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Manullang C, Singh T, Sakai K, Miyagi A, Iwasaki A, Nojiri Y, Iguchi A. Separate and combined effects of elevated pCO 2 and temperature on the branching reef corals Acropora digitifera and Montipora digitata. MARINE ENVIRONMENTAL RESEARCH 2023; 188:106030. [PMID: 37267662 DOI: 10.1016/j.marenvres.2023.106030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 05/18/2023] [Accepted: 05/22/2023] [Indexed: 06/04/2023]
Abstract
Ocean acidification (OA) and warming (OW) are major global threats to coral reef ecosystems; however, studies on their combined effects (OA + OW) are scarce. Therefore, we evaluated the effects of OA, OW, and OA + OW in the branching reef corals Acropora digitifera and Montipora digitata, which have been found to respond differently to environmental changes. Our results indicate that OW has a greater impact on A. digitifera and M. digitata than OA and that the former species is more vulnerable to OW than the latter. OW was the main stressor for increased mortality and decreased calcification in the OA + OW group, and the effect of OA + OW was additive in both species. Our findings suggest that the relative abundance and cover of M. digitata are expected to increase whereas those of A. digitifera may decrease in the near future in Okinawa.
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Affiliation(s)
- Cristiana Manullang
- Sesoko Station, Tropical Biosphere Research Center, University of the Ryukyus, Motobu, Okinawa, Japan
| | - Tanya Singh
- Sesoko Station, Tropical Biosphere Research Center, University of the Ryukyus, Motobu, Okinawa, Japan
| | - Kazuhiko Sakai
- Sesoko Station, Tropical Biosphere Research Center, University of the Ryukyus, Motobu, Okinawa, Japan.
| | - Aika Miyagi
- Department of Bioresources Engineering, National Institute of Technology, Okinawa College, Nago-City, Okinawa, Japan
| | - Aiko Iwasaki
- Asamushi Research Center for Marine Biology, Graduate School of Life Sciences, Tohoku University, Aomori, Aomori, Japan
| | - Yukihiro Nojiri
- Center for Global Environmental Research, National Institute for Environmental Studies, Tsukuba, Ibaraki, Japan; Graduate School of Earth and Environmental Sciences, Hirosaki University, Hirosaki, Aomori, Japan
| | - Akira Iguchi
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan; Research Laboratory on Environmentally-conscious Developments and Technologies [E-code], National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
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2
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Mersal GAM, Hessien MM, Taleb MFA, Al-Juaid SS, Ibrahim MM. Solid–Liquid Phase Structural Studies of Bis(2-Picolyl)Amine-Based Zinc(II) Complexes as Functional Hydrolase Models: The Detoxification of Fenitrothion. J Inorg Organomet Polym Mater 2021. [DOI: 10.1007/s10904-021-02105-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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3
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Verma M, Bhaduri GA, Phani Kumar VS, Deshpande PA. Biomimetic Catalysis of CO 2 Hydration: A Materials Perspective. Ind Eng Chem Res 2021. [DOI: 10.1021/acs.iecr.0c06203] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Manju Verma
- Department of Chemical Engineering, Motilal Nehru National Institute of Technology Allahabad, Prayagraj 211004, India
| | - Gaurav A. Bhaduri
- Department of Chemical Engineering, Indian Institute of Technology Jammu, Jammu and Kashmir, 181221, India
| | - V. Sai Phani Kumar
- Quantum and Molecular Engineering Laboratory, Department of Chemical Engineering Indian Institute of Technology Kharagpur, Kharagpur, 721302, India
| | - Parag A. Deshpande
- Quantum and Molecular Engineering Laboratory, Department of Chemical Engineering Indian Institute of Technology Kharagpur, Kharagpur, 721302, India
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4
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Matsuzaki Y, Yamamoto S, Yamada H, Chowdhury FA, Goto K. Catalysis of CO 2 Absorption in an Aqueous Alkanolamine Solution by Boron Compounds: A Combined Computational and Experimental Study. Ind Eng Chem Res 2020. [DOI: 10.1021/acs.iecr.0c02756] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yoichi Matsuzaki
- Advanced Technology Research Laboratories, Nippon Steel Corporation, 20-1 Shintomi, Futtsu, Chiba 293-8511, Japan
| | - Shin Yamamoto
- Chemical Research Group, Research Institute of Innovative Technology for the Earth, 9-2 Kizugawadai, Kizugawa, Kyoto 619-0292, Japan
| | - Hidetaka Yamada
- Chemical Research Group, Research Institute of Innovative Technology for the Earth, 9-2 Kizugawadai, Kizugawa, Kyoto 619-0292, Japan
| | - Firoz A. Chowdhury
- Chemical Research Group, Research Institute of Innovative Technology for the Earth, 9-2 Kizugawadai, Kizugawa, Kyoto 619-0292, Japan
| | - Kazuya Goto
- Chemical Research Group, Research Institute of Innovative Technology for the Earth, 9-2 Kizugawadai, Kizugawa, Kyoto 619-0292, Japan
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Pinter TBJ, Koebke KJ, Pecoraro VL. Catalysis and Electron Transfer in De Novo Designed Helical Scaffolds. Angew Chem Int Ed Engl 2020; 59:7678-7699. [PMID: 31441170 PMCID: PMC7035182 DOI: 10.1002/anie.201907502] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Indexed: 12/31/2022]
Abstract
The relationship between protein structure and function is one of the greatest puzzles within biochemistry. De novo metalloprotein design is a way to wipe the board clean and determine what is required to build in function from the ground up in an unrelated structure. This Review focuses on protein design efforts to create de novo metalloproteins within alpha-helical scaffolds. Examples of successful designs include those with carbonic anhydrase or nitrite reductase activity by incorporating a ZnHis3 or CuHis3 site, or that recapitulate the spectroscopic properties of unique electron-transfer sites in cupredoxins (CuHis2 Cys) or rubredoxins (FeCys4 ). This work showcases the versatility of alpha helices as scaffolds for metalloprotein design and the progress that is possible through careful rational design. Our studies cover the invariance of carbonic anhydrase activity with different site positions and scaffolds, refinement of our cupredoxin models, and enhancement of nitrite reductase activity up to 1000-fold.
