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Lee Y, Kim H, Lee E, Hahn H, Heo Y, Jang DM, Kwak K, Kim HJ, Kim HS. Structural insights into N-terminal methionine cleavage by the human mitochondrial methionine aminopeptidase, MetAP1D. Sci Rep 2023; 13:22326. [PMID: 38102161 PMCID: PMC10724148 DOI: 10.1038/s41598-023-49332-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 12/07/2023] [Indexed: 12/17/2023] Open
Abstract
Isozymes are enzymes that catalyze identical biological reactions, yet exhibit slight variations in structures and catalytic efficiency, which enables the precise adjustment of metabolism to fulfill the specific requirements of a particular tissue or stage of development. Methionine aminopeptidase (MetAP) isozymes function a critical role in cleaving N-terminal methionine from nascent proteins to generate functional proteins. In humans, two distinct MetAP types I and II have been identified, with type I further categorized into cytosolic (MetAP1) and mitochondrial (MetAP1D) variants. However, despite extensive structural studies on both bacterial and human cytosolic MetAPs, the structural information remains unavailable for human mitochondrial MetAP. This study was aimed to elucidate the high-resolution structures of human mitochondrial MetAP1D in its apo-, cobalt-, and methionine-bound states. Through a comprehensive analysis of the determined structures and a docking simulation model with mitochondrial substrate peptides, we present mechanistic insights into the cleavage process of the initiator methionine from mitochondrial proteins. Notably, despite the shared features at the active site between the cytosolic and mitochondrial MetAP type I isozymes, we identified distinct structural disparities within the active-site pocket primarily contributed by two specific loops that could play a role in accommodating specific substrates. These structural insights offer a basis for the further exploration of MetAP isozymes as critical players in cellular processes and potential therapeutic applications.
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Affiliation(s)
- Yeon Lee
- Research Institute, National Cancer Center, Goyang, 10408, Republic of Korea
| | - Hayoung Kim
- Research Institute, National Cancer Center, Goyang, 10408, Republic of Korea
- Division of Medical Sciences, College of Medicine, Yonsei University, Seoul, 03722, Republic of Korea
| | - Eunji Lee
- Research Institute, National Cancer Center, Goyang, 10408, Republic of Korea
| | - Hyunggu Hahn
- Research Institute, National Cancer Center, Goyang, 10408, Republic of Korea
| | - Yoonyoung Heo
- Research Institute, National Cancer Center, Goyang, 10408, Republic of Korea
| | - Dong Man Jang
- Research Institute, National Cancer Center, Goyang, 10408, Republic of Korea
| | - Kihyuck Kwak
- Division of Medical Sciences, College of Medicine, Yonsei University, Seoul, 03722, Republic of Korea
| | - Hyo Jung Kim
- College of Pharmacy, Woosuk University, Wanju, 55338, Republic of Korea.
| | - Hyoun Sook Kim
- Research Institute, National Cancer Center, Goyang, 10408, Republic of Korea.
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2
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Diment WT, Lindeboom W, Fiorentini F, Deacy AC, Williams CK. Synergic Heterodinuclear Catalysts for the Ring-Opening Copolymerization (ROCOP) of Epoxides, Carbon Dioxide, and Anhydrides. Acc Chem Res 2022; 55:1997-2010. [PMID: 35863044 PMCID: PMC9350912 DOI: 10.1021/acs.accounts.2c00197] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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The development of sustainable
plastic materials is an essential
target of chemistry in the 21st century. Key objectives toward this
goal include utilizing sustainable monomers and the development of
polymers that can be chemically recycled/degraded. Polycarbonates
synthesized from the ring-opening copolymerization (ROCOP) of epoxides
and CO2, and polyesters synthesized from the ROCOP of epoxides
and anhydrides, meet these criteria. Despite this, designing efficient
catalysts for these processes remains challenging. Typical issues
include the requirement for high catalyst loading; low catalytic activities
in comparison with other commercialized polymerizations; and the requirement
of costly, toxic cocatalysts. The development of efficient catalysts
for both types of ROCOP is highly desirable. This Account details
our work on the development of catalysts for these two related polymerizations
and, in particular, focuses on dinuclear complexes, which are typically
applied without any cocatalyst. We have developed mechanistic hypotheses
in tandem with our catalysts, and throughout the Account, we describe
the kinetic, computational, and structure–activity studies
that underpin the performance of these catalysts. Our initial research
on homodinuclear M(II)M(II) complexes for cyclohexene oxide (CHO)/CO2 ROCOP provided data to support a chain shuttling catalytic
mechanism, which implied different roles for the two metals in the
catalysis. This mechanistic hypothesis inspired the development of
mixed-metal, heterodinuclear catalysts. The first of this class of
catalysts was a heterodinuclear Zn(II)Mg(II) complex, which showed
higher rates than either of the homodinuclear [Zn(II)Zn(II) and Mg(II)Mg(II)]
analogues for CHO/CO2 ROCOP. Expanding on this finding,
we subsequently developed a Co(II)Mg(II) complex that showed field
leading rates for CHO/CO2 ROCOP and allowed for unique
insight into the role of the two metals in this complex, where it
was established that the Mg(II) center reduced transition state entropy
and the Co(II) center reduced transition state enthalpy. Following
these discoveries, we subsequently developed a range of heterodinuclear
M(III)M(I) catalysts that were capable of catalyzing a broad range
of copolymerizations, including the ring-opening copolymerization
of CHO/CO2, propylene oxide (PO)/CO2, and CHO/phthalic
anhydride (PA). Catalysts featuring Co(III)K(I) and Al(III)K(I) were
found to be exceptionally effective for PO/CO2 and CHO/PA
ROCOP, respectively. Such M(III)M(I) complexes operate through a dinuclear
metalate mechanism, where the M(III) binds and activates monomers
while the M(I) species binds the polymer change in close proximity
to allow for insertion into the activated monomer. Our research illustrates
how careful catalyst design can yield highly efficient systems and
how the development of mechanistic understanding aids this process.
Avenues of future research are also discussed, including the applicability
of these heterodinuclear catalysts in the synthesis of sustainable
materials.
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Affiliation(s)
- Wilfred T Diment
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Wouter Lindeboom
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Francesca Fiorentini
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Arron C Deacy
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Charlotte K Williams
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
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Muderspach SJ, Fredslund F, Volf V, Poulsen JCN, Blicher TH, Clausen MH, Rasmussen KK, Krogh KBRM, Jensen K, Lo Leggio L. Engineering the substrate binding site of the hyperthermostable archaeal endo-β-1,4-galactanase from Ignisphaera aggregans. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:183. [PMID: 34530892 PMCID: PMC8447715 DOI: 10.1186/s13068-021-02025-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 08/23/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Endo-β-1,4-galactanases are glycoside hydrolases (GH) from the GH53 family belonging to the largest clan of GHs, clan GH-A. GHs are ubiquitous and involved in a myriad of biological functions as well as being widely used industrially. Endo-β-1,4-galactanases, in particular hydrolyse galactan and arabinogalactan in pectin, a major component of the primary plant cell wall, with important functions in plant defence and application in the food and other industries. Here, we explore the family's biological diversity by characterizing the first archaeal and hyperthermophilic GH53 galactanase, and utilize it as a scaffold for engineering enzymes with different product lengths. RESULTS A galactanase gene was identified in the genome of the anaerobic hyperthermophilic archaeon Ignisphaera aggregans, and the isolated catalytic domain expressed and characterized (IaGal). IaGal presents the typical (βα)8 barrel structure of clan GH-A enzymes, with catalytic carboxylates at the end of the 4th and 7th barrel strands. Its activity optimum of at least 95 °C and melting point over 100 °C indicate extreme thermostability, a very advantageous property for industrial applications. If enzyme depletion is reduced, so is the need for re-addition, and thus costs. The main stabilizing features of IaGal compared to other structurally characterized members are π-π and cation-π interactions. The length of the substrate binding site-and thus produced oligosaccharide products-is intermediate compared to previously characterized galactanases. Variants inspired by the structural diversity in the GH53 family were rationally designed to shorten or extend the substrate binding groove, in order to modulate product length. Subsite-deleted variants produced shorter products than IaGal, as do the fungal galactanases inspiring the design. IaGal variants engineered with a longer binding site produced a less expected degradation pattern, though still different from that of wild-type IaGal. All variants remained extremely stable. CONCLUSIONS We have characterized in detail the most thermophilic endo-β-1,4-galactanase known to date and successfully engineered it to modify the degradation profile, while maintaining much of its desirable thermostability. This is an important achievement as oligosaccharide products length is an important property for industrial and natural GHs alike.
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Affiliation(s)
- Sebastian J Muderspach
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen, Denmark
| | - Folmer Fredslund
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen, Denmark
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Verena Volf
- Novozymes A/S, Biologiens vej 2, 2800, Kongens Lyngby, Denmark
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | | | | | - Mads Hartvig Clausen
- Center for Nanomedicine and Theranostics, Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800, Kgs. Lyngby, Denmark
| | - Kim Krighaar Rasmussen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen, Denmark
| | | | - Kenneth Jensen
- Novozymes A/S, Biologiens vej 2, 2800, Kongens Lyngby, Denmark.
| | - Leila Lo Leggio
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen, Denmark.
