1
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Is the phosphorous atom a stereogenic center? Crystallographic findings in five new dithiophosphonate compounds supported with non covalent interaction index (NCI), theoretical approach and spectroscopic analysis. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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2
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Xiao Z, Zhong L, Du C, Du W, Zheng H, Cheung CS, Wang L, Gao H. Unprecedented Steric and Positioning Effects of Comonomer Substituents on α-Diimine Palladium-Catalyzed Vinyl Arene/CO Copolymerization. Macromolecules 2021. [DOI: 10.1021/acs.macromol.0c02227] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Zefan Xiao
- School of Materials Science and Engineering, PCFM Lab, GD HPPC Lab, Sun Yat-sen University, Guangzhou 510275, China
| | - Liu Zhong
- School of Materials Science and Engineering, PCFM Lab, GD HPPC Lab, Sun Yat-sen University, Guangzhou 510275, China
| | - Cheng Du
- School of Materials Science and Engineering, PCFM Lab, GD HPPC Lab, Sun Yat-sen University, Guangzhou 510275, China
| | - Wenbo Du
- School of Materials Science and Engineering, PCFM Lab, GD HPPC Lab, Sun Yat-sen University, Guangzhou 510275, China
| | - Handou Zheng
- School of Materials Science and Engineering, PCFM Lab, GD HPPC Lab, Sun Yat-sen University, Guangzhou 510275, China
| | - Chi Shing Cheung
- School of Materials Science and Engineering, PCFM Lab, GD HPPC Lab, Sun Yat-sen University, Guangzhou 510275, China
| | - Lingzhi Wang
- School of Materials Science and Engineering, PCFM Lab, GD HPPC Lab, Sun Yat-sen University, Guangzhou 510275, China
| | - Haiyang Gao
- School of Materials Science and Engineering, PCFM Lab, GD HPPC Lab, Sun Yat-sen University, Guangzhou 510275, China
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3
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Leone L, Chino M, Nastri F, Maglio O, Pavone V, Lombardi A. Mimochrome, a metalloporphyrin‐based catalytic Swiss knife†. Biotechnol Appl Biochem 2020; 67:495-515. [DOI: 10.1002/bab.1985] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 07/09/2020] [Indexed: 12/20/2022]
Affiliation(s)
- Linda Leone
- Department of Chemical Sciences University of Napoli “Federico II” Napoli Italy
| | - Marco Chino
- Department of Chemical Sciences University of Napoli “Federico II” Napoli Italy
| | - Flavia Nastri
- Department of Chemical Sciences University of Napoli “Federico II” Napoli Italy
| | - Ornella Maglio
- Department of Chemical Sciences University of Napoli “Federico II” Napoli Italy
- IBB ‐ National Research Council Napoli Italy
| | - Vincenzo Pavone
- Department of Chemical Sciences University of Napoli “Federico II” Napoli Italy
| | - Angela Lombardi
- Department of Chemical Sciences University of Napoli “Federico II” Napoli Italy
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4
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Xiao Z, Zheng H, Du C, Zhong L, Liao H, Gao J, Gao H, Wu Q. Enhancement on Alternating Copolymerization of Carbon Monoxide and Styrene by Dibenzobarrelene-Based α-Diimine Palladium Catalysts. Macromolecules 2018. [DOI: 10.1021/acs.macromol.8b01786] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Zefan Xiao
- School of Materials Science and Engineering, PCFM Lab, GD HPPC Lab, Sun Yat-sen University, Guangzhou 510275, China
| | - Handou Zheng
- School of Materials Science and Engineering, PCFM Lab, GD HPPC Lab, Sun Yat-sen University, Guangzhou 510275, China
| | - Cheng Du
- School of Materials Science and Engineering, PCFM Lab, GD HPPC Lab, Sun Yat-sen University, Guangzhou 510275, China
| | - Liu Zhong
- School of Materials Science and Engineering, PCFM Lab, GD HPPC Lab, Sun Yat-sen University, Guangzhou 510275, China
| | - Heng Liao
- School of Materials Science and Engineering, PCFM Lab, GD HPPC Lab, Sun Yat-sen University, Guangzhou 510275, China
| | - Jie Gao
- School of Materials Science and Engineering, PCFM Lab, GD HPPC Lab, Sun Yat-sen University, Guangzhou 510275, China
| | - Haiyang Gao
- School of Materials Science and Engineering, PCFM Lab, GD HPPC Lab, Sun Yat-sen University, Guangzhou 510275, China
| | - Qing Wu
- School of Materials Science and Engineering, PCFM Lab, GD HPPC Lab, Sun Yat-sen University, Guangzhou 510275, China
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5
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Danielson TA, Stine JM, Dar TA, Briknarova K, Bowler BE. Effect of an Imposed Contact on Secondary Structure in the Denatured State of Yeast Iso-1-cytochrome c. Biochemistry 2017; 56:6662-6676. [PMID: 29148740 DOI: 10.1021/acs.biochem.7b01002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
There is considerable evidence that long-range interactions stabilize residual protein structure under denaturing conditions. However, evaluation of the effect of a specific contact on structure in the denatured state has been difficult. Iso-1-cytochrome c variants with a Lys54 → His mutation form a particularly stable His-heme loop in the denatured state, suggestive of loop-induced residual structure. We have used multidimensional nuclear magnetic resonance methods to assign 1H and 15N backbone amide and 13C backbone and side chain chemical shifts in the denatured state of iso-1-cytochrome c carrying the Lys54 → His mutation in 3 and 6 M guanidine hydrochloride and at both pH 6.4, where the His54-heme loop is formed, and pH 3.6, where the His54-heme loop is broken. Using the secondary structure propensity score, with the 6 M guanidine hydrochloride chemical shift data as a random coil reference state for data collected in 3 M guanidine hydrochloride, we found residual helical structure in the denatured state for the 60s helix and the C-terminal helix, but not in the N-terminal helix in the presence or absence of the His54-heme loop. Non-native helical structure is observed in two regions that form Ω-loops in the native state. There is more residual helical structure in the C-terminal helix at pH 6.4 when the loop is formed. Loop formation also appears to stabilize helical structure near His54, consistent with induction of helical structure observed when His-heme bonds form in heme-peptide model systems. The results are discussed in the context of the folding mechanism of cytochrome c.
