1apc Citations

Solution structure of apocytochrome b562.

Nat Struct Biol 1 30-5 (1994)
Cited: 61 times
EuropePMC logo PMID: 7656004

Abstract

The apoprotein is an important intermediate on the folding pathways of many haem proteins, yet a detailed structure of such an intermediate has remained elusive. Here we present the structure of apocytochrome b562 obtained by NMR spectroscopy. The apoprotein has a topology similar to the holoprotein. Nevertheless, significant differences in helix-helix packing between the two are evident. Much of the haem binding pocket in the apoprotein is preserved but exposed to solvent creating a large cavern. As apocytochrome b562 displays many of the physical characteristics ascribed to the molten globule state, these results help ellucidate the origin of several properties of the protein molten globule.

Reviews - 1apc mentioned but not cited (1)

Articles - 1apc mentioned but not cited (5)

  1. Toward an accurate theoretical framework for describing ensembles for proteins under strongly denaturing conditions. Tran HT, Pappu RV. Biophys J 91 1868-1886 (2006)
  2. Linking the functions of unrelated proteins using a novel directed evolution domain insertion method. Edwards WR, Busse K, Allemann RK, Jones DD. Nucleic Acids Res 36 e78 (2008)
  3. In-frame amber stop codon replacement mutagenesis for the directed evolution of proteins containing non-canonical amino acids: identification of residues open to bio-orthogonal modification. Arpino JA, Baldwin AJ, McGarrity AR, Tippmann EM, Jones DD. PLoS One 10 e0127504 (2015)
  4. Light-Driven CO2 Reduction by Co-Cytochrome b 562. Alcala-Torano R, Halloran N, Gwerder N, Sommer DJ, Ghirlanda G. Front Mol Biosci 8 609654 (2021)
  5. Computationally Guided Redesign of a Heme-free Cytochrome with Native-like Structure and Stability. Hoffnagle AM, Eng VH, Markel U, Tezcan FA. Biochemistry 61 2063-2072 (2022)


Reviews citing this publication (13)

  1. Theory of protein folding: the energy landscape perspective. Onuchic JN, Luthey-Schulten Z, Wolynes PG. Annu Rev Phys Chem 48 545-600 (1997)
  2. Principles of protein folding--a perspective from simple exact models. Dill KA, Bromberg S, Yue K, Fiebig KM, Yee DP, Thomas PD, Chan HS. Protein Sci 4 561-602 (1995)
  3. Protein folding intermediates and pathways studied by hydrogen exchange. Englander SW. Annu Rev Biophys Biomol Struct 29 213-238 (2000)
  4. Mechanisms and uses of hydrogen exchange. Englander SW, Sosnick TR, Englander JJ, Mayne L. Curr Opin Struct Biol 6 18-23 (1996)
  5. Kinetic role of early intermediates in protein folding. Roder H, Colón W. Curr Opin Struct Biol 7 15-28 (1997)
  6. The nature of protein folding pathways: the classical versus the new view. Baldwin RL. J Biomol NMR 5 103-109 (1995)
  7. Structures of folding intermediates. Ptitsyn OB. Curr Opin Struct Biol 5 74-78 (1995)
  8. Protein folding. Solid evidence for molten globules. Dobson CM. Curr Biol 4 636-640 (1994)
  9. Fast-folding experiments and the topography of protein folding energy landscapes. Wolynes P, Luthey-Schulten Z, Onuchic J. Chem Biol 3 425-432 (1996)
  10. From Synthesis to Utilization: The Ins and Outs of Mitochondrial Heme. Swenson SA, Moore CM, Marcero JR, Medlock AE, Reddi AR, Khalimonchuk O. Cells 9 E579 (2020)
  11. Designing redox metalloproteins from bottom-up and top-down perspectives. Barker PD. Curr Opin Struct Biol 13 490-499 (2003)
  12. Structural and thermodynamic consequences of b heme binding for monomeric apoglobins and other apoproteins. Landfried DA, Vuletich DA, Pond MP, Lecomte JT. Gene 398 12-28 (2007)
  13. Contacting the protein folding funnel with NMR. Onuchic JN. Proc Natl Acad Sci U S A 94 7129-7131 (1997)

Articles citing this publication (42)

