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Iacovelli R, Bovenberg RAL, Driessen AJM. Nonribosomal peptide synthetases and their biotechnological potential in Penicillium rubens. J Ind Microbiol Biotechnol 2021; 48:6324005. [PMID: 34279620 PMCID: PMC8788816 DOI: 10.1093/jimb/kuab045] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 07/12/2021] [Indexed: 01/23/2023]
Abstract
Nonribosomal peptide synthetases (NRPS) are large multimodular enzymes that synthesize a diverse variety of peptides. Many of these are currently used as pharmaceuticals, thanks to their activity as antimicrobials (penicillin, vancomycin, daptomycin, echinocandin), immunosuppressant (cyclosporin) and anticancer compounds (bleomycin). Because of their biotechnological potential, NRPSs have been extensively studied in the past decades. In this review, we provide an overview of the main structural and functional features of these enzymes, and we consider the challenges and prospects of engineering NRPSs for the synthesis of novel compounds. Furthermore, we discuss secondary metabolism and NRP synthesis in the filamentous fungus Penicillium rubens and examine its potential for the production of novel and modified β-lactam antibiotics.
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Affiliation(s)
- Riccardo Iacovelli
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Roel A L Bovenberg
- Synthetic Biology and Cell Engineering, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands.,DSM Biotechnology Centre, 2613 AX Delft, The Netherlands
| | - Arnold J M Driessen
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
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2
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Chapman NC, Rutledge PJ. Isopenicillin N Synthase: Crystallographic Studies. Chembiochem 2021; 22:1687-1705. [PMID: 33415840 DOI: 10.1002/cbic.202000743] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 01/01/2021] [Indexed: 02/02/2023]
Abstract
Isopenicillin N synthase (IPNS) is a non-heme iron oxidase (NHIO) that catalyses the cyclisation of tripeptide δ-(l-α-aminoadipoyl)-l-cysteinyl-d-valine (ACV) to bicyclic isopenicillin N (IPN). Over the last 25 years, crystallography has shed considerable light on the mechanism of IPNS catalysis. The first crystal structure, for apo-IPNS with Mn bound in place of Fe at the active site, reported in 1995, was also the first structure for a member of the wider NHIO family. This was followed by the anaerobic enzyme-substrate complex IPNS-Fe-ACV (1997), this complex plus nitric oxide as a surrogate for co-substrate dioxygen (1997), and an enzyme product complex (1999). Since then, crystallography has been used to probe many aspects of the IPNS reaction mechanism, by crystallising the protein with a diversity of substrate analogues and triggering the oxidative reaction by using elevated oxygen pressures to force the gaseous co-substrate throughout protein crystals and maximise synchronicity of turnover in crystallo. In this way, X-ray structures have been elucidated for a range of complexes closely related to and/or directly derived from key intermediates in the catalytic cycle, thereby answering numerous mechanistic questions that had arisen from solution-phase experiments, and posing many new ones. The results of these crystallographic studies have, in turn, informed computational experiments that have brought further insight. These combined crystallographic and computational investigations augment and extend the results of earlier spectroscopic analyses and solution phase studies of IPNS turnover, to enrich our understanding of this important protein and the wider NHIO enzyme family.
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Affiliation(s)
- Nicole C Chapman
- School of Chemistry, The University of Sydney, Sydney, New South Wales, 2006, Australia
| | - Peter J Rutledge
- School of Chemistry, The University of Sydney, Sydney, New South Wales, 2006, Australia
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3
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Hsieh CC, Liu YC, Tseng MC, Chiang MH, Horng YC. Dioxygen activation by a dinuclear thiolate-ligated Fe(ii) complex. Dalton Trans 2019; 48:379-386. [PMID: 30516213 DOI: 10.1039/c8dt04491k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Dioxygen activation by FeII thiolate complexes is relatively rare in biological and chemical systems because the sulfur site is at least as vulnerable as the iron site to oxidative modification. O2 activation by FeII-SR complexes with thiolate bound trans to the O2 binding site generally affords the FeIV[double bond, length as m-dash]O intermediate and oxidized thiolate. On the other hand, O2 activation by Fe(ii)-SR complexes with thiolate bound cis to the O2 binding site generates FeIII-O-FeIII or S-oxygenated complexes. The postulated FeIV[double bond, length as m-dash]O intermediate has only been identified in isopenicillin N synthase recently. We demonstrated here that O2 activation by a dinuclear FeII thiolate-rich complex produces a mononuclear FeIII complex and water with a supply of electron donors. The thiolate is bound cis to the postulated dioxygen binding site, and no FeIII-O-FeIII or S-oxygenated complex was observed. Although we have not detected the transient intermediate by spectroscopic measurements, the FeIV[double bond, length as m-dash]O intermediate is suggested to exist by theoretical calculation, and P-oxidation and hydride-transfer experiments. In addition, an unprecedented FeIII-O2-FeIII complex supported by thiolates was observed during the reaction by using a coldspray ionization time-of-flight mass (CSI-TOF MS) instrument. This is also supported by low-temperature UV-vis measurements. The intramolecular NHO[double bond, length as m-dash]FeIV hydrogen bonding, calculated by DFT, probably fine tunes the O2-activation process for intramolecular hydrogen abstraction, avoiding the S-oxygenation at cis-thiolate.
