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White MA, Li S, Tsalkova T, Mei FC, Liu T, Woods VL, Cheng X. Structural analyses of a constitutively active mutant of exchange protein directly activated by cAMP. PLoS One 2012; 7:e49932. [PMID: 23189173 PMCID: PMC3506601 DOI: 10.1371/journal.pone.0049932] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2012] [Accepted: 10/16/2012] [Indexed: 01/08/2023] Open
Abstract
Exchange proteins directly activated by cAMP (EPACs) are important allosteric regulators of cAMP-mediated signal transduction pathways. To understand the molecular mechanism of EPAC activation, we have combined site-directed mutagenesis, X-ray crystallography, and peptide amide hydrogen/deuterium exchange mass spectrometry (DXMS) to probe the structural and conformational dynamics of EPAC2-F435G, a constitutively active EPAC2 mutant. Our study demonstrates that conformational dynamics plays a critical role in cAMP-induced EPAC activation. A glycine mutation at 435 position shifts the equilibrium of conformational dynamics towards the extended active conformation.
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Affiliation(s)
- Mark A. White
- Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch, Galveston, Texas, United States of America
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Sheng Li
- Department of Medicine and Biomedical Sciences Graduate program, University of California San Diego, La Jolla, California United States of America
| | - Tamara Tsalkova
- Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch, Galveston, Texas, United States of America
- Department of Pharmacology and Toxicology, The University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Fang C. Mei
- Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch, Galveston, Texas, United States of America
- Department of Pharmacology and Toxicology, The University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Tong Liu
- Department of Medicine and Biomedical Sciences Graduate program, University of California San Diego, La Jolla, California United States of America
| | - Virgil L. Woods
- Department of Medicine and Biomedical Sciences Graduate program, University of California San Diego, La Jolla, California United States of America
| | - Xiaodong Cheng
- Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch, Galveston, Texas, United States of America
- Department of Pharmacology and Toxicology, The University of Texas Medical Branch, Galveston, Texas, United States of America
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Abstract
betaB2-crystallin, the major component of beta-crystallin, is a dimer at low concentrations but can form oligomers under physiological conditions. The interaction domains have been speculated to be the beta-sheets, each of which is formed by two or more beta-strands. betaB2-crystallin consists of 16 beta-strands, 8 in the N-terminal domain and 8 in the C-terminal domain. Domain interaction sites may be removed by destroying the beta-strands, which can be done by site-specific mutations, substituting the beta-formers (Val, Phe, Leu) with Glu or Asn, strong beta-breakers. We have cloned the following beta-strand-deleted mutants, I20E, L34E, V54E, V60E, V73E, L97E, I109E, I124E, V144E, V152E, L162E, L165E, and V187E and their corresponding X --> Asn mutants. We also made two mutants, V46E and V129E, that were not on the beta-strand as controls. Disruption of protein-protein interactions was screened by a mammalian two-hybrid system assay. Protein-protein interactions decreased for all beta-strand-deleted mutants except I20E, L34E, and L162E mutants; this effect was not seen in the two mutant controls, V46E and V129E. The sequences around Val-54, Val-60, Val-73, and Leu-97 in the N-terminal region and Ile-109, Ile-124, Val-144, Val-152, Leu-165, and Val-187 in the C-terminal region that formed beta-strands appear to be important in dimerization. Some selected mutant proteins that showed strong (V46E and V129E) and reduced (V60E, V144E, V60N, and V144N) interactions were expressed in bacterial culture and were studied with spectroscopy and chromatography. The V60E and V144E mutants were found to be partially unfolded and incapable of forming a complete dimer.
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Affiliation(s)
- Bing-Fen Liu
- Center for Ophthalmic Research/Surgery, Brigham and Women's Hospital, and Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts 02115, USA
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Bunting KA, Cooper JB, Tickle IJ, Young DB. Engineering of an intersubunit disulfide bridge in the iron-superoxide dismutase of Mycobacterium tuberculosis. Arch Biochem Biophys 2002; 397:69-76. [PMID: 11747311 DOI: 10.1006/abbi.2001.2635] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
With the aim of enhancing interactions involved in dimer formation, an intersubunit disulfide bridge was engineered in the superoxide dismutase enzyme of Mycobacterium tuberculosis. Ser-123 was chosen for mutation to cysteine since it resides at the dimer interface where the serine side chain interacts with the same residue in the opposite subunit. Gel electrophoresis and X-ray crystallographic studies of the expressed mutant confirmed formation of the disulfide bond under nonreducing conditions. However, the mutant protein was found to be less stable than the wild type as judged by susceptibility to denaturation in the presence of guanidine hydrochloride. Decreased stability probably results from formation of a disulfide bridge with a suboptimal torsion angle and exclusion of solvent molecules from the dimer interface.
