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Balakrishnan S, Sarma SP. Engineering Aromatic–Aromatic Interactions To Nucleate Folding in Intrinsically Disordered Regions of Proteins. Biochemistry 2017; 56:4346-4359. [DOI: 10.1021/acs.biochem.7b00437] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Swati Balakrishnan
- Molecular
Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Siddhartha P. Sarma
- Molecular
Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka 560012, India
- NMR
Research Center, Indian Institute of Science, Bangalore, Karnataka 560012, India
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2
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Basova LV, Tiktopulo EI, Kutyshenko VP, Mauk AG, Bychkova VE. Phospholipid membranes affect tertiary structure of the soluble cytochrome b5 heme-binding domain. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2008; 1778:1015-26. [PMID: 18275841 DOI: 10.1016/j.bbamem.2007.12.028] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2007] [Revised: 12/21/2007] [Accepted: 12/28/2007] [Indexed: 11/30/2022]
Abstract
The influence of charged phospholipid membranes on the conformational state of the water-soluble fragment of cytochrome b5 has been investigated by a variety of techniques at neutral pH. The results of this work provide the first evidence that aqueous solutions with high phospholipid/protein molar ratios (pH 7.2) induce the cytochrome to undergo a structural transition from the native conformation to an intermediate state with molten-globule like properties that occur in the presence of an artificial membrane surface and that leads to binding of the protein to the membrane. At other phospholipid/protein ratios, equilibrium was observed between cytochrome free in solution and cytochrome bound to the surface of vesicles. Inhibition of protein binding to the vesicles with increasing ionic strength indicated for the most part an electrostatic contribution to the stability of cytochrome b5-vesicle interactions at pH 7.2. The possible physiological role of membrane-induced conformational change in the structure of cytochrome b5 upon the interaction with its redox partners is discussed.
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Affiliation(s)
- Liana V Basova
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290 Russia
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3
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Dürr UH, Waskell L, Ramamoorthy A. The cytochromes P450 and b5 and their reductases—Promising targets for structural studies by advanced solid-state NMR spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2007; 1768:3235-59. [DOI: 10.1016/j.bbamem.2007.08.007] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2007] [Accepted: 08/08/2007] [Indexed: 02/02/2023]
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4
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Lecomte JTJ, Mukhopadhyay K, Pond MP. Structural and thermodynamic encoding in the sequence of rat microsomal cytochrome b(5). Biopolymers 2007; 89:428-42. [PMID: 18041061 DOI: 10.1002/bip.20892] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The water-soluble domain of rat microsomal cytochrome b(5) is a convenient protein with which to inspect the connection between amino acid sequence and thermodynamic properties. In the absence of its single heme cofactor, cytochrome b(5) contains a partially folded stretch of 30 residues. This region is recognized as prone to disorder by programs that analyze primary structures for such intrinsic features. The cytochrome was subjected to amino acid replacements in the folded core (I12A), in the portion that refolds only when in contact with the heme group (N57P), and in both (F35H/H39A/L46Y). Despite the difficulties associated with measuring thermodynamic quantities for the heme-bound species, it was possible to rationalize the energetic consequences of both types of replacements and test a simple equation relating apoprotein and holoprotein stability. In addition, a phenomenological relationship between the change in T(m) (the temperature at the midpoint of the thermal transition) and the change in thermodynamic stability determined by chemical denaturation was observed that could be used to extend the interpretation of incomplete holoprotein stability data. Structural information was obtained by nuclear magnetic resonance spectroscopy toward an atomic-level analysis of the effects.
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Affiliation(s)
- Juliette T J Lecomte
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA.