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Evolution of Protein Structure and Stability in Global Warming. Int J Mol Sci 2020; 21:ijms21249662. [PMID: 33352933 PMCID: PMC7767258 DOI: 10.3390/ijms21249662] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/15/2020] [Accepted: 12/16/2020] [Indexed: 12/12/2022] Open
Abstract
This review focuses on the molecular signatures of protein structures in relation to evolution and survival in global warming. It is based on the premise that the power of evolutionary selection may lead to thermotolerant organisms that will repopulate the planet and continue life in general, but perhaps with different kinds of flora and fauna. Our focus is on molecular mechanisms, whereby known examples of thermoresistance and their physicochemical characteristics were noted. A comparison of interactions of diverse residues in proteins from thermophilic and mesophilic organisms, as well as reverse genetic studies, revealed a set of imprecise molecular signatures that pointed to major roles of hydrophobicity, solvent accessibility, disulfide bonds, hydrogen bonds, ionic and π-electron interactions, and an overall condensed packing of the higher-order structure, especially in the hydrophobic regions. Regardless of mutations, specialized protein chaperones may play a cardinal role. In evolutionary terms, thermoresistance to global warming will likely occur in stepwise mutational changes, conforming to the molecular signatures, such that each "intermediate" fits a temporary niche through punctuated equilibrium, while maintaining protein functionality. Finally, the population response of different species to global warming may vary substantially, and, as such, some may evolve while others will undergo catastrophic mass extinction.
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5
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P1' Residue-Oriented Virtual Screening for Potent and Selective Phosphinic (Dehydro) Dipeptide Inhibitors of Metallo-Aminopeptidases. Biomolecules 2020; 10:biom10040659. [PMID: 32344658 PMCID: PMC7225938 DOI: 10.3390/biom10040659] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 04/17/2020] [Accepted: 04/20/2020] [Indexed: 01/01/2023] Open
Abstract
Designing side chain substituents complementary to enzyme binding pockets is of great importance in the construction of potent and selective phosphinic dipeptide inhibitors of metallo-aminopeptidases. Proper structure selection makes inhibitor construction more economic, as the development process typically consists of multiple iterative preparation/bioassay steps. On the basis of these principles, using noncomplex computation and modeling methodologies, we comprehensively screened 900 commercial precursors of the P1′ residues of phosphinic dipeptide and dehydrodipeptide analogs to identify the most promising ligands of 52 metallo-dependent aminopeptidases with known crystal structures. The results revealed several nonproteinogenic residues with an improved energy of binding compared with the best known inhibitors. The data are discussed taking into account the selectivity and stereochemical implications of the enzymes. Using this approach, we were able to identify nontrivial structural elements substituting the recognized phosphinic peptidomimetic scaffold of metallo-aminopeptidase inhibitors.
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6
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Moriarty NW, Janowski PA, Swails JM, Nguyen H, Richardson JS, Case DA, Adams PD. Improved chemistry restraints for crystallographic refinement by integrating the Amber force field into Phenix. Acta Crystallogr D Struct Biol 2020; 76:51-62. [PMID: 31909743 PMCID: PMC6939439 DOI: 10.1107/s2059798319015134] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 11/08/2019] [Indexed: 02/01/2023] Open
Abstract
The refinement of biomolecular crystallographic models relies on geometric restraints to help to address the paucity of experimental data typical in these experiments. Limitations in these restraints can degrade the quality of the resulting atomic models. Here, an integration of the full all-atom Amber molecular-dynamics force field into Phenix crystallographic refinement is presented, which enables more complete modeling of biomolecular chemistry. The advantages of the force field include a carefully derived set of torsion-angle potentials, an extensive and flexible set of atom types, Lennard-Jones treatment of nonbonded interactions and a full treatment of crystalline electrostatics. The new combined method was tested against conventional geometry restraints for over 22 000 protein structures. Structures refined with the new method show substantially improved model quality. On average, Ramachandran and rotamer scores are somewhat better, clashscores and MolProbity scores are significantly improved, and the modeling of electrostatics leads to structures that exhibit more, and more correct, hydrogen bonds than those refined using traditional geometry restraints. In general it is found that model improvements are greatest at lower resolutions, prompting plans to add the Amber target function to real-space refinement for use in electron cryo-microscopy. This work opens the door to the future development of more advanced applications such as Amber-based ensemble refinement, quantum-mechanical representation of active sites and improved geometric restraints for simulated annealing.
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Affiliation(s)
- Nigel W. Moriarty
- Molecular Biosciences and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235, USA
| | - Pawel A. Janowski
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Jason M. Swails
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Hai Nguyen
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | | | - David A. Case
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Paul D. Adams
- Molecular Biosciences and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235, USA
- Department of Bioengineering, University of California at Berkeley, Berkeley, CA 94720, USA
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7
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Matsuura Y, Joti Y, Bagautdinov B, Yutani K. Evaluating the strengths of salt bridges in the CutA1 protein using molecular dynamic simulations: a comparison of different force fields. FEBS Open Bio 2019; 9:1939-1956. [PMID: 31509647 PMCID: PMC6823277 DOI: 10.1002/2211-5463.12731] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 09/01/2019] [Accepted: 09/06/2019] [Indexed: 11/15/2022] Open
Abstract
Ion–ion interactions (salt bridges) between favorable pairs of charged residues are important for the conformational stability of proteins. Molecular dynamic (MD) simulations are useful for elucidating the interactions among charged residues fluctuating in solution. However, the quality of MD results depends strongly on the force fields used. In this study, we compared the strengths of salt bridges among force fields by performing MD simulations using the CutA1 protein (trimer) from the hyperthermophile Pyrococcus horikoshii (PhCutA1), which has an unusually large proportion of charged residues. The force fields Chemistry at HARvard Macromolecular Mechanics (Charmm)27, Assisted Model Building and Energy Refinement (Amber)99sb, Amber14sb, GROningen Molecular Simulation (Gromos)43a1, and Gromos53a6 were used in combination with two different water models, tip3p (for Charmm27, Amber99sb, and Amber14sb) and simple point charge/extended (for Amber99sb, Gromos43a1, and Gromos53a6), yielding a total of six combinations. The RMSDs of all Cα atoms of PhCutA1 were similar among force fields, except for Charmm27, during 400‐ns MD simulations at 300 K; however, the radius of gyration (Rg) was greater for Amber99sb and shorter for Gromos43a1. The average strengths of salt bridges for each positively charged residue did not differ greatly among force fields, but the strengths at specific sites within the structure depended sensitively on the force field used. In the case of the Gromos group, positively charged residues could engage in favorable interactions with many more charged residues than in the other force fields, especially in loop regions; consequently, the apparent strength at each site was lower.
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Affiliation(s)
| | - Yasumasa Joti
- RIKEN SPring-8 Center, Sayo, Hyogo, Japan.,Japan Synchrotron Radiation Research Institute, Sayo, Hyogo, Japan
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Matsuura Y, Takehira M, Makhatadze GI, Joti Y, Naitow H, Kunishima N, Yutani K. Strategy for Stabilization of CutA1 Proteins Due to Ion-Ion Interactions at Temperatures of over 100 °C. Biochemistry 2018; 57:2649-2656. [PMID: 29648806 DOI: 10.1021/acs.biochem.8b00103] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
In order to elucidate the contribution of charged residues to protein stabilization at temperatures of over 100 °C, we constructed many mutants of the CutA1 protein ( EcCutA1) from Escherichia coli. The goal was to see if one can achieve the same stability as for a CutA1 from hyperthermophile Pyrococcus horikoshii that has the denaturation temperature near 150 °C. The hydrophobic mutant of EcCutA1 ( Ec0VV) with denaturation temperature ( Td) of 113.2 °C was used as a template for mutations. The highest Td of Ec0VV mutants substituted by a single charged residue was 118.4 °C. Multiple ion mutants were also constructed by combination of single mutants and found to have an increased thermostability. The highest stability of multiple mutants was a mutant substituted by nine charged residues that had a Td of 142.2 °C. To evaluate the energy of ion-ion interactions of mutant proteins, we used the structural ensemble obtained by a molecular dynamics simulation at 300 K. The Td of ionic mutants linearly increases with the increments of the computed energy of ion-ion interactions for ionic mutant proteins even up to the temperatures near 140 °C, suggesting that ion-ion interactions cumulatively contribute to the stabilization of a protein at high temperatures.
