MAGNETYCZNY REZONANS JĄDROWY W BADANIACH STRUKTURALNYCH BIOMOLEKUŁ NA PRZYKŁADZIE BADANIA MODELOWYCH UKŁADÓW HELIKALNYCH

Marta Oleszczuk

doi:10.56782/pps.55

Published : 2006-07-31

Vol. 4 No. 1 (2006)

NUCLEAR MAGNETIC RESONANCE IN THE STRUCTURAL INVESTIGATION OF BIOMOLECULES: APPLICATION IN THE STUDY OF MODEL HELICAL SYSTEMS

Marta Oleszczuk

DOI: https://doi.org/10.56782/pps.55

Abstract

Nuclear Magnetic Resonance (NMR) is a powerful tool in the structural investigation of biomolecules. It enables the study not only on large macromolecules such as proteins with rigid conformation, but also on small peptides evincing conformational equilibrium in solution. In this paper the basic information about nuclear magnetic resonance and a short description of the most commonly used methods for calculating 3D structures of biomolecules are presented. Structural investigations of a model helical system carried out at the Institute of Biochemistry and Biophysics PAS in Warsaw are included to exemplify the protocols.

Keywords:

Nuclear Magnetic Resonance (NMR), protein, peptide, helix

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Oleszczuk, M. (2006). NUCLEAR MAGNETIC RESONANCE IN THE STRUCTURAL INVESTIGATION OF BIOMOLECULES: APPLICATION IN THE STUDY OF MODEL HELICAL SYSTEMS. Prospects in Pharmaceutical Sciences, 4(1), 1–16. https://doi.org/10.56782/pps.55

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References

Wüthrich, K., (1995), Acta.Cryst.D, 51, 249-270 DOI: https://doi.org/10.1107/S0907444994010188

Akke, M., Palmer, A.G., III (1996), J.Am.Chem.Soc., 118, 911-912 DOI: https://doi.org/10.1021/ja953503r

Lundström, P., Akke, M., (2004), J.Am.Chem.Soc., 123, 928-935 DOI: https://doi.org/10.1021/ja037529r

Kay, L.E., (1998), Nat.Struct.Biol., 5, (suplement NMR), 513-517 DOI: https://doi.org/10.1038/755

Ejchart, A., (1999a),”Zjawiska relaksacji molekularnej”; rozdział “Relaksacja jądrowa w badaniach dynamiki szkieletów białek”, edytor Hawranek, P., Sobczyk, L., Wydawnictwo Uniwersytetu Wrocławskiego, str. 117-134

Buck, M., Rosen, M.K., (2001), Science, 291, 2329-2330 DOI: https://doi.org/10.1126/science.1060383

Abragam, A., (1978), “The Principles of Nuclear Magnetism”, Oxford University Press

Hennel, J., (1997), „Wstęp do teorii magnetycznego rezonansu jądrowego”, Wydawnictwo Instytutu Fizyki Jądrowej im. H. Niewodniczańskiego

Ejchart, A., Kozerski, L., (1988), „Spektroskopia magnetycznego rezonansu jądrowego 13C” PWN

Ejchart, A., Gryff-Keller, A., (2004) „NMR w cieczach. Zarys teorii i metodologii”, Oficyna Wydawnicza Politechniki Warszawskiej

Günther, H., (1983) „Spektroskopia magnetycznego rezonansu jądrowego”, PWN

Cavanagh, J., Fairbrother, W.J., Palmer III, A.G., Skelton, N.J., (1996), “Protein NMR Spectroscopy”, Academic Press

Karplus, M., (1959), J.Phys.Chem., 30, 11-15 DOI: https://doi.org/10.1063/1.1729860

van de Ven, F.J.M., (1995), „Multidimensional NMR in Liquids“, VCH Publishers, Inc

IUPAC-IUB Commission on Biochemical Nomeclature, (1970), Biochemistry, 9, 3471-3479 DOI: https://doi.org/10.1021/bi00820a001

Bystrov, V.F., Gavrilov, Y.D., Solkan, V.N., J. Magn. Reson. (1975), 19, 123 DOI: https://doi.org/10.1016/0022-2364(75)90061-X

Noggle, J.H., Schirmer, R.E., (1971), “The Nuclear Overhauser Effect”, Academic, New York DOI: https://doi.org/10.1016/B978-0-12-520650-1.50008-2