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5
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Nakanishi N, Takeuchi F, Okamoto H, Tamura A, Hori H, Tsubaki M. Characterization of Heme-Coordinating Histidyl Residues of Cytochrome b5 Based on the Reactivity with Diethylpyrocarbonate: A Mechanism for the Opening of Axial Imidazole Rings. ACTA ACUST UNITED AC 2006; 140:561-71. [PMID: 16963788 DOI: 10.1093/jb/mvj189] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
We investigated the reactivity of heme-coordinating imidazole with diethylpyrocarbonate using a soluble domain of cytochrome b(5). Analyses with various spectroscopic methods including MALDI-TOF-MS indicated that two axial His residues (His44 and His68) of cytochrome b(5) were protected from the modification by several factors, i.e., limited steric exposure of the axial imidazole to the solvent, the Fe-N(epsilon2) coordination bond, and protonation of the N(delta1) position by forming a hydrogen bond with its immediate surroundings. However, once N-carbethoxylation at the N(epsilon2) position of the axial His residues occurred with a higher concentration of diethylpyrocarbonate, displacement of heme prosthetic group from the protein moiety continued. Simultaneously, it facilitated the second N-carbethoxylation to take place at the N(epsilon1) position of the same imidazole ring, leading to a bis-N-carbethoxylated derivative and further to a ring-opened derivative. A similar mechanism seemed in operation for one non-axial His residue (His85), in which the N(delta1) atom works as a hydrogen acceptor in a strong hydrogen-bond and the other N(epsilon2) atom is in a protonated form, resulting in a formation of the ring-opened derivative upon treatment with a higher concentration of diethylpyrocarbonate. These results suggested that the use of diethylpyrocarbonate for MALDI-TOF-MS analysis might provide a unique method to characterize the protonation state of His residues and the strength of their hydrogen-bondings at the active site of enzymes.
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Affiliation(s)
- Nobuyuki Nakanishi
- Department of Molecular Science and Material Engineering, Graduate School of Science and Technology, Kobe University, Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501
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6
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Martin CE, Oh CS, Jiang Y. Regulation of long chain unsaturated fatty acid synthesis in yeast. Biochim Biophys Acta Mol Cell Biol Lipids 2006; 1771:271-85. [PMID: 16920014 DOI: 10.1016/j.bbalip.2006.06.010] [Citation(s) in RCA: 163] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2006] [Revised: 06/13/2006] [Accepted: 06/14/2006] [Indexed: 12/20/2022]
Abstract
Saccharomyces cerevisiae forms monounsaturated fatty acids using the ER membrane-bound Delta-9 fatty acid desaturase, Ole1p, an enzyme system that forms a double bond in saturated fatty acyl CoA substrates. Ole1p is a chimeric protein consisting of an amino terminal desaturase domain fused to cytochrome b5. It catalyzes the formation of the double bond through an oxygen-dependent mechanism that requires reducing equivalents from NADH. These are transferred to the enzyme via NADH cytochrome b5 reductase to the Ole1p cytochrome b5 domain and then to the diiron-oxo catalytic center of the enzyme. The control of OLE1 gene expression appears to mediated through the ER membrane proteins Spt23p and Mga2p. N-terminal fragments of these proteins are released by an ubiquitin/proteasome mediated proteolysis system and translocated to the nucleus where they appear to act as transcription coactivators of OLE1. OLE1 is regulated through Spt23p and Mga2p by multiple systems that control its transcription and mRNA stability in response to diverse stimuli that include nutrient fatty acids, carbon source, metal ions and the availability of oxygen.
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Affiliation(s)
- Charles E Martin
- Rutgers University, Department of Cell Biology and Neuroscience, Nelson Laboratories, 604 Allison Road, Piscataway, NJ 08854-8082, USA.