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Affiliation(s)
- Karen A Bunting
- Department of Crystallography, Birkbeck College, Malet Street, London WC1E 7HX, United Kingdom.
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Kamińska A, Kowalska M. A study of the lens crystallin's photodegradation in the presence of β-carotene. Polym Degrad Stab 1999. [DOI: 10.1016/s0141-3910(99)00046-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Hülsmeyer M, Hecht HJ, Niefind K, Hofer B, Eltis LD, Timmis KN, Schomburg D. Crystal structure of cis-biphenyl-2,3-dihydrodiol-2,3-dehydrogenase from a PCB degrader at 2.0 A resolution. Protein Sci 1998; 7:1286-93. [PMID: 9655331 PMCID: PMC2144030 DOI: 10.1002/pro.5560070603] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
cis-Biphenyl-2,3-dihydrodiol-2,3-dehydrogenase (BphB) is involved in the aerobic biodegradation of polychlorinated biphenyls (PCBs). The crystal structure of the NAD+-enzyme complex was determined by molecular replacement and refined to an R-value of 17.9% at 2.0 A. As a member of the short-chain alcohol dehydrogenase/reductase (SDR) family, the overall protein fold and positioning of the catalytic triad in BphB are very similar to those observed in other SDR enzymes, although small differences occur in the cofactor binding site. Modeling studies indicate that the substrate is bound in a deep hydrophobic cleft close to the nicotinamide moiety of the NAD+ cofactor. These studies further suggest that Asn143 is a key determinant of substrate specificity. A two-step reaction mechanism is proposed for cis-dihydrodiol dehydrogenases.
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Affiliation(s)
- M Hülsmeyer
- National Institute for Biotechnological Research (GBF), Department of Structure Research, Braunschweig, Germany
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Wright G, Basak AK, Wieligmann K, Mayr EM, Slingsby C. Circular permutation of betaB2-crystallin changes the hierarchy of domain assembly. Protein Sci 1998; 7:1280-5. [PMID: 9655330 PMCID: PMC2144035 DOI: 10.1002/pro.5560070602] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The betagamma-crystallins form a superfamily of eye lens proteins comprised of multiple Greek motifs that are symmetrically organized into domains and higher assemblies. In the betaB2-crystallin dimer each polypeptide folds into two similar domains that are related to monomeric gamma-crystallin by domain swapping. The crystal structure of the circularly permuted two-domain betaB2 polypeptide shows that permutation converts intermolecular domain pairing into intramolecular pairing. However, the dimeric permuted protein is, in fact, half a native tetramer. This result shows how the sequential order of domains in multi-domain proteins can affect quaternary domain assembly.
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Affiliation(s)
- G Wright
- Birkbeck College, Department of Crystallography, London, United Kingdom
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Norledge BV, Mayr EM, Glockshuber R, Bateman OA, Slingsby C, Jaenicke R, Driessen HP. The X-ray structures of two mutant crystallin domains shed light on the evolution of multi-domain proteins. NATURE STRUCTURAL BIOLOGY 1996; 3:267-74. [PMID: 8605629 DOI: 10.1038/nsb0396-267] [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
We use protein engineering and crystallography to simulate aspects of the early evolution of beta gamma-crystallins by observing how a single domain oligomerizes in response to changes in a sequence extension. The crystal structure of the C-terminal domain of gamma beta-crystallin with its four-residue C-terminal extension shows that the domain does not form a symmetric homodimer analogous to the two-domain pairing in beta gamma-crystallins. Instead the C-terminal extension now forms heterologous interactions with other domains leading to the solvent exposure of the natural hydrophobic interface with a consequent loss in protein solubility. However, this domain truncated by just the C-terminal tyrosine forms a symmetric homodimer of domains in the crystal lattice.
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Affiliation(s)
- B V Norledge
- Department of Crystallography, Birkbeck College, London, UK
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Husain J, Tickle IJ, Wood SP. Crystal structure of momordin, a type I ribosome inactivating protein from the seeds of Momordica charantia. FEBS Lett 1994; 342:154-8. [PMID: 8143869 DOI: 10.1016/0014-5793(94)80491-5] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
A type I ribosome-inactivating protein, extracted and purified from M. charantia seeds, was crystallised by vapour diffusion with polyethylene glycol at pH 7.2. X-ray data were collected to 2.1 A resolution and the structure solved by molecular replacement using the A-chain coordinates of ricin. The overall fold of the protein is similar to ricin but there are differences in secondary structure, on the surface and in the active site cleft. These differences are probably due in part to the evolution of the protein without a B-chain partner. The most extensive reorganisation occurs at the C-terminus whereas Tyr70 shows the greatest change in the active site cleft.