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Affiliation(s)
- Travis A Danielson
- Department of Chemistry and Biochemistry, University of Montana , Missoula, Montana 59812, United States
| | - Jessica M Stine
- Department of Chemistry and Biochemistry, University of Montana , Missoula, Montana 59812, United States
| | - Tanveer A Dar
- Department of Chemistry and Biochemistry, University of Montana , Missoula, Montana 59812, United States
| | - Klara Briknarova
- Department of Chemistry and Biochemistry, University of Montana , Missoula, Montana 59812, United States.,Center for Biomolecular Structure and Dynamics, University of Montana , Missoula, Montana 59812, United States
| | - Bruce E Bowler
- Department of Chemistry and Biochemistry, University of Montana , Missoula, Montana 59812, United States.,Center for Biomolecular Structure and Dynamics, University of Montana , Missoula, Montana 59812, United States
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6
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Valiente-Gabioud AA, Miotto MC, Chesta ME, Lombardo V, Binolfi A, Fernández CO. Phthalocyanines as Molecular Scaffolds to Block Disease-Associated Protein Aggregation. Acc Chem Res 2016; 49:801-8. [PMID: 27136297 DOI: 10.1021/acs.accounts.5b00507] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The aggregation of proteins into toxic conformations plays a critical role in the development of different neurodegenerative diseases such as Alzheimer's disease (AD), Parkinson's disease (PD), and Creutzfled-Jakob's disease (CJD). These disorders share a common pathological mechanism that involves the formation of aggregated protein species including toxic oligomers and amyloid fibrils. The aggregation of alpha-synuclein (αS) in PD and the amyloid beta peptide (Aβ) and tau protein in AD results in neuronal death and disease onset. In the case of CJD, the misfolding of the physiological prion protein (PrP) induces a chain reaction that results in accumulation of particles that elicit brain damage. Currently, there is no preventive therapy for these diseases and the available therapeutic approaches are based on the treatment of the symptoms rather than the underlying causes of the disease. Accordingly, the aggregation pathway of these proteins represents a useful target for therapeutic intervention. Therefore, understanding the mechanism of amyloid formation and its inhibition is of high clinical importance. The design of small molecules that efficiently inhibit the aggregation process and/or neutralize its associated toxicity constitutes a promising tool for the development of therapeutic strategies against these disorders. In this accounts, we discuss current knowledge on the anti-amyloid activity of phthalocyanines and their potential use as drug candidates in neurodegeneration. These tetrapyrrolic compounds modulate the amyloid assembly of αS, tau, Aβ, and the PrP in vitro, and protect cells from the toxic effects of amyloid aggregates. In addition, in scrapie-infected mice, these compounds showed important prophylactic antiscrapie properties. The structural basis for the inhibitory effect of phthalocyanines on amyloid filament assembly relies on specific π-π interactions between the aromatic ring system of these molecules and aromatic residues in the amyloidogenic proteins. Analysis of the structure-activity relationship in phthalocyanines revealed that their anti-amyloid activity is highly dependent on the type of metal ion coordinated to the tetrapyrrolic system but is not sensitive to the number of peripheral charged substituents. The tendency of phthalocyanines to oligomerize (self-association) via aromatic-aromatic stacking interactions correlates precisely with their binding capabilities to target proteins and, more importantly, determines their efficiency as anti-amyloid agents. The ability to block different types of disease-associated protein aggregation raises the possibility that these cyclic tetrapyrrole compounds have a common mechanism of action to impair the formation of a variety of pathological aggregates. Because the structural and molecular basis for the anti-amyloid effects of these molecules is starting to emerge, combined efforts from the fields of structural, cellular, and animal biology will result critical for the rational design and discovery of new drugs for the treatment of amyloid related neurological disorders.
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Affiliation(s)
- Ariel A. Valiente-Gabioud
- Max Planck Laboratory for Structural Biology,
Chemistry and Molecular
Biophysics of Rosario (MPLbioR, UNR-MPIbpC) and ‡Instituto de Investigaciones para
el Descubrimiento de Fármacos de Rosario (IIDEFAR, UNR-CONICET), Universidad Nacional de Rosario, Ocampo y Esmeralda, S2002LRK Rosario, Argentina
| | - Marco C. Miotto
- Max Planck Laboratory for Structural Biology,
Chemistry and Molecular
Biophysics of Rosario (MPLbioR, UNR-MPIbpC) and ‡Instituto de Investigaciones para
el Descubrimiento de Fármacos de Rosario (IIDEFAR, UNR-CONICET), Universidad Nacional de Rosario, Ocampo y Esmeralda, S2002LRK Rosario, Argentina
| | - María E. Chesta
- Max Planck Laboratory for Structural Biology,
Chemistry and Molecular
Biophysics of Rosario (MPLbioR, UNR-MPIbpC) and ‡Instituto de Investigaciones para
el Descubrimiento de Fármacos de Rosario (IIDEFAR, UNR-CONICET), Universidad Nacional de Rosario, Ocampo y Esmeralda, S2002LRK Rosario, Argentina
| | - Verónica Lombardo
- Max Planck Laboratory for Structural Biology,
Chemistry and Molecular
Biophysics of Rosario (MPLbioR, UNR-MPIbpC) and ‡Instituto de Investigaciones para
el Descubrimiento de Fármacos de Rosario (IIDEFAR, UNR-CONICET), Universidad Nacional de Rosario, Ocampo y Esmeralda, S2002LRK Rosario, Argentina
| | - Andres Binolfi
- Max Planck Laboratory for Structural Biology,
Chemistry and Molecular
Biophysics of Rosario (MPLbioR, UNR-MPIbpC) and ‡Instituto de Investigaciones para
el Descubrimiento de Fármacos de Rosario (IIDEFAR, UNR-CONICET), Universidad Nacional de Rosario, Ocampo y Esmeralda, S2002LRK Rosario, Argentina
| | - Claudio O. Fernández
- Max Planck Laboratory for Structural Biology,
Chemistry and Molecular
Biophysics of Rosario (MPLbioR, UNR-MPIbpC) and ‡Instituto de Investigaciones para
el Descubrimiento de Fármacos de Rosario (IIDEFAR, UNR-CONICET), Universidad Nacional de Rosario, Ocampo y Esmeralda, S2002LRK Rosario, Argentina
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7
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Hosseinzadeh P, Lu Y. Design and fine-tuning redox potentials of metalloproteins involved in electron transfer in bioenergetics. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1857:557-581. [PMID: 26301482 PMCID: PMC4761536 DOI: 10.1016/j.bbabio.2015.08.006] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 08/20/2015] [Indexed: 12/25/2022]
Abstract
Redox potentials are a major contributor in controlling the electron transfer (ET) rates and thus regulating the ET processes in the bioenergetics. To maximize the efficiency of the ET process, one needs to master the art of tuning the redox potential, especially in metalloproteins, as they represent major classes of ET proteins. In this review, we first describe the importance of tuning the redox potential of ET centers and its role in regulating the ET in bioenergetic processes including photosynthesis and respiration. The main focus of this review is to summarize recent work in designing the ET centers, namely cupredoxins, cytochromes, and iron-sulfur proteins, and examples in design of protein networks involved these ET centers. We then discuss the factors that affect redox potentials of these ET centers including metal ion, the ligands to metal center and interactions beyond the primary ligand, especially non-covalent secondary coordination sphere interactions. We provide examples of strategies to fine-tune the redox potential using both natural and unnatural amino acids and native and nonnative cofactors. Several case studies are used to illustrate recent successes in this area. Outlooks for future endeavors are also provided. This article is part of a Special Issue entitled Biodesign for Bioenergetics--the design and engineering of electronic transfer cofactors, proteins and protein networks, edited by Ronald L. Koder and J.L. Ross Anderson.