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Affiliation(s)
| | - Michiyo Takehira
- RIKEN SPring-8 Center , 1-1-1 Kouto , Sayo, Hyogo 679-5148 , Japan
| | - George I Makhatadze
- Department of Biology , Rensselaer Polytechnic Institute , 110 Eighth Street , Troy , New York 12180-3590 , United States
| | - Yasumasa Joti
- Japan Synchrotron Radiation Research Institute , 1-1-1, Kouto , Sayo, Hyogo 679-5198 Japan
| | - Hisashi Naitow
- RIKEN SPring-8 Center , 1-1-1 Kouto , Sayo, Hyogo 679-5148 , Japan
| | - Naoki Kunishima
- RIKEN SPring-8 Center , 1-1-1 Kouto , Sayo, Hyogo 679-5148 , Japan
| | - Katsuhide Yutani
- RIKEN SPring-8 Center , 1-1-1 Kouto , Sayo, Hyogo 679-5148 , Japan
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Hendriks A, van Lier J, de Kreuk M. Growth media in anaerobic fermentative processes: The underestimated potential of thermophilic fermentation and anaerobic digestion. Biotechnol Adv 2018; 36:1-13. [DOI: 10.1016/j.biotechadv.2017.08.004] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 07/08/2017] [Accepted: 08/30/2017] [Indexed: 11/24/2022]
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10
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Bose H, Satyanarayana T. Microbial Carbonic Anhydrases in Biomimetic Carbon Sequestration for Mitigating Global Warming: Prospects and Perspectives. Front Microbiol 2017; 8:1615. [PMID: 28890712 PMCID: PMC5574912 DOI: 10.3389/fmicb.2017.01615] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 08/08/2017] [Indexed: 11/13/2022] Open
Abstract
All the leading cities in the world are slowly becoming inhospitable for human life with global warming playing havoc with the living conditions. Biomineralization of carbon dioxide using carbonic anhydrase (CA) is one of the most economical methods for mitigating global warming. The burning of fossil fuels results in the emission of large quantities of flue gas. The temperature of flue gas is quite high. Alkaline conditions are necessary for CaCO3 precipitation in the mineralization process. In order to use CAs for biomimetic carbon sequestration, thermo-alkali-stable CAs are, therefore, essential. CAs must be stable in the presence of various flue gas contaminants too. The extreme environments on earth harbor a variety of polyextremophilic microbes that are rich sources of thermo-alkali-stable CAs. CAs are the fastest among the known enzymes, which are of six basic types with no apparent sequence homology, thus represent an elegant example of convergent evolution. The current review focuses on the utility of thermo-alkali-stable CAs in biomineralization based strategies. A variety of roles that CAs play in various living organisms, the use of CA inhibitors as drug targets and strategies for overproduction of CAs to meet the demand are also briefly discussed.
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11
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Garg DK, Kundu B. Hyperthermophilic l -asparaginase bypasses monomeric intermediates during folding to retain cooperativity and avoid amyloid assembly. Arch Biochem Biophys 2017; 622:36-46. [DOI: 10.1016/j.abb.2017.04.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Revised: 04/26/2017] [Accepted: 04/27/2017] [Indexed: 10/19/2022]
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12
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Thermodynamics of protein denaturation at temperatures over 100 °C: CutA1 mutant proteins substituted with hydrophobic and charged residues. Sci Rep 2015; 5:15545. [PMID: 26497062 PMCID: PMC4620440 DOI: 10.1038/srep15545] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 09/28/2015] [Indexed: 11/08/2022] Open
Abstract
Although the thermodynamics of protein denaturation at temperatures over 100 °C is essential for the rational design of highly stable proteins, it is not understood well because of the associated technical difficulties. We designed certain hydrophobic mutant proteins of CutA1 from Escherichia coli, which have denaturation temperatures (Td) ranging from 101 to 113 °C and show a reversible heat denaturation. Using a hydrophobic mutant as a template, we successfully designed a hyperthermostable mutant protein (Td = 137 °C) by substituting six residues with charged ones. Thermodynamic analyses of these mutant proteins indicated that the hydrophobic mutants were stabilized by the accumulation of denaturation enthalpy (ΔH) with no entropic gain from hydrophobic solvation around 100 °C, and that the stabilization due to salt bridges resulted from both the increase in ΔH from ion-ion interactions and the entropic effect of the electrostatic solvation over 113 °C. This is the first experimental evidence that has successfully overcome the typical technical difficulties.
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13
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Thermostable Carbonic Anhydrases in Biotechnological Applications. Int J Mol Sci 2015; 16:15456-80. [PMID: 26184158 PMCID: PMC4519908 DOI: 10.3390/ijms160715456] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 07/01/2015] [Accepted: 07/02/2015] [Indexed: 01/10/2023] Open
Abstract
Carbonic anhydrases are ubiquitous metallo-enzymes which catalyze the reversible hydration of carbon dioxide in bicarbonate ions and protons. Recent years have seen an increasing interest in the utilization of these enzymes in CO2 capture and storage processes. However, since this use is greatly limited by the harsh conditions required in these processes, the employment of thermostable enzymes, both those isolated by thermophilic organisms and those obtained by protein engineering techniques, represents an interesting possibility. In this review we will provide an extensive description of the thermostable carbonic anhydrases so far reported and the main processes in which these enzymes have found an application.
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14
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Boone CD, Rasi V, Tu C, McKenna R. Structural and catalytic effects of proline substitution and surface loop deletion in the extended active site of human carbonic anhydrase II. FEBS J 2015; 282:1445-57. [PMID: 25683338 PMCID: PMC4400229 DOI: 10.1111/febs.13232] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 02/04/2015] [Accepted: 02/10/2015] [Indexed: 01/07/2023]
Abstract
UNLABELLED Bioengineering of a thermophilic enzyme starting from a mesophilic scaffold has proven to be a significant challenge, as several stabilizing elements have been proposed to be the foundation of thermal stability, including disulfide bridges, surface loop reduction, ionic pair networks, proline substitutions and aromatic clusters. This study emphasizes the effect of increasing the rigidity of human carbonic anhydrase II (HCA II; EC 4.2.1.1) via incorporation of proline residues at positions 170 and 234, which are located in surface loops that are able to accommodate restrictive main-chain conformations without rearrangement of the surrounding peptide backbone. Additionally, the effect of the compactness of HCA II was examined by deletion of a surface loop (residues 230-240) that had been previously identified as a possible source of thermal stability for the hyperthermophilic carbonic anhydrase isolated from the bacterium Sulfurihydrogenibium yellowstonense YO3AOP1. Differential scanning calorimetry analysis of these HCA II variants revealed that these structural modifications had a minimum effect on the thermal stability of the enzyme, while kinetic studies showed unexpected effects on the catalytic efficiency and proton transfer rates. X-ray crystallographic analysis of these HCA II variants showed that the electrostatic potential and configuration of the highly acidic loop (residues 230-240) play an important role in its high catalytic activity. Based on these observations and previous studies, a picture is emerging of the various components within the general structural architecture of HCA II that are key to stability. These elements may provide blueprints for rational thermal stability engineering of other enzymes. DATABASE Structural data have been submitted to the Protein Data Bank under accession numbers 4QK1 (K170P), 4QK2 (E234P) and 4QK3 (Δ230-240).
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Affiliation(s)
- Christopher D. Boone
- Biochemistry & Molecular Biology, University of Florida, P.O. Box 100245, Gainesville, FL, 32610, USA
| | - Valerio Rasi
- Biochemistry & Molecular Biology, University of Florida, P.O. Box 100245, Gainesville, FL, 32610, USA
| | - Chingkuang Tu
- Pharmacology & Therapeutics, University of Florida, P.O. Box 100267, Gainesville, FL, 32610, USA
| | - Robert McKenna
- Biochemistry & Molecular Biology, University of Florida, P.O. Box 100245, Gainesville, FL, 32610, USA,Corresponding author. FAX (352) 392-3422;
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Reddi R, Arya T, Kishor C, Gumpena R, Ganji RJ, Bhukya S, Addlagatta A. Selective targeting of the conserved active site cysteine ofMycobacterium tuberculosismethionine aminopeptidase with electrophilic reagents. FEBS J 2014; 281:4240-8. [DOI: 10.1111/febs.12847] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 05/07/2014] [Accepted: 05/14/2014] [Indexed: 11/29/2022]
Affiliation(s)
- Ravikumar Reddi
- Center for Chemical Biology; CSIR-Indian Institute of Chemical Technology; Hyderabad Telengana India
| | - Tarun Arya
- Center for Chemical Biology; CSIR-Indian Institute of Chemical Technology; Hyderabad Telengana India
| | - Chandan Kishor
- Center for Chemical Biology; CSIR-Indian Institute of Chemical Technology; Hyderabad Telengana India
| | - Rajesh Gumpena
- Center for Chemical Biology; CSIR-Indian Institute of Chemical Technology; Hyderabad Telengana India
| | - Roopa J. Ganji
- Center for Chemical Biology; CSIR-Indian Institute of Chemical Technology; Hyderabad Telengana India
| | - Supriya Bhukya
- Center for Chemical Biology; CSIR-Indian Institute of Chemical Technology; Hyderabad Telengana India
| | - Anthony Addlagatta
- Center for Chemical Biology; CSIR-Indian Institute of Chemical Technology; Hyderabad Telengana India
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16
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Zeng J, Gao X, Dai Z, Tang B, Tang XF. Effects of metal ions on stability and activity of hyperthermophilic pyrolysin and further stabilization of this enzyme by modification of a Ca2+-binding site. Appl Environ Microbiol 2014; 80:2763-72. [PMID: 24561589 PMCID: PMC3993279 DOI: 10.1128/aem.00006-14] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Accepted: 02/16/2014] [Indexed: 11/20/2022] Open
Abstract
Pyrolysin is an extracellular subtilase produced by the marine hyperthermophilic archaeon Pyrococcus furiosus. This enzyme functions at high temperatures in seawater, but little is known about the effects of metal ions on the properties of pyrolysin. Here, we report that the supplementation of Na(+), Ca(2+), or Mg(2+) salts at concentrations similar to those in seawater destabilizes recombinant pyrolysin but leads to an increase in enzyme activity. The destabilizing effect of metal ions on pyrolysin appears to be related to the disturbance of surface electrostatic interactions of the enzyme. In addition, mutational analysis of two predicted high-affinity Ca(2+)-binding sites (Ca1 and Ca2) revealed that the binding of Ca(2+) is important for the stabilization of this enzyme. Interestingly, Asn substitutions at residues Asp818 and Asp820 of the Ca2 site, which is located in the C-terminal extension of pyrolysin, resulted in improvements in both enzyme thermostability and activity without affecting Ca(2+)-binding affinity. These effects were most likely due to the elimination of unfavorable electrostatic repulsion at the Ca2 site. Together, these results suggest that metal ions play important roles in modulating the stability and activity of pyrolysin.
