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Structure—activity relationship of a recombinant hybrid Manganese superoxide dismutase of Staphylococcus saprophyticus / S. equorum. Int J Biol Macromol 2017; 98:222-227. [DOI: 10.1016/j.ijbiomac.2017.01.096] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 01/11/2017] [Accepted: 01/23/2017] [Indexed: 11/24/2022]
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2
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Suresh A, Karthikraja V, Lulu S, Kangueane U, Kangueane P. A decision tree model for the prediction of homodimer folding mechanism. Bioinformation 2009; 4:197-205. [PMID: 20461159 PMCID: PMC2859576 DOI: 10.6026/97320630004197] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2009] [Accepted: 11/09/2009] [Indexed: 11/25/2022] Open
Abstract
The formation of protein homodimer complexes for molecular catalysis and regulation is fascinating. The homodimer formation through 2S (2 state), 3SMI (3 state with monomer intermediate) and 3SDI (3 state with dimer intermediate) folding mechanism is known for 47 homodimer structures. Our dataset of forty-seven homodimers consists of twenty-eight 2S, twelve 3SMI and seven 3SDI. The dataset is characterized using monomer length, interface area and interface/total (I/T) residue ratio. It is found that 2S are often small in size with large I/T ratio and 3SDI are frequently large in size with small I/T ratio. Nonetheless, 3SMI have a mixture of these features. Hence, we used these parameters to develop a decision tree model. The decision tree model produced positive predictive values (PPV) of 72% for 2S, 58% for 3SMI and 57% for 3SDI in cross validation. Thus, the method finds application in assigning homodimers with folding mechanism.
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Affiliation(s)
- Abishek Suresh
- Biomedical Informatics, Pondicherry 607402
- AIMST University, Semeling 08100, Malaysia
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3
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Multistate folding of a hyperthermostable Fe-superoxide dismutase (TcSOD) in guanidinium hydrochloride: The importance of the quaternary structure. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2008; 1784:445-54. [DOI: 10.1016/j.bbapap.2007.12.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2007] [Revised: 11/15/2007] [Accepted: 12/03/2007] [Indexed: 11/22/2022]
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4
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He Y, Qin S, Pan XM. A novel procedure for identification of the folding/unfolding patterns of dimeric proteins. J Theor Biol 2008; 250:461-7. [PMID: 18022646 DOI: 10.1016/j.jtbi.2007.10.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2007] [Revised: 09/23/2007] [Accepted: 10/12/2007] [Indexed: 11/20/2022]
Abstract
The unfolding of proteins has been widely used for investigating the thermodynamic properties of monomeric proteins but has been used infrequently for dimeric (or oligomeric) proteins, because of the inherent cooperation of denaturation and dissociation of the dimers (oligomers). Here, we introduce a thermodynamic parameter K(obs) to discriminate the diverse folding patterns of dimeric proteins. K(obs) remains constant as the protein concentration increases for the true one-step curve of unfolding pattern (A), increases and reaches a plateau for one-step curves with monomeric intermediate pattern (B), and increases steadily with no plateau for one-step curves with dimeric intermediate pattern (C).
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Affiliation(s)
- Yun He
- The Key Laboratory of Bioinformatics, Ministry of Education, Department of Biological Sciences and Biotechnology, Tsinghua University, Beijing 100084, China
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5
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Li L, Gunasekaran K, Gan JGK, Zhanhua C, Shapshak P, Sakharkar MK, Kangueane P. Structural features differentiate the mechanisms between 2S (2 state) and 3S (3 state) folding homodimers. Bioinformation 2005; 1:42-9. [PMID: 17597851 PMCID: PMC1891634 DOI: 10.6026/97320630001042] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2005] [Revised: 08/28/2005] [Accepted: 09/02/2005] [Indexed: 11/23/2022] Open
Abstract
The formation of homodimer complexes for interface stability, catalysis and regulation is intriguing. The mechanisms of homodimer complexations are even more interesting. Some homodimers form without intermediates (two-state (2S)) and others through the formation of stable intermediates (three-state (3S)). Here, we analyze 41 homodimer (25 2S and 16 3S) structures determined by X-ray crystallography to estimate structural differences between them. The analysis suggests that a combination of structural properties such as monomer length, subunit interface area, ratio of interface to interior hydrophobicity can predominately distinguish 2S and 3S homodimers. These findings are useful in the prediction of homodimer folding and binding mechanisms using structural data.