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Affiliation(s)
- Parisa Hosseinzadeh
- Department of Chemistry and Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews St., Urbana, IL, 61801, USA
| | - Yi Lu
- Department of Chemistry and Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews St., Urbana, IL, 61801, USA.
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8
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Amdursky N. Electron Transfer across Helical Peptides. Chempluschem 2015; 80:1075-1095. [DOI: 10.1002/cplu.201500121] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 05/06/2015] [Indexed: 02/05/2023]
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9
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Liu J, Chakraborty S, Hosseinzadeh P, Yu Y, Tian S, Petrik I, Bhagi A, Lu Y. Metalloproteins containing cytochrome, iron-sulfur, or copper redox centers. Chem Rev 2014; 114:4366-469. [PMID: 24758379 PMCID: PMC4002152 DOI: 10.1021/cr400479b] [Citation(s) in RCA: 559] [Impact Index Per Article: 55.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Indexed: 02/07/2023]
Affiliation(s)
- Jing Liu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Saumen Chakraborty
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Parisa Hosseinzadeh
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yang Yu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Shiliang Tian
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Igor Petrik
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Ambika Bhagi
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yi Lu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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10
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Venanzi M, Cianfanelli S, Palleschi A. Mimicking hemoproteins: a new synthetic metalloenzyme based on a Fe(III)-mesoporphyrin functionalized by two helical decapeptides. J Pept Sci 2013; 20:36-45. [DOI: 10.1002/psc.2586] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 10/15/2013] [Accepted: 10/16/2013] [Indexed: 01/16/2023]
Affiliation(s)
- Mariano Venanzi
- Department of Chemical Sciences and Technologies; University of Rome Tor Vergata; Rome Italy
| | - Sabrina Cianfanelli
- Department of Chemical Sciences and Technologies; University of Rome Tor Vergata; Rome Italy
| | - Antonio Palleschi
- Department of Chemical Sciences and Technologies; University of Rome Tor Vergata; Rome Italy
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11
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Weinert EE, Phillips-Piro CM, Marletta MA. Porphyrin π-stacking in a heme protein scaffold tunes gas ligand affinity. J Inorg Biochem 2013; 127:7-12. [PMID: 23831583 DOI: 10.1016/j.jinorgbio.2013.06.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Revised: 06/04/2013] [Accepted: 06/05/2013] [Indexed: 10/26/2022]
Abstract
The role of π-stacking in controlling redox and ligand binding properties of porphyrins has been of interest for many years. The recent discovery of H-NOX domains has provided a model system to investigate the role of porphyrin π-stacking within a heme protein scaffold. Removal of a phenylalanine-porphyrin π-stack dramatically increased O2, NO, and CO affinities and caused changes in redox potential (~40mV) without any structural changes. These results suggest that small changes in redox potential affect ligand affinity and that π-stacking may provide a novel route to engineer heme protein properties for new functions.
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Affiliation(s)
- Emily E Weinert
- Department of Chemistry, Emory University, Atlanta, GA 30322, United States
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12
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Non-canonical interactions of porphyrins in porphyrin-containing proteins. Amino Acids 2013; 43:1535-46. [PMID: 22302367 DOI: 10.1007/s00726-012-1228-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Accepted: 01/19/2012] [Indexed: 10/14/2022]
Abstract
In this study we have described the noncanonical interactions between the porphyrin ring and the protein part of porphyrin-containing proteins to better understand their stabilizing role. The analysis reported in this study shows that the predominant type of non-canonical interactions at porphyrins are CH····O and CH····N interactions, with a small percentage of CH···π and noncanonical interactions involving sulfur atoms. The majority of non-canonical interactions are formed from side-chains of charged and polar amino acids, whereas backbone groups are not frequently involved. The main-chain noncanonical interactions might be slightly more linear than the side-chain interactions, and they have somewhat shorter median distances. The analysis, performed in this study, shows that about 44% of the total interactions in the dataset are involved in the formation of multiple (furcated) noncanonical interactions. The high number of porphyrin-water interactions show importance of the inclusion of solvent in protein-ligand interaction studies. Furthermore, in the present study we have observed that stabilization centers are composed predominantly from nonpolar amino acid residues. Amino acids deployed in the environment of porphyrin rings are deposited in helices and coils. The results from this study might be used for structure-based porphyrin protein prediction and as scaffolds for future porphyrin-containing protein design.
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13
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Yuan C, Gao Z. Aβ Interacts with Both the Iron Center and the Porphyrin Ring of Heme: Mechanism of Heme’s Action on Aβ Aggregation and Disaggregation. Chem Res Toxicol 2013; 26:262-9. [DOI: 10.1021/tx300441e] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Can Yuan
- Hubei Key Laboratory of Bioinorganic
Chemistry and Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan,
Hubei 430074, People’s Republic of China
- Key Laboratory of Molecular Biophysics of
Ministry of Education, College of Life Science and Technology, Center
for Human Genome Research, Huazhong University of Science and Technology, Wuhan, Hubei 430074, People’s
Republic of China
| | - Zhonghong Gao
- Hubei Key Laboratory of Bioinorganic
Chemistry and Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan,
Hubei 430074, People’s Republic of China
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14
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Moore TC, Newmister SA, Rayment I, Escalante-Semerena JC. Structural insights into the mechanism of four-coordinate Cob(II)alamin formation in the active site of the Salmonella enterica ATP:Co(I)rrinoid adenosyltransferase enzyme: critical role of residues Phe91 and Trp93. Biochemistry 2012; 51:9647-57. [PMID: 23148601 DOI: 10.1021/bi301378d] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
ATP:co(I)rrinoid adenosyltransferases (ACATs) are enzymes that catalyze the formation of adenosylcobalamin (AdoCbl, coenzyme B(12)) from cobalamin and ATP. There are three families of ACATs, namely, CobA, EutT, and PduO. In Salmonella enterica, CobA is the housekeeping enzyme that is required for de novo AdoCbl synthesis and for salvaging incomplete precursors and cobalamin from the environment. Here, we report the crystal structure of CobA in complex with ATP, four-coordinate cobalamin, and five-coordinate cobalamin. This provides the first crystallographic evidence of the existence of cob(II)alamin in the active site of CobA. The structure suggests a mechanism in which the enzyme adopts a closed conformation and two residues, Phe91 and Trp93, displace 5,6-dimethylbenzimidazole, the lower nucleotide ligand base of cobalamin, to generate a transient four-coordinate cobalamin, which is critical in the formation of the AdoCbl Co-C bond. In vivo and in vitro mutational analyses of Phe91 and Trp93 emphasize the important role of bulky hydrophobic side chains in the active site. The proposed manner in which CobA increases the redox potential of the cob(II)alamin/cob(I)alamin couple to facilitate formation of the Co-C bond appears to be analogous to that utilized by the PduO-type ACATs, where in both cases the polar coordination of the lower ligand to the cobalt ion is eliminated by placing that face of the corrin ring adjacent to a cluster of bulky hydrophobic side chains.
