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fd coat protein structure in membrane environments: structural dynamics of the loop between the hydrophobic trans-membrane helix and the amphipathic in-plane helix.

Almeida FC, Opella SJ
J Mol Biol 270 481-95 (1997)
Cited: 64 times
EuropePMC logo PMID: 9237913

Abstract

By performing multidimensional solution NMR experiments on micelle samples it was possible to determine the structure of the membrane-bound form of fd coat protein based on short-range distance and dihedral angle constraints using distance geometry and simulated annealing calculations. Its dynamics were described by 15N relaxation measurements (T1, T2, heteronuclear nuclear Overhauser enhancement (NOE)) fitted with the Lipari-Szabo model-free formalism adapted for the transmembrane and in-plane helices of a membrane protein. The overall correlation time of the protein in micelles was found to be approximately 9 ns, and the local motion of each backbone N-H vector was described by an order parameter and an effective correlation time. The 50 residue protein has an amphipathic alpha-helix (residues 7 to 16) and a hydrophobic alpha-helix (residues 27 to 44), which were found to be approximately perpendicular on the basis of NOEs in the residues that connect the two helices. The residues connecting the helices are of particular interest in membrane proteins, and in this case the loop consists of two turns. The relaxation data show the presence of an extra motion in the amphipathic alpha-helix on the nanosecond timescale and additional flexibility of several residues in the loop connecting the two helices.

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  3. Application of solid-state NMR restraint potentials in membrane protein modeling. Lee J, Chen J, Brooks CL, Im W. J Magn Reson 193 68-76 (2008)
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  1. Structure determination of membrane proteins by NMR spectroscopy. Opella SJ, Marassi FM. Chem Rev 104 3587-3606 (2004)
  2. NMR structural studies of membrane proteins. Marassi FM, Opella SJ. Curr Opin Struct Biol 8 640-648 (1998)
  3. NMR solution structure determination of membrane proteins reconstituted in detergent micelles. Fernández C, Wüthrich K. FEBS Lett 555 144-150 (2003)
  4. Structure, dynamics, and assembly of filamentous bacteriophages by nuclear magnetic resonance spectroscopy. Opella SJ, Zeri AC, Park SH. Annu Rev Phys Chem 59 635-657 (2008)
  5. Viruses: incredible nanomachines. New advances with filamentous phages. Hemminga MA, Vos WL, Nazarov PV, Koehorst RB, Wolfs CJ, Spruijt RB, Stopar D. Eur Biophys J 39 541-550 (2010)
  6. Anchoring mechanisms of membrane-associated M13 major coat protein. Stopar D, Spruijt RB, Hemminga MA. Chem Phys Lipids 141 83-93 (2006)
  7. Structure determination of membrane proteins by NMR spectroscopy. Opella SJ, Nevzorov A, Mesleh MF, Marassi FM. Biochem Cell Biol 80 597-604 (2002)
  8. Structure determination of membrane proteins by nuclear magnetic resonance spectroscopy. Opella SJ. Annu Rev Anal Chem (Palo Alto Calif) 6 305-328 (2013)
  9. NMR structures of membrane proteins in phospholipid bilayers. Radoicic J, Lu GJ, Opella SJ. Q Rev Biophys 47 249-283 (2014)
  10. Techniques and applications of NMR to membrane proteins. Nielsen N, Malmendal A, Vosegaard T. Mol Membr Biol 21 129-141 (2004)
  11. Interpretation of biomolecular NMR spin relaxation parameters. Reddy T, Rainey JK. Biochem Cell Biol 88 131-142 (2010)
  12. Strategies for dealing with conformational sampling in structural calculations of flexible or kinked transmembrane peptides. Rainey JK, Fliegel L, Sykes BD. Biochem Cell Biol 84 918-929 (2006)
  13. From 'I' to 'L' and back again: the odyssey of membrane-bound M13 protein. Vos WL, Nazarov PV, Koehorst RB, Spruijt RB, Hemminga MA. Trends Biochem Sci 34 249-255 (2009)
  14. Deuterated detergents for structural and functional studies of membrane proteins: Properties, chemical synthesis and applications. Hiruma-Shimizu K, Shimizu H, Thompson GS, Kalverda AP, Patching SG. Mol Membr Biol 32 139-155 (2015)
  15. Application of Solution NMR to Structural Studies on α-Helical Integral Membrane Proteins. Sim DW, Lu Z, Won HS, Lee SN, Seo MD, Lee BJ, Kim JH. Molecules 22 E1347 (2017)