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Affiliation(s)
- Jing Zeng
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Xiaowei Gao
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Zheng Dai
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Bing Tang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
- Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Wuhan, China
| | - Xiao-Feng Tang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
- Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Wuhan, China
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17
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Besio R, Baratto MC, Gioia R, Monzani E, Nicolis S, Cucca L, Profumo A, Casella L, Basosi R, Tenni R, Rossi A, Forlino A. A Mn(II)–Mn(II) center in human prolidase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:197-204. [DOI: 10.1016/j.bbapap.2012.09.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Revised: 09/10/2012] [Accepted: 09/12/2012] [Indexed: 12/20/2022]
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18
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Eichler J, Maupin-Furlow J. Post-translation modification in Archaea: lessons from Haloferax volcanii and other haloarchaea. FEMS Microbiol Rev 2012; 37:583-606. [PMID: 23167813 DOI: 10.1111/1574-6976.12012] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Revised: 11/13/2012] [Accepted: 11/13/2012] [Indexed: 01/11/2023] Open
Abstract
As an ever-growing number of genome sequences appear, it is becoming increasingly clear that factors other than genome sequence impart complexity to the proteome. Of the various sources of proteomic variability, post-translational modifications (PTMs) most greatly serve to expand the variety of proteins found in the cell. Likewise, modulating the rates at which different proteins are degraded also results in a constantly changing cellular protein profile. While both strategies for generating proteomic diversity are adopted by organisms across evolution, the responsible pathways and enzymes in Archaea are often less well described than are their eukaryotic and bacterial counterparts. Studies on halophilic archaea, in particular Haloferax volcanii, originally isolated from the Dead Sea, are helping to fill the void. In this review, recent developments concerning PTMs and protein degradation in the haloarchaea are discussed.
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Affiliation(s)
- Jerry Eichler
- Department of Life Sciences, Ben Gurion University, Beersheva, Israel.
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19
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Fujii Y, Dohmae N, Takio K, Kawsar SMA, Matsumoto R, Hasan I, Koide Y, Kanaly RA, Yasumitsu H, Ogawa Y, Sugawara S, Hosono M, Nitta K, Hamako J, Matsui T, Ozeki Y. A lectin from the mussel Mytilus galloprovincialis has a highly novel primary structure and induces glycan-mediated cytotoxicity of globotriaosylceramide-expressing lymphoma cells. J Biol Chem 2012; 287:44772-83. [PMID: 23093409 DOI: 10.1074/jbc.m112.418012] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A novel lectin structure was found for a 17-kDa α-D-galactose-binding lectin (termed "MytiLec") isolated from the Mediterranean mussel, Mytilus galloprovincialis. The complete primary structure of the lectin was determined by Edman degradation and mass spectrometric analysis. MytiLec was found to consist of 149 amino acids with a total molecular mass of 16,812.59 Da by Fourier transform-ion cyclotron resonance mass spectrometry, in good agreement with the calculated value of 16,823.22 Da. MytiLec had an N terminus of acetylthreonine and a primary structure that was highly novel in comparison with those of all known lectins in the structure database. The polypeptide structure consisted of three tandem-repeat domains of ∼50 amino acids each having 45-52% homology with each other. Frontal affinity chromatography technology indicated that MytiLec bound specifically to globotriose (Gb3; Galα1-4Galβ1-4Glc), the epitope of globotriaosylceramide. MytiLec showed a dose-dependent cytotoxic effect on human Burkitt lymphoma Raji cells (which have high surface expression of Gb3) but had no such effect on erythroleukemia K562 cells (which do not express Gb3). The cytotoxic effect of MytiLec was specifically blocked by the co-presence of an α-galactoside. MytiLec treatment of Raji cells caused increased binding of anti-annexin V antibody and incorporation of propidium iodide, which are indicators of cell membrane inversion and perforation. MytiLec is the first reported lectin having a primary structure with the highly novel triple tandem-repeat domain and showing transduction of apoptotic signaling against Burkitt lymphoma cells by interaction with a glycosphingolipid-enriched microdomain containing Gb3.
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Affiliation(s)
- Yuki Fujii
- Laboratory of Glycobiology and Marine Biochemistry, Department of Life and Environmental System Science, Graduate School of NanoBio Sciences, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama 236-0027, Japan
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20
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Matsuura Y, Takehira M, Sawano M, Ogasahara K, Tanaka T, Yamamoto H, Kunishima N, Katoh E, Yutani K. Role of charged residues in stabilization of Pyrococcus horikoshii CutA1, which has a denaturation temperature of nearly 150 °C. FEBS J 2011; 279:78-90. [DOI: 10.1111/j.1742-4658.2011.08400.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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21
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Bao-Hui Y, Xiao-Ming C. Syntheses, Characterization and Equilibrium between Mono-and Aqua-bridged Dicobalt(II) Complexes. A Structural Model for Methionine Aminopeptidase. CHINESE J CHEM 2010. [DOI: 10.1002/cjoc.20030210512] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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23
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Structure of a microsporidian methionine aminopeptidase type 2 complexed with fumagillin and TNP-470. Mol Biochem Parasitol 2009; 168:158-67. [PMID: 19660503 DOI: 10.1016/j.molbiopara.2009.07.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2009] [Revised: 07/21/2009] [Accepted: 07/26/2009] [Indexed: 01/14/2023]
Abstract
Microsporidia are protists that have been reported to cause infections in both vertebrates and invertebrates. They have emerged as human pathogens particularly in patients that are immunosuppressed and cases of gastrointestinal infection, encephalitis, keratitis, sinusitis, myositis and disseminated infection are well described in the literature. While benzimidazoles are active against many species of microsporidia, these drugs do not have significant activity against Enterocytozoon bieneusi. Fumagillin and its analogues have been demonstrated to have activity invitro and in animal models of microsporidiosis and human infections due to E. bieneusi. Fumagillin and its analogues inhibit methionine aminopeptidase type 2. Encephalitozoon cuniculi MetAP2 (EcMetAP2) was cloned and expressed as an active enzyme using a baculovirus system. The crystal structure of EcMetAP2 was determined with and without the bound inhibitors fumagillin and TNP-470. This structure classifies EcMetAP2 as a member of the MetAP2c family. The EcMetAP2 structure was used to generate a homology model of the E. bieneusi MetAP2. Comparison of microsporidian MetAP2 structures with human MetAP2 provides insights into the design of inhibitors that might exhibit specificity for microsporidian MetAP2.
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Theriot CM, Tove SR, Grunden AM. Biotechnological applications of recombinant microbial prolidases. ADVANCES IN APPLIED MICROBIOLOGY 2009; 68:99-132. [PMID: 19426854 DOI: 10.1016/s0065-2164(09)01203-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Prolidase is a metallopeptidase that is ubiquitous in nature and has been isolated from mammals, bacteria and archaea. Prolidase specifically hydrolyzes dipeptides with a prolyl residue in the carboxy terminus (NH(2)-X-/-Pro-COOH). Currently, the only solved structure of prolidase is from the hyperthermophilic archaeon Pyrococcus furiosus. This enzyme is of particular interest because it can be used in many biotechnological applications. Prolidase is able to degrade toxic organophosphorus (OP) compounds, namely, by cleaving the P-F and P-O bonds in the nerve agents, sarin and soman. Applications using prolidase to detoxify OP nerve agents include its incorporation into fire-fighting foams and as biosensors for OP compound detection. Prolidases are also employed in the cheese-ripening process to improve cheese taste and texture. In humans, prolidase deficiency (PD) is a rare autosomal recessive disorder that affects the connective tissue. Symptoms of PD include skin lesions, mental retardation and recurrent respiratory infections. Enzyme replacement therapies are currently being studied in an effort to optimize enzyme delivery and stability for this application. Previously, prolidase has been linked to collagen metabolism and more recently is being associated with melanoma. Increased prolidase activity in melanoma cell lines has lead investigators to create cancer prodrugs targeting this enzyme. Thus, there are many biotechnological applications using recombinant and native forms of prolidase and this review will describe the biochemical and structural properties of prolidases as well as discuss their most current applications.