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Affiliation(s)
- Tyler B. J. Pinter
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, United States, 48109-1055
| | - Karl J. Koebke
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, United States, 48109-1055
| | - Vincent L. Pecoraro
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, United States, 48109-1055
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Pinter TBJ, Koebke KJ, Pecoraro VL. Katalyse und Elektronentransfer in helikalen De‐novo‐Gerüststrukturen. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201907502] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Tyler B. J. Pinter
- Department of Chemistry University of Michigan Ann Arbor Michigan 48109-1055 USA
| | - Karl J. Koebke
- Department of Chemistry University of Michigan Ann Arbor Michigan 48109-1055 USA
| | - Vincent L. Pecoraro
- Department of Chemistry University of Michigan Ann Arbor Michigan 48109-1055 USA
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7
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Park D, Lee MS. Kinetic Study of CO 2 Hydration by Small-Molecule Catalysts with A Second Coordination Sphere that Mimic the Effect of the Thr-199 Residue of Carbonic Anhydrase. Biomimetics (Basel) 2019; 4:E66. [PMID: 31581538 PMCID: PMC6963681 DOI: 10.3390/biomimetics4040066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 09/11/2019] [Accepted: 09/27/2019] [Indexed: 02/06/2023] Open
Abstract
Zinc complexes were synthesized as catalysts that mimic the ability of carbonic anhydrase (CA) for the CO2 hydration reaction (H2O + CO2 → H+ + HCO3-). For these complexes, a tris(2-pyridylmethyl)amine (TPA) ligand mimicking only the active site, and a 6-((bis(pyridin-2-ylmethyl)amino)methyl)pyridin-2-ol (TPA-OH) ligand mimicking the hydrogen-bonding network of the secondary coordination sphere of CA were used. Potentiometric pH titration was used to determine the deprotonation ability of the Zn complexes, and their pKa values were found to be 8.0 and 6.8, respectively. Stopped-flow spectrophotometry was used to confirm the CO2 hydration rate. The rate constants were measured to be 648.4 and 730.6 M-1s-1, respectively. The low pKa value was attributed to the hydrogen-bonding network of the secondary coordination sphere of the catalyst that mimics the behavior of CA, and this was found to increase the CO2 hydration rate of the catalyst.
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Affiliation(s)
- DongKook Park
- Green Materials & Processes Group, Korea Institute of Industrial Technology (KITECH), 55, Jongga-ro, Jung-gu, Ulsan 44413, Korea.
| | - Man Sig Lee
- Green Materials & Processes Group, Korea Institute of Industrial Technology (KITECH), 55, Jongga-ro, Jung-gu, Ulsan 44413, Korea.
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Park D, Lee MS. Kinetic study of catalytic CO 2 hydration by metal-substituted biomimetic carbonic anhydrase model complexes. ROYAL SOCIETY OPEN SCIENCE 2019; 6:190407. [PMID: 31598240 PMCID: PMC6731748 DOI: 10.1098/rsos.190407] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 07/01/2019] [Indexed: 05/20/2023]
Abstract
The rapid rise of the CO2 level in the atmosphere has spurred the development of CO2 capture methods such as the use of biomimetic complexes that mimic carbonic anhydrase. In this study, model complexes with tris(2-pyridylmethyl)amine (TPA) were synthesized using various transition metals (Zn2+, Cu2+ and Ni2+) to control the intrinsic proton-donating ability. The pKa of the water coordinated to the metal, which indicates its proton-donating ability, was determined by potentiometric pH titration and found to increase in the order [(TPA)Cu(OH2)]2+ < [(TPA)Ni(OH2)]2+ < [(TPA)Zn(OH2)]2+. The effect of pKa on the CO2 hydration rate was investigated by stopped-flow spectrophotometry. Because the water ligand in [(TPA)Zn(OH2)]2+ had the highest pKa, it would be more difficult to deprotonate it than those coordinated to Cu2+ and Ni2+. It was, therefore, expected that the complex would have the slowest rate for the reaction of the deprotonated water with CO2 to form bicarbonate. However, it was confirmed that [(TPA)Zn(OH2)]2+ had the fastest CO2 hydration rate because the substitution of bicarbonate with water (bicarbonate release) occurred easily.
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Affiliation(s)
| | - Man Sig Lee
- Author for correspondence: Man Sig Lee e-mail:
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9
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Rains JGD, O’Donnelly K, Oliver T, Woscholski R, Long NJ, Barter LMC. Bicarbonate Inhibition of Carbonic Anhydrase Mimics Hinders Catalytic Efficiency: Elucidating the Mechanism and Gaining Insight toward Improving Speed and Efficiency. ACS Catal 2019. [DOI: 10.1021/acscatal.8b04077] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jonathan G. D. Rains
- Institute of Chemical Biology, Department of Chemistry, Imperial College, Molecular Science Research Hub, White City Campus, London W12 0BZ, United Kingdom
| | - Kerry O’Donnelly
- Institute of Chemical Biology, Department of Chemistry, Imperial College, Molecular Science Research Hub, White City Campus, London W12 0BZ, United Kingdom
| | - Thomas Oliver
- Institute of Chemical Biology, Department of Chemistry, Imperial College, Molecular Science Research Hub, White City Campus, London W12 0BZ, United Kingdom
| | - Rudiger Woscholski
- Institute of Chemical Biology, Department of Chemistry, Imperial College, Molecular Science Research Hub, White City Campus, London W12 0BZ, United Kingdom
| | - Nicholas J. Long
- Institute of Chemical Biology, Department of Chemistry, Imperial College, Molecular Science Research Hub, White City Campus, London W12 0BZ, United Kingdom
| | - Laura M. C. Barter
- Institute of Chemical Biology, Department of Chemistry, Imperial College, Molecular Science Research Hub, White City Campus, London W12 0BZ, United Kingdom
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10
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The Carbonation of Wollastonite: A Model Reaction to Test Natural and Biomimetic Catalysts for Enhanced CO2 Sequestration. MINERALS 2018. [DOI: 10.3390/min8050209] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
One of the most promising strategies for the safe and permanent disposal of anthropogenic CO2 is its conversion into carbonate minerals via the carbonation of calcium and magnesium silicates. However, the mechanism of such a reaction is not well constrained, and its slow kinetics is a handicap for the implementation of silicate mineral carbonation as an effective method for CO2 capture and storage (CCS). Here, we studied the different steps of wollastonite (CaSiO3) carbonation (silicate dissolution → carbonate precipitation) as a model CCS system for the screening of natural and biomimetic catalysts for this reaction. Tested catalysts included carbonic anhydrase (CA), a natural enzyme that catalyzes the reversible hydration of CO2(aq), and biomimetic metal-organic frameworks (MOFs). Our results show that dissolution is the rate-limiting step for wollastonite carbonation. The overall reaction progresses anisotropically along different [hkl] directions via a pseudomorphic interface-coupled dissolution–precipitation mechanism, leading to partial passivation via secondary surface precipitation of amorphous silica and calcite, which in both cases is anisotropic (i.e., (hkl)-specific). CA accelerates the final carbonate precipitation step but hinders the overall carbonation of wollastonite. Remarkably, one of the tested Zr-based MOFs accelerates the dissolution of the silicate. The use of MOFs for enhanced silicate dissolution alone or in combination with other natural or biomimetic catalysts for accelerated carbonation could represent a potentially effective strategy for enhanced mineral CCS.