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7
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D'Auria G, Maglio O, Nastri F, Lombardi A, Mazzeo M, Morelli G, Paolillo L, Pedone C, Pavone V. Hemoprotein Models Based on a Covalent Helix-Heme-Helix Sandwich: 2. Structural Characterization of CoIII Mimochrome I δ and δ Isomers. Chemistry 2006. [DOI: 10.1002/chem.19970030306] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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8
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Wu Y, Wang Y, Qian C, Lu J, Li E, Wang W, Lu J, Xie Y, Wang J, Zhu D, Huang Z, Tang W. Solution structure of cytochromeb5mutant (E44/48/56A/D60A) and its interaction with cytochromec. ACTA ACUST UNITED AC 2003. [DOI: 10.1046/j.1432-1327.2001.02033.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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9
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Cao C, Zhang Q, Xue LL, Ma J, Wang YH, Wu H, Huang ZX. The solution structure of the oxidized bovine microsomal cytochrome b(5) mutant V61H. Biochem Biophys Res Commun 2003; 307:600-9. [PMID: 12893266 DOI: 10.1016/s0006-291x(03)01225-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Using 1488 NOE constraints, 19 stereo-specific assignments, 13 pairs of H-bond constraints, and 140 pseudo-contact shift constraints, a family of 35 structures of bovine microsomal cytochrome b(5) mutant V61H has been obtained through the program PSEUDYANA. The family has been further refined by restrained energy minimization to give a family of final structures. The RMSD values of final structures with respect to the average structure are 0.45+/-0.11 and 0.96+/-0.10A for backbone and heavy atoms, respectively. The final Deltachi(ax) and Deltachi(rh) values are 2.34 x 10(-32) and -0.67 x 10(-32)m(3), respectively. The comparisons between the solution structures of mutant V61H and WT cytochrome b(5), and X-ray structure of the mutant V61H show that the global folding of the molecule in solution is unchanged and the side-chain of His61 deviates from the heme pocket and extends into the solvent like in its crystal structure. However, the helices around the heme pocket undergo outward global displacement while their local conformations are well maintained. Meanwhile, the heme ring shows a little off the heme pocket, which accounts for the lower stability of the mutant. Additionally, the axial ligand rings counterclockwise rotate around His39 N-Fe axis due to the mutation, which is confirmed by variation of the hyperfine shifts of the heme protons of V61H compared to those of WT cytochrome b(5).
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Affiliation(s)
- Chunyang Cao
- State Key Laboratory of Bio-Organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, PR China
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10
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Wolff N, Deniau C, Létoffé S, Simenel C, Kumar V, Stojiljkovic I, Wandersman C, Delepierre M, Lecroisey A. Histidine pK(a) shifts and changes of tautomeric states induced by the binding of gallium-protoporphyrin IX in the hemophore HasA(SM). Protein Sci 2002; 11:757-65. [PMID: 11910020 PMCID: PMC2373534 DOI: 10.1110/ps.3630102] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
The HasA(SM) hemophore, secreted by Serratia marcescens, binds free or hemoprotein bound heme with high affinity and delivers it to a specific outer membrane receptor, HasR. In HasA(SM), heme is held by two loops and coordinated to iron by two residues, His 32 and Tyr 75. A third residue His 83 was shown recently to play a crucial role in heme ligation. To address the mechanistic issues of the heme capture and release processes, the histidine protonation states were studied in both apo- and holo-forms of HasA(SM) in solution. Holo-HasA(SM) was formed with gallium-protoporphyrin IX (GaPPIX), giving rise to a diamagnetic protein. By use of heteronuclear correlation NMR spectroscopy, the imidazole side-chain (15)N and (1)H resonances of the six HasA(SM) histidines were assigned and their pKa values and predominant tautomeric states according to pH were determined. We show that protonation states of the heme pocket histidines can modulate the nucleophilic character of the two axial ligands and, consequently, control the heme binding. In particular, the essential role of the His 83 is emphasized according to its direct interaction with Tyr 75.
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Affiliation(s)
- Nicolas Wolff
- Unité de Résonance Magnétique Nucléaire des Biomolécules, CNRS URA 2185, Institut Pasteur, Paris, France.
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11
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Banci L, Bertini I, Rosato A, Scacchieri S. Solution structure of oxidized microsomal rabbit cytochrome b5. Factors determining the heterogeneous binding of the heme. EUROPEAN JOURNAL OF BIOCHEMISTRY 2000; 267:755-66. [PMID: 10651812 DOI: 10.1046/j.1432-1327.2000.01054.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Cytochrome b5 is heterogeneous in solution because of the presence of two isomers (A and B), differing in the rotation of the heme plane around the axis defined by the alpha and gamma meso protons. For rabbit cytochrome b5, the A/B ratio is 5 : 1. The solution structure of the major form of the oxidized soluble fragment of rabbit microsomal cytochrome b5 (94 amino acids) is here solved through NMR spectroscopy. From 1908 NOEs, of which 1469 were meaningful, there were 246 pseudocontact shifts and 18 3J couplings, a family of 40 energy-minimized conformers were obtained with average backbone rmsd (for residues 4-84) of 0.060 +/- 0.016 nm and average target function of 0.0078 nm2, no distance violations being larger than 0.03 nm. The structure was compared with the solution structures of the A (major) and B (minor) isomers of the rat cytochrome in the oxidized form. The A/B ratio for the rat cytochrome is 1.5 : 1, despite the very high sequence similarity (93%) to the rabbit protein. This comparison has provided insights into the factors determining the distribution in solution of the two isomers differing with respect to heme orientation. It appears that residues 23 and 74 are both important in determining this distribution, through interaction of their side chains with the prosthetic group. Hydrophobic and steric interactions are the key factors in determining the relative stability of one isomer with respect to the other.