  1. Toward an outline of the topography of a realistic protein-folding funnel. Onuchic JN, Wolynes PG, Luthey-Schulten Z, Socci ND. Proc Natl Acad Sci U S A 92 3626-3630 (1995)
  2. LINUS: a hierarchic procedure to predict the fold of a protein. Srinivasan R, Rose GD. Proteins 22 81-99 (1995)
  3. Protein secondary structural types are differentially coded on messenger RNA. Thanaraj TA, Argos P. Protein Sci 5 1973-1983 (1996)
  4. Bipartite structure of the alpha-lactalbumin molten globule. Wu LC, Peng ZY, Kim PS. Nat Struct Biol 2 281-286 (1995)
  5. Heme proteins--diversity in structural characteristics, function, and folding. Smith LJ, Kahraman A, Thornton JM. Proteins 78 2349-2368 (2010)
  6. An amino acid code for protein folding. Rumbley J, Hoang L, Mayne L, Englander SW. Proc Natl Acad Sci U S A 98 105-112 (2001)
  7. Stably folded de novo proteins from a designed combinatorial library. Wei Y, Liu T, Sazinsky SL, Moffet DA, Pelczer I, Hecht MH. Protein Sci 12 92-102 (2003)
  8. Amyloid fibril formation by a helical cytochrome. Pertinhez TA, Bouchard M, Tomlinson EJ, Wain R, Ferguson SJ, Dobson CM, Smith LJ. FEBS Lett 495 184-186 (2001)
  9. Partially folded structure of monomeric bovine beta-lactoglobulin. Molinari H, Ragona L, Varani L, Musco G, Consonni R, Zetta L, Monaco HL. FEBS Lett 381 237-243 (1996)
  10. Redesign of a four-helix bundle protein by phage display coupled with proteolysis and structural characterization by NMR and X-ray crystallography. Chu R, Takei J, Knowlton JR, Andrykovitch M, Pei W, Kajava AV, Steinbach PJ, Ji X, Bai Y. J Mol Biol 323 253-262 (2002)
  11. The HP-1 maquette: from an apoprotein structure to a structured hemoprotein designed to promote redox-coupled proton exchange. Huang SS, Koder RL, Lewis M, Wand AJ, Dutton PL. Proc Natl Acad Sci U S A 101 5536-5541 (2004)
  12. Nanodiscs: A Controlled Bilayer Surface for the Study of Membrane Proteins. McLean MA, Gregory MC, Sligar SG. Annu Rev Biophys 47 107-124 (2018)
  13. Constructing a man-made c-type cytochrome maquette in vivo: electron transfer, oxygen transport and conversion to a photoactive light harvesting maquette. Anderson JLR, Armstrong CT, Kodali G, Lichtenstein BR, Watkins DW, Mancini JA, Boyle AL, Farid TA, Crump MP, Moser CC, Dutton PL. Chem Sci 5 507-514 (2014)
  14. Conformational properties of native sperm whale apomyoglobin in solution. Lecomte JT, Sukits SF, Bhattacharya S, Falzone CJ. Protein Sci 8 1484-1491 (1999)
  15. Molten globular characteristics of the native state of apomyoglobin. Lin L, Pinker RJ, Forde K, Rose GD, Kallenbach NR. Nat Struct Biol 1 447-452 (1994)
  16. Molten globule of bovine alpha-lactalbumin at neutral pH induced by heat, trifluoroethanol, and oleic acid: a comparative analysis by circular dichroism spectroscopy and limited proteolysis. Polverino de Laureto P, Frare E, Gottardo R, Fontana A. Proteins 49 385-397 (2002)
  17. Partially folded, molten globule and molten coil states of bovine pancreatic trypsin inhibitor. Ferrer M, Barany G, Woodward C. Nat Struct Biol 2 211-217 (1995)
  18. Heme Gazing: Illuminating Eukaryotic Heme Trafficking, Dynamics, and Signaling with Fluorescent Heme Sensors. Hanna DA, Martinez-Guzman O, Reddi AR. Biochemistry 56 1815-1823 (2017)
  19. Hydrophobic sequence minimization of the alpha-lactalbumin molten globule. Wu LC, Kim PS. Proc Natl Acad Sci U S A 94 14314-14319 (1997)
  20. Thermal unfolding of tetrameric melittin: comparison with the molten globule state of cytochrome c. Hagihara Y, Oobatake M, Goto Y. Protein Sci 3 1418-1429 (1994)
  21. Effects of heme on the structure of the denatured state and folding kinetics of cytochrome b562. Garcia P, Bruix M, Rico M, Ciofi-Baffoni S, Banci L, Ramachandra Shastry MC, Roder H, de Lumley Woodyear T, Johnson CM, Fersht AR, Barker PD. J Mol Biol 346 331-344 (2005)