Wüthrich, K., (1986), „NMR of Proteins and Nucleic Acids” Wiley-Interscience Publication DOI: https://doi.org/10.1051/epn/19861701011

Neuhaus, D., Williamson, M., (1989), “The Nuclear Overhauser Effect in Structural and Conformational Analysis”, VCH Publishers, New York

Bothner-By, A.A., Stephens, R.L., Lee, J-M., Warren, C.D., Jeanloz, R.W., (1984), J. Am. Chem. Soc., 106, 811-813 DOI: https://doi.org/10.1021/ja00315a069

Hull, W.E., (1994), “Experimental Aspects of Two-Dimensional NMR”, rozdział 2 z „Two-Dimensional NMR Spectroscopy” (second edition), edytorzy: Croasmun, W.R., Carlson, R.M.K.,VCH, str. 67-457

Aue, P.W., Bartholdi, W.P., Ernst, R.R, (1976), J. Chem. Phys., 64, 2229-2246 DOI: https://doi.org/10.1063/1.432450

Bax, A., Davis, D.G., (1985), J. Magn. Reson., 63, 207-213 DOI: https://doi.org/10.1016/0022-2364(85)90171-4

Bax, A., Davis, D.G., (1985), J.Magn.Reson., 65, 355-360 DOI: https://doi.org/10.1016/0022-2364(85)90018-6

Braunschweiler, L., Ernst, R.R., (1983), J. Magn. Reson., 53, 521-528 DOI: https://doi.org/10.1016/0022-2364(83)90226-3

Jeener, J., Meier, Megier, H., Bachmann, P., Ernst, R.R., (1979), J. Chem. Phys, 71, 4546-4553 DOI: https://doi.org/10.1063/1.438208

Bodenhausen, G., Ruben, G.J., (1980), Chem.Phys.Lett., 69, 185-189 DOI: https://doi.org/10.1016/0009-2614(80)80041-8

Kay, L.E., Keifer, P., Saarinen, T., (1992), J. Am. Chem. Soc. 114, 10663-10665 DOI: https://doi.org/10.1021/ja00052a088

Palmer III, A.G., Cavanagh, J., Wright, P.E., Rance, M., (1991), J. Magn. Reson., 93, 151-170 DOI: https://doi.org/10.1016/0022-2364(91)90036-S

Kontraxis, G., Stonehouse, J., Laue, E.D., Keeler, J., (1994), J. Magn. Reson. Ser. A, 111, 70-76 DOI: https://doi.org/10.1006/jmra.1994.1227

Levitt, M.H., Freeman, R., (1981), J.Magn.Reson, 43, 502-507 DOI: https://doi.org/10.1016/0022-2364(81)90066-4

Levitt, M.H., Freeman, R., Frenkiel, T., (1982), J.Magn.Reson, 50, 345-348 DOI: https://doi.org/10.1016/0022-2364(82)90066-X

Hurd, R.E., John, B.K., (1991), J.Magn.Reson., 91, 648 DOI: https://doi.org/10.1016/0022-2364(91)90395-A

Vuister, G.W., Boelens, R., Kaptein, R., Hurd, R.E., John, B., van Zijl, P.C.M., (1991), J.Am.Chem.Soc., 113, 9688-9690 DOI: https://doi.org/10.1021/ja00025a053

Ruiz-Cabello, J., Vuister, G.W., Moonen, C.T.W., van Geldener, P., Cohen, J.C., van Zijl, P.C.M., (1992), J.Magn.Reson., 100, 282 DOI: https://doi.org/10.1016/0022-2364(92)90262-6

Braun, S., Kalinowski, H.-O., Berger, S., (1996), “100 and More Basic NMR Experiments”, VCH Publishers, Weinheim

Ejchart, A., (1998), Bulletin of the PAS, Chem., 46, 117-131 DOI: https://doi.org/10.1248/cpb.46.131

Blumenthal, L.M., (1953), “Theory and Applications of Distance Geometry”, Cambridge University Press

Crippen, G.M., Havel, T. F., (1988), “Distance Geometry and Molecular Conformation”, Taunton, UK: Research Studies Press

Güntert, P., (1998), Quat.Rev.Biophys., 31, 145-237 DOI: https://doi.org/10.1017/S0033583598003436

Allen, M.P., Tildesley, D.J., (1987), “Computer Simulation in Liquids”, Oxford: Clarendon Press

