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Ereño-Orbea J, Oyenarte I, Martínez-Cruz LA. CBS domains: Ligand binding sites and conformational variability. Arch Biochem Biophys 2013; 540:70-81. [DOI: 10.1016/j.abb.2013.10.008] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 10/08/2013] [Accepted: 10/11/2013] [Indexed: 02/07/2023]
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Doyle CM, Rumfeldt JA, Broom HR, Broom A, Stathopulos PB, Vassall KA, Almey JJ, Meiering EM. Energetics of oligomeric protein folding and association. Arch Biochem Biophys 2012; 531:44-64. [PMID: 23246784 DOI: 10.1016/j.abb.2012.12.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Revised: 11/29/2012] [Accepted: 12/05/2012] [Indexed: 12/11/2022]
Abstract
In nature, proteins most often exist as complexes, with many of these consisting of identical subunits. Understanding of the energetics governing the folding and misfolding of such homooligomeric proteins is central to understanding their function and misfunction, in disease or biotechnology. Much progress has been made in defining the mechanisms and thermodynamics of homooligomeric protein folding. In this review, we outline models as well as calorimetric and spectroscopic methods for characterizing oligomer folding, and describe extensive results obtained for diverse proteins, ranging from dimers to octamers and higher order aggregates. To our knowledge, this area has not been reviewed comprehensively in years, and the collective progress is impressive. The results provide evolutionary insights into the development of subunit interfaces, mechanisms of oligomer folding, and contributions of oligomerization to protein stability, function and regulation. Thermodynamic analyses have also proven valuable for understanding protein misfolding and aggregation mechanisms, suggesting new therapeutic avenues. Successful recent designs of novel, functional proteins demonstrate increased understanding of oligomer folding. Further rigorous analyses using multiple experimental and computational approaches are still required, however, to achieve consistent and accurate prediction of oligomer folding energetics. Modeling the energetics remains challenging but is a promising avenue for future advances.
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Affiliation(s)
- Colleen M Doyle
- Guelph-Waterloo Centre for Graduate Studies in Chemistry and Biochemistry, and Department of Chemistry, University of Waterloo, 200 University Ave. West, Waterloo, ON, Canada
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Oyenarte I, Lucas M, Gómez García I, Martínez-Cruz LA. Purification, crystallization and preliminary crystallographic analysis of the CBS-domain protein MJ1004 from Methanocaldococcus jannaschii. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:318-24. [PMID: 21393835 PMCID: PMC3053155 DOI: 10.1107/s1744309110053479] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2010] [Accepted: 12/20/2010] [Indexed: 11/10/2022]
Abstract
The purification and preliminary crystallographic analysis of the archaeal CBS-domain protein MJ1004 from Methanocaldococcus jannaschii are described. The native protein was overexpressed, purified and crystallized in the monoclinic space group P2(1), with unit-cell parameters a=54.4, b=53.8, c=82.6 Å, β=106.1°. The crystals diffracted X-rays to 2.7 Å resolution using synchrotron radiation. Matthews-volume calculations suggested the presence of two molecules in the asymmetric unit that are likely to correspond to a dimeric species, which is also observed in solution.
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Affiliation(s)
- Iker Oyenarte
- Structural Biology Unit, CIC bioGUNE, Parque Tecnológico de Bizkaia, Edificio 800, 48160 Derio, Bizkaia, Spain
| | - María Lucas
- Center for Integrated Protein Sciences and Munich Center for Advanced Photonics at the Gene Center, Department of Biochemistry, Ludwig-Maximilians-University Munich, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Inmaculada Gómez García
- Structural Biology Unit, CIC bioGUNE, Parque Tecnológico de Bizkaia, Edificio 800, 48160 Derio, Bizkaia, Spain
| | - Luis Alfonso Martínez-Cruz
- Structural Biology Unit, CIC bioGUNE, Parque Tecnológico de Bizkaia, Edificio 800, 48160 Derio, Bizkaia, Spain
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Botana A, Aguilar JA, Nilsson M, Morris GA. J-modulation effects in DOSY experiments and their suppression: the Oneshot45 experiment. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2011; 208:270-278. [PMID: 21185209 DOI: 10.1016/j.jmr.2010.11.012] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2010] [Revised: 11/17/2010] [Accepted: 11/18/2010] [Indexed: 05/30/2023]
Abstract
Diffusion-ordered spectroscopy (DOSY) is a powerful NMR method for identifying compounds in mixtures. DOSY experiments are very demanding of spectral quality; even small deviations from expected behaviour in NMR signals can cause significant distortions in the diffusion domain. This is a particular problem when signals overlap, so it is very important to be able to acquire clean data with as little overlap as possible. DOSY experiments all suffer to a greater or lesser extent from multiplet phase distortions caused by J-modulation, requiring a trade-off between such distortions and gradient pulse width. Multiplet distortions increase spectral overlap and may cause unexpected and misleading apparent diffusion coefficients in DOSY spectra. These effects are described here and a simple and effective remedy, the addition of a 45° purging pulse immediately before the onset of acquisition to remove the unwanted anti-phase terms, is demonstrated. As well as affording significantly cleaner results, the new method allows much longer diffusion-encoding pulses to be used without problems from J-modulation, and hence greatly increases the range of molecular sizes that can be studied for coupled spin systems. The sensitivity loss is negligible and the added phase cycling is modest. The new method is illustrated for a widely-used general purpose DOSY pulse sequence, Oneshot.