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11
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Sahoo PC, Kumar M, Puri S, Ramakumar S. Enzyme inspired complexes for industrial CO2 capture: Opportunities and challenges. J CO2 UTIL 2018. [DOI: 10.1016/j.jcou.2018.02.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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12
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Sivanesan D, Youn MH, Murnandari A, Kang JM, Park KT, Kim HJ, Jeong SK. Enhanced CO2 absorption and desorption in a tertiary amine medium with a carbonic anhydrase mimic. J IND ENG CHEM 2017. [DOI: 10.1016/j.jiec.2017.03.058] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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13
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Nath I, Chakraborty J, Verpoort F. Metal organic frameworks mimicking natural enzymes: a structural and functional analogy. Chem Soc Rev 2016; 45:4127-70. [DOI: 10.1039/c6cs00047a] [Citation(s) in RCA: 299] [Impact Index Per Article: 37.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In this review, we have portrayed the structure, synthesis and applications of a variety of biomimetic MOFs from an unprecedented angle.
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Affiliation(s)
- Ipsita Nath
- Laboratory of Organometallics
- Catalysis and Ordered Materials
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing
- Center for Chemical and Material Engineering
- Wuhan University of Technology
| | - Jeet Chakraborty
- Laboratory of Organometallics
- Catalysis and Ordered Materials
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing
- Center for Chemical and Material Engineering
- Wuhan University of Technology
| | - Francis Verpoort
- Laboratory of Organometallics
- Catalysis and Ordered Materials
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing
- Center for Chemical and Material Engineering
- Wuhan University of Technology
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14
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Kelsey RA, Miller DA, Parkin SR, Liu K, Remias JE, Yang Y, Lightstone FC, Liu K, Lippert CA, Odom SA. Carbonic anhydrase mimics for enhanced CO2 absorption in an amine-based capture solvent. Dalton Trans 2016; 45:324-33. [DOI: 10.1039/c5dt02943k] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Carbonic anhydrase converts CO2 to HCO3− in physiological conditions, but in the highly basic amine-containing solutions used industrially for carbon capture, the enzyme does not function. Instead small molecule mimics can catalyze CO2 hydration.
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Affiliation(s)
| | | | - Sean R. Parkin
- Department of Chemistry
- University of Kentucky
- Lexington
- USA
| | - Kun Liu
- Center for Applied Energy Research
- University of Kentucky
- Lexington
- USA
| | - Joe E. Remias
- Center for Applied Energy Research
- University of Kentucky
- Lexington
- USA
| | - Yue Yang
- Division
- Lawrence Livermore National Laboratory
- Livermore
- USA
| | | | - Kunlei Liu
- Center for Applied Energy Research
- University of Kentucky
- Lexington
- USA
- Department of Mechanical Engineering
| | | | - Susan A. Odom
- Department of Chemistry
- University of Kentucky
- Lexington
- USA
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15
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Sivanesan D, Kim YE, Youn MH, Park KT, Kim HJ, Grace AN, Jeong SK. The salt-based catalytic enhancement of CO2 absorption by a tertiary amine medium. RSC Adv 2016. [DOI: 10.1039/c6ra13978g] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
An improved CO2 sequestration method is proposed that uses new catalysts, specifically a series of tertiary amine nitrate salts, in an aqueous tertiary amine medium.
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Affiliation(s)
| | - Young Eun Kim
- Green Energy Process Laboratory
- Korea Institute of Energy Research
- Daejeon 305-343
- Korea
| | - Min Hye Youn
- Green Energy Process Laboratory
- Korea Institute of Energy Research
- Daejeon 305-343
- Korea
| | - Ki Tae Park
- Green Energy Process Laboratory
- Korea Institute of Energy Research
- Daejeon 305-343
- Korea
| | - Hak-Joo Kim
- Green Energy Process Laboratory
- Korea Institute of Energy Research
- Daejeon 305-343
- Korea
| | | | - Soon Kwan Jeong
- Green Energy Process Laboratory
- Korea Institute of Energy Research
- Daejeon 305-343
- Korea
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16
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Sivanesan D, Choi Y, Lee J, Youn MH, Park KT, Grace AN, Kim HJ, Jeong SK. Carbon Dioxide Sequestration by Using a Model Carbonic Anhydrase Complex in Tertiary Amine Medium. CHEMSUSCHEM 2015; 8:3977-3982. [PMID: 26564396 DOI: 10.1002/cssc.201501139] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Revised: 10/12/2015] [Indexed: 06/05/2023]
Abstract
Globally, the elevation of carbon dioxide (CO2 ) levels due to the anthropogenic effect poses a serious threat to the ecosystem. Hence, it is important to control and/or mitigate the level of CO2 in the atmosphere, which necessitates novel tools. Herein, it is proposed to improve CO2 sequestration by using model complexes based on the enzyme carbonic anhydrase (CA) in aqueous tertiary amine medium. The effect of substituents on the model CA model complexes on CO2 absorption and desorption was determined by using a stopped-flow spectrophotometer to follow pH changes through coupling to pH indicator and a continuous stirred-tank reactor (CSTR). The CO2 hydration rate constants were determined under basic conditions and compound 6, which contained a hydrophilic group, showed the highest absorption or hydration levels of CO2 (2.860×10(3) L mol(-1) s(-1) ). In addition, CSTR results for the absorption and desorption of CO2 suggest that simple model CA complexes could be used in post-combustion processing.