Kirkpatrick, S., Gelatt, Jr., C.D., Vecchi, M.P., (1983), Science, 220, 671-680 DOI: https://doi.org/10.1126/science.220.4598.671

Brünger, A.T., Nigels, M., (1993), Q.Rev.Biophys., 26, 49-125 DOI: https://doi.org/10.1017/S0033583500003966

Nigels, M., Clore, G.M., Gronenborn, A.M., (1988), FEBS Lett., 229, 317-324 DOI: https://doi.org/10.1016/0014-5793(88)81148-7

Bae, D.S., Huang, D.J., (1987), Mech.Struct.Mech., 15, 359-382 DOI: https://doi.org/10.1080/08905458708905124

Güntert, P., Mumenthaler, C., Wüthrich, K., (1997), J.Mol.Biol., 273, 283-298 DOI: https://doi.org/10.1006/jmbi.1997.1284

Jain, A., Vaidehi, N., Rodrigues, G., (1993), J.Comp.Phys., 106, 258-268 DOI: https://doi.org/10.1016/S0021-9991(83)71106-X

Katz, H., Walter, R., Somorjay, R.L., (1979), Compurets&Chemistry, 3, 25-32 DOI: https://doi.org/10.1016/0097-8485(79)80005-4

Kneller, G.R., Hinsen, K., (1994), Phys.Rev.E, 50, 1559-1564 DOI: https://doi.org/10.1103/PhysRevE.50.1559

Mathiowetz, A. M., Jain, A., Karasawa, N., Goddard III, W. A. (1994). Proteins, 20, 227-247 DOI: https://doi.org/10.1002/prot.340200304

Mazur, A.K., Abagyan, R.A. (1989), J.Biomol.Struct.Dynam., 4, 815-832 DOI: https://doi.org/10.1080/07391102.1989.10507739

Mazur, A. K., Dorofeev, V.E., Abagyan, R.A. (1991), J.Comp.Phys., 92, 261-272 DOI: https://doi.org/10.1016/0021-9991(91)90210-C

Rice, L.M., Brünger, A.T. (1994), Proteins,19, 277-290 DOI: https://doi.org/10.1002/prot.340190403

Stein, E. G., Rice, L.M., Brünger, A. T. (1997), J.Magn.Reson., 124, 154-164 DOI: https://doi.org/10.1006/jmre.1996.1027

Groth, M., Malicka, J., Czapiewski, C., Ołdziej, S., Łankiewicz, L, Wiczk, W., Liwo, A., (1999), J.Biomol.NMR, 69, 315-330 DOI: https://doi.org/10.1023/A:1008349424452

Oleszczuk, M., (2005), „Badania konformacyjne modelowych fragmentów białek wiążących jony wapnia”, praca doktorska, Instytut Biochemii i Biofizyki PAN

Barlow, D.J., Thornton, J.M., (1988), J.Mol.Biol., 201, 601-619 DOI: https://doi.org/10.1016/0022-2836(88)90641-9

Fodje, M.N., Al-Karadaghi, S., (2002), Prot.Eng., 15, 353-358 DOI: https://doi.org/10.1093/protein/15.5.353

Schultz, G.E., Schirmer, R.H., (1990), “Principles of Protein Structure”, Springer-Verlag (ninth printing)

Zimm, B.H., Bragg, J.K., (1959), J.Chem.Phys., 31, 526-535 DOI: https://doi.org/10.1063/1.1730390

Lifson, S., Roig, A., (1961), J.Chem.Phys., 34, 1963-1974 DOI: https://doi.org/10.1063/1.1731802

Davies, D.R., (1964), J.Mol.Biol., 9, 605-612 DOI: https://doi.org/10.1016/S0022-2836(64)80232-1

Prothero, J.W., (1966), Biophys.J., 6, 367-370 DOI: https://doi.org/10.1016/S0006-3495(66)86662-6

Cook, D.A., (1967), J.Mol.Biol., 29, 167-171 DOI: https://doi.org/10.1016/0022-2836(67)90188-X

Ptitsyn, O.B., (1969), J.Mol.Biol., 42, 501-510 DOI: https://doi.org/10.1016/0022-2836(69)90238-1

Ptitsyn, O.B., Finkelstein, A.V., (1970), Biofizika (ZSRR), 15, 757-768

Blagdon, D.E., Goodman, M., (1975), Biopolymers, 14, 241-245 DOI: https://doi.org/10.1002/bip.1975.360140118