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Affiliation(s)
- Casey M Theriot
- Department of Microbiology, North Carolina State University, Raleigh, North Carolina 27695-7615, USA
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25
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X-ray structure and spectroscopic characterization of divalent dinuclear cobalt complexes containing carboxylate- and phosphodiester- auxiliary bridges. Inorganica Chim Acta 2009. [DOI: 10.1016/j.ica.2009.02.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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26
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Crystal Structural and Functional Analysis of the Putative Dipeptidase from Pyrococcus horikoshii OT3. JOURNAL OF BIOPHYSICS 2009; 2009:434038. [PMID: 20130794 PMCID: PMC2814137 DOI: 10.1155/2009/434038] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2009] [Accepted: 04/30/2009] [Indexed: 12/05/2022]
Abstract
The crystal structure of a putative dipeptidase (Phdpd) from Pyrococcus horikoshii OT3 was solved using X-ray data at 2.4 Å resolution. The protein is folded into two distinct entities. The N-terminal domain consists of the general topology of the α/β fold, and the C-terminal domain consists of five long mixed strands, four helices, and two 310 helices. The structure of Phdpd is quite similar to reported structures of prolidases from P. furiosus (Zn-Pfprol) and P. horikoshii (Zn-Phdpd), where Zn ions are observed in the active site resulting in an inactive form. However, Phdpd did not contain metals in the crystal structure and showed prolidase activity in the absence of additional Co ions, whereas the specific activities increased by 5 times in the presence of a sufficient concentration (1.2 mM) of Co ions. The substrate specificities (X-Pro) of Phdpd were broad compared with those of Zn-Phdpd in the presence of Co ions, whose relative activities are 10% or less for substrates other than Met-Pro, which is the most favorable substrate. The binding constants of Zn-Phdpd with three metals (Zn, Co, and Mn) were higher than those of Phdpd and that with Zn was higher by greater than 2 orders, which were determined by DSC experiments. From the structural comparison of both forms and the above experimental results, it could be elucidated why the protein with Zn2+ ions is inactive.
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27
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Besio R, Alleva S, Forlino A, Lupi A, Meneghini C, Minicozzi V, Profumo A, Stellato F, Tenni R, Morante S. Identifying the structure of the active sites of human recombinant prolidase. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2009; 39:935-45. [DOI: 10.1007/s00249-009-0459-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2009] [Revised: 03/26/2009] [Accepted: 04/07/2009] [Indexed: 10/20/2022]
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28
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Ganguli S, Yoshimoto K, Tomita S, Sakuma H, Matsuoka T, Shiraki K, Nagasaki Y. Regulation of Lysozyme Activity Based on Thermotolerant Protein/Smart Polymer Complex Formation. J Am Chem Soc 2009; 131:6549-53. [DOI: 10.1021/ja900786z] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sumon Ganguli
- Graduate School of Pure and Applied Science, University of Tsukuba, 1-1-1 Ten-noudai, Tsukuba, Ibaraki 305-8573, Japan, Center for Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Ten-noudai 1-1-1, Tsukuba 305-8577, Japan, Tsukuba Research Center for Interdisciplinary Materials Science (TIMS), University of Tsukuba, 1-1-1 Ten-noudai, Tsukuba, Ibaraki 305-8571, Japan, Master’s School of Medical Science, Graduate School of Comprehensive Human Sciences, University of Tsukuba, 1-1-1 Ten
| | - Keitaro Yoshimoto
- Graduate School of Pure and Applied Science, University of Tsukuba, 1-1-1 Ten-noudai, Tsukuba, Ibaraki 305-8573, Japan, Center for Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Ten-noudai 1-1-1, Tsukuba 305-8577, Japan, Tsukuba Research Center for Interdisciplinary Materials Science (TIMS), University of Tsukuba, 1-1-1 Ten-noudai, Tsukuba, Ibaraki 305-8571, Japan, Master’s School of Medical Science, Graduate School of Comprehensive Human Sciences, University of Tsukuba, 1-1-1 Ten
| | - Shunsuke Tomita
- Graduate School of Pure and Applied Science, University of Tsukuba, 1-1-1 Ten-noudai, Tsukuba, Ibaraki 305-8573, Japan, Center for Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Ten-noudai 1-1-1, Tsukuba 305-8577, Japan, Tsukuba Research Center for Interdisciplinary Materials Science (TIMS), University of Tsukuba, 1-1-1 Ten-noudai, Tsukuba, Ibaraki 305-8571, Japan, Master’s School of Medical Science, Graduate School of Comprehensive Human Sciences, University of Tsukuba, 1-1-1 Ten
| | - Hiroshi Sakuma
- Graduate School of Pure and Applied Science, University of Tsukuba, 1-1-1 Ten-noudai, Tsukuba, Ibaraki 305-8573, Japan, Center for Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Ten-noudai 1-1-1, Tsukuba 305-8577, Japan, Tsukuba Research Center for Interdisciplinary Materials Science (TIMS), University of Tsukuba, 1-1-1 Ten-noudai, Tsukuba, Ibaraki 305-8571, Japan, Master’s School of Medical Science, Graduate School of Comprehensive Human Sciences, University of Tsukuba, 1-1-1 Ten
| | - Tsuneyoshi Matsuoka
- Graduate School of Pure and Applied Science, University of Tsukuba, 1-1-1 Ten-noudai, Tsukuba, Ibaraki 305-8573, Japan, Center for Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Ten-noudai 1-1-1, Tsukuba 305-8577, Japan, Tsukuba Research Center for Interdisciplinary Materials Science (TIMS), University of Tsukuba, 1-1-1 Ten-noudai, Tsukuba, Ibaraki 305-8571, Japan, Master’s School of Medical Science, Graduate School of Comprehensive Human Sciences, University of Tsukuba, 1-1-1 Ten
| | - Kentaro Shiraki
- Graduate School of Pure and Applied Science, University of Tsukuba, 1-1-1 Ten-noudai, Tsukuba, Ibaraki 305-8573, Japan, Center for Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Ten-noudai 1-1-1, Tsukuba 305-8577, Japan, Tsukuba Research Center for Interdisciplinary Materials Science (TIMS), University of Tsukuba, 1-1-1 Ten-noudai, Tsukuba, Ibaraki 305-8571, Japan, Master’s School of Medical Science, Graduate School of Comprehensive Human Sciences, University of Tsukuba, 1-1-1 Ten
| | - Yukio Nagasaki
- Graduate School of Pure and Applied Science, University of Tsukuba, 1-1-1 Ten-noudai, Tsukuba, Ibaraki 305-8573, Japan, Center for Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Ten-noudai 1-1-1, Tsukuba 305-8577, Japan, Tsukuba Research Center for Interdisciplinary Materials Science (TIMS), University of Tsukuba, 1-1-1 Ten-noudai, Tsukuba, Ibaraki 305-8571, Japan, Master’s School of Medical Science, Graduate School of Comprehensive Human Sciences, University of Tsukuba, 1-1-1 Ten
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Analyzing the binding of Co(II)-specific inhibitors to the methionyl aminopeptidases from Escherichia coli and Pyrococcus furiosus. J Biol Inorg Chem 2009; 14:573-85. [PMID: 19198897 DOI: 10.1007/s00775-009-0471-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2008] [Accepted: 12/31/2008] [Indexed: 10/21/2022]
Abstract
Methionine aminopeptidases (MetAPs) represent a unique class of protease that is capable of the hydrolytic removal of an N-terminal methionine residue from nascent polypeptide chains. MetAPs are physiologically important enzymes; hence, there is considerable interest in developing inhibitors that can be used as antiangiogenic and antimicrobial agents. A detailed kinetic and spectroscopic study has been performed to probe the binding of a triazole-based inhibitor and a bestatin-based inhibitor to both Mn(II)- and Co(II)-loaded type-I (Escherichia coli) and type-II (Pyrococcus furiosus) MetAPs. Both inhibitors were found to be moderate competitive inhibitors. The triazole-type inhibitor was found to interact with both active-site metal ions, while the bestatin-type inhibitor was capable of switching its mode of binding depending on the metal in the active site and the type of MetAP enzyme.
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Mitra S, Bennett B, Holz RC. Mutation of H63 and its catalytic affect on the methionine aminopeptidase from Escherichia coli. BIOCHIMICA ET BIOPHYSICA ACTA 2009; 1794:137-143. [PMID: 18952013 PMCID: PMC2674292 DOI: 10.1016/j.bbapap.2008.09.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2008] [Revised: 09/11/2008] [Accepted: 09/13/2008] [Indexed: 05/27/2023]
Abstract
In order to gain insight into the mechanistic role of a flexible exterior loop near the active site, made up of Y62, H63, G64, and Y65, that has been proposed to play an important role in substrate binding and recognition in the methionyl aminopeptidase from Escherichia coli (EcMetAP-I), the H63A enzyme was prepared. Mutation of H63 to alanine does not affect the ability of the enzyme to bind divalent metal ions. The specific activity of H63A EcMetAP-I was determined using four different substrates of varying lengths, namely, l-Met-p-NA, MAS, MGMM and MSSHRWDW. For the smallest/shortest substrate (l-Met-p-NA) the specific activity decreased nearly seven fold but as the peptide length increased, the specific activity also increased and became comparable to WT EcMetAP-I. This decrease in specific activity is primarily due to a decrease in the observed k(cat) values, which decreases nearly sixty-fold for l-Met-p-NA while only a four-fold decrease is observed for the tri- and tetra-peptide substrates. Interestingly, no change in k(cat) was observed when the octa-peptide MSSHRWDW was used as a substrate. These data suggest that H63 affects the hydrolysis of small peptide substrates whereas large peptides can overcome the observed loss in binding energy, as predicted from K(m) values, by additional hydrophilic and hydrophobic interactions.
