sadee W (1999) The Venus flytrap of periplasmic binding proteins: an ancient protein module present in multiple drug receptors. AAPS PharmSci 1 (2):E2.
- Szurmant H, Ordal GW (2004) Diversity in chemotaxis mechanisms among the bacteria and archaea. Microbiol Mol Biol Rev 68 (2):301−319.
- Neiditch MB, Federle MJ, Pompeani AJ, Kelly RC, Swem DL, Jeffrey PD, Bassler BL, Hughson FM (2006) Ligand-induced asymmetry in histidine sensor kinase complex regulates quorum sensing. Cell 126 (6): 1095−1108.
- Schauder S, Bassler BL (2001) The languages of bacteria. Genes Dev 15 (12): 14 681 480.
- Dalken B, Jabulowsky RA, Oberoi P, Benhar I, Wels WS (2010) Maltose-binding protein enhances secretion of recombinant human granzyme B accompanied by in vivo processing of a precursor MBP fusion protein. PLoS One 5 (12):el4404.
- Richarme G, Caldas TD (1997) Chaperone properties of the bacterial periplasmic substrate-binding proteins. J Biol Chem 272 (25):15 607−15 612.
- Fukami-Kobayashi K, Tateno Y, Nishikawa K (1999) Domain dislocation: a change of core structure in periplasmic binding proteins in their evolutionary history. J Mol Biol 286 (l):279−290.
- Lewis RJ, Muchova K, Brannigan JA, Barak I, Leonard G, Wilkinson AJ (2000) Domain swapping in the sporulation response regulator SpoOA. J Mol Biol 297 (3):757−770.
- Vyas NK, Vyas MN, Quiocho FA (1988) Sugar and signal-transducer binding sites of the Escherichia coli galactose chemoreceptor protein. Science 242 (4883):1290−1295.
- Hsiao CD, Sun YJ, Rose J, Wang BC (1996) The crystal structure of glutamine-binding protein from Escherichia coli. J Mol Biol 262 (2):225−242.
- Sun YJ, Rose J, Wang BC, Hsiao CD (1998) The structure of glutamine-binding protein complexed with glutamine at 1.94 A resolution: comparisons with other amino acid binding proteins. J Mol Biol 278 (l):219−229.
- Nickitenko AV, Trakhanov S, Quiocho FA (1995) 2 A resolution structure of DppA, a periplasmic dipeptide transport/chemosensory receptor. Biochemistry 34 (51):16 585−16 595.
- Sleigh SH, Seavers PR, Wilkinson AJ, Ladbury JE, Tame JR (1999) Crystallographic and calorimetric analysis of peptide binding to OppA protein. J Mol Biol 291 (2):393−415.
- Lee YH, Dorwart MR, Hazlett KR, Deka RK, Norgard MV, Radolf JD, Hasemann CA (2002) The crystal structure of Zn (II)-free Treponema pallidum TroA, a periplasmic metal-binding protein, reveals a closed conformation. J Bacteriol 184 (8):2300−2304.
- Karpowich NK, Huang HH, Smith PC, Hunt JF (2003) Crystal structures of the BtuF periplasmic-binding protein for vitamin B12 suggest a functionally important reduction in protein mobility upon ligand binding. J Biol Chem 278 (10):8429−8434.
- Shilton BH, Flocco MM, Nilsson M, Mowbray SL (1996) Conformational changes of three periplasmic receptors for bacterial chemotaxis and transport: the maltose-, glucose/galactose- and ribose-binding proteins. J Mol Biol 264 (2):350−363.
- Pang A, Arinaminpathy Y, Sansom MS, Biggin PC (2003) Interdomain dynamics and ligand binding: molecular dynamics simulations of glutamine binding protein. FEBS Lett 550 (1−3):168−174.
- Hollenstein K, Frei DC, Locher KP (2007) Structure of an ABC transporter in complex with its binding protein. Nature 446 (7132):213−216.
- Bermejo GA, Strub MP, Ho C, Tjandra N (2010) Ligand-free open-closed transitions of periplasmic binding proteins: the case of glutamine-binding protein. Biochemistry 49 (9): 1893−1902.
- Bucher D, Grant BJ, Markwick PR, McCammon JA (2011) Accessing a hidden conformation of the maltose binding protein using accelerated molecular dynamics. PLoS Comput Biol 7 (4):el002034.