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Affiliation(s)
- Lei Li
- School of Mechanical and Aerospace Engineering,
Nanyang Technological University, Singapore 639798
| | - Kannan Gunasekaran
- Basic Research Program, SAIC-Frederick, Inc., Laboratory of Experimental and
Computational Biology, National Cancer Institute, Frederick, MD 21702, USA
| | - Jacob Gah-Kok Gan
- School of Mechanical and Aerospace Engineering,
Nanyang Technological University, Singapore 639798
| | - Cui Zhanhua
- School of Mechanical and Aerospace Engineering,
Nanyang Technological University, Singapore 639798
| | - Paul Shapshak
- Dementia/HIV Laboratory, Elliot Building Room 2013, Department of Psychiatry
and Beh Sci, University of Miami Miller Medical School, 1800 NW 10th Avenue, Miami, Florida 33136
| | - Meena Kishore Sakharkar
- School of Mechanical and Aerospace Engineering,
Nanyang Technological University, Singapore 639798
| | - Pandjassarame Kangueane
- School of Mechanical and Aerospace Engineering,
Nanyang Technological University, Singapore 639798
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6
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Lindberg MJ, Byström R, Boknäs N, Andersen PM, Oliveberg M. Systematically perturbed folding patterns of amyotrophic lateral sclerosis (ALS)-associated SOD1 mutants. Proc Natl Acad Sci U S A 2005; 102:9754-9. [PMID: 15987780 PMCID: PMC1174986 DOI: 10.1073/pnas.0501957102] [Citation(s) in RCA: 188] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2005] [Indexed: 11/18/2022] Open
Abstract
Amyotrophic lateral sclerosis is a neurodegenerative syndrome associated with 114 mutations in the gene encoding the cytosolic homodimeric enzyme Cu/Zn superoxide dismutase (SOD). In this article, we report that amyotrophic lateral sclerosis-associated SOD mutations with distinctly different disease progression can be rationalized in terms of their folding patterns. The mutations are found to perturb the protein in multiple ways; they destabilize the precursor monomers (class 1), weaken the dimer interface (class 2), or both at the same time (class 1 + 2). A shared feature of the mutational perturbations is a shift of the folding equilibrium toward poorly structured SOD monomers. We observed a link, coupled to the altered folding patterns, between protein stability, net charge, and survival time for the patients carrying the mutations.
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Affiliation(s)
- Mikael J Lindberg
- Departments of Biochemistry and Clinical Neuroscience, Umeå University, S-901 87 Umeå, Sweden
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7
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Cioni P, Pesce A, Morozzo della Rocca B, Castelli S, Falconi M, Parrilli L, Bolognesi M, Strambini G, Desideri A. Active-site copper and zinc ions modulate the quaternary structure of prokaryotic Cu,Zn superoxide dismutase. J Mol Biol 2003; 326:1351-60. [PMID: 12595249 DOI: 10.1016/s0022-2836(03)00047-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The influence of the constitutive metal ions on the equilibrium properties of dimeric Photobacterium leiognathi Cu,Zn superoxide dismutase has been studied for the wild-type and for two mutant protein forms bearing a negative charge in the amino acid clusters at the dimer association interface. Depletion of copper and zinc dissociates the two mutant proteins into monomers, which reassemble toward the dimeric state upon addition of stoichiometric amounts of zinc. Pressure-dependent dissociation is observed for the copper-depleted wild-type and mutated enzymes, as monitored by the fluorescence shift of a unique tryptophan residue located at the subunit association interface. The spectral shift occurs slowly, reaching a plateau after 15-20 minutes, and is fully reversible. The recovery of the original fluorescence properties, after decompression, is fast (less than four minutes), suggesting that the isolated subunit has a relatively stable structure, and excluding the presence of stable intermediates during the dimer-monomer transition. The dimer dissociation process is still incomplete at 6.5 kbar for the copper-depleted wild-type and mutated enzymes, at variance with what is generally observed for oligomeric proteins that dissociate below 3 kbar. Measurement of the degree of dissociation, at two different protein concentrations, allows us to calculate the standard volume variation upon association, Delta V, and the dissociation constant K(d0), at atmospheric pressure, (25 ml/mol and 3 x 10(-7)M, respectively). The holoprotein is fully dimeric even at 6.5 kbar, which allows us to evaluate a lower Delta G degrees limit of 11.5 kcal/mol, corresponding to a dissociation constant K(d0)<10(-9)M.
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Affiliation(s)
- P Cioni
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche, Area della Ricerca di Pisa, Pisa, Italy
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8
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Bonaccorsi di Patti MC, Giartosio A, Rotilio G, Battistoni A. Analysis of Cu,ZnSOD conformational stability by differential scanning calorimetry. Methods Enzymol 2002; 349:49-61. [PMID: 11912929 DOI: 10.1016/s0076-6879(02)49320-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
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9
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Malvezzi-Campeggi F, Rosato N, Finazzi-Agrò A, Maccarrone M. Effect of denaturants on the structural properties of soybean lipoxygenase-1. Biochem Biophys Res Commun 2001; 289:1295-300. [PMID: 11741336 DOI: 10.1006/bbrc.2001.6109] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The effect of chemical (urea) and physical (temperature and high pressure) denaturation on the structural properties of soybean lipoxygenase-1 (LOX1) was analyzed through dynamic fluorescence spectroscopy and circular dichroism. We show that the fluorescence decay of the native protein could be fitted by two lorentzian distributions of lifetimes, centered at 1 and 4 ns. The analysis of the urea-denatured protein suggested that the shorter distribution is mostly due to the tryptophan residues located in the N-terminal domain of LOX1. We also show that a pressure of 2400 bar and a temperature of 55 degrees C brought LOX-1 to a state similar to a recently described stable intermediate "I." Analysis of circular dichroism spectra indicated a substantial decrease of alpha-helix compared with beta-structure under denaturing conditions, suggesting a higher stability of the N-terminal compared with the C-terminal domain in the denaturation process.