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Affiliation(s)
- Theodore C Moore
- Department of Bacteriology, University of Wisconsin, Madison, WI 53706, USA
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15
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Shaw WJ. The Outer-Coordination Sphere: Incorporating Amino Acids and Peptides as Ligands for Homogeneous Catalysts to Mimic Enzyme Function. CATALYSIS REVIEWS-SCIENCE AND ENGINEERING 2012. [DOI: 10.1080/01614940.2012.679453] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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16
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17
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Park K, Mera PE, Escalante-Semerena JC, Brunold TC. Spectroscopic characterization of active-site variants of the PduO-type ATP:corrinoid adenosyltransferase from Lactobacillus reuteri: insights into the mechanism of four-coordinate Co(II)corrinoid formation. Inorg Chem 2012; 51:4482-94. [PMID: 22480351 DOI: 10.1021/ic202096x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The PduO-type adenosine 5'-triphosphate (ATP):corrinoid adenosyltransferase from Lactobacillus reuteri (LrPduO) catalyzes the transfer of the adenosyl-group of ATP to Co(1+)cobalamin (Cbl) and Co(1+)cobinamide (Cbi) substrates to synthesize adenosylcobalamin (AdoCbl) and adenosylcobinamide (AdoCbi(+)), respectively. Previous studies revealed that to overcome the thermodynamically challenging Co(2+) → Co(1+) reduction, the enzyme drastically weakens the axial ligand-Co(2+) bond so as to generate effectively four-coordinate (4c) Co(2+)corrinoid species. To explore how LrPduO generates these unusual 4c species, we have used magnetic circular dichroism (MCD) and electron paramagnetic resonance (EPR) spectroscopic techniques. The effects of active-site amino acid substitutions on the relative yield of formation of 4c Co(2+)corrinoid species were examined by performing eight single-amino acid substitutions at seven residues that are involved in ATP-binding, an intersubunit salt bridge, and the hydrophobic region surrounding the bound corrin ring. A quantitative analysis of our MCD and EPR spectra indicates that the entire hydrophobic pocket below the corrin ring, and not just residue F112, is critical for the removal of the axial ligand from the cobalt center of the Co(2+)corrinoids. Our data also show that a higher level of coordination among several LrPduO amino acid residues is required to exclude the dimethylbenzimidazole moiety of Co(II)Cbl from the active site than to remove the water molecule from Co(II)Cbi(+). Thus, the hydrophilic interactions around and above the corrin ring are more critical to form 4c Co(II)Cbl than 4c Co(II)Cbi(+). Finally, when ATP analogues were used as cosubstrate, only "unactivated" five-coordinate (5c) Co(II)Cbl was observed, disclosing an unexpectedly large role of the ATP-induced active-site conformational changes with respect to the formation of 4c Co(II)Cbl. Collectively, our results indicate that the level of control exerted by LrPduO over the timing for the formation of the 4c Co(2+)corrinoid intermediates is even more exquisite than previously anticipated.
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Affiliation(s)
- Kiyoung Park
- University of Wisconsin-Madison, Department of Chemistry, Madison, Wisconsin 53706, USA
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18
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Shinde S, Cordova JM, Woodrum BW, Ghirlanda G. Modulation of function in a minimalist heme-binding membrane protein. J Biol Inorg Chem 2012; 17:557-64. [PMID: 22307279 DOI: 10.1007/s00775-012-0876-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Accepted: 01/14/2012] [Indexed: 12/21/2022]
Abstract
De novo designed heme-binding proteins have been used successfully to recapitulate features of natural hemoproteins. This approach has now been extended to membrane-soluble model proteins. Our group designed a functional hemoprotein, ME1, by engineering a bishistidine binding site into a natural membrane protein, glycophorin A (Cordova et al. in J Am Chem Soc 129:512-518, 2007). ME1 binds iron(III) protoporphyrin IX with submicromolar affinity, has a redox potential of -128 mV, and displays peroxidase activity. Here, we show the effect of aromatic residues in modulating the redox potential in the context of a membrane-soluble model system. We designed aromatic interactions with the heme through a single-point mutant, G25F, in which a phenylalanine is designed to dock against the porphyrin ring. This mutation results in roughly tenfold tighter binding to iron(III) protoporphyrin IX (K(d,app) = 6.5 × 10(-8) M), and lowers the redox potential of the cofactor to -172 mV. This work demonstrates that specific design features aimed at controlling the properties of bound cofactors can be introduced in a minimalist membrane hemoprotein model. The ability to modulate the redox potential of cofactors embedded in artificial membrane proteins is crucial for the design of electron transfer chains across membranes in functional photosynthetic devices.
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Affiliation(s)
- Sandip Shinde
- Department of Chemistry and Biochemistry, ASU, Tempe, AZ 85287, USA
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Dimitrijević BP, Borozan SZ, Stojanović SĐ. π–π and cation–π interactions in protein–porphyrin complex crystal structures. RSC Adv 2012. [DOI: 10.1039/c2ra21937a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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Yang CM, Zhang J. Insights into intramolecular Trp and His side-chain orientation and stereospecific π interactions surrounding metal centers: an investigation using protein metal-site mimicry in solution. Chemistry 2011; 16:10854-65. [PMID: 20669189 DOI: 10.1002/chem.200903149] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Metal-binding scaffolds incorporating a Trp/His-paired epitope are instrumental in giving novel insights into the physicochemical basis of functional and mechanistic versatility conferred by the Trp-His interplay at a metal site. Herein, by coupling biometal site mimicry and (1)H and (13)C NMR spectroscopy experiments, modular constructs EDTA-(L-Trp, L-His) (EWH; EDTA=ethylenediamino tetraacetic acid) and DTPA-(L-Trp, L-His) (DWH; DTPA=diethylenetriamino pentaacetic acid) were employed to dissect the static and transient physicochemical properties of hydrophobic/hydrophilic aromatic interactive modes surrounding biometal centers. The binding feature and identities of the stoichiometric metal-bound complexes in solution were investigated by using (1)H and (13)C NMR spectroscopy, which facilitated a cross-validation of the carboxylate, amide oxygen, and tertiary amino groups as the primary ligands and indole as the secondary ligand, with the imidazole (Im) N3 nitrogen being weakly bound to metals such as Ca(2+) owing to a multivalency effect. Surrounding the metal centers, the stereospecific orientation of aromatic rings in the diastereoisomerism is interpreted with the Ca(2+)-EWH complex. With respect to perturbed Trp side-chain rotamer heterogeneity, drastically restricted Trp side-chain flexibility and thus a dynamically constrained rotamer interconversion due to π interactions is evident from the site-selective (13)C NMR spectroscopic signal broadening of the Trp indolyl C3 atom. Furthermore, effects of Trp side-chain fluctuation on indole/Im orientation were the subject of a 2D NMR spectroscopy study by using the Ca(2+)-bound state; a C-H2(indolyl)/C-H5(Im(+)) connectivity observed in the NOESY spectra captured direct evidence that the N-H1 of the Ca(2+)-Im(+) unit interacted with the pyrrole ring of the indole unit in Ca(2+)-bound EWH but not in DWH, which is assignable to a moderately static, anomalous, T-shaped, interplanar π(+)-π stacking alignment. Nevertheless, a comparative (13)C NMR spectroscopy study of the two homologous scaffolds revealed that the overall response of the indole unit arises predominantly from global attractions between the indole ring and the entire positively charged first coordination sphere. The study thus demonstrates the coordination-sphere/geometry dependence of the Trp/His side-chain interplay, and established that π interactions allow (13)C NMR spectroscopy to offer a new window for investigating Trp rotamer heterogeneity near metal-binding centers.