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Affiliation(s)
- Dharmalingam Sivanesan
- Green Energy Process Laboratory, Korea Institute of Energy Research, 102 Gajeong-ro, Yuseong-gu, Daejeon, 305-343, Republic of Korea), Fax: (+82) 42-860-3134
| | - Youngju Choi
- Green Energy Process Laboratory, Korea Institute of Energy Research, 102 Gajeong-ro, Yuseong-gu, Daejeon, 305-343, Republic of Korea), Fax: (+82) 42-860-3134
| | - Jiyeon Lee
- Green Energy Process Laboratory, Korea Institute of Energy Research, 102 Gajeong-ro, Yuseong-gu, Daejeon, 305-343, Republic of Korea), Fax: (+82) 42-860-3134
| | - Min Hye Youn
- Green Energy Process Laboratory, Korea Institute of Energy Research, 102 Gajeong-ro, Yuseong-gu, Daejeon, 305-343, Republic of Korea), Fax: (+82) 42-860-3134
| | - Ki Tae Park
- Green Energy Process Laboratory, Korea Institute of Energy Research, 102 Gajeong-ro, Yuseong-gu, Daejeon, 305-343, Republic of Korea), Fax: (+82) 42-860-3134
| | - Andrew Nirmala Grace
- Centre for Nanotechnology Research, VIT University, Vellore 632014, Tamil Nadu, India
| | - Hak-Joo Kim
- Green Energy Process Laboratory, Korea Institute of Energy Research, 102 Gajeong-ro, Yuseong-gu, Daejeon, 305-343, Republic of Korea), Fax: (+82) 42-860-3134
| | - Soon Kwan Jeong
- Green Energy Process Laboratory, Korea Institute of Energy Research, 102 Gajeong-ro, Yuseong-gu, Daejeon, 305-343, Republic of Korea), Fax: (+82) 42-860-3134.
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18
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Plegaria JS, Pecoraro VL. Sculpting Metal-binding Environments in De Novo Designed Three-helix Bundles. Isr J Chem 2015; 55:85-95. [PMID: 29353917 PMCID: PMC5771423 DOI: 10.1002/ijch.201400146] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
De novo protein design is a biologically relevant approach used to study the active centers of native metalloproteins. In this review, we will first discuss the design process in achieving α3D, a de novo designed three-helix bundle peptide with a well-defined fold. We will then cover our recent work in functionalizing the α3D framework by incorporating a tris(cysteine) and tris(histidine) motif. Our first design contains the thiol-rich sites found in metalloregulatory proteins that control the levels of toxic metal ions (Hg, Cd, and Pb). The latter design recapitulates the catalytic site and activity of a natural metalloenzyme carbonic anhydrase. The review will conclude with future design goals aimed at introducing an asymmetric metal-binding site in the α3D framework.
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Affiliation(s)
- Jefferson S Plegaria
- 930 North University Ave, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109 (USA)
| | - Vincent L Pecoraro
- 930 North University Ave, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109 (USA)
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19
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Suwa R, Hatta M, Ichikawa K. Proton-transfer reaction dynamics and energetics in calcification and decalcification. Chemistry 2014; 20:13656-61. [PMID: 25179204 DOI: 10.1002/chem.201402210] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2014] [Revised: 06/30/2014] [Indexed: 11/07/2022]
Abstract
CaCO3 -saturated saline waters at pH values below 8.5 are characterized by two stationary equilibrium states: reversible chemical calcification/decalcification associated with acid dissociation, Ca(2+) +HCO3 (-) ⇌CaCO3 +H(+) ; and reversible static physical precipitation/dissolution, Ca(2+) +CO3 (2-) ⇌CaCO3 . The former reversible reaction was determined using a strong base and acid titration. The saturation state described by the pH/PCO2 -independent solubility product, [Ca(2+) ][CO3 (2-) ], may not be observed at pH below 8.5 because [Ca(2+) ][CO3 (2-) ]/([Ca(2+) ][HCO3 (-) ]) ≪1. Since proton transfer dynamics controls all reversible acid dissociation reactions in saline waters, the concentrations of calcium ion and dissolved inorganic carbon (DIC) were expressed as a function of dual variables, pH and PCO2 . The negative impact of ocean acidification on marine calcifying organisms was confirmed by applying the experimental culture data of each PCO2 /pH-dependent coral polyp skeleton weight (Wskel) to the proton transfer idea. The skeleton formation of each coral polyp was performed in microspaces beneath its aboral ectoderm. This resulted in a decalcification of 14 weight %, a normalized CaCO3 saturation state Λ of 1.3 at PCO2 ≈400 ppm and pH ≈8.0, and serious decalcification of 45 % and Λ 2.5 at PCO2 ≈1000 ppm and pH ≈7.8.
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Affiliation(s)
- Ryota Suwa
- Seto Marine Biological Laboratory, Field Science Education and Research Center, Kyoto University, Wakayama, 649-2211 (Japan); Present address: Marine Ecology Research Institute, Kashiwazaki, Niigata, 945-0017 (Japan)
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20
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Cangelosi VM, Deb A, Penner-Hahn JE, Pecoraro VL. A De Novo Designed Metalloenzyme for the Hydration of CO2. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201404925] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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21
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Cangelosi VM, Deb A, Penner-Hahn JE, Pecoraro VL. A de novo designed metalloenzyme for the hydration of CO2. Angew Chem Int Ed Engl 2014; 53:7900-3. [PMID: 24943466 DOI: 10.1002/anie.201404925] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Indexed: 11/07/2022]
Abstract
Protein design will ultimately allow for the creation of artificial enzymes with novel functions and unprecedented stability. To test our current mastery of nature's approach to catalysis, a Zn(II) metalloenzyme was prepared using de novo design. α3DH3 folds into a stable single-stranded three-helix bundle and binds Zn(II) with high affinity using His3 O coordination. The resulting metalloenzyme catalyzes the hydration of CO2 better than any small molecule model of carbonic anhydrase and with an efficiency within 1400-fold of the fastest carbonic anhydrase isoform, CAII, and 11-fold of CAIII.