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Affiliation(s)
- Sanghamitra Mitra
- Department of Chemistry, Boston University, Boston, MA 02215-2521, USA
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Mitra S, Job KM, Meng L, Bennett B, Holz RC. Analyzing the catalytic role of Asp97 in the methionine aminopeptidase from Escherichia coli. FEBS J 2008; 275:6248-59. [PMID: 19019076 DOI: 10.1111/j.1742-4658.2008.06749.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An active site aspartate residue, Asp97, in the methionine aminopeptidase (MetAPs) from Escherichia coli (EcMetAP-I) was mutated to alanine, glutamate, and asparagine. Asp97 is the lone carboxylate residue bound to the crystallographically determined second metal-binding site in EcMetAP-I. These mutant EcMetAP-I enzymes have been kinetically and spectroscopically characterized. Inductively coupled plasma-atomic emission spectroscopy analysis revealed that 1.0 +/- 0.1 equivalents of cobalt were associated with each of the Asp97-mutated EcMetAP-Is. The effect on activity after altering Asp97 to alanine, glutamate or asparagine is, in general, due to a approximately 9000-fold decrease in k(ca) towards Met-Gly-Met-Met as compared to the wild-type enzyme. The Co(II) d-d spectra for wild-type, D97E and D97A EcMetAP-I exhibited very little difference in form, in each case, between the monocobalt(II) and dicobalt(II) EcMetAP-I, and only a doubling of intensity was observed upon addition of a second Co(II) ion. In contrast, the electronic absorption spectra of [Co_(D97N EcMetAP-I)] and [CoCo(D97N EcMetAP-I)] were distinct, as were the EPR spectra. On the basis of the observed molar absorptivities, the Co(II) ions binding to the D97E, D97A and D97N EcMetAP-I active sites are pentacoordinate. Combination of these data suggests that mutating the only nonbridging ligand in the second divalent metal-binding site in MetAPs to an alanine, which effectively removes the ability of the enzyme to form a dinuclear site, provides a MetAP enzyme that retains catalytic activity, albeit at extremely low levels. Although mononuclear MetAPs are active, the physiologically relevant form of the enzyme is probably dinuclear, given that the majority of the data reported to date are consistent with weak cooperative binding.
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Affiliation(s)
- Sanghamitra Mitra
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT, USA
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Watterson SJ, Mitra S, Swierczek SI, Bennett B, Holz RC. Kinetic and spectroscopic analysis of the catalytic role of H79 in the methionine aminopeptidase from Escherichia coli. Biochemistry 2008; 47:11885-93. [PMID: 18855426 DOI: 10.1021/bi801499g] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
To gain insight into the role of the strictly conserved histidine residue, H79, in the reaction mechanism of the methionyl aminopeptidase from Escherichia coli ( EcMetAP-I), the H79A mutated enzyme was prepared. Co(II)-loaded H79A exhibits an overall >7000-fold decrease in specific activity. The almost complete loss of activity is primarily due to a >6000-fold decrease in k cat. Interestingly, the K m value obtained for Co(II)-loaded H79A was approximately half the value observed for wild-type (WT) EcMetAP-I. Consequently, k cat/ K m values decreased only 3000-fold. On the other hand, the observed specific activity of Mn(II)-loaded H79A EcMetAP-I decreased by approximately 2.6-fold while k cat decreased by approximately 3.5-fold. The observed K m value for Mn(II)-loaded H79A EcMetAP-I was approximately 1.4-fold larger than that observed for WT EcMetAP-I, resulting in a k cat/ K m value that is lower by approximately 3.4-fold. Metal binding, UV-vis, and EPR data indicate that the active site is unperturbed by mutation of H79, as suggested by X-ray crystallographic data. Kinetic isotope data indicate that H79 does not transfer a proton to the newly forming amine since a single proton is transferred in the transition state for both the WT and H79A EcMetAP-I enzymes. Therefore, H79 functions to position the substrate by hydrogen bonding to either the amine group of the peptide linkage or a backbone carbonyl group. Together, these data provide new insight into the catalytic mechanism of EcMetAP-I.
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Affiliation(s)
- Sarah J Watterson
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, USA
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Hernández-Rocamora VM, Maestro B, Mollá-Morales A, Sanz JM. Rational stabilization of the C-LytA affinity tag by protein engineering. Protein Eng Des Sel 2008; 21:709-20. [PMID: 18840883 DOI: 10.1093/protein/gzn046] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The C-LytA protein constitutes the choline-binding module of the LytA amidase from Streptococcus pneumoniae. Owing to its affinity for choline and analogs, it is regularly used as an affinity tag for the purification of proteins in a single chromatographic step. In an attempt to build a robust variant against thermal denaturation, we have engineered several salt bridges on the protein surface. All the stabilizing mutations were pooled in a single variant, C-LytAm7, which contained seven changes: Y25K, F27K, M33E, N51K, S52K, T85K and T108K. The mutant displays a 7 degrees C thermal stabilization compared with the wild-type form, together with a complete reversibility upon heating and a higher kinetic stability. Moreover, the accumulation of intermediates in the unfolding of C-LytA is virtually abolished for C-LytAm7. The differences in stability become more evident when the proteins are bound to a DEAE-cellulose affinity column, as most of wild-type C-LytA is denatured at approximately 65 degrees C, whereas C-LytAm7 may stand temperatures up to 90 degrees C. Finally, the change in the isoelectric point of C-LytAm7 enhances its solubility at acidic pHs. Therefore, C-LytAm7 behaves as an improved affinity tag and supports the engineering of surface salt bridges as an effective approach for protein stabilization.
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Affiliation(s)
- Víctor M Hernández-Rocamora
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Avda Universidad s/n, Elche 03202, Spain
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Yamamoto H, Miwa H, Kunishima N. Crystal Structure of Glucose-6-Phosphate Isomerase from Thermus thermophilus HB8 Showing a Snapshot of Active Dimeric State††H.Y. performed structural determination and biochemical and biophysical experiments, and wrote this paper. H.M. contributed to large-scale protein production. N.K. supervised this work. J Mol Biol 2008; 382:747-62. [DOI: 10.1016/j.jmb.2008.07.041] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2008] [Revised: 07/11/2008] [Accepted: 07/16/2008] [Indexed: 11/26/2022]
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Hu XV, Chen X, Han KC, Mildvan AS, Liu JO. Kinetic and Mutational Studies of the Number of Interacting Divalent Cations Required by Bacterial and Human Methionine Aminopeptidases. Biochemistry 2007; 46:12833-43. [DOI: 10.1021/bi701127x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xiaoyi V. Hu
- Departments of Pharmacology and Molecular Sciences and Biological Chemistry and Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, Maryland 21205
| | - Xiaochun Chen
- Departments of Pharmacology and Molecular Sciences and Biological Chemistry and Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, Maryland 21205
| | - Kee Chung Han
- Departments of Pharmacology and Molecular Sciences and Biological Chemistry and Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, Maryland 21205
| | - Albert S. Mildvan
- Departments of Pharmacology and Molecular Sciences and Biological Chemistry and Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, Maryland 21205
| | - Jun O. Liu
- Departments of Pharmacology and Molecular Sciences and Biological Chemistry and Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, Maryland 21205
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Takano K, Katagiri Y, Mukaiyama A, Chon H, Matsumura H, Koga Y, Kanaya S. Conformational contagion in a protein: structural properties of a chameleon sequence. Proteins 2007; 68:617-25. [PMID: 17510955 DOI: 10.1002/prot.21451] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Certain sequences, known as chameleon sequences, take both alpha- and beta-conformations in natural proteins. We demonstrate that a wild chameleon sequence fused to the C-terminal alpha-helix or beta-sheet in foreign stable proteins from hyperthermophiles forms the same conformation as the host secondary structure. However, no secondary structural formation is observed when the sequence is attached to the outside of the secondary structure. These results indicate that this sequence inherently possesses an ability to make either alpha- or beta-conformation, depending on the sequentially neighboring secondary structure if little other nonlocal interaction occurs. Thus, chameleon sequences take on a satellite state through contagion by the power of a secondary structure. We propose this "conformational contagion" as a new nonlocal determinant factor in protein structure and misfolding related to protein conformational diseases.
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Affiliation(s)
- Kazufumi Takano
- Department of Material and Life Science, Osaka University, Suita, Japan.