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  2. Coarse-grained molecular dynamics simulations of membrane proteins and peptides. Bond PJ, Holyoake J, Ivetac A, Khalid S, Sansom MS. J Struct Biol 157 593-605 (2007)
  3. Simultaneous assignment and structure determination of a membrane protein from NMR orientational restraints. Marassi FM, Opella SJ. Protein Sci 12 403-411 (2003)
  4. Complete resolution of the solid-state NMR spectrum of a uniformly 15N-labeled membrane protein in phospholipid bilayers. Marassi FM, Ramamoorthy A, Opella SJ. Proc Natl Acad Sci U S A 94 8551-8556 (1997)
  5. Structure of the coat protein in fd filamentous bacteriophage particles determined by solid-state NMR spectroscopy. Zeri AC, Mesleh MF, Nevzorov AA, Opella SJ. Proc Natl Acad Sci U S A 100 6458-6463 (2003)
  6. NMR spectroscopy in studies of light-induced structural changes in mammalian rhodopsin: applicability of solution (19)F NMR. Klein-Seetharaman J, Getmanova EV, Loewen MC, Reeves PJ, Khorana HG. Proc Natl Acad Sci U S A 96 13744-13749 (1999)
  7. Dipolar waves map the structure and topology of helices in membrane proteins. Mesleh MF, Lee S, Veglia G, Thiriot DS, Marassi FM, Opella SJ. J Am Chem Soc 125 8928-8935 (2003)
  8. Positively and negatively charged residues have different effects on the position in the membrane of a model transmembrane helix. Monné M, Nilsson I, Johansson M, Elmhed N, von Heijne G. J Mol Biol 284 1177-1183 (1998)
  9. Large-scale molecular dynamics simulations of general anesthetic effects on the ion channel in the fully hydrated membrane: the implication of molecular mechanisms of general anesthesia. Tang P, Xu Y. Proc Natl Acad Sci U S A 99 16035-16040 (2002)
  10. (1)H/(15)N heteronuclear NMR spectroscopy shows four dynamic domains for phospholamban reconstituted in dodecylphosphocholine micelles. Metcalfe EE, Zamoon J, Thomas DD, Veglia G. Biophys J 87 1205-1214 (2004)
  11. Magic angle-oriented sample spinning (MAOSS): A new approach toward biomembrane studies. Glaubitz C, Watts A. J Magn Reson 130 305-316 (1998)
  12. Structure and dynamics of the membrane-bound form of Pf1 coat protein: implications of structural rearrangement for virus assembly. Park SH, Marassi FM, Black D, Opella SJ. Biophys J 99 1465-1474 (2010)
  13. Solution structure of the M13 major coat protein in detergent micelles: a basis for a model of phage assembly involving specific residues. Papavoine CH, Christiaans BE, Folmer RH, Konings RN, Hilbers CW. J Mol Biol 282 401-419 (1998)
  14. Transmembrane domain mediated self-assembly of major coat protein subunits from Ff bacteriophage. Melnyk RA, Partridge AW, Deber CM. J Mol Biol 315 63-72 (2002)
  15. De novo folding of membrane proteins: an exploration of the structure and NMR properties of the fd coat protein. Im W, Brooks CL. J Mol Biol 337 513-519 (2004)
  16. Filamentous bacteriophage stability in non-aqueous media. Olofsson L, Ankarloo J, Andersson PO, Nicholls IA. Chem Biol 8 661-671 (2001)
  17. Deuterium/hydrogen exchange factors measured by solution nuclear magnetic resonance spectroscopy as indicators of the structure and topology of membrane proteins. Veglia G, Zeri AC, Ma C, Opella SJ. Biophys J 82 2176-2183 (2002)
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  20. Structure and dynamics of a membrane protein in micelles from three solution NMR experiments. Lee S, Mesleh MF, Opella SJ. J Biomol NMR 26 327-334 (2003)
  21. Structural and orientational information of the membrane embedded M13 coat protein by (13)C-MAS NMR spectroscopy. Glaubitz C, Gröbner G, Watts A. Biochim Biophys Acta 1463 151-161 (2000)
  22. Structural biology of transmembrane domains: efficient production and characterization of transmembrane peptides by NMR. Hu J, Qin H, Li C, Sharma M, Cross TA, Gao FP. Protein Sci 16 2153-2165 (2007)
  23. Backbone structure of a small helical integral membrane protein: A unique structural characterization. Page RC, Lee S, Moore JD, Opella SJ, Cross TA. Protein Sci 18 134-146 (2009)
  24. Solution structure of the antimicrobial peptide gaegurin 4 by H and 15N nuclear magnetic resonance spectroscopy. Park SH, Kim YK, Park JW, Lee B, Lee BJ. Eur J Biochem 267 2695-2704 (2000)
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  32. NMR-Based amide hydrogen-deuterium exchange measurements for complex membrane proteins: development and critical evaluation. Czerski L, Vinogradova O, Sanders CR. J Magn Reson 142 111-119 (2000)
  33. Proton-decoupled 15N and 31P solid-state NMR investigations of the Pf3 coat protein in oriented phospholipid bilayers. Aisenbrey C, Harzer U, Bauer-Manz G, Bär G, Chotimah IN, Bertani P, Sizun C, Kuhn A, Bechinger B. FEBS J 273 817-828 (2006)
  34. Site-specific tryptophan dynamics in class A amphipathic helical peptides at a phospholipid bilayer interface. Clayton AH, Sawyer WH. Biophys J 79 1066-1073 (2000)
  35. Solid-State NMR-Restrained Ensemble Dynamics of a Membrane Protein in Explicit Membranes. Cheng X, Jo S, Qi Y, Marassi FM, Im W. Biophys J 108 1954-1962 (2015)
  36. Enhanced Sampling of Coarse-Grained Transmembrane-Peptide Structure Formation from Hydrogen-Bond Replica Exchange. Bereau T, Deserno M. J Membr Biol 248 395-405 (2015)
  37. Influence of assignment on the prediction of transmembrane helices in protein structures. Pylouster J, Bornot A, Etchebest C, de Brevern AG. Amino Acids 39 1241-1254 (2010)
  38. Probing the structure of the Ff bacteriophage major coat protein transmembrane helix dimer by solution NMR. Wu Y, Shih SC, Goto NK. Biochim Biophys Acta 1768 3206-3215 (2007)
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  40. Structural studies of MS2 bacteriophage virus particle disassembly by nuclear magnetic resonance relaxation measurements. Anobom CD, Albuquerque SC, Albernaz FP, Oliveira AC, Silva JL, Peabody DS, Valente AP, Almeida FC. Biophys J 84 3894-3903 (2003)
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  43. NMR studies of membrane proteins. Cook GA, Opella SJ. Methods Mol Biol 637 263-275 (2010)
  44. Impact of Differential Detergent Interactions on Transmembrane Helix Dimerization Affinities. Qureshi T, Goto NK. ACS Omega 1 277-285 (2016)


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