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Yu F, Cangelosi VM, Zastrow ML, Tegoni M, Plegaria JS, Tebo AG, Mocny CS, Ruckthong L, Qayyum H, Pecoraro VL. Protein design: toward functional metalloenzymes. Chem Rev 2014; 114:3495-578. [PMID: 24661096 PMCID: PMC4300145 DOI: 10.1021/cr400458x] [Citation(s) in RCA: 340] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Fangting Yu
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | | | | | | | - Alison G. Tebo
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | - Leela Ruckthong
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Hira Qayyum
- University of Michigan, Ann Arbor, Michigan 48109, United States
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23
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Zastrow M, Pecoraro VL. Designing hydrolytic zinc metalloenzymes. Biochemistry 2014; 53:957-78. [PMID: 24506795 PMCID: PMC3985962 DOI: 10.1021/bi4016617] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2013] [Revised: 01/23/2014] [Indexed: 12/15/2022]
Abstract
Zinc is an essential element required for the function of more than 300 enzymes spanning all classes. Despite years of dedicated study, questions regarding the connections between primary and secondary metal ligands and protein structure and function remain unanswered, despite numerous mechanistic, structural, biochemical, and synthetic model studies. Protein design is a powerful strategy for reproducing native metal sites that may be applied to answering some of these questions and subsequently generating novel zinc enzymes. From examination of the earliest design studies introducing simple Zn(II)-binding sites into de novo and natural protein scaffolds to current studies involving the preparation of efficient hydrolytic zinc sites, it is increasingly likely that protein design will achieve reaction rates previously thought possible only for native enzymes. This Current Topic will review the design and redesign of Zn(II)-binding sites in de novo-designed proteins and native protein scaffolds toward the preparation of catalytic hydrolytic sites. After discussing the preparation of Zn(II)-binding sites in various scaffolds, we will describe relevant examples for reengineering existing zinc sites to generate new or altered catalytic activities. Then, we will describe our work on the preparation of a de novo-designed hydrolytic zinc site in detail and present comparisons to related designed zinc sites. Collectively, these studies demonstrate the significant progress being made toward building zinc metalloenzymes from the bottom up.
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Affiliation(s)
| | - Vincent L. Pecoraro
- Department of Chemistry, University
of Michigan, Ann Arbor, Michigan 48109, United
States
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24
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Lippert CA, Liu K, Sarma M, Parkin SR, Remias JE, Brandewie CM, Odom SA, Liu K. Improving carbon capture from power plant emissions with zinc- and cobalt-based catalysts. Catal Sci Technol 2014. [DOI: 10.1039/c4cy00766b] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A carbonic anhydrase mimic converting CO2 to carbonic acid, deprotonated under highly basic conditions, and being converted to a carbamate upon reaction with monoethanolamine, a solvent reported for carbon capture reactions.
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Affiliation(s)
| | - Kun Liu
- University of Kentucky
- Center for Applied Energy Research
- Lexington, USA
| | - Moushumi Sarma
- University of Kentucky
- Center for Applied Energy Research
- Lexington, USA
| | - Sean R. Parkin
- University of Kentucky
- Department of Chemistry
- Lexington, USA
| | - Joseph E. Remias
- University of Kentucky
- Center for Applied Energy Research
- Lexington, USA
| | | | - Susan A. Odom
- University of Kentucky
- Department of Chemistry
- Lexington, USA
| | - Kunlei Liu
- University of Kentucky
- Center for Applied Energy Research
- Lexington, USA
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25
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Wanjari S, Prabhu C, Labhsetwar N, Rayalu S. Biomimetic carbon dioxide sequestration using immobilized bio-composite materials. ACTA ACUST UNITED AC 2013. [DOI: 10.1016/j.molcatb.2013.03.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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26
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Zastrow ML, Pecoraro VL. Designing functional metalloproteins: from structural to catalytic metal sites. Coord Chem Rev 2013; 257:2565-2588. [PMID: 23997273 PMCID: PMC3756834 DOI: 10.1016/j.ccr.2013.02.007] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Metalloenzymes efficiently catalyze some of the most important and difficult reactions in nature. For many years, coordination chemists have effectively used small molecule models to understand these systems. More recently, protein design has been shown to be an effective approach for mimicking metal coordination environments. Since the first designed proteins were reported, much success has been seen for incorporating metal sites into proteins and attaining the desired coordination environment but until recently, this has been with a lack of significant catalytic activity. Now there are examples of designed metalloproteins that, although not yet reaching the activity of native enzymes, are considerably closer. In this review, we highlight work leading up to the design of a small metalloprotein containing two metal sites, one for structural stability (HgS3) and the other a separate catalytic zinc site to mimic carbonic anhydrase activity (ZnN3O). The first section will describe previous studies that allowed for a high affinity thiolate site that binds heavy metals in a way that stabilizes three-stranded coiled coils. The second section will examine ways of preparing histidine rich environments that lead to metal based hydrolytic catalysts. We will also discuss other recent examples of the design of structural metal sites and functional metalloenzymes. Our work demonstrates that attaining the proper first coordination geometry of a metal site can lead to a significant fraction of catalytic activity, apparently independent of the type of secondary structure of the surrounding protein environment. We are now in a position to begin to meet the challenge of building a metalloenzyme systematically from the bottom-up by engineering and analyzing interactions directly around the metal site and beyond.