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Affiliation(s)
- Chi Ming Yang
- Neurochemistry & Biophysical Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China.
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Ming Yang C. Biometal binding-site mimicry with modular, hetero-bifunctionally modified architecture encompassing a Trp/His motif: Insights into spatiotemporal noncovalent interactions from a comparative spectroscopic study. Dalton Trans 2011; 40:3008-27. [DOI: 10.1039/c0dt00237b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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22
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Mera PE, St Maurice M, Rayment I, Escalante-Semerena JC. Residue Phe112 of the human-type corrinoid adenosyltransferase (PduO) enzyme of Lactobacillus reuteri is critical to the formation of the four-coordinate Co(II) corrinoid substrate and to the activity of the enzyme. Biochemistry 2009; 48:3138-45. [PMID: 19236001 DOI: 10.1021/bi9000134] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
ATP:Corrinoid adenosyltransferases (ACAs) catalyze the transfer of the adenosyl moiety from ATP to cob(I)alamin via a four-coordinate cob(II)alamin intermediate. At present, it is unknown how ACAs promote the formation of the four-coordinate corrinoid species needed for activity. The published high-resolution crystal structure of the ACA from Lactobacillus reuteri (LrPduO) in complex with ATP and cob(II)alamin shows that the environment around the alpha face of the corrin ring consists of bulky hydrophobic residues. To understand how these residues promote the generation of the four-coordinate cob(II)alamin, variants of the human-type ACA enzyme from L. reuteri (LrPduO) were kinetically and structurally characterized. These studies revealed that residue Phe112 is critical in the displacement of 5,6-dimethylbenzimidazole (DMB) from its coordination bond with the Co ion of the ring, resulting in the formation of the four-coordinate species. An F112A substitution resulted in a 80% drop in the catalytic efficiency of the enzyme. The explanation for this loss of activity was obtained from the crystal structure of the mutant protein, which showed cob(II)alamin bound in the active site with DMB coordinated to the cobalt ion. The crystal structure of an LrPduO(F112H) variant showed a DMB-off/His-on interaction between the corrinoid and the enzyme, whose catalytic efficiency was 4 orders of magnitude lower than that of the wild-type protein. The analysis of the kinetic parameters of LrPduO(F112H) suggests that the F112H substitution negatively impacts product release. Substitutions of other hydrophobic residues in the Cbl binding pocket did not result in significant defects in catalytic efficiency in vitro; however, none of the variant enzymes analyzed in this work supported AdoCbl biosynthesis in vivo.
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Affiliation(s)
- Paola E Mera
- Department of Bacteriology, University of Wisconsin, Madison, Wisconsin 53706, USA
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Tzul FO, Bowler BE. Importance of contact persistence in denatured state loop formation: kinetic insights into sequence effects on nucleation early in folding. J Mol Biol 2009; 390:124-34. [PMID: 19426739 DOI: 10.1016/j.jmb.2009.04.075] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2009] [Revised: 04/23/2009] [Accepted: 04/30/2009] [Indexed: 10/20/2022]
Abstract
Protein folding is dependent on the formation and persistence of simple loops early in folding. Ease of loop formation and persistence is believed to be dependent on the steric interactions of the residues involved in loop formation. We have previously investigated this factor in the denatured state of iso-1-cytochrome c using a five-amino-acid insert in front of a unique histidine in the N-terminal region of the protein. Previously, we reported that the apparent pK(a) values of loop formation for the most flexible (all Gly) and least flexible (all Ala) insert were, within error, the same. We evaluate whether this observation is due to differences in the persistence of loop contacts or due to effects of local sequence sterics and main-chain hydration on the persistence length of the chain. We also test whether sequence order affects loop formation. Here, we report kinetic results coupled to further mutagenesis of the insert to discern between these possibilities. We find that the amino acid-glycine versus alanine-next to the loop forming histidine has a dominant effect on loop kinetics and equilibria. A glycine in this position speeds loop breakage relative to alanine, resulting in less stable loops. At high percentage of Gly in the insert, rates of loop formation and breakage exactly compensate, leading to a leveling out in loop stability. Loop formation rates also increase with glycine content, inconsistent with poly-Gly segments being more extended than previously suspected due to main-chain hydration or local sterics. Unlike loop breakage rates, loop formation rates are insensitive to local sequence. Together, these observations suggest that contact persistence plays a more important role in defining the "folding code" than rates of loop formation.
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Affiliation(s)
- Franco O Tzul
- Department of Chemistry and Biochemistry and Center for Biomolecular Structure and Dynamics, The University of Montana, Missoula, 59812, USA
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24
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Negron C, Fufezan C, Koder RL. Geometric constraints for porphyrin binding in helical protein binding sites. Proteins 2009; 74:400-16. [PMID: 18636480 DOI: 10.1002/prot.22143] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Helical bundles which bind heme and porphyrin cofactors have been popular targets for cofactor-containing de novo protein design. By analyzing a highly nonredundant subset of the protein databank we have determined a rotamer distribution for helical histidines bound to heme cofactors. Analysis of the entire nonredundant database for helical sequence preferences near the ligand histidine demonstrated little preference for amino acid side chain identity, size, or charge. Analysis of the database subdivided by ligand histidine rotamer, however, reveals strong preferences in each case, and computational modeling illuminates the structural basis for some of these findings. The majority of the rotamer distribution matches that predicted by molecular simulation of a single porphyrin-bound histidine residue placed in the center of an all-alanine helix, and the deviations explain two prominent features of natural heme protein binding sites: heme distortion in the case of the cytochromes C in the m166 histidine rotamer, and a highly prevalent glycine residue in the t73 histidine rotamer. These preferences permit derivation of helical consensus sequence templates which predict optimal side chain-cofactor packing interactions for each rotamer. These findings thus promise to guide future design endeavors not only in the creation of higher affinity heme and porphyrin binding sites, but also in the direction of bound cofactor geometry.