Chou, P.Y., Fasman, G.D., (1974), Biochemystry, 13, 211-222 DOI: https://doi.org/10.1021/bi00699a001

Chakrabartty, A. and Baldwin, R.L., (1995) Adv.Protein Chem., 46, 141-176 DOI: https://doi.org/10.1016/S0065-3233(08)60334-4

Cierpicki, T., Zhukov, I., Byrd, R.A., Otlewski, J., (2002), J.Magn.Reson., 157, 178-180 DOI: https://doi.org/10.1006/jmre.2002.2597

Forsen, S., Hoffman, R.A., (1963), J.Chem.Phys., 39, 2892-2901 DOI: https://doi.org/10.1063/1.1734121

Wójcik, J., Ruszczyńska, K., Zhukov, I., Ejchart, A., (1999), Acta Biochim.Polon., 46, 651-663 DOI: https://doi.org/10.18388/abp.1999_4137

Forsen, S., Hoffman, R.A., (1964), J.Chem.Phys., 40, 1189 DOI: https://doi.org/10.1063/1.1725295

Led, J.J., Gesman, H., Abildgaard, F., (1989), Methods in Enzymology, 176, 311-329 DOI: https://doi.org/10.1016/0076-6879(89)76017-1

Vold, R.L., Waugh, J.S., Klein, M.P., Phepls, D.D., (1968), J.Chem.Phys., 48, 3831 DOI: https://doi.org/10.1063/1.1669699

Lian, L-Y., Roberts, G.C.K., (1993), rozdział 6 z Roberts, G.C.K “NMR of Macromolecules. A Practical Approach”, Oxford University Press

Rhol, C.A., Doig, A.J., (1996), Protein Sci., 5, 1687-1696 DOI: https://doi.org/10.1002/pro.5560050822

Wang, L., O’Connell, T., Tropsha, A., Hermans, J., (1995), Proc. Natl. Acad. Sci. USA, 92, 10924-10928 DOI: https://doi.org/10.1073/pnas.92.24.10924

Gariepy, J., Sykes, B.D., Hodges, R.S., (1983), Biochemistry, 22, 1765-1772 DOI: https://doi.org/10.1021/bi00277a004

Dadlez, M., Góral, J., Bierzyński, A., (1991), FEBS Lett., 282, 143-146 DOI: https://doi.org/10.1016/0014-5793(91)80464-E

Horrocs, W.DeW., Jr, (1993), Methods Enzymol., 226, 495-538 DOI: https://doi.org/10.1016/0076-6879(93)26023-3

Lee, L., Sykes, B.D., (1983), Biochemistry, 22, 4366-4373 DOI: https://doi.org/10.1021/bi00288a004

Wójcik, J., Góral, J., Pawłowski, K., Bierzyński, A., (1997), Biochemistry, 36, 680-587 DOI: https://doi.org/10.1021/bi961821c

Siedlecka, M., Goch, G., Ejchart, A., Sticht, H., Bierzyński, A., (1999), Proc.Natl.Acad.Sci.USA, 96, 903-908 DOI: https://doi.org/10.1073/pnas.96.3.903

Goch, G., Maciejczyk, M., Oleszczuk, M., Stachowiak, D., Malicka, J., Bierzyński, A., (2003), Biochemistry, 42, 6840-6847 DOI: https://doi.org/10.1021/bi027339d

Kulawińska, R., (2001), „Badanie struktury peptydu analogu trzeciej pętli wiążącej kalmoduliny”, praca magisterska, Uniwersytet Warszawski, Wydział Fizyki

Ruszczyńska, K., (1999), „Badanie magnetycznego rezonansu jądrowego struktur i stabilności analogów III pętli białka kalmoduliny”, praca magisterska, Uniwersytet Warszawski, Wydział Fizyki

Brünger, A.T., (1992), “X-PLOR, version3.1. A system for X-ray crystallography and NMR”, New Haven: Yale University Press

Lin, J.C., Barua, B., Andersen, N.H., (2004), J.Am.Chem.Soc., 126, 13679-13684 DOI: https://doi.org/10.1021/ja047265o

Gething, M-J., Sambrook, J., (1992), Nature, 355, 33-45 DOI: https://doi.org/10.1038/355033a0

Thomas, P.J., Qu, B-H., Pedersen, P.L., (1995), Trends Biochem. Sci.¸ 20, 456-459 DOI: https://doi.org/10.1016/S0968-0004(00)89100-8