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Affiliation(s)
- L Banci
- Department of Chemistry and Centro di Risonanze Magnetiche, University of Florence, Sesto Fiorentino, Italy
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12
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Banci L, Bertini I, Ferroni F, Rosato A. Solution structure of reduced microsomal rat cytochrome b5. EUROPEAN JOURNAL OF BIOCHEMISTRY 1997; 249:270-9. [PMID: 9363779 DOI: 10.1111/j.1432-1033.1997.t01-1-00270.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The solution structure of the major form of the reduced soluble fragment of rat microsomal cytochrome b5 has been solved through 1H-NMR spectroscopy. The protein contains 98 amino acids. Proton assignment was available for residues 1-94, except 90 [Guiles, R. D., Basus, V. J., Kuntz, I. D. & Waskell, L. (1992) Biochemistry 31, 11,365-11,375] and has been confirmed. From 1722 NOEs, of which 1203 were found to be meaningful, a family of 40 energy-minimized structures has been obtained with average backbone rmsd (for residues 5-89) of 0.078 +/- 0.018 nm and average target function of 0.0045 nm2, no distance violations being larger than 0.029 nm. The structure has been compared with the X-ray structure of the oxidized rat mitochondrial isoenzyme and with that of the highly similar bovine microsomal isoenzyme in the oxidized form. The analysis of the elements of secondary structure is instructive in terms of their stability and of their occurrence in related structures, and of the capability of NMR and X-ray spectroscopy to observe them. Some detailed structural variations are noticed among the solved structures of the various isoenzymes and between solid and solution. The structural features in solution of the residues proposed to be involved in protein-protein recognition are found to be largely conserved with respect to the solid state.
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Affiliation(s)
- L Banci
- Department of Chemistry, University of Florence, Italy
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13
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Abstract
A comparison of the primary sequences of the heme binding domains of bovine and rat microsomal cytochrome reveal differences at only six residues. These residues must therefore provide the origin for the observed variation in the ratio of the heme orientational isomers, the equilibrium constant of which ranges from approximately 9 in the bovine protein to 1.6 for rat cytochrome b5. Residues 7, 20, 21, and 30 are distant from the exposed heme edge whilst Leu27 and Phe78 are located close to different parts of the porphyrin macrocycle. 1H NMR spectra of the heme and heme ligand resonances of a recombinant tobacco cytochrome b5 extending from Gly1 to Lys89 suggest, in combination with NMR data acquired for other forms of cytochrome b5 and an inspection of their sequence homology, that the identity of residue 78 influences the relative ratios of heme isomers. The Gly1-Lys89 domain of tobacco cytochrome b5 has two equally abundant heme orientational isomers but retains the leucine side chain at position 27 whilst phenylalanine 78 is replaced by tyrosine. A more direct role for residue 78 in modulating the heme ratio is shown by site directed mutagenesis of bovine microsomal cytochrome b5 where the mutation Phe78 > Tyr shifts the equilibrium constant for the heme orientational isomers from 9 to 3.5. Whilst the ratio is clearly shifted towards that exhibited by the rat protein the incomplete transition suggested the involvement of other residues. The mutation of Leu27 > Val was shown to result in a slightly smaller change in ratios of each isomer (from 9 to 4.0). Together these results point to the importance of these residues in modulating the ratio of heme isomers.