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Affiliation(s)
- Adolfo Botana
- School of Chemistry, University of Manchester, Manchester M13 9PL, UK
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Martínez-Cruz LA, Encinar JA, Sevilla P, Oyenarte I, Gómez-García I, Aguado-Llera D, García-Blanco F, Gómez J, Neira JL. Nucleotide-induced conformational transitions in the CBS domain protein MJ0729 of Methanocaldococcus jannaschii. Protein Eng Des Sel 2010; 24:161-9. [PMID: 20959390 DOI: 10.1093/protein/gzq073] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Nucleotide-binding cystathionine β-synthase (CBS) domains function as regulatory motifs in several proteins distributed through all kingdoms of life. This function has been proposed based on their affinity for adenosyl-derivatives, although the exact binding mechanisms remain largely unknown. The question of how CBS domains exactly work is relevant because in humans, several genetic diseases have been associated with mutations in those motifs. In this work, we describe the adenosyl-ligand (AMP, ATP, NADP and SAM) properties of the wild-type CBS domain protein MJ0729 from Methanocaldococcus jannaschii by using a combination of spectroscopic techniques (fluorescence, FTIR and FRET). The fluorescence results show that binding to AMP and ATP occurs with an apparent dissociation constant of ~10 µM, and interestingly enough, binding induces protein conformational changes, as shown by FTIR. On the other hand, fluorescence spectra (FRET and steady-state) did not change upon addition of NADP and SAM to MJ0729, suggesting that tryptophan and/or tyrosine residues were not involved in the recognition of those ligands; however, there were changes in the secondary structure of the protein upon addition of NADP and SAM, as shown by FTIR (thus, indicating binding to the nucleotide). Taken together, these results suggest that: (i) the adenosyl ligands bind to MJ0729 in different ways, and (ii) there are changes in the protein secondary structure upon binding of the nucleotides.
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Affiliation(s)
- Luis Alfonso Martínez-Cruz
- Unidad de Biología Estructural, CIC bioGUNE, Parque Tecnológico de Bizkaia, 48160 Derio (Vizcaya), Spain.
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Aguado-Llera D, Oyenarte I, Martínez-Cruz LA, Neira JL. The CBS domain protein MJ0729 of Methanocaldococcus jannaschii binds DNA. FEBS Lett 2010; 584:4485-9. [PMID: 20934423 DOI: 10.1016/j.febslet.2010.10.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2010] [Revised: 09/29/2010] [Accepted: 10/04/2010] [Indexed: 12/16/2022]
Abstract
The cystathionine beta-synthase (CBS) domains function as regulatory motifs in several proteins. Elucidating how CBS domains exactly work is relevant because several genetic human diseases have been associated with mutations in those motifs. Here, we show, for the first time, that a CBS domain binds calf-thymus DNA and E-boxes recognized by transcription factors. We have carried out the DNA-binding characterization of the CBS domain protein MJ0729 from Methanocaldococcus jannaschii by biochemical and spectroscopic techniques. Binding induces conformational changes in the protein, and involves the sole tryptophan residue. The apparent dissociation constant for the E-boxes is ∼10 μM. These results suggest that CBS domains might interact with DNA.
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Affiliation(s)
- David Aguado-Llera
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche (Alicante), Spain
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Caliendo G, Cirino G, Santagada V, Wallace JL. Synthesis and biological effects of hydrogen sulfide (H2S): development of H2S-releasing drugs as pharmaceuticals. J Med Chem 2010; 53:6275-86. [PMID: 20462257 DOI: 10.1021/jm901638j] [Citation(s) in RCA: 209] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Giuseppe Caliendo
- Dipartimento di Chimica Farmaceutica e Tossicologica, Universitá degli Studi di Napoli Federico II, Via Domenico Montesano, 49, 80131 Napoli, Italy.
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Gómez-García I, Oyenarte I, Martínez-Cruz LA. The crystal structure of protein MJ1225 from Methanocaldococcus jannaschii shows strong conservation of key structural features seen in the eukaryal gamma-AMPK. J Mol Biol 2010; 399:53-70. [PMID: 20382158 DOI: 10.1016/j.jmb.2010.03.045] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2009] [Revised: 03/23/2010] [Accepted: 03/23/2010] [Indexed: 11/27/2022]
Abstract
In mammals, 5'-AMP-activated protein kinase (AMPK) is a heterotrimeric protein composed of a catalytic serine/threonine kinase subunit (alpha) and two regulatory subunits (beta and gamma). The gamma-subunit senses the intracellular energy status by competitively binding AMP and ATP and is thought to be responsible for allosteric regulation of the whole complex. We describe herein the crystal structure of protein MJ1225 from Methanocaldococcus jannaschii complexed to AMP, ADP, and ATP. Our data provide evidence of a strong conservation of the key functional features seen in the gamma-subunit of the eukaryotic AMPK, and more importantly, it reveals a novel AMP binding site, herein denoted as site E, which had not been previously described in cystathionine beta-synthase domains so far. Site E is located in a small cavity existing between the alpha-helices structurally equivalent to those disrupting the internal symmetry of each Bateman domain in gamma-AMPKs and shows striking similarities with a symmetry-related crevice of the mammalian enzyme that hosts the pathological mutation N488I.