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Monie TP, Perrin AJ, Birtley JR, Sweeney TR, Karakasiliotis I, Chaudhry Y, Roberts LO, Matthews S, Goodfellow IG, Curry S. Structural insights into the transcriptional and translational roles of Ebp1. EMBO J 2007; 26:3936-44. [PMID: 17690690 PMCID: PMC1994118 DOI: 10.1038/sj.emboj.7601817] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2007] [Accepted: 07/11/2007] [Indexed: 11/08/2022] Open
Abstract
The ErbB3-binding protein 1 (Ebp1) is an important regulator of transcription, affecting eukaryotic cell growth, proliferation, differentiation and survival. Ebp1 can also affect translation and cooperates with the polypyrimidine tract-binding protein (PTB) to stimulate the activity of the internal ribosome entry site (IRES) of foot-and-mouth disease virus (FMDV). We report here the crystal structure of murine Ebp1 (p48 isoform), providing the first glimpse of the architecture of this versatile regulator. The structure reveals a core domain that is homologous to methionine aminopeptidases, coupled to a C-terminal extension that contains important motifs for binding proteins and RNA. It sheds new light on the conformational differences between the p42 and p48 isoforms of Ebp1, the disposition of the key protein-interacting motif ((354)LKALL(358)) and the RNA-binding activity of Ebp1. We show that the primary RNA-binding site is formed by a Lys-rich motif in the C terminus and mediates the interaction with the FMDV IRES. We also demonstrate a specific functional requirement for Ebp1 in FMDV IRES-directed translation that is independent of a direct interaction with PTB.
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Affiliation(s)
- Tom P Monie
- Division of Cell and Molecular Biology, Imperial College, South Kensington Campus, London, UK
| | - Andrew J Perrin
- Division of Cell and Molecular Biology, Imperial College, South Kensington Campus, London, UK
| | - James R Birtley
- Division of Cell and Molecular Biology, Imperial College, South Kensington Campus, London, UK
| | - Trevor R Sweeney
- Division of Cell and Molecular Biology, Imperial College, South Kensington Campus, London, UK
| | | | - Yasmin Chaudhry
- Department of Virology, Faculty of Medicine, Imperial College London, London, UK
| | - Lisa O Roberts
- School of Biomedical and Molecular Sciences, University of Surrey, Guildford, Surrey, UK
| | | | - Ian G Goodfellow
- Department of Virology, Faculty of Medicine, Imperial College London, London, UK
| | - Stephen Curry
- Division of Cell and Molecular Biology, Imperial College, South Kensington Campus, London, UK
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Tanaka Y, Sasaki T, Kumagai I, Yasutake Y, Yao M, Tanaka I, Tsumoto K. Molecular properties of two proteins homologous to PduO-type ATP:cob(I)alamin adenosyltransferase from Sulfolobus tokodaii. Proteins 2007; 68:446-57. [PMID: 17492665 DOI: 10.1002/prot.21303] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
In the thermophilic archaeon Sulfolobus tokodaii, there are two genes homologous to PduO-type ATP:cob(I)alamin adenosyltransferase, ST1454 and ST2180. To address the structure and function of these two sequence-related proteins from one organism, we prepared them by using the Escherichia coli expression system and analyzed them by immunoblotting, matrix-assisted laser desorption ionization-time-of-flight mass spectroscopy, circular dichroism spectrometry, ATP:cobalamin adenosyltransferase assay, and X-ray crystallography. Immunoblotting and matrix-assisted laser desorption ionization-time-of-flight mass spectroscopy analyses showed that both these proteins are expressed in S. tokodaii cells as soluble proteins and are spontaneously digested at the N-terminal region. ATP:cob(I)alamin adenosyltransferase activity was detected for ST1454 but not for ST2180. ST2180 reduced the concentration of cob(I)alamin, suggesting that ST2180 might recognize cob(I)alamin as a ligand. The secondary structure of ST1454 was retained even in 7 M guanidine hydrochroride, whereas that of ST2180 was melted in 4.5 M guanidine hydrochloride. The X-ray crystal structural analysis revealed that the proteins shared a common structure: a trimer of five-helix bundles with a clockwise kink. There is a pocket surrounded by highly conserved residues, in which a polypropylene glycol 400 in the crystal structure of ST1454 was captured, suggesting that it is an active site. Structural comparison between these two proteins showed the difference in the number of ion pairs around the proposed active site. On the basis of these results, we propose that ST1454 and ST2180 have related but distinct functions.
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Affiliation(s)
- Yoshikazu Tanaka
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
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40
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Meinnel T, Serero A, Giglione C. Impact of the N-terminal amino acid on targeted protein degradation. Biol Chem 2006; 387:839-51. [PMID: 16913833 DOI: 10.1515/bc.2006.107] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The N-terminus of any protein may be used as a destabilization signal for targeted protein degradation. In the eukaryotic cytosol, the signal - the so-called N-degron--is recognized for degradation by (i) the N-end rule, a well-described degradation process involving epsilon-ubiquitination; or (ii) N-terminal ubiquitination, a more recently described pathway. Dedicated E3 ubiquitin ligases known as N-recognins then act on the protein. The proteolytic pathways involve ATP-dependent chambered proteases, such as the 26S proteasome in the cytosol, which generate short oligopeptides. The N-terminus of the polypeptide chain is also important for post-proteasome degradation by specific aminopeptidases, which complete peptide cleavage to generate free amino acids. Finally, in each compartment of the eukaryotic cell, N-terminal methionine excision creates a variety of N-termini for mature proteins. It has recently been shown that the N-terminal methionine excision pathway has a major impact early in targeted protein degradation.
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Affiliation(s)
- Thierry Meinnel
- Protein Maturation, Cell Fate and Therapeutics, Institut des Sciences du Végétal, UPR2355, Centre National de la Recherche Scientifique, Bâtiment 23, 1 avenue de la Terrasse, F-91198 Gif-sur-Yvette cedex, France.
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41
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Tanaka T, Sawano M, Ogasahara K, Sakaguchi Y, Bagautdinov B, Katoh E, Kuroishi C, Shinkai A, Yokoyama S, Yutani K. Hyper-thermostability of CutA1 protein, with a denaturation temperature of nearly 150 °C. FEBS Lett 2006; 580:4224-30. [PMID: 16831434 DOI: 10.1016/j.febslet.2006.06.084] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2006] [Revised: 06/06/2006] [Accepted: 06/27/2006] [Indexed: 10/24/2022]
Abstract
We found that the CutA1 protein, from Pyrococcus horikoshii (PhCutA1), has an extremely high denaturation temperature (T(d)) of nearly 150 degrees C, which exceeds the highest record determined by DSC by about 30 degrees C. To elucidate the mechanism of the ultra-high stability of PhCutA1, we analyzed the crystal structures of CutA1 proteins from three different sources, P. horikoshii, Thermus thermophilus, and Escherichia coli, with different growth temperatures (98, 75, and 37 degrees C). This analysis revealed that the remarkably increased number of ion pairs in the monomeric structure contributes to the stabilization of the trimeric structure and plays an important role in enhancing the T(d), up to 150 degrees C, for PhCutA1.
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Affiliation(s)
- Tomoyuki Tanaka
- RIKEN SPring-8 Center, Harima Institute, Kouto, Sayo, Hyogo 679-5148, Japan
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42
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Lee HS, Kim YJ, Bae SS, Jeon JH, Lim JK, Jeong BC, Kang SG, Lee JH. Cloning, expression, and characterization of a methionyl aminopeptidase from a hyperthermophilic archaeon Thermococcus sp. NA1. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2006; 8:425-32. [PMID: 16761197 DOI: 10.1007/s10126-005-6124-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2005] [Accepted: 01/13/2006] [Indexed: 05/10/2023]
Abstract
Genomic analysis of a hyperthermophilic archaeon Thermococcus sp. NA1 revealed the presence of an 885-bp open reading frame encoding a protein of 295 amino acids with a calculated molecular mass of 32,981 Da. Analysis of the deduced amino acid sequence showed that amino acid residues important for catalytic activity and the metal binding ligands conserved in all of methionyl aminopeptidases (MetAP) were also conserved and belonged to type IIa MetAP. The protein, designated TNA1_MetAP (Thermococcus sp. NA1 MetAP), was cloned and expressed in Escherichia coli. The recombinant enzyme was a Mn(2+)-, Ni(2+)-, Fe(2+)-, or Co(2+)-dependent metallopeptidase. Optimal MetAP activity against L: -methionine p-nitroanilide (Met-pNA) (K (m) = 0.68 mM) occurred at pH 7.0 and 80 to 90 degrees C. The MetAP was very unstable compared to Pyrococcus furiosus MetAP, which was completely inactivated by heating at 80 degrees C for 5 min. It seemed likely that the cysteine residue (Cys53) played a critical role in regulating the thermostability of TNA1_MetAP.
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Affiliation(s)
- H S Lee
- Korean Ocean Research & Development Institute, Ansan, P.O. Box 29, Seoul, 425-600, Korea.