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Affiliation(s)
- Christopher Negron
- Department of Physics, the City College of New York, New York, New York 10031, USA
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Dawn A, Fujita N, Haraguchi S, Sada K, Shinkai S. An organogel system can control the stereochemical course of anthracene photodimerization. Chem Commun (Camb) 2009:2100-2. [DOI: 10.1039/b820565e] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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26
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Dawn A, Fujita N, Haraguchi S, Sada K, Tamaru SI, Shinkai S. Studies on a new class of organogelator containing 2-anthracenecarboxylic acid: Influence of gelator and solvent on stereochemistry of the photodimers. Org Biomol Chem 2009; 7:4378-85. [DOI: 10.1039/b910741j] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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27
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Affiliation(s)
- Guy A Hembury
- Japan Science and Technology Agency and Department of Applied Chemistry, Osaka University, 2-1 Yamada-oka, Suita 565-0871, Japan
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28
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Stojanović SD, Medaković VB, Predović G, Beljanski M, Zarić SD. XH/pi interactions with the pi system of porphyrin ring in porphyrin-containing proteins. J Biol Inorg Chem 2007; 12:1063-71. [PMID: 17659366 DOI: 10.1007/s00775-007-0276-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2007] [Accepted: 06/28/2007] [Indexed: 11/29/2022]
Abstract
Searching structures of porphyrin-containing proteins from the Protein Data Bank revealed that the pi system of every porphyrin ring is involved in XH/pi interactions, with most of the porphyrins having several interactions. Both five-membered pyrrole rings and six-membered chelate rings are involved in XH/pi interactions; the number of interactions with five-membered rings is larger than the number of interactions with six-membered rings. We found interactions with C-H and N-H groups as hydrogen-atom donors; however, the number of CH/pi interactions is much larger than the number of NH/pi interactions. The amino acids involved in the interactions show a high conservation score. Our results that every porphyrin is involved in XH/pi interactions and that amino acids involved in these interactions are highly conserved demonstrate that XH/pi interactions play an important role in porphyrin-protein stability.
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Affiliation(s)
- Srdan D Stojanović
- Department of Chemistry, University of Belgrade, Studentski trg 16, 11001 Belgrade, Serbia
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29
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Bulmer AC, Ried K, Coombes JS, Blanchfield JT, Toth I, Wagner KH. The anti-mutagenic and antioxidant effects of bile pigments in the Ames Salmonella test. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2007; 629:122-32. [PMID: 17350329 DOI: 10.1016/j.mrgentox.2007.01.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2006] [Revised: 01/22/2007] [Accepted: 01/25/2007] [Indexed: 10/23/2022]
Abstract
The aim of this study was to explore the potential pro- and anti-mutagenic effects of endogenous bile pigments unconjugated bilirubin (BR), biliverdin (BV) and a synthetic, water soluble conjugate, bilirubin ditaurate (BRT) in the Ames Salmonella test. The bile pigments were tested over a wide concentration range (0.01-2 micromol/plate) in the presence of three bacterial strains (TA98, TA100, TA102). A variety of mutagens including benzo[alpha]pyrene (B[alpha]P), 2,4,7 trinitrofluorenone (TNFone), 2-aminofluorene (2-AF), sodium azide (NaN(3)) and tertiary-butyl hydroperoxide (t-BuOOH), were used to promote the formation of mutant revertants. Tests were conducted with (B[alpha]P, 2-AF, t-BuOOH) and without (TNFone, NaN(3), t-BuOOH) metabolic activation incorporating the addition of the microsomal liver preparation, S9. The bile pigments alone did not induce mutagenicity in any of the strains tested (p>0.05). Anti-mutagenic effects of the bile pigments were observed in the presence of all mutagens except for NaN(3) and the anti-mutagenic effects appeared independent of the strain tested. For TNFone induced genotoxicity, the order of effectiveness was BR> or =BRT>BV. However, the order was BV> or =BRT> or =BR for 2-AF. Antioxidant testing in the TA102 strain revealed bile pigments could effectively inhibit the genotoxic effect of t-BuOOH induced oxidative stress. The apparent antioxidant and anti-mutagenic behaviour of bile pigments further suggests their presence in biological systems is of possible physiological importance.
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Affiliation(s)
- A C Bulmer
- School of Human Movement Studies, University of Queensland, Brisbane 4072, Australia.
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30
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Mooibroek TJ, Gamez P. The s-triazine ring, a remarkable unit to generate supramolecular interactions. Inorganica Chim Acta 2007. [DOI: 10.1016/j.ica.2006.07.061] [Citation(s) in RCA: 135] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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31
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Hodgson MJ, Borovkov VV, Inoue Y, Arnold DP. A new type of chiral porphyrin: Organopalladium porphyrins with chiral chelating diphosphine ligands. J Organomet Chem 2006. [DOI: 10.1016/j.jorganchem.2005.10.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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32
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Wang F, Yang J, Wu X, Wang X, Sun C, Liu S, Guo C. Molecular self-assembling and the fluorescence enhancement in morin–Al3+–cetyltrimethylammonium bromide–protein system. Biochimie 2006; 88:121-9. [PMID: 16181723 DOI: 10.1016/j.biochi.2005.08.002] [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: 05/12/2005] [Accepted: 08/16/2005] [Indexed: 11/18/2022]
Abstract
Fluorescence enhancement effect of the morin-Al3+-cetyltrimethylammonium bromide (CTAB)-bovine serum albumin (BSA) system is reported here and the interaction mechanism is studied using fluorescence, resonance light scattering (RLS), absorption spectroscopy, Far-UV circular dichroism (CD) spectrum and small angle X-ray scattering (SAXS) measurement. It is considered that protein can bind with Al3+, morin and CTAB through self-assembling function with electrostatic attraction, hydrogen bond, hydrophobic interaction and Vander Waal force etc, and forms a supermolecular association with multilayer structure, in which morin-Al3+ is clamped between BSA and CTAB. In this system, the fluorescence enhancement of morin originates from both intermolecular energy transfer between BSA and morin, and the hydrophobic microenvironment provided by BSA and CTAB. Whereas Al3+ plays a key role for the enhancement of energy transfer efficiency because it provides an efficient channel for the energy transfer between BSA and morin.
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Affiliation(s)
- Fei Wang
- Key Laboratory of Colloid and Interface Chemistry (Shandong University), Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
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Sun C, Yang J, Wu X, Huang X, Wang F, Liu S. Unfolding and refolding of bovine serum albumin induced by cetylpyridinium bromide. Biophys J 2005; 88:3518-24. [PMID: 15731386 PMCID: PMC1305498 DOI: 10.1529/biophysj.104.051516] [Citation(s) in RCA: 137] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2004] [Accepted: 02/04/2005] [Indexed: 11/18/2022] Open
Abstract
The interaction of bovine serum albumin (BSA) with cationic surfactant cetylpyridinium bromide (CPB) in aqueous solution (pH 7.00) was studied quantitatively with ultraviolet (UV)-visible, far-UV, and near-UV circular dichroism, fluorescence, small angle x-ray scattering, and nuclear magnetic resonance measurement. It was found that CPB at low and high concentrations could induce the unfolding and refolding of BSA, respectively. We suggest that in the unfolding process, there existed BSA-CPB complex with the "necklace and bead" structure in which the unfolded BSA wrapped around CPB micelles, and that the hydrophobic interaction between the complexes led to the formation of large aggregates. The aromatic headgroup of CPB interacted with the tryptophan residues of BSA, resulting in the aromatic ring stacking between BSA and CPB. During the refolding process, the BSA molecule was penetrated into the rod micelle of CPB and the hydrophobic moiety of the BSA molecule was exposed outside while its hydrophilic part was hidden inside, thereby disrupting the aromatic ring stacking.