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Affiliation(s)
- Chang-Chih Hsieh
- Department of Chemistry, National Changhua University of Education, Changhua 50058, Taiwan.
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4
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Kleinlein C, Bendelsmith AJ, Zheng SL, Betley TA. C-H Activation from Iron(II)-Nitroxido Complexes. Angew Chem Int Ed Engl 2017; 56:12197-12201. [PMID: 28766325 PMCID: PMC5672810 DOI: 10.1002/anie.201706594] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 07/31/2017] [Indexed: 11/08/2022]
Abstract
The reaction of nitroxyl radicals TEMPO (2,2',6,6'-tetramethylpiperidinyloxyl) and AZADO (2-azaadamantane-N-oxyl) with an iron(I) synthon affords iron(II)-nitroxido complexes (Ar L)Fe(κ1 -TEMPO) and (Ar L)Fe(κ2 -N,O-AZADO) (Ar L=1,9-(2,4,6-Ph3 C6 H2 )2 -5-mesityldipyrromethene). Both high-spin iron(II)-nitroxido species are stable in the absence of weak C-H bonds, but decay via N-O bond homolysis to ferrous or ferric iron hydroxides in the presence of 1,4-cyclohexadiene. Whereas (Ar L)Fe(κ1 -TEMPO) reacts to give a diferrous hydroxide [(Ar L)Fe]2 (μ-OH)2 , the reaction of four-coordinate (Ar L)Fe(κ2 -N,O-AZADO) with hydrogen atom donors yields ferric hydroxide (Ar L)Fe(OH)(AZAD). Mechanistic experiments reveal saturation behavior in C-H substrate and are consistent with rate-determining hydrogen atom transfer.
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Affiliation(s)
- Claudia Kleinlein
- Department of Chemistry & Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA
| | - Andrew J Bendelsmith
- Department of Chemistry & Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA
| | - Shao-Liang Zheng
- Department of Chemistry & Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA
| | - Theodore A Betley
- Department of Chemistry & Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA
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5
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Kleinlein C, Bendelsmith AJ, Zheng S, Betley TA. C−H Activation from Iron(II)‐Nitroxido Complexes. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201706594] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Claudia Kleinlein
- Department of Chemistry & Chemical Biology Harvard University 12 Oxford Street Cambridge MA 02138 USA
| | - Andrew J. Bendelsmith
- Department of Chemistry & Chemical Biology Harvard University 12 Oxford Street Cambridge MA 02138 USA
| | - Shao‐Liang Zheng
- Department of Chemistry & Chemical Biology Harvard University 12 Oxford Street Cambridge MA 02138 USA
| | - Theodore A. Betley
- Department of Chemistry & Chemical Biology Harvard University 12 Oxford Street Cambridge MA 02138 USA
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Kleespies ST, Oloo WN, Mukherjee A, Que L. C-H Bond Cleavage by Bioinspired Nonheme Oxoiron(IV) Complexes, Including Hydroxylation of n-Butane. Inorg Chem 2015; 54:5053-64. [PMID: 25751610 DOI: 10.1021/ic502786y] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The development of efficient and selective hydrocarbon oxidation processes with low environmental impact remains a major challenge of the 21st century because of the strong and apolar nature of the C-H bond. Naturally occurring iron-containing metalloenzymes can, however, selectively functionalize strong C-H bonds on substrates under mild and environmentally benign conditions. The key oxidant in a number of these transformations is postulated to possess an S = 2 Fe(IV)═O unit in a nonheme ligand environment. This oxidant has been trapped and spectroscopically characterized and its reactivity toward C-H bonds demonstrated for several nonheme iron enzyme classes. In order to obtain insight into the structure-activity relationships of these reactive intermediates, over 60 synthetic nonheme Fe(IV)(O) complexes have been prepared in various laboratories and their reactivities investigated. This Forum Article summarizes the current status of efforts in the characterization of the C-H bond cleavage reactivity of synthetic Fe(IV)(O) complexes and provides a snapshot of the current understanding of factors that control this reactivity, such as the properties of the supporting ligands and the spin state of the iron center. In addition, new results on the oxidation of strong C-H bonds such as those of cyclohexane and n-butane by a putative S = 2 synthetic Fe(IV)(O) species that is generated in situ using dioxygen at ambient conditions are presented.