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43
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Mitra S, Dygas-Holz AM, Jiracek J, Zertova M, Zakova L, Holz RC. A new colorimetric assay for methionyl aminopeptidases: examination of the binding of a new class of pseudopeptide analog inhibitors. Anal Biochem 2006; 357:43-9. [PMID: 16844071 DOI: 10.1016/j.ab.2006.06.012] [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] [Received: 04/20/2006] [Revised: 06/07/2006] [Accepted: 06/09/2006] [Indexed: 11/18/2022]
Abstract
A direct and convenient spectrophotometric assay has been developed for methionine aminopeptidases (MetAPs). The method employs the hydrolysis of a substrate that is a methionyl analogue of p-nitroaniline (L-Met-p-NA), which releases the chromogenic product p-nitroaniline. This chromogenic product can be monitored continuously using a UV-Vis spectrophotometer set at 405 nm. The assay was tested with the type I MetAP from Escherichia coli (EcMetAP-I) and the type II MetAP from Pyrococcus furiosus (PfMetAP-II). Using L-Met-p-NA, the kinetic constants k(cat) and K(m) were determined for EcMetAP-I and PfMetAP-II and were compared with those obtained with a "standard" high-performance liquid chromatography (HPLC) discontinuous assay. The assay has also been used to determine the temperature dependence of the kinetic constant k(cat) for PfMetAP-II as well as to screen two novel pseudopeptide inhibitors of MetAPs. The results demonstrate that L-Met-p-NA provides a fast, convenient, and effective substrate for both type I and type II MetAPs and that this substrate can be used to quickly screen inhibitors of MetAPs.
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Affiliation(s)
- Sanghamitra Mitra
- Department of Chemistry and Biochemistry, Utah State University, Logan, 84322, USA
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44
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Asada Y, Sawano M, Ogasahara K, Nakamura J, Ota M, Kuroishi C, Sugahara M, Yutani K, Kunishima N. Stabilization mechanism of the tryptophan synthase alpha-subunit from Thermus thermophilus HB8: X-ray crystallographic analysis and calorimetry. J Biochem 2006; 138:343-53. [PMID: 16272128 DOI: 10.1093/jb/mvi133] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In order to elucidate the thermo-stabilization mechanism of the tryptophan synthase alpha-subunit from the extreme thermophile Thermus thermophilus HB8 (Tt-alpha-subunit), its crystal structure was determined and its stability was examined using DSC. The results were compared to those of other orthologs from mesophilic and hyperthermophilic organisms. The denaturation temperature of the Tt-alpha-subunit was higher than that of the alpha-subunit from S. typhimurium (St-alpha-subunit) but lower than that of the alpha-subunit from P. furiosus (Pf-alpha-subunit). Specific denaturation enthalpy and specific denaturation heat capacity values of the Tt-alpha-subunit were the lowest among the three proteins, suggesting that entropy effects are responsible for the stabilization of the Tt-alpha-subunit. Based on a structural comparison with the St-alpha-subunit, two deletions in loop regions, an increase in the number of ion pairs and a decrease in cavity volume seem to be responsible for the stabilization of the Tt-alpha-subunit. The results of structural comparison suggest that the native structure of the Tt-alpha-subunit is better adapted to an ideally stable structure than that of the St-alpha-subunit, but worse than that of the Pf-alpha-subunit. The results of calorimetry suggest that the residual structure of the Tt-alpha-subunit in the denatured state contributes to the stabilization.
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Affiliation(s)
- Yukuhiko Asada
- Advanced Protein Crystallography Research Group, RIKEN Harima Institute at SPring-8, 1-1-1 Kouto, Mikazuki-cho, Sayo-gun, Hyogo 679-5148
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45
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De Castro RE, Maupin-Furlow JA, Giménez MI, Herrera Seitz MK, Sánchez JJ. Haloarchaeal proteases and proteolytic systems. FEMS Microbiol Rev 2006; 30:17-35. [PMID: 16438678 DOI: 10.1111/j.1574-6976.2005.00003.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Proteases play key roles in many biological processes and have numerous applications in biotechnology and industry. Recent advances in the genetics, genomics and biochemistry of the halophilic Archaea provide a tremendous opportunity for understanding proteases and their function in the context of an archaeal cell. This review summarizes our current knowledge of haloarchaeal proteases and provides a reference for future research.
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Affiliation(s)
- Rosana E De Castro
- Instituto de Investigaciones Biológicas, Facultad de Ciencias Exactas y Naturales Universidad Nacional de Mar del Plata, Mar del Plata, Argentina.
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46
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47
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Du X, Tove S, Kast-Hutcheson K, Grunden AM. Characterization of the dinuclear metal center ofPyrococcus furiosusprolidase by analysis of targeted mutants. FEBS Lett 2005; 579:6140-6. [PMID: 16243319 DOI: 10.1016/j.febslet.2005.09.086] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2005] [Revised: 09/27/2005] [Accepted: 09/28/2005] [Indexed: 11/24/2022]
Abstract
Prolidases are dipeptidases specific for cleavage of Xaa-Pro dipeptides. Pyrococcus furiosus prolidase is a homodimer having one Co-bound dinuclear metal cluster per monomer with one tightly bound Co(II) site and the other loosely bound (Kd 0.24 mM). To identify which Co site is tight-binding and which is loose-binding, site-directed mutagenesis was used to modify amino acid residues that participate in binding the Co1 (E-313 and H-284), the Co2 site (D-209) or the bidentate ligand (E-327). Metal-content, enzyme activity and CD-spectra analyses of D209A-, H284L-, and E327L-prolidase mutants show that Co1 is the tight-binding and Co2 the loose-binding metal center.
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Affiliation(s)
- Xuelian Du
- Department of Microbiology, North Carolina State University, Box 7615, Raleigh, NC 27695, USA
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Swierczek K, Copik AJ, Swierczek SI, Holz RC. Molecular Discrimination of Type-I over Type-II Methionyl Aminopeptidases. Biochemistry 2005; 44:12049-56. [PMID: 16142902 DOI: 10.1021/bi047752g] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Two residues that are conserved in type-I methionyl aminopeptidases (MetAPs) but are absent in all type-II MetAPs are the cysteine residues (Escherichia coli MetAP-I: C59 and C70) that reside at the back of the substrate recognition pocket. These Cys residues are 4.4 A apart and do not form a disulfide bond. Since bacteria and fungi contain only type-I MetAPs while all human cells contain both type-I and type-II MetAPs, type-I MetAPs represent a novel antibiotic/antifungal target if type-I MetAPs can be specifically targeted over type-II. Based on reaction of the thiol-specific binding reagent 5,5'-dithio-bis(2-nitrobenzoic acid) (DTNB) with the type-I MetAP from E. coli and the type-II MetAP from Pyrococcus furiosus, the type-I MetAP can be selectively inhibited. Verification that DTNB covalently binds to C59 in EcMetAP-I was obtained by mass spectrometry (MS) from reaction of DTNB with the C59A and C70A mutant EcMetAP-I enzymes. In addition, two inhibitors of EcMetAP-I, 5-iodopentaphosphonic acid (1) and 6-phosphonohexanoic acid (2), were designed and synthesized. The first was designed as a selective-C59 binding reagent while the second was designed as a simple competitive inhibitor of EcMetAP. Indeed, inhibitor 1 forms a covalent interaction with C59 based on activity assays and MS measurements, while 2 does not. These data indicate that type-I MetAPs can be selectively targeted over type-II MetAPs, suggesting that type-I MetAPs represent a new enzymatic target for antibacterial or antifungal agents.
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Affiliation(s)
- Krzysztof Swierczek
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, USA
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49
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Vetro JA, Dummitt B, Micka WS, Chang YH. Evidence of a dominant negative mutant of yeast methionine aminopeptidase type 2 in Saccharomyces cerevisiae. J Cell Biochem 2005; 94:656-68. [PMID: 15547949 DOI: 10.1002/jcb.20285] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Eukaryotic methionine aminopeptidase type 2 (MetAP2, MetAP2 gene (MAP2)), together with eukaryotic MetAP1, cotranslationally hydrolyzes initiator methionine from nascent polypeptides when the side chain of the second residue is small and uncharged. In this report, we took advantage of the yeast (Saccharomyces cerevisiae) map1 null strain's reliance on MetAP2 activity for the growth and viability to provide evidence of the first dominant negative mutant of eukaryotic MetAP2. Replacement of the conserved His(174) with alanine within the C-terminal catalytic domain of yeast MetAP2 eliminated detectable catalytic activity against a peptide substrate in vitro. Overexpression of MetAP2 (H174A) under the strong GPD promoter in a yeast map1 null strain was lethal, whereas overexpression under the weaker GAL1 promoter slightly inhibited map1 null growth. Deletion mutants further revealed that the N-terminal region of MetAP2 (residues 2-57) is essential but not sufficient for MetAP2 (H174A) to fully interfere with map1 null growth. Together, these results indicate that catalytically inactive MetAP2 is a dominant negative mutant that requires its N-terminal region to interfere with wild-type MetAP2 function.
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Affiliation(s)
- Joseph A Vetro
- Edward A. Doisy Department of Biochemistry and Molecular Biology, St. Louis University Health Sciences Center, 1402 S. Grand Blvd., St. Louis, MO 63104, USA
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50
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Lo HF, Chen YH, Hsiao NW, Chen HL, Hu HY, Hsu WH, Lin LL. Stabilization of a truncated Bacillus sp. strain TS-23 α-amylase by replacing histidine-436 with aspartate. World J Microbiol Biotechnol 2005. [DOI: 10.1007/s11274-004-1764-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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