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Affiliation(s)
- G B Mortuza
- Laboratory of Structural Biochemistry, Queen Mary and Westfield College, London, UK
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14
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Liu G, Shao W, Huang X, Wu H, Tang W. Structural studies of imidazole-cytochrome c: resonance assignments and structural comparison with cytochrome c. BIOCHIMICA ET BIOPHYSICA ACTA 1996; 1277:61-82. [PMID: 8950372 DOI: 10.1016/s0005-2728(96)00038-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Two-dimensional nuclear magnetic resonance spectroscopy (2D NMR) was used to obtain extensive proton resonance assignments of Im-cyt c complex which is a possible analog of a late folding intermediate of cytochrome c. Assignments were made nearly completely for the main-chain and the side-chain protons (all except Gly29). As starting points for the assignment of the Im-cyt c, a limited set of protons was initially assigned by use of 2D NMR magnetization transfer methods to correlated resonances in the Im-cyt c with assigned resonances in the native cyt c. The subsequent search focused on recognition of main-chain NOE connectivity patterns, with use of previously assigned residues to place NOE-connected segments within the amino acid sequence. The observed patterns of main-chain NOEs provided some structural information and suggested potentially significant differences between Im-cyt c and the native cyt c. Differences in NOEs involving side-chain protons were reported and analyzed. There was evidence for conformational changes induced by the breakage of Fe-S bond. It was concluded that the Im-cyt c had undergone a rearrangement of several regions forming the heme pocket of the protein. The structural understanding of these effects of the mutation may be essential to elucidate the changes in function and kinetic mechanism of cyt c folding.
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Affiliation(s)
- G Liu
- State Key Laboratory of Coordination Chemistry, Nanjing University, China
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15
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Guiles RD, Sarma S, DiGate RJ, Banville D, Basus VJ, Kuntz ID, Waskell L. Pseudocontact shifts used in the restraint of the solution structures of electron transfer complexes. NATURE STRUCTURAL BIOLOGY 1996; 3:333-9. [PMID: 8599759 DOI: 10.1038/nsb0496-333] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The geometry of the ferricytochrome b5-ferricytochrome c complex has been analysed using long-range interprotein paramagnetic dipolar shifts. Heteronuclear filtered NMR spectra of samples containing 15N-labelled cytochrome b5 in complex with unlabelled cytochrome c allowed unambiguous assessment of pseudocontact shifts relative to diamagnetic reference states. Because pseudocontact shifts can be observed for protons as much as 20 A from the paramagnetic centre, this approach allows study of electron transfer proteins in fast exchange. Our findings provide the first physical evidence confirming hypotheses presented in previous theoretical studies. This absence of certain predicted shifts that are expected based on the best fit to a static model of the complex suggests that cytochrome b5 is more dynamic in solution than in the crystal, in agreement with molecular dynamics simulations.
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Affiliation(s)
- R D Guiles
- Department of Pharmaceutical Sciences, University of Maryland at Baltimore, 21201, USA
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16
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Storch EM, Daggett V. Molecular dynamics simulation of cytochrome b5: implications for protein-protein recognition. Biochemistry 1995; 34:9682-93. [PMID: 7626638 DOI: 10.1021/bi00030a005] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Cytochrome b5 participates in electron-transfer reactions with a variety of different proteins. To explore how this protein might discern between structurally varied proteins, we have performed a molecular dynamics simulation focusing on its structural stability and dynamic behavior in solution. The protein was simulated in water at 298 K and pH 6.9 for 2.5 ns. The protein deviated significantly from the crystal structure midway through the simulation, but ultimately the crystalline conformation was regained. The simulation was at all times well behaved as judged by comparison to structural NMR data obtained in solution. One region of the protein backbone that deviated from the crystal conformation contains acidic residues implicated in electrostatic-based protein-protein recognition. The mobility in this region caused the protein to display different patterns of residues at the surface with time, as well as the formation of a large cleft partially exposing the hydrophobic core lining the heme pocket. Furthermore, the position and cyclical formation of this cleft suggest that hydrophobic interactions may be important in protein-protein recognition events and possibly even electron transfer, as the cleft allows for easy access to the heme group. These results indicate that thermal motion could provide a low-energy mechanism for controlling recognition events. Thus, the dynamical behavior observed through the varying solution conformations sampled may be important in influencing the diverse range of protein-protein interactions in which cytochrome b5 participates.