- Stepanenko O, Fonin A, Kuznetsova I, Turoverov K (2012) Ligand-binding proteins: structure, stability and practical application. Protein Structure, InTech, Rijeka:265−290
- Anraku Y (1968) Transport of sugars and amino acids in bacteria. II. Properties of galactose- and leucine-binding proteins. J Biol Chem 243 (11):3123−3127
- Hazelbauer GL, Adler J (1971) Role of the galactose binding protein in chemotaxis of Escherichia coli toward galactose. Nat New Biol 230 (12):101−104
- Borrok MJ, Kiessling LL, Forest KT (2007) Conformational changes of glucose/galactose-binding protein illuminated by open, unliganded, and ultra-highresolution ligand-bound structures. Protein Sci 16 (6): 1032−1041.
- Berman H, Henrick K, Nakamura H, Markley JL (2007) The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Res 35 (Database issue):D301−303.
- Diez J, Diederichs K, Greller G, Horlacher R, Boos W, Welte W (2001) The crystal structure of a liganded trehalose/maltose-binding protein from the hyperthermophilic Archaeon Thermococcus litoralis at 1.85 A. J Mol Biol 305 (4):905−915.
- Oliver NS, Toumazou C, Cass AE, Johnston DG (2009) Glucose sensors: a review of current and emerging technology. Diabet Med 26 (3): 197−210.
- Tura A, Maran A, Pacini G (2007) Non-invasive glucose monitoring: assessment of technologies and devices according to quantitative criteria. Diabetes Res Clin Pract 77 (1): 16−40.
- Ferrante do Amaral CE, Wolf B (2008) Current development in non-invasive glucose monitoring. Med Eng Phys 30 (5):541−549.
- Nelson LA, McCann JC, Loepke AW, Wu J, Ben Dor B, Kurth CD (2006) Development and validation of a multiwavelength spatial domain near-infrared oximeter to detect cerebral hypoxia-ischemia. J Biomed Opt 11 (6):64 022.
- Lambert JL, Morookian JM, Sirk SJ, Borchert MS (2002) Measurement of aqueous glucose in a model anterior chamber using Raman spectroscopy. Journal of Raman Spectroscopy 33 (7):524−529.
- Cameron BD, Anumula H (2006) Development of a real-time corneal birefringence compensated glucose sensing polarimeter. Diabetes Technol Ther 8 (2):156−164.
- MacKenzie HA, Ashton HS, Spiers S, Shen Y, Freeborn SS, Hannigan J, Lindberg J, Rae P (1999) Advances in photoacoustic noninvasive glucose testing. Clin Chem 45 (9): 1587−1595
- Rao G, Glikfeld P, Guy RH (1993) Reverse iontophoresis: development of a noninvasive approach for glucose monitoring. Pharm Res 10 (12): 1751−1755
- Kost J, Mitragotri S, Gabbay RA, Pishko M, Langer R (2000) Transdermal monitoring of glucose and other analytes using ultrasound. Nat Med 6 (3):347−350.
- Jensen BM, Bjerring P, Christiansen JS, Orskov H (1995) Glucose content in human skin: relationship with blood glucose levels. Scand J Clin Lab Invest 55 (5):427−432
- Tolosa L (2010) On the design of low-cost fluorescent protein biosensors. Adv Biochem Eng Biotechnol 116:143−157.
- Amiss TJ, Sherman DB, Nycz CM, Andaluz SA, Pitner JB (2007) Engineering and rapid selection of a low-affinity glucose/galactose-binding protein for a glucose biosensor. Protein Sci 16 (11):2350−2359.
- Khan F, Saxl TE, Pickup JC (2010) Fluorescence intensity- and lifetime-based glucose sensing using an engineered high-Kd mutant of glucose/galactose-binding protein. Anal Biochem 399 (l):39−43.
- Thomas KJ, Sherman DB, Amiss TJ, Andaluz SA, Pitner JB (2006) A long-wavelength fluorescent glucose biosensor based on bioconjugates of galactose/glucose binding protein and Nile Red derivatives. Diabetes Technol Ther 8 (3):261−268.
- Thomas J, Sherman DB, Amiss TJ, Andaluz SA, Pitner JB (2007) Synthesis and biosensor performance of a near-IR thiol-reactive fluorophore based on benzothiazolium squaraine. Bioconjug Chem 18 (6): 1841−1846.
- Ge X, Tolosa L, Rao G (2004) Dual-labeled glucose binding protein for ratiometric measurements of glucose. Anal Chem 76 (5): 1403−1410.
- Ye K, Schultz JS (2003) Genetic engineering of an allosterically based glucose indicator protein for continuous glucose monitoring by fluorescence resonance energy transfer. Anal Chem 75 (14):3451−3459
- Pickup JC, Zhi ZL, Khan F, Saxl T, Birch DJ (2008) Nanomedicine and its potential in diabetes research and practice. Diabetes Metab Res Rev 24 (8):604−610.