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Affiliation(s)
- Melissa L. Zastrow
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
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27
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Comparison and analysis of zinc and cobalt-based systems as catalytic entities for the hydration of carbon dioxide. PLoS One 2013; 8:e66187. [PMID: 23840420 PMCID: PMC3688778 DOI: 10.1371/journal.pone.0066187] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Accepted: 05/05/2013] [Indexed: 11/19/2022] Open
Abstract
In nature, the zinc metalloenzyme carbonic anhydrase II (CAII) efficiently catalyzes the conversion of carbon dioxide (CO2) to bicarbonate under physiological conditions. Many research efforts have been directed towards the development of small molecule mimetics that can facilitate this process and thus have a beneficial environmental impact, but these efforts have met very limited success. Herein, we undertook quantum mechanical calculations of four mimetics, 1,5,9-triazacyclododedacane, 1,4,7,10-tetraazacyclododedacane, tris(4,5-dimethyl-2-imidazolyl)phosphine, and tris(2-benzimidazolylmethyl)amine, in their complexed form either with the Zn2+ or the Co2+ ion and studied their reaction coordinate for CO2 hydration. These calculations demonstrated that the ability of the complex to maintain a tetrahedral geometry and bind bicarbonate in a unidentate manner were vital for the hydration reaction to proceed favorably. Furthermore, these calculations show that the catalytic activity of the examined zinc complexes was insensitive to coordination states for zinc, while coordination states above four were found to have an unfavorable effect on product release for the cobalt counterparts.
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Koziol L, Essiz SG, Wong SE, Lau EY, Valdez CA, Satcher JH, Aines RD, Lightstone FC. Computational Analysis of a Zn-Bound Tris(imidazolyl) Calix[6]arene Aqua Complex: Toward Incorporating Second-Coordination Sphere Effects into Carbonic Anhydrase Biomimetics. J Chem Theory Comput 2013; 9:1320-7. [DOI: 10.1021/ct3008793] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Lucas Koziol
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California
94550, United States
| | - Sebnem G. Essiz
- Bioinformatics and Genetics
Department, Faculty of Engineering and Natural Sciences, Kadir Has University, 34083 Fatih, Istanbul, Turkey
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California
94550, United States
| | - Sergio E. Wong
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California
94550, United States
| | - Edmond Y. Lau
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California
94550, United States
| | - Carlos A. Valdez
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California
94550, United States
| | - Joe H. Satcher
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California
94550, United States
| | - Roger D. Aines
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California
94550, United States
| | - Felice C. Lightstone
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California
94550, United States
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Koziol L, Valdez CA, Baker SE, Lau EY, Floyd WC, Wong SE, Satcher JH, Lightstone FC, Aines RD. Toward a Small Molecule, Biomimetic Carbonic Anhydrase Model: Theoretical and Experimental Investigations of a Panel of Zinc(II) Aza-Macrocyclic Catalysts. Inorg Chem 2012; 51:6803-12. [DOI: 10.1021/ic300526b] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lucas Koziol
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore,
California 94550, United States
| | - Carlos A. Valdez
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore,
California 94550, United States
| | - Sarah E. Baker
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore,
California 94550, United States
| | - Edmond Y. Lau
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore,
California 94550, United States
| | - William C. Floyd
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore,
California 94550, United States
| | - Sergio E. Wong
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore,
California 94550, United States
| | - Joe H. Satcher
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore,
California 94550, United States
| | - Felice C. Lightstone
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore,
California 94550, United States
| | - Roger D. Aines
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore,
California 94550, United States
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30
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Lee D, Kanai Y. Biomimetic Carbon Nanotube for Catalytic CO2 Hydrolysis: First-Principles Investigation on the Role of Oxidation State and Metal Substitution in Porphyrin. J Phys Chem Lett 2012; 3:1369-1373. [PMID: 26286784 DOI: 10.1021/jz300419u] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Hydrolysis of carbon dioxide is an important reaction for CO2 collection. Using accurate first-principles electronic structure calculations, we predict how the catalytic hydrolysis reaction in carbonic anhydrase (CA) can be mimicked in a metal-porphyrin carbon nanotube. The two-step catalytic process can be improved remarkably by controlling the porphyrin oxidation state via the nanotube charge state and by substituting the porphyrin metal atom. The oxidation state and the metal substitution both have profound effects on the reaction energetics for the initial hydration reaction step. For the subsequent product-release reaction step, two different reaction mechanisms could take place. These mechanisms are distinctively sensitive to either the oxidation state change or the metal substitution, but not to both. For the overall catalytic cycle, a significant dependence on the nanotube charge state at low pH and on the metal substitution at high pH is expected.
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Affiliation(s)
- Donghwa Lee
- Condensed Matter and Materials Division, Lawrence Livermore National Laboratory, Department of Chemistry, The University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Yosuke Kanai
- Condensed Matter and Materials Division, Lawrence Livermore National Laboratory, Department of Chemistry, The University of North Carolina, Chapel Hill, North Carolina 27599, United States
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31
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Hydrolytic catalysis and structural stabilization in a designed metalloprotein. Nat Chem 2011; 4:118-23. [PMID: 22270627 PMCID: PMC3270697 DOI: 10.1038/nchem.1201] [Citation(s) in RCA: 251] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2011] [Accepted: 10/18/2011] [Indexed: 12/18/2022]
Abstract
Metal ions are an important part of many natural proteins, providing structural, catalytic and electron transfer functions. Reproducing these functions in a designed protein is the ultimate challenge to our understanding of them. Here, we present an artificial metallohydrolase, which has been shown by X-ray crystallography to contain two different metal ions – a Zn(II) ion which is important for catalytic activity and a Hg(II) ion which provides structural stability. This metallohydrolase displays catalytic activity that compares well with several characteristic reactions of natural enzymes. It catalyses p-nitrophenyl acetate hydrolysis (pNPA) to within ~100-fold of the efficiency of human carbonic anhydrase (CA)II and is at least 550-fold better than comparable synthetic complexes. Similarly, CO2 hydration occurs with an efficiency within ~500-fold of CAII. While histidine residues in the absence of Zn(II) exhibit pNPA hydrolysis, miniscule apopeptide activity is observed for CO2 hydration. The kinetic and structural analysis of this first de novo designed hydrolytic metalloenzyme uncovers necessary design features for future metalloenzymes containing one or more metals.