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Affiliation(s)
- E M Storch
- Department of Medicinal Chemistry, University of Washington, Seattle 98195-7610, USA
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17
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Gill DS, Roush DJ, Willson RC. Tertiary structure of the heme-binding domain of rat cytochrome b5 based on homology modeling. J Biomol Struct Dyn 1994; 11:1003-15. [PMID: 7946056 DOI: 10.1080/07391102.1994.10508048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The in vitro complexes formed between cytochrome b5 and other proteins (e.g. cytochrome c) have served as a useful means to probe electrostatic contributions to macromolecular recognition. Extensive experimentation has been carried out to test the specificity and stability of these complexes, including site-directed mutagenesis based on the heterologous expression of rat cytochrome b5 in E. coli. Despite this interest, there has not been a determination of the complete structure of cytochrome b5. Here we report coordinates for the complete tertiary structure of the heme-binding domain of rat cytochrome b5 based on homology modeling. Protein Data Bank (PDB) coordinates derived from the crystal structure of the highly homologous bovine cytochrome b5 were used for main chain scaffolding. Secondary structures for the termini missing in the bovine structure were generated using homologous sequences derived from an exhaustive search of the PDB database. The model structure was solvated and further refined using energy minimization techniques. The N-terminal residues of the model appear to be in a beta sheet conformation while the carboxy terminus is in a helical conformation. The rest of the rat model is folded virtually identically to the bovine x-ray crystal structure (r.m.s. deviation 1.28 A), despite six sequence differences between the two cores. This homology-based structure should be useful for structure-function analyses of molecular recognition involving cytochrome b5.
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Affiliation(s)
- D S Gill
- Department of Chemical Engineering, University of Houston, TX 77204-4792
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18
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Abstract
The family of b5-like cytochromes encompasses, besides cytochrome b5 itself, hemoprotein domains covalently associated with other redox proteins, in flavocytochrome b2 (L-lactate dehydrogenase), sulfite oxidase and assimilatory nitrate reductase. A comparison of about 40 amino acid sequences deposited in data banks shows that eight residues are invariant and about 15 positions carry strongly conservative substitutions. Examination of the location of these invariant and conserved positions in the light of the three-dimensional structures of beef cytochrome b5 and S cerevisiae flavocytochrome b2 suggests a strongly conserved protein structure for the b5-like heme-binding domain throughout evolution. Numerous NMR studies have demonstrated the existence of a positional isomerism for the heme, which involves both a 180 degree-rotation around the heme alpha,gamma-meso carbon atoms and a rotation through an axis normal to the heme plane at the iron. NMR studies did not detect significant differences in protein structure between reduced and oxidized states, or between species. The role of a number of side chains was probed by site-directed mutagenesis. Studies of complex formation and of electron transfer rates between cytochrome b5 and redox partners have led to the idea that complexation is driven by electrostatic forces, that it is generally the exposed heme edge which makes contact with electron donors and acceptors, but that there are multiple overlapping sites within this general area. For the bi- and trifunctional members of the family, extrapolation of available data would suggest a mobile heme-binding domain within a complex structure. In these cases the existence of a single interaction area for both electron donor and acceptor, or of two different ones, remains open to discussion.
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Affiliation(s)
- F Lederer
- CNRS-URA 1461, Hôpital Necker, Paris, France
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19
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Guiles RD, Basus VJ, Sarma S, Malpure S, Fox KM, Kuntz ID, Waskell L. Novel heteronuclear methods of assignment transfer from a diamagnetic to a paramagnetic protein: application to rat cytochrome b5. Biochemistry 1993; 32:8329-40. [PMID: 8347629 DOI: 10.1021/bi00083a037] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
15N and 1H resonance assignments for backbone and side-chain resonances of both equilibrium forms of rat ferricytochrome b5 have been obtained, using a combination of novel heteronuclear assignment transfer methods from the known assignments of the diamagnetic protein [Guiles, R. D., Basus, V. J., Kuntz, I. D., & Waskell, L. A. (1992) Biochemistry 31, 11365-11375] and computational methods which depend on an accurate determination of the orientation of the components of the susceptibility tensor. The transfer of amide proton resonance assignments takes advantage of the apparent insensitivity of amide 15N resonances to pseudocontact effects, evident in overlays of 15N-1H heteronuclear correlation spectra. Amide-proton resonance assignments tentatively transferred from the known diamagnetic assignments to the paramagnetic form of the protein were confirmed using conventional assignment strategies employing 600-MHz COSY, HOHAHA, and NOESY spectra of the oxidized protein. As was observed in rat ferrocytochrome b5, more than 40% of all residues exhibited NMR detectable heterogeneity due to the two different orientations of the heme. Complete assignment of both forms enabled accurate determination of the orientation of the susceptibility tensor for both conformations of the heme. The orientation of the z-component of the susceptibility tensors for the two forms are indistinguishable, while the in-plane components appear to differ by about 6 degrees. Differences in the orientation of the in-plane susceptibility components are undoubtedly due dominantly to the relative axial rotation of the heme of between 5 degrees and 10 degrees indicated by the NOESY contacts to the protein observed in the spectra of the ferrocytochrome [Guiles, R. D., Basus, V. J., Kuntz, I. D., & Waskell, L. A. (1992) Biochemistry 31, 11365-11375; Pochapsky, T. C., Sligar, S. G., McLachlan, S. J., & LaMar, G. N. (1990) J. Am. Chem. Soc. 112, 5258-5263].