- Saxl T, Khan F, Ferla M, Birch D, Pickup J (2011) A fluorescence lifetime-based fibre-optic glucose sensor using glucose/galactose-binding protein. Analyst 136 (5):968−972.
- Birnboim HC, Doly J (1979) A rapid alkaline extraction procedure for screening recombinant plasmid DNA. Nucleic Acids Res 7 (6):1513−1523
- Laemmli UK (1970) Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227 (5259):680−685
- Turoverov KK, Kuznetsova IM, Zaitsev VN (1985) The environment of the tryptophan residue in Pseudomonas aeruginosa azurin and its fluorescence properties. Biophys Chem 23 (l-2):79−89.
- Туроверов KK, Бикташев АГ, Дорофеюк AB, Кузнецова ИМ (1998) Комплекс аппаратных и программных средств для измерения спектральных, поляризационных и кинетических характеристик флуоресценции в растворе. Цитология 40 (8−9):806−817
- Lakowicz JR (2006) Principles of Fluorescence Spectroscopy. 3 edn. Springer, New York, 698 p.
- Kuznetsova IM, Sulatskaya AI, Povarova OI, Turoverov KK (2012) Reevaluation of ANS binding to human and bovine serum albumins: key role of equilibrium microdialysis in ligand receptor binding characterization. PLoS One 7 (7):e40845.
- Nolting В (1999) Calculation of the kinetic rate constants. In: Protein Folding Kinetics. Springer, 222 p.
- Marquardt DW (1963) An algorithm for least-squares estimation of nonlinear parameters. J Soc Indust Appl Math 11 (2):431−441
- Zuker M, Szabo AG, Bramall L, Krajcarski DT, Seiinger В (1985) Delta fonction convolution method (DFCM) for fluorescence decay experiments. Rev Sei Instrum 56 (l):14−22.
- Levitsky DI, Rostkova EV, Orlov VN, Nikolaeva OP, Moiseeva LN, Teplova MV, Gusev NB (2000) Complexes of smooth muscle tropomyosin with F-actin studied by differential scanning calorimetry. Eur J Biochem 267 (6): 1869−1877.
- Levitsky D (2005) Structural and functional studies of muscle proteins by using differential scanning calorimetry. In: The Nature of Biological Systems as Revealed by Thermal Methods. Springer, pp 127−158
- Privalov PL, Potekhin SA (1986) Scanning microcalorimetry in studying temperature-induced changes in proteins. Methods Enzymol 131:4−51
- Turoverov KK, Kuznetsova IM (2003) Intrinsic fluorescence of actin. J Fluorescence 13:41−57
- Kuznetsova IM, Stepanenko OV, Turoverov KK, Staiano M, Scognamiglio V, Rossi M, D’Auria S (2005) Fluorescence properties of glutamine-binding protein from Escherichia coli and its complex with glutamine. J Proteome Res 4 (2):417−423
- Bushmarina NA, Kuznetsova IM, Biktashev AG, Turoverov KK, Uversky VN (2001) Partially folded conformations in the folding pathway of bovine carbonic anhydrase II: a fluorescence spectroscopic analysis. Chembiochem 2 (11):813−821.
- Chen Y, Barkley MD (1998) Toward understanding tryptophan fluorescence in proteins. Biochemistry 37 (28):9976−9982.
- Piszczek G, DAuria S, Staiano M, Rossi M, Ginsburg A (2004) Conformational stability and domain coupling in D-glucose/D-galactose-binding protein from Escherichia coli. Biochem J 381 (Pt 1):97−103.
- Permyakov SE, Bakunts AG, Denesyuk AI, Knyazeva EL, Uversky VN, Permyakov EA (2008) Apo-parvalbumin as an intrinsically disordered protein. Proteins 72:822−836
- Povarova OI, Kuznetsova IM, Turoverov KK (2010) Differences in the pathways of proteins unfolding induced by urea and guanidine hydrochloride: molten globule state and aggregates. PLoS One 5 (1 l):el5035.
- Bongrand Р (1999) Ligand-receptor interactions. Rep Prog Phys 62 (6):921−968.
- Dintenfass L (1985) Blood viscosity. Kluwer Academic Pub 482 p.
- Фонин AB, Степаненко OB, Верхуша BB, Щербакова ДМ, Кузнецова ИМ, Туроверов КК (2011). Перспективы создания чувствительного элемента биосенсорной системы на глюкозу. Вестник СпбГУ 4(4): 180−185.