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Affiliation(s)
- J Husain
- Department of Crystallography, Birkbeck College, London, UK
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Nalini V, Bax B, Driessen H, Moss DS, Lindley PF, Slingsby C. Close packing of an oligomeric eye lens beta-crystallin induces loss of symmetry and ordering of sequence extensions. J Mol Biol 1994; 236:1250-8. [PMID: 8120900 DOI: 10.1016/0022-2836(94)90025-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
beta-Crystallins are oligomeric eye lens proteins that are related to monomeric gamma-crystallins. The main sequence difference between the two families is the presence of sequence extensions in the beta-crystallins. A major question concerns the role that these extensions play in mediating interactions at the high protein concentrations found in the lens. The predominant beta-crystallin polypeptide, beta B2, can be crystallized in two different space groups, I222 and C222. The I222 crystal structure revealed that the protein packed as a tetramer with perfect 222 symmetry but that the extensions were disordered. The X-ray structure of the C222 lattice of beta B2 has now been refined at 3.3 A, the structure analysed and compared with the I222 lattice. The protein is also a tetramer with 222 symmetry in the C222 lattice but differs in that parts of the N-terminal extensions have been visualized. In the asymmetric unit of the C222 lattice there are four subunits, each comprising a single polypeptide chain, in which certain flexible loops in the N-terminal domains and the N-terminal extensions have various conformations. The tetramers in the C222 lattice are more tightly packed than in the I222 form. Analysis of the tetramer contacts shows that the sites of interaction break the 222 symmetry of the tetramers. The N-terminal extensions play a major role in directing interactions between tetramers. One of the N-terminal extensions interacts with a hydrophobic patch on the N-terminal domain of another tetramer. These crystallographic observations obtained over a physiological concentration range indicate how, in beta-crystallin oligomers, the N-terminal extensions of beta B2 can switch from interacting with water to interacting with protein depending on their relative concentrations. This could be useful in maintaining a gradient of refractive index.
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Affiliation(s)
- V Nalini
- Laboratory of Molecular Biology, Birkbeck College, London University, UK
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Koenig SH, Brown RD, Kenworthy AK, Magid AD, Ugolini R. Intermolecular protein interactions in solutions of bovine lens beta L-crystallin. Results from 1/T1 nuclear magnetic relaxation dispersion profiles. Biophys J 1993; 64:1178-86. [PMID: 8388267 PMCID: PMC1262435 DOI: 10.1016/s0006-3495(93)81483-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
We report the magnetic field dependence of 1/T1 of solvent water protons and deuterons (nuclear magnetic relaxation dispersion, or NMRD, profiles) for solutions of steer lens beta L-crystallin. Such data allow the study of intermolecular protein interactions over a wide concentration range, here 1-34% vol/vol, by providing a measure of the rotational relaxation time of solute macromolecules. We conclude that, for approximately less than 5% protein, the solute particles are noncompact, with a rotationally averaged volume approximately three times that of a compact 60-kD sphere. (Earlier results for alpha-crystallin, approximately 1,000 kD, from optical and osmotic measurements (Vérétout and Tardieu, 1989. J. Mol. Biol. 205:713-728), show a similar, approximately twofold, effect). At intermediate concentrations, to approximately 20% protein, there is evidence for limited association or oligomerization, as found for the structurally related gamma II-crystallin (Koenig et al. 1990. Biophys. J. 57:461-469), to a limiting size about two-thirds that of alpha-crystallin. The difference in NMRD behavior of the three classes of crystallins is consonant with their differing osmotic properties (Vérétout and Tardieu. J. Mol. Biol. 1989, 205:713-728; Kenworthy, McIntosh, and Magid. Biophys. J. 1992. 61:A477; Tardieu et al. 1992. Eur. Biophys. J. 21:1-12). We indicate how the unusual structures and interactions of these three classes of proteins can be combined to optimize transparency and minimize colloid osmotic difficulties in eye lens.
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Affiliation(s)
- S H Koenig
- IBM T. J. Watson Research Center, Yorktown Heights, New York 10598
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Dhanaraj V, Dealwis CG, Frazao C, Badasso M, Sibanda BL, Tickle IJ, Cooper JB, Driessen HP, Newman M, Aguilar C. X-ray analyses of peptide-inhibitor complexes define the structural basis of specificity for human and mouse renins. Nature 1992; 357:466-72. [PMID: 1608447 DOI: 10.1038/357466a0] [Citation(s) in RCA: 102] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
X-ray analyses have defined the three-dimensional structures of crystals of mouse and human renins complexed with peptide inhibitors at resolutions of 1.9 and 2.8 A, respectively. The exquisite specificity of renin arises partly from ordered loop regions at the periphery of the binding cleft. Although the pattern of main-chain hydrogen bonding in other aspartic proteinase inhibitor complexes is conserved in renins, differences in the positions of secondary structure elements (particularly helices) also lead to improved specificity in renins for angiotensinogen substrates.
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Affiliation(s)
- V Dhanaraj
- Department of Crystallography, Birkbeck College, London, UK
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