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Affiliation(s)
- R D Guiles
- Department of Pharmaceutical Chemistry, University of California, San Francisco 94143
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Wishart DS, Sykes BD, Richards FM. Relationship between nuclear magnetic resonance chemical shift and protein secondary structure. J Mol Biol 1991; 222:311-33. [PMID: 1960729 DOI: 10.1016/0022-2836(91)90214-q] [Citation(s) in RCA: 1503] [Impact Index Per Article: 45.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
An analysis of the 1H nuclear magnetic resonance chemical shift assignments and secondary structure designations for over 70 proteins has revealed some very strong and unexpected relationships. Similar studies, performed on smaller databases, for 13C and 15N chemical shifts reveal equally strong correlations to protein secondary structure. Among the more interesting results to emerge from this work is the finding that all 20 naturally occurring amino acids experience a mean alpha-1H upfield shift of 0.39 parts per million (from the random coil value) when placed in a helical configuration. In a like manner, the alpha-1H chemical shift is found to move downfield by an average of 0.37 parts per million when the residue is placed in a beta-strand or extended configuration. Similar changes are also found for amide 1H, carbonyl 13C, alpha-13C and amide 15N chemical shifts. Other relationships between chemical shift and protein conformation are also uncovered; in particular, a correlation between helix dipole effects and amide proton chemical shifts as well as a relationship between alpha-proton chemical shifts and main-chain flexibility. Additionally, useful relationships between alpha-proton chemical shifts and backbone dihedral angles as well as correlations between amide proton chemical shifts and hydrogen bond effects are demonstrated.
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Affiliation(s)
- D S Wishart
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511
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21
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Wishart DS, Sykes BD, Richards FM. Simple techniques for the quantification of protein secondary structure by 1H NMR spectroscopy. FEBS Lett 1991; 293:72-80. [PMID: 1959674 DOI: 10.1016/0014-5793(91)81155-2] [Citation(s) in RCA: 88] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Previous work by Wishart et al. (in press) and others [(1989) J. Magn. Reson. 83, 441-449; (1990) J. Magn. Reson. 90, 165-176] has shown a strong tendency for protein secondary structure to be manifested in 1H NMR chemical shifts. Based on these earlier results, two techniques have been developed for the quantification of secondary structure in proteins. Both methods allow for the rapid and accurate determination of the percent content of helix, coil, and beta-strand based on the integration (or peak enumeration) of selected portions of either 1-D or 2-D 1H NMR spectra. These new and very simple procedures have been found to compare quite favorably to other well established techniques for secondary structure determination such as CD, Raman and IR spectroscopy.