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32
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Huang D, Makhlynets OV, Tan LL, Lee SC, Rybak-Akimova EV, Holm RH. Fast Carbon Dioxide Fixation by 2,6-Pyridinedicarboxamidato-nickel(II)-hydroxide Complexes: Influence of Changes in Reactive Site Environment on Reaction Rates. Inorg Chem 2011; 50:10070-81. [DOI: 10.1021/ic200942u] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Deguang Huang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Olga V. Makhlynets
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Lay Ling Tan
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L3G1, Canada
| | - Sonny C. Lee
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L3G1, Canada
| | | | - R. H. Holm
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
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33
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Ibrahim MM, Amin MA, Ichikawa K. Synthesis and characterization of benzimidazole-based zinc complexes as structural carbonic anhydrase models and their applications towards CO2 hydration. J Mol Struct 2011. [DOI: 10.1016/j.molstruc.2010.10.041] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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34
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Satcher J, Baker S, Kulik H, Valdez C, Krueger R, Lightstone F, Aines R. Modeling, synthesis and characterization of zinc containing carbonic anhydrase active site mimics. ACTA ACUST UNITED AC 2011. [DOI: 10.1016/j.egypro.2011.02.092] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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35
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Schulzke C. Temperature dependent electrochemistry--a versatile tool for investigations of biology related topics. Dalton Trans 2009:6683-91. [PMID: 19690674 DOI: 10.1039/b904361f] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Temperature dependent electrochemistry can be efficiently used to determine very different properties of the investigated system, such as thermodynamic parameters of redox processes (especially the entropy), the degeneration temperature of a protein or kinetic parameters, for instance activation energy. It can even be used in biotechnology for improved catalysis and detection of substances. This perspective describes a selection of different experiments that used temperature dependent electrochemistry in order to determine these different values or achieve an enhancement of biotechnological applications, respectively, and hence gives an overview of its versatile use in studies aimed at biological issues.
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Affiliation(s)
- Carola Schulzke
- School of Chemistry, Trinity College Dublin, Dublin 2, Ireland.
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36
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Davy R. Development of catalysts for fast, energy efficient post combustion capture of CO2 into water; an alternative to monoethanolamine (MEA) solvents. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.egypro.2009.01.118] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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37
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Eger WA, Jahn BO, Anders E. The zinc complex catalyzed hydration of alkyl isothiocyanates. J Mol Model 2008; 15:433-46. [PMID: 19085026 DOI: 10.1007/s00894-008-0385-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2008] [Accepted: 10/09/2008] [Indexed: 11/25/2022]
Abstract
Based upon our preceding studies of the hydration of CO(2), COS and CS(2), accelerated by the carbonic anhydrase (CA) using simplified [ZnL(3)OH](+) complexes as model catalysts, we calculated the hydration mechanisms of both the uncatalyzed and the [ZnL(3)OH](+)-catalyzed reactions (L = NH(3)) of isothiocyanates RNCS on the B3LYP/6-311+G(d,p) level of theory. Interestingly, the transition state for the favored metal mediated reaction with the lowest Gibbs free energy is only slightly higher than in the case of CO(2) (depending on the attacking atom (N or S). Calculations under inclusion of solvent corrections show a reduction of the selectivity and a slight decrease of the Gibbs free energy in the rate-determining steps. The most plausible pathway prefers the mechanism via a Lindskog proton-shift transition state leading to the thermodynamically most stable product, the carbamatic-S-acid. Furthermore, powerful electron withdrawing substituents R of the cumulenic substrates influence the selectivity of the reaction to a significant extent. Especially the CF(3)-group in trifluoromethylisothiocyanate reverses the selectivity. This investigation demonstrates that reaction principles developed by nature can be translated to develop efficient catalytic methods, in this case presumably for the transformation of a wide variety of heterocumulenes aside from CO(2), COS and CS(2).
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Affiliation(s)
- Wilhelm A Eger
- Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, Humboldtstrasse 10, 07743, Jena, Germany
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38
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da Silva Miranda F, Signori AM, Vicente J, de Souza B, Priebe J, Szpoganicz B, Gonçalves NS, Neves A. Synthesis of substituted dipyrido[3,2-a:2′,3′-c]phenazines and a new heterocyclic dipyrido[3,2-f:2′,3′-h]quinoxalino[2,3-b]quinoxaline. Tetrahedron 2008. [DOI: 10.1016/j.tet.2008.02.097] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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39
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Abstract
The oscillating stability of coral reef seawater pH has been maintained at around physiological pH values over the past 300 years (Pelejero et al., 2005). The stability mechanism of its pH has been interpreted in terms of the buffering dissolution/formation reaction of CaCO(3) as well as the proton consumption/generation reaction in CaCO(3)-saturated water. Here the pH-dependent solubility product [HCO(3)(-)][Ca(2+)] has been derived on the basis of the actual pH-dependent reactions for the atmospheric CO(2)/CO(2 (aq.))/HCO(3)(-)/CO(3)(2-)/Ca(2+)/CaCO(3) system. Overbasic pH peaks appeared between pH approximately 8 and approximately 9.5 during sodium hydroxide titration, as a result of simultaneous CaCO(3) formation and proton generation. The spontaneous and prompt water pH recovery from the acidic to the physiological range has been confirmed by the observation of acid/base time evolution, because of simultaneous CaCO(3) dissolution and proton consumption. The dissolution/formation of CaCO(3) in water at pH 7.5-9 does not take place without a proton consumption/generation reaction, or a buffering chemical reaction of HCO(3)(-)+Ca(2+)right arrow over left arrowCaCO(3)+H(+). SEM images of the CaCO(3) fragments showed that the acid water ate away at the CaCO(3) formed at physiological pH values. Natural coral reefs can thus recover the physiological pH levels of seawater from the acidic range through partial dissolution of their own skeletons.
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Affiliation(s)
- Kazuhiko Ichikawa
- Graduate School of Environmental Earth Science, Hokkaido University, Sapporo 060-0810, Japan.