  22. Gatekeepers in the ribosomal protein s6: thermodynamics, kinetics, and folding pathways revealed by a minimalist protein model. Stoycheva AD, Brooks CL, Onuchic JN. J Mol Biol 340 571-585 (2004)
  23. Heme bioavailability and signaling in response to stress in yeast cells. Hanna DA, Hu R, Kim H, Martinez-Guzman O, Torres MP, Reddi AR. J Biol Chem 293 12378-12393 (2018)
  24. A differential scanning calorimetric study of the thermal unfolding of apo- and holo-cytochrome b562. Robinson CR, Liu Y, O'Brien R, Sligar SG, Sturtevant JM. Protein Sci 7 961-965 (1998)
  25. Dynamic alpha-helices: conformations that do not conform. Sandhu KS, Dash D. Proteins 68 109-122 (2007)
  26. Glucose enzyme electrode using cytochrome b(562) as an electron mediator. Okuda J, Wakai J, Yuhashi N, Sode K. Biosens Bioelectron 18 699-704 (2003)
  27. Heme is not required for Aquifex aeolicus cytochrome c(555) polypeptide folding. Yamanaka M, Mita H, Yamamoto Y, Sambongi Y. Biosci Biotechnol Biochem 73 2022-2025 (2009)
  28. Molecular dynamics simulations of apocytochrome b562--the highly ordered limit of molten globules. Laidig KE, Daggett V. Fold Des 1 335-346 (1996)
  29. How does heme axial ligand deletion affect the structure and the function of cytochrome b(562)? Kamiya N, Okimoto Y, Ding Z, Ohtomo H, Shimizu M, Kitayama A, Morii H, Nagamune T. Protein Eng 14 415-419 (2001)
  30. Heterologous synthesis of cytochrome c' by Escherichia coli is not dependent on the System I cytochrome c biogenesis machinery. Inoue H, Wakai S, Nishihara H, Sambongi Y. FEBS J 278 2341-2348 (2011)
  31. Structure of the essential Plasmodium host cell traversal protein SPECT1. Hamaoka BY, Ghosh P. PLoS One 9 e114685 (2014)
  32. Design and characterisation of an artificial DNA-binding cytochrome. Jones DD, Barker PD. Chembiochem 5 964-971 (2004)
  33. Designing heterotropically activated allosteric conformational switches using supercharging. Schnatz PJ, Brisendine JM, Laing CC, Everson BH, French CA, Molinaro PM, Koder RL. Proc Natl Acad Sci U S A 117 5291-5297 (2020)
  34. Structural organization in peptide fragments of cytochrome c by heme binding. Kang X, Carey J. J Mol Biol 285 463-468 (1999)
  35. Estimates for the potential accuracy required in realistic protein folding simulations and structure recognition experiments. de Araújo AF, Pochapsky TC. Fold Des 2 135-139 (1997)
  36. Redox tuning of cytochrome b562 through facile metal porphyrin substitution. Della Pia EA, Chi Q, Elliott M, Macdonald JE, Ulstrup J, Jones DD. Chem Commun (Camb) 48 10624-10626 (2012)
  37. Repacking of hydrophobic residues in a stable mutant of apocytochrome b562 selected by phage-display and proteolysis. Feng H, Bai Y. Proteins 56 426-429 (2004)
  38. Rational design of photosynthetic reaction center protein maquettes. Ennist NM, Stayrook SE, Dutton PL, Moser CC. Front Mol Biosci 9 997295 (2022)
  39. Lysozyme among the Lilliputians. Rose GD. Proc Natl Acad Sci U S A 97 526-528 (2000)
  40. Process of maturation of tetraheme cytochrome c3 in a Shewanella expression system. Takayama Y, Shen Y, Akutsu H. J Biochem 141 121-126 (2007)
  41. Controlled Ligand Exchange Between Ruthenium Organometallic Cofactor Precursors and a Naïve Protein Scaffold Generates Artificial Metalloenzymes Catalysing Transfer Hydrogenation. Biggs GS, Klein OJ, Maslen SL, Skehel JM, Rutherford TJ, Freund SMV, Hollfelder F, Boss SR, Barker PD. Angew Chem Int Ed Engl 60 10919-10927 (2021)
  42. Getting Deeper into the Molecular Events of Heme Binding Mechanisms: A Comparative Multi-level Computational Study of HasAsm and HasAyp Hemophores. Tiessler-Sala L, Sciortino G, Alonso-Cotchico L, Masgrau L, Lledós A, Maréchal JD. Inorg Chem 61 17068-17079 (2022)


Related citations provided by authors (1)