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Affiliation(s)
- Changxia Sun
- Key Laboratory of Colloid and Interface Chemistry (Shandong University), Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
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Fluorescent enhancement effect in terbium–gadolinium–protein–cetylpyridine bromide system and its application for the determination of protein at nanogram level. Chem Phys Lett 2004. [DOI: 10.1016/j.cplett.2004.09.094] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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35
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Ghirlanda G, Osyczka A, Liu W, Antolovich M, Smith KM, Dutton PL, Wand AJ, DeGrado WF. De novo design of a D2-symmetrical protein that reproduces the diheme four-helix bundle in cytochrome bc1. J Am Chem Soc 2004; 126:8141-7. [PMID: 15225055 DOI: 10.1021/ja039935g] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An idealized, water-soluble D(2)-symmetric diheme protein is constructed based on a mathematical parametrization of the backbone coordinates of the transmembrane diheme four-helix bundle in cytochrome bc(1). Each heme is coordinated by two His residues from diagonally apposed helices. In the model, the imidazole rings of the His ligands are held in a somewhat unusual perpendicular orientation as found in cytochrome bc(1), which is maintained by a second-shell hydrogen bond to a Thr side chain on a neighboring helix. The resulting peptide is unfolded in the apo state but assembles cooperatively upon binding to heme into a well-folded tetramer. Each tetramer binds two hemes with high affinity at low micromolar concentrations. The equilibrium reduction midpoint potential varies between -76 mV and -124 mV vs SHE in the reducing and oxidizing direction, respectively. The EPR spectrum of the ferric complex indicates the presence of a low-spin species, with a g(max) value of 3.35 comparable to those obtained for hemes b of cytochrome bc(1) (3.79 and 3.44). This provides strong support for the designed perpendicular orientation of the imidazole ligands. Moreover, NMR spectra show that the protein exists in solution in a unique conformation and is amenable to structural studies. This protein may provide a useful scaffold for determining how second-shell ligands affect the redox potential of the heme cofactor.
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Affiliation(s)
- Giovanna Ghirlanda
- Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA.
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36
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Cowley AB, Rivera M, Benson DR. Stabilizing roles of residual structure in the empty heme binding pockets and unfolded states of microsomal and mitochondrial apocytochrome b5. Protein Sci 2004; 13:2316-29. [PMID: 15295112 PMCID: PMC2280026 DOI: 10.1110/ps.04817704] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2004] [Revised: 06/03/2004] [Accepted: 06/04/2004] [Indexed: 10/26/2022]
Abstract
The microsomal (Mc) and mitochondrial (OM) isoforms of mammalian cytochrome b5 are the products of different genes, which likely arose via duplication of a primordial gene and subsequent functional divergence. Despite sharing essentially identical folds, heme-polypeptide interactions are stronger in OM b5s than in Mc b5s due to the presence of two conserved patches of hydrophobic amino acid side chains in the OM heme binding pockets. This is of fundamental interest in terms of understanding heme protein structure-function relationships, because stronger heme-polypeptide interactions in OM b5s in comparison to Mc b5s may represent a key source of their more negative reduction potentials. Herein we provide evidence that interactions amongst the amino acid side chains contributing to the hydrophobic patches in rat OM (rOM) b5 persist when heme is removed, rendering the empty heme binding pocket of rOM apo-b5 more compact and less conformationally dynamic than that in bovine Mc (bMc) apo-b5. This may contribute to the stronger heme binding by OM apo-b5 by reducing the entropic penalty associated with polypeptide folding. We also show that when bMc apo-b5 unfolds it adopts a structure that is more compact and contains greater nonrandom secondary structure content than unfolded rOM apo-b5. We propose that a more robust beta-sheet in Mc apo-b5s compensates for the absence of the hydrophobic packing interactions that stabilize the heme binding pocket in OM apo-b5s.
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Affiliation(s)
- Aaron B Cowley
- Department of Chemistry, University of Kansas, 1251 Wescoe Hall Drive, 2010 Malott Hall, Lawrence, KS 66045-7582, USA
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Sun C, Yang J, Wu X, Liu S, Su B. Study on the fluorescent enhancement effect in terbium–gadolinium–protein–sodium dodecyl benzene sulfonate system and its application on sensitive detection of protein at nanogram level. Biochimie 2004; 86:569-78. [PMID: 15388234 DOI: 10.1016/j.biochi.2004.07.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2004] [Accepted: 07/05/2004] [Indexed: 11/24/2022]
Abstract
The co-luminescence effect in a terbium-gadolinium-protein-sodium dodecyl benzene sulfonate (SDBS) system is reported here. Based on it, the sensitive quantitative analysis of protein at nanogram levels is established. The co-luminescence mechanism is studied using fluorescence, resonance light scattering (RLS), absorption spectroscopy and NMR measurement. It is considered that protein could be unfolded by SDBS, then a efficacious intramolecular fluorescent energy transfer occurs from unfolded protein to rare earth ions through SDBS acting as a "transfer bridge" to enhance the emission fluorescence of Tb3+ in this ternary complex of Tb-SDBS-BSA, where energy transfer from protein to SDBS by aromatic ring stacking is the most important step. Cooperating with the intramolecular energy transfer above is the intermolecular energy transfer between the simultaneous existing complexes of both Tb3+ and Gd3+. The fluorescence quantum yield is increased by an energy-insulating sheath, which is considered to be another reason for the resulting enhancement of the fluorescence. Förster theory is used to calculate the distribution of enhancing factors and has led to a greater understanding of the mechanisms of energy transfer.
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Affiliation(s)
- Changxia Sun
- Key Laboratory of Colloid and Interface Chemistry (Shandong University), Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, PR China
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Affiliation(s)
- Charles J Reedy
- Department of Chemistry, Columbia University, 3000 Broadway, MC 3121, New York, New York 10027, USA
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39
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Tsukube H, Shinoda S. Lanthanide complexes in molecular recognition and chirality sensing of biological substrates. Chem Rev 2002; 102:2389-403. [PMID: 12059273 DOI: 10.1021/cr010450p] [Citation(s) in RCA: 470] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hiroshi Tsukube
- Department of Chemistry, Graduate School of Science, Osaka City University, Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan
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40
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Schneider HJ, Tianjun L, Sirish M, Malinovski V. Dispersive interactions in supramolecular porphyrin complexes. Tetrahedron 2002. [DOI: 10.1016/s0040-4020(01)01103-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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41
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Affiliation(s)
- A Lombardi
- Department of Chemistry, University of Napoli Federico II, Complesso Universitario Monte S. Angelo, Via Cynthia 45, I-80126 Napoli, Italy.