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Affiliation(s)
- D S Wishart
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511
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22
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Whitford D, Gao Y, Pielak GJ, Williams RJ, McLendon GL, Sherman F. The role of the internal hydrogen bond network in first-order protein electron transfer between Saccharomyces cerevisiae iso-1-cytochrome c and bovine microsomal cytochrome b5. EUROPEAN JOURNAL OF BIOCHEMISTRY 1991; 200:359-67. [PMID: 1653702 DOI: 10.1111/j.1432-1033.1991.tb16193.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
An internal water molecule (designated WAT166) is found in iso-1-cytochrome c which is part of a redox-state-dependent hydrogen bond network. The position of this water molecule with respect to the polypeptide fold can be altered or even displaced by site-directed mutagenesis leading to structural perturbations and associated changes in redox potential. Using saturation transfer 1H-NMR methods, this study measures changes in the electron transfer reactivity for three variants of yeast iso-1-cytochromes c in which the position of this water molecule is altered. In particular, the reverse electron transfer rate is measured within a complex formed between either wild-type or variant yeast iso-1-cytochromes c and the tryptic fragment of bovine liver microsomal cytochrome b5. For three variants of yeast iso-1-cytochrome c the rate constants measured by saturation transfer are wild-type (Asn52, E0 = 270 mV, kex = 0.3 s-1), Asn52----Ala (E0 = 240 mV, kex = 0.6 s-1), Asn52----Ile (E0 = 220 mV, kex = 1.0 s-1). The first-order rates are compared with that of a fourth variant Phe82----Gly which has been measured previously (E0 = 220 mV, kex = 0.7 s-1). An analysis of the variation in the observed cross exchange rate using Marcus theory shows that these changes can be predicted quantitatively by the shift in redox potential that accompanies mutagenesis. So, although the perturbation of the internal water molecule by mutagenesis alters both the structure and redox potential of cytochrome c, surprisingly it does not significantly influence the intrinsic electron transfer reactivity of the protein. Studies of the activation parameters suggests that a variation of temperature changes both delta G* and also the prefactor. These data are discussed in terms of models involving dynamic molecular recognition between proteins.
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Affiliation(s)
- D Whitford
- Department of Biochemistry, University of Oxford, England
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Gibson BW, Falick AM, Lipka JJ, Waskell LA. Mass spectrometric analysis of rabbit and bovine trypsin-solubilized cytochrome b5. JOURNAL OF PROTEIN CHEMISTRY 1990; 9:695-703. [PMID: 2073321 DOI: 10.1007/bf01024764] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The sequence and blocking group of the amino-terminal 15 amino acids of rabbit trypsin-solubilized cytochrome b5 were determined by liquid secondary ion mass spectrometry (LSIMS) and tandem mass spectrometry (MS/MS). The molecular weights of peptides generated from a Staphylococcus aureus V8 protease digest of this protein were determined by LSIMS analysis and the two peptides containing the blocked amino-terminus were sequenced by tandem mass spectrometry to yield the sequence; N-acetyl-Ala-Ala-Glu-Ser-Asp-Lys-Asp-Val-Lys-Tyr-Tyr-Thr-Leu-Glu-Glu. Comparison of this sequence with a recently reported cDNA sequence (Dariush et al., 1988) indicates that Gln at position 3 is selectively deamidated, although no other discrepancies were found. Intact rabbit and bovine trypsin-solubilized cytochrome b5 were also analyzed by LSIMS on a high-field mass spectrometer equipped with a diode array detector. Mass measurement of the unresolved protonated molecular ion peak tops gave average molecular weights of 9462.2 +/- 2 and 9502.3 +/- 2 for bovine and rabbit trypsin-solubilized cytochrome b5, respectively. In both cases, these molecular weights correspond to a cytochrome b5 fragment consisting of amino acids Asp(7)-Arg(88). The average molecular weight for the rabbit amino-terminal-blocked form of trypsin-solubilized cytochrome b5 was found to be 10,144.5 +/- 2, which was consistent with the molecular weight predicted for the extended N-acetylated form (residues 1-88) of Mr 10,146.1.
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Affiliation(s)
- B W Gibson
- Department of Pharmaceutical Chemistry, University of California, San Francisco 94143-0446
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Veitch NC, Whitford D, Williams RJ. An analysis of pseudocontact shifts and their relationship to structural features of the redox states of cytochrome b5. FEBS Lett 1990; 269:297-304. [PMID: 2401354 DOI: 10.1016/0014-5793(90)81180-v] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The assignment of proton resonances in both redox states of a heme protein is necessary for the evaluation of pseudocontact shift data. Many new assignments are presented here for cytochrome b5, particularly in the paramagnetic oxidised state, thereby allowing both the calculation of electronic g-tensor values with the magnetic axis orientation and a comparison of observed and calculated pseudocontact shifts utilising a computational procedure. The possible redox linked conformational changes are found to be minimal in contrast with cytochrome c although the procedure additionally highlights aspects of the mobility of certain residues in cytochrome b5. In this respect the residue Gly-42 appears mobile both by this method and by the observation from NMR spectra of a major and minor conformation in this region.
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Affiliation(s)
- N C Veitch
- Inorganic Chemistry Laboratory, University of Oxford, UK
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