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Affiliation(s)
- Inmaculada Gómez-García
- Structural Biology Unit, CIC bioGUNE, Parque Tecnológico de Bizkaia, Edificio 800, 48160 Derio, Bizkaia, Spain
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Binding of S-methyl-5'-thioadenosine and S-adenosyl-L-methionine to protein MJ0100 triggers an open-to-closed conformational change in its CBS motif pair. J Mol Biol 2009; 396:800-20. [PMID: 20026078 DOI: 10.1016/j.jmb.2009.12.012] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2009] [Revised: 12/09/2009] [Accepted: 12/09/2009] [Indexed: 02/03/2023]
Abstract
Cystathionine beta-synthase (CBS) domains are small motifs that are present in proteins with completely different functions. Several genetic diseases in humans have been associated with mutations in their sequence, which has made them promising targets for rational drug design. The protein MJ0100 from Methanocaldococcus jannaschii includes a DUF39 domain of so far unknown function and a CBS domain pair (Bateman domain) at its C-terminus. This work presents the crystallographic analysis of four different states of the CBS motif pair of MJ0100 in complex with different numbers of S-adenosyl-L-methionine (SAM) and S-methyl-5'-thioadenosine (MTA) ligands, providing evidence that ligand-induced conformational reorganization of Bateman domain dimers could be an important regulatory mechanism. These observations are in contrast to what is known from most of the other Bateman domain structures but are supported by recent studies on the magnesium transporter MgtE. Our structures represent the first example of a CBS domain protein complexed with SAM and/or MTA and might provide a structural basis for understanding the molecular mechanisms regulated by SAM upon binding to the C-terminal domain of human CBS, whose structure remains unknown.
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Gómez García I, Kortázar D, Oyenarte I, Mato JM, Martínez-Chantar ML, Martínez-Cruz LA. Purification, crystallization and preliminary crystallographic analysis of protein MJ1225 from Methanocaldococcus jannaschii, a putative archaeal homologue of gamma-AMPK. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:813-7. [PMID: 19652347 PMCID: PMC2720341 DOI: 10.1107/s1744309109026475] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2009] [Accepted: 07/07/2009] [Indexed: 01/05/2023]
Abstract
In mammals, AMP-activated protein kinase (AMPK) is a heterotrimeric protein composed of a catalytic serine/threonine kinase subunit (alpha) and two regulatory subunits (beta and gamma). The gamma subunit senses the intracellular energy status by competitively binding AMP and ATP and is thought to be responsible for allosteric regulation of the whole complex. This work describes the purification and preliminary crystallographic analysis of protein MJ1225 from Methanocaldococcus jannaschii, an archaeal homologue of gamma-AMPK. The purified protein was crystallized using the hanging-drop vapour-diffusion method. Diffraction data for MJ1225 were collected to 2.3 A resolution using synchrotron radiation. The crystals belonged to space group H32, with unit-cell parameters a = b = 108.95, c = 148.08 A, alpha = beta = 90.00, gamma = 120.00 degrees . Preliminary analysis of the X-ray data indicated that there was one molecule per asymmetric unit.
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Affiliation(s)
- Inmaculada Gómez García
- Structural Biology Unit, CIC bioGUNE, Parque Tecnológico de Bizkaia, Edificio 800, 48160 Derio, Bizkaia, Spain
| | - Danel Kortázar
- Structural Biology Unit, CIC bioGUNE, Parque Tecnológico de Bizkaia, Edificio 800, 48160 Derio, Bizkaia, Spain
| | - Iker Oyenarte
- Structural Biology Unit, CIC bioGUNE, Parque Tecnológico de Bizkaia, Edificio 800, 48160 Derio, Bizkaia, Spain
| | - José María Mato
- Metabolomics Unit, CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (Ciberedh), Parque Tecnológico de Bizkaia, Edificio 801, 48160 Derio Bizkaia, Spain
| | - María Luz Martínez-Chantar
- Metabolomics Unit, CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (Ciberedh), Parque Tecnológico de Bizkaia, Edificio 801, 48160 Derio Bizkaia, Spain
| | - Luis Alfonso Martínez-Cruz
- Structural Biology Unit, CIC bioGUNE, Parque Tecnológico de Bizkaia, Edificio 800, 48160 Derio, Bizkaia, Spain
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