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Hammack BN, Smith CR, Bowler BE. Denatured state thermodynamics: residual structure, chain stiffness and scaling factors. J Mol Biol 2001; 311:1091-104. [PMID: 11531342 DOI: 10.1006/jmbi.2001.4909] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A set of nine variants of yeast iso-1-cytochrome c with zero or one surface histidine have been engineered such that the N-terminal amino group is acetylated in vivo. N-terminal acetylation has been confirmed by mass spectral analysis of intact and proteolytically digested protein. The histidine-heme loop-forming equilibrium, under denaturing conditions (3 M guanidine hydrochloride), has been measured by pH titration providing an observed pK(a), pK(a)(obs), for each variant. N-terminal acetylation prevents the N-terminal amino group-heme binding equilibrium from interfering with measurements of histidine-heme affinity. Significant deviation is observed from the linear dependence of pK(a)(obs) on the log of the number of monomers in the loop formed, expected for a random coil denatured state. The maximum histidine-heme affinity occurs for a loop size of 37 monomers. For loop sizes of 37-83 monomers, histidine-heme pK(a)(obs) values are consistent with a scaling factor of -4.2+/-0.3. This value is much larger than the scaling factor of -1.5 for a freely jointed random coil, which is commonly used to represent the conformational properties of protein denatured states. For loop sizes of nine to 22 monomers, chain stiffness is likely responsible for the decreases in histidine-heme affinity relative to a loop size of 37. The results are discussed in terms of residual structure and sequence composition effects on the conformational properties of the denatured states of proteins.
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Affiliation(s)
- B N Hammack
- Department of Chemistry & Biochemistry, University of Denver, 2190 East Iliff Avenue, Denver, CO 80208-2436, USA
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Kennedy ML, Silchenko S, Houndonougbo N, Gibney BR, Dutton PL, Rodgers KR, Benson DR. Model hemoprotein reduction potentials: the effects of histidine-to-iron coordination equilibrium. J Am Chem Soc 2001; 123:4635-6. [PMID: 11457264 DOI: 10.1021/ja0156441] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- M L Kennedy
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, USA
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Sampath V, Zhao XJ, Caughey WS. Anesthetic-like interactions of nitric oxide with albumin and hemeproteins. A mechanism for control of protein function. J Biol Chem 2001; 276:13635-43. [PMID: 11278308 DOI: 10.1074/jbc.m006588200] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Noncovalent bonding interactions of nitric oxide (NO) with human serum albumin (HSA), human hemoglobin A, bovine myoglobin, and bovine cytochrome c oxidase (CcO) have been explored. The anesthetic nitrous oxide (NNO) occupies multiple sites within each protein, but does not bind to heme iron. Infrared (IR) spectra of NNO molecules sequestered within albumin, with NO present, support the binding of NO and NNO to the same sites with comparable affinities. Perturbations of IR spectra of the Cys(34) thiol of HSA indicate NO, NNO, halothane, and chloroform can induce similar changes in protein structure. Experiments evaluating the relative affinities of binding of NO and carbon monoxide (CO) to iron(II) sites of the hemeproteins led to evidence of NO binding to noniron, nonsulfur sites as well. With HbA, IR spectra of cysteine thiols and/or the iron(II) N-O stretching region denote changes in protein structure due to NO, NNO, or CO occupying noniron sites with an order of decreasing affinities of NO > NNO > CO. Loss of NO from some, not all, noniron sites in hemeproteins is very slow (t(1/2) approximately hours). These findings provide examples in which NO and anesthetics alter the structure and properties of protein similarly, and support the hypothesis that some physiological effects of NO (and possibly CO) result from anesthetic-like noncovalent bonding to sites within protein or other tissue components. Such bonding may be involved in mechanisms for control of oxygen transport, mitochondrial respiration, and activation of soluble guanylate cyclase by NO.
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Affiliation(s)
- V Sampath
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, USA
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Taber DF, Nakajima K. Unsymmetrical ozonolysis of a Diels-Alder adduct: practical preparation of a key intermediate for heme total synthesis. J Org Chem 2001; 66:2515-7. [PMID: 11281801 DOI: 10.1021/jo001732c] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- D F Taber
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA.
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Abstract
Recent progress in the rational design of metal sites within peptide model systems shows increasing control in the placement of metals within helical bundles and inclusion of sophisticated elements such as second-sphere ligand interactions. A crystallographically characterized two-metal peptide model for diiron proteins represents a major achievement in de novo design methodologies. Increasingly complex and robust models for electron transfer through and between helices, and electrode-supported electron-transfer peptides, have been constructed. Design elements for peptide-supported ferredoxins and mononuclear Fe(II) and Zn(II) sites have been refined.
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Affiliation(s)
- G Xing
- Department of Chemistry, Texas A&M University, College Station 77842-3012, USA
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47
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Borovkov VV, Yamamoto N, Lintuluoto JM, Tanaka T, Inoue Y. Supramolecular chirality induction in bis(zinc porphyrin) by amino acid derivatives: Rationalization and applications of the ligand bulkiness effect. Chirality 2001; 13:329-35. [PMID: 11370023 DOI: 10.1002/chir.1039] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The achiral syn conformer (face-to-face) of the ethane-bridged bis(zinc porphyrin) (syn-ZnD) transforms into the corresponding chiral extended anti bis-ligated species (anti-ZnD.L2) in the presence of enantiopure ligands (L: amino acid derivatives). The mechanism of the supramolecular chirality induction is based on chiral ligand binding to zinc porphyrins and subsequent formation of either right- or left-handed screw structures in anti-ZnD.L2. The screw structure formation arises from steric interactions between the bulkiest substituent at the asymmetric carbon of the ligand and the peripheral ethyl groups of the neighboring porphyrin ring directed towards the covalent bridge. The sign and amplitude of the induced circular dichroism (CD) are dependent on the steric bulk of the substituents at the chiral center. The greater difference in size between the chiral center's substituents gives the stronger induced CD signal. Rationalization of the ligand bulkiness effect on chirality induction by amino acid derivatives, application of this supramolecular system for the determination of ligand absolute configuration, and relative bulkiness of the substituents at the asymmetric carbon are discussed.
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Affiliation(s)
- V V Borovkov
- Inoue Photochirogenesis Project, ERATO, JST, Osaka, Japan.
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48
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Lee KH, Kennedy ML, Buchalova M, Benson DR. Thermodynamics of Carbon Monoxide Binding by Helical Hemoprotein Models: the Effect of a Competing Intramolecular Ligand. Tetrahedron 2000. [DOI: 10.1016/s0040-4020(00)00879-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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49
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Gibney BR, Dutton P. De novo design and synthesis of heme proteins. ADVANCES IN INORGANIC CHEMISTRY 2000. [DOI: 10.1016/s0898-8838(00)51008-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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