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Falconi M, Stroppolo ME, Cioni P, Strambini G, Sergi A, Ferrario M, Desideri A. Dynamics-function correlation in Cu, Zn superoxide dismutase: a spectroscopic and molecular dynamics simulation study. Biophys J 2001; 80:2556-67. [PMID: 11371434 PMCID: PMC1301445 DOI: 10.1016/s0006-3495(01)76227-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
A single mutation (Val29-->Gly) at the subunit interface of a Cu, Zn superoxide dismutase dimer leads to a twofold increase in the second order catalytic rate, when compared to the native enzyme, without causing any modification of the structure or the electric field distribution. To check the role of dynamic processes in this catalytic enhancement, the flexibility of the dimeric protein at the subunit interface region has been probed by the phosphorescence and fluorescence properties of the unique tryptophan residue. Multiple spectroscopic data indicate that Trp83 experiences a very similar, and relatively hydrophobic, environment in both wild-type and mutant protein, whereas its mobility is distinctly more restrained in the latter. Molecular dynamics simulation confirms this result, and provides, at the molecular level, details of the dynamic change felt by tryptophan. Moreover, the simulation shows that the loops surrounding the active site are more flexible in the mutant than in the native enzyme, making the copper more accessible to the incoming substrate, and being thus responsible for the catalytic rate enhancement. Evidence for increased, dynamic copper accessibility also comes from faster copper removal in the mutant by a metal chelator. These results indicate that differences in dynamic, rather than structural, features of the two enzymes are responsible for the observed functional change.
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Affiliation(s)
- M Falconi
- INFM and Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
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11
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Cioni P, Stroppolo ME, Desideri A, Strambini GB. Dynamic features of the subunit interface of Cu,Zn superoxide dismutase as probed by tryptophan phosphorescence. Arch Biochem Biophys 2001; 391:111-8. [PMID: 11414691 DOI: 10.1006/abbi.2001.2407] [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: 11/22/2022]
Abstract
As part of the more general inquiry on the molecular basis of specific recognition between macromolecules, the subunit-subunit interface structure of dimeric superoxide dismutase from Photobacterium leiognathi has been probed selectively by the phosphorescence emission of Trp-73, located at the subunit contact region. Copper at the catalytic site was found to quench completely the delayed emission and therefore all studies were conducted with the copper-free or Cd(2+)-substituted protein. The spectrum at 140 K is diagnostic for an indole ring located in a hydrophobic environment whereas a degree of spectral broadening indicates that the local structure is not unique. Environmental heterogeneity is confirmed by the nonuniform phosphorescence decay in buffer, at 274 K, with lifetime components of 44 and 20 ms of practically equal amplitude. Information on the flexibility of the interface region was gathered from both the intrinsic lifetime and the accessibility of acrylamide to the site of the chromophore. The magnitude of the intrinsic lifetime, its temperature dependence, and the accessibility to solutes like acrylamide describe a tight dimeric structure in which hydrophobic interactions seem to play an important role. In particular the acrylamide bimolecular rate constant is 1.4 x 10(4) M(-1) s(-1) and indicates highly hindered diffusion of the solute through the interface region. Cd(2+) complexation to the apoprotein caused no detectable changes in protein conformation although the metal was able to influence the flexibility of the Trp-73 environment, indicating the occurrence of a long-range communication between the intersubunit surface and the active site, which is more than 16 A away.
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Affiliation(s)
- P Cioni
- Istituto di Biofisica Consiglio Nazionale delle Ricerche Area della Ricerca di Pisa, Via G. Moruzzi, 1, Pisa, Italy.
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12
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Stroppolo ME, Malvezzi-Campeggi F, Mei G, Rosato N, Desideri A. Role of the tertiary and quaternary structures in the stability of dimeric copper, zinc superoxide dismutases. Arch Biochem Biophys 2000; 377:215-8. [PMID: 10845696 DOI: 10.1006/abbi.2000.1780] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The equilibrium unfolding process of human Cu,Zn superoxide dismutase has been quantitatively monitored through circular dichroism and fluorescence spectroscopy as a function of increasing guanidinium hydrochloride concentration. The process occurs through the formation of a monomeric intermediate species following a three-state transition equilibrium. Comparison with the stability of the prokaryotic Cu,Zn SOD from P. leiognathi shows that the eukaryotic enzyme is more stable than the prokaryotic enzyme by approximately 3 kcal/mol. This difference is due to the monomer-to-unfolded equilibrium, while the dimer-to-monomer equilibrium is comparable for the two enzymes despite their different intersubunit interactions. These results are confirmed by the unfolding of the copper-depleted derivatives. The Cu,Zn superoxide dismutase represents a good example of how evolution has found two independent quaternary assemblies maintaining the same dimer stability.
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Affiliation(s)
- M E Stroppolo
- INFM and Department of Biology, University of Rome Tor Vergata, Italy
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