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40
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Ichikawa K, Shimomura N. Calcium-Binding Membrane Influence on Polymorph and Morphology of Calcium Carbonate Formed by Biomimetic Mineralization. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2006. [DOI: 10.1246/bcsj.79.580] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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41
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Lonnon DG, Craig DC, Colbran SB. Rhodium, palladium and platinum complexes of tris(pyridylalkyl)amine and tris(benzimidazolylmethyl)amine N4-tripodal ligands. Dalton Trans 2006:3785-97. [PMID: 16883405 DOI: 10.1039/b602556k] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
To investigate the influence of a potentially N4-tripodal amine ligand on the structure and internal exchange processes of its complexes with late transition metals, five rhodium, six palladium and two platinum complexes have been prepared from seven alkyl-bridged N-heterocyclic amine tripodal ligands: tris(2-pyridylmethyl)amine, (2-(2-pyridylethyl))bis(2-pyridylmethyl)amine, bis(2-(2-pyridylethyl))-2-pyridylmethylamine, bis(2-(2-pyridylethyl))amine, ((6-(hydroxymethyl)-2-pyridyl)methyl)bis(2-pyridylmethyl)amine, tris(2-benzimidazolylmethyl)amine (tbima) and tris(3-ethyl-2-benzimidazolylmethyl)amine. Single-crystal X-ray diffraction studies were completed for ten complexes: the d6-rhodium(III) complexes are octahedral with kappa 4 N-bound ligands, whereas the d8-palladium(II) and d8-platinum(II) complexes are square planar, kappa 3 N-bound by the tripodal ligand with a dangling N-donor leg, except for the unusual [Pd2(tbima)2Cl2]Cl2 dimer in which each palladium(II) ion is square planar and bound by two benzimidazole legs from one tbima ligand, one leg from the other tbima ligand and a chloride ancillary ligand. Cation bilayers are a common structural motif in the crystal structures. Variable-temperature 1H NMR studies reveal exchange occurs between the coordinated and dangling N-donor legs in the palladium and platinum complexes. Exchange free energy (Delta G++ c) values have been calculated and some general rules governing the favoured complex structures and exchange pathways elucidated. The palladium(II) and platinum(II) complexes of a ligand with an pyridylethyl leg are unstable with respect to elimination of vinylpyridine.
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Affiliation(s)
- David G Lonnon
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia
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42
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Kinetic and mechanistic studies of the reactivity of Zn–OHn (n=1 or 2) species in small molecule analogs of zinc-containing metalloenzymes. ADVANCES IN PHYSICAL ORGANIC CHEMISTRY 2006. [DOI: 10.1016/s0065-3160(06)41002-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/13/2023]
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43
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44
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Nomura A, Sugiura Y. Hydrolytic Reaction by Zinc Finger Mutant Peptides: Successful Redesign of Structural Zinc Sites into Catalytic Zinc Sites. Inorg Chem 2004; 43:1708-13. [PMID: 14989663 DOI: 10.1021/ic034931y] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To redesign a metal site originally required for the stabilization of a folded protein structure into a functional metal site, we constructed a series of zinc finger mutant peptides such as zf(CCHG) and zf(GCHH), in which one zinc-coordinating residue is substituted into a noncoordinating one. The mutant peptides having water bound to the zinc ion catalyzed the hydrolysis of 4-nitrophenyl acetate as well as the enantioselective hydrolysis of amino acid esters. All the zinc complexes of the mutant peptides showed hydrolytic activity, depending on their peptide sequences. In contrast, the zinc complex of the wild-type, zf(CCHH), and zinc ion alone exhibited no hydrolytic ability. These results clearly indicate that the catalytic abilities are predominantly attributed to the zinc center in the zinc complexes of the mutant peptides. Kinetic studies of the mutant peptides demonstrated that the catalytic hydrolysis is affected by the electron-donating ability of the protein ligands and the coordination environment. In addition, the pH dependence of the hydrolysis strongly suggests that the zinc-coordinated hydroxide ion participates the catalytic reaction. This report is the first successful study of catalytically active zinc finger peptides.
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Affiliation(s)
- Akiko Nomura
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
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45
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Affiliation(s)
- Gerard Parkin
- Department of Chemistry, Columbia University, New York, New York 10027, USA
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46
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Loferer MJ, Tautermann CS, Loeffler HH, Liedl KR. Influence of backbone conformations of human carbonic anhydrase II on carbon dioxide hydration: hydration pathways and binding of bicarbonate. J Am Chem Soc 2003; 125:8921-7. [PMID: 12862489 DOI: 10.1021/ja035072f] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this study, the hydration of carbon dioxide and the formation of bicarbonate in human carbonic anhydrase II have been examined. From semiempirical QM/MM molecular dynamics studies, dominant conformations of the protein backbone, possibly contributing to the catalytic activity, have been isolated and further examined by means of density functional QM/MM methods. In agreement with experimental observations, a binding site for cyanate, which acts as an inhibitor, has been located, whereas for carbon dioxide, depending on the conformation of the protein environment, either a different binding site or no binding site has been found. In the latter case, carbon dioxide diffuses barrierless to the zinc-bound oxygen, and then a weakly bound bicarbonate complex is formed. The formed complex is characterized by a long C-O bond to the zinc-bound hydroxide. The nature of the calculated stationary points was verified by determination of vibrational frequencies. Finally, the dissociation of the formed bicarbonate from zinc has been considered. Therefore, a water molecule was included in the QM zone of the QM/MM hybrid potential, and minimization yielded a pentacoordinated intermediate. From a potential energy scan, an activation energy of 6.2 kcal/mol for dissociation of bicarbonate from Zn has been found.
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Affiliation(s)
- Markus J Loferer
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
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Yamaguchi S, Tokairin I, Wakita Y, Funahashi Y, Jitsukawa K, Masuda H. Preparation and Characterization of Hydroxo-zinc(II) Complex Surrounded with Hydrogen Bonding and Hydrophobic Interaction Groups. A Structural/Functional Model of Carbonic Anhydrases. CHEM LETT 2003. [DOI: 10.1246/cl.2003.406] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Shimomura N, Ohkubo N, Ichikawa K. Control of the Production Amount and Polymorphism of Calcium Carbonate by Biomimetic Mineralization. CHEM LETT 2002. [DOI: 10.1246/cl.2002.902] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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