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Affiliation(s)
- Scott T Kleespies
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Williamson N Oloo
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Anusree Mukherjee
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Lawrence Que
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
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Abstract
In order to address how diverse metalloprotein active sites, in particular those containing iron and copper, guide O₂binding and activation processes to perform diverse functions, studies of synthetic models of the active sites have been performed. These studies have led to deep, fundamental chemical insights into how O₂coordinates to mono- and multinuclear Fe and Cu centers and is reduced to superoxo, peroxo, hydroperoxo, and, after O-O bond scission, oxo species relevant to proposed intermediates in catalysis. Recent advances in understanding the various factors that influence the course of O₂activation by Fe and Cu complexes are surveyed, with an emphasis on evaluating the structure, bonding, and reactivity of intermediates involved. The discussion is guided by an overarching mechanistic paradigm, with differences in detail due to the involvement of disparate metal ions, nuclearities, geometries, and supporting ligands providing a rich tapestry of reaction pathways by which O₂is activated at Fe and Cu sites.
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9
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McDonald AR, Que L. High-valent nonheme iron-oxo complexes: Synthesis, structure, and spectroscopy. Coord Chem Rev 2013. [DOI: 10.1016/j.ccr.2012.08.002] [Citation(s) in RCA: 397] [Impact Index Per Article: 36.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Maeda S, Abe E, Hatanaka M, Taketsugu T, Morokuma K. Exploring Potential Energy Surfaces of Large Systems with Artificial Force Induced Reaction Method in Combination with ONIOM and Microiteration. J Chem Theory Comput 2012; 8:5058-63. [DOI: 10.1021/ct300633e] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Satoshi Maeda
- Department of Chemistry,
Faculty
of Science, Hokkaido University, Sapporo
060-0810, Japan
| | - Erika Abe
- Fukui Institute
for Fundamental
Chemistry, Kyoto University, Kyoto 606-8103,
Japan
| | - Miho Hatanaka
- Fukui Institute
for Fundamental
Chemistry, Kyoto University, Kyoto 606-8103,
Japan
| | - Tetsuya Taketsugu
- Department of Chemistry,
Faculty
of Science, Hokkaido University, Sapporo
060-0810, Japan
| | - Keiji Morokuma
- Fukui Institute
for Fundamental
Chemistry, Kyoto University, Kyoto 606-8103,
Japan
- Department of Chemistry
and Cherry
L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
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Abstract
The S-oxygenation of cysteine with dioxygen to give cysteine sulfinic acid occurs at the non-heme iron active site of cysteine dioxygenase. Similar S-oxygenation events occur in other non-heme iron enzymes, including nitrile hydratase and isopenicillin N synthase, and these enzymes have inspired the development of a class of [N(x)S(y)]-Fe model complexes. Certain members of this class have provided some intriguing examples of S-oxygenation, and this article summarizes these results, focusing on the non-heme iron(II/III)-thiolate model complexes that are known to react with O(2) or other O-atom transfer oxidants to yield sulfur oxygenates. Key aspects of the synthesis, structure, and reactivity of these systems are presented, along with any mechanistic information available on the oxygenation reactions. A number of iron(III)-thiolate complexes react with O(2) to give S-oxygenates, and the degree to which the thiolate sulfur donors are oxidized varies among the different complexes, depending upon the nature of the ligand, metal geometry, and spin state. The first examples of iron(II)-thiolate complexes that react with O(2) to give selective S-oxygenation are just emerging. Mechanistic information on these transformations is limited, with isotope labeling studies providing much of the current mechanistic data. The many questions that remain unanswered for both models and enzymes provide strong motivation for future work in this area.
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Affiliation(s)
- Alison C. McQuilken
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - David P. Goldberg
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, USA
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12
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Cowley RE, Holland PL. Ligand effects on hydrogen atom transfer from hydrocarbons to three-coordinate iron imides. Inorg Chem 2012; 51:8352-61. [PMID: 22800175 DOI: 10.1021/ic300870y] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A new β-diketiminate ligand with 2,4,6-tri(phenyl)phenyl N-substituents provides protective bulk around the metal without exposing any weak C-H bonds. This ligand improves the stability of reactive iron(III) imido complexes with Fe═NAd and Fe═NMes functional groups (Ad = 1-adamantyl; Mes = mesityl). The new ligand gives iron(III) imido complexes that are significantly more reactive toward 1,4-cyclohexadiene than the previously reported 2,6-diisopropylphenyl diketiminate variants. Analysis of X-ray crystal structures implicates Fe═N-C bending, a longer Fe═N bond, and greater access to the metal as potential reasons for the increase in C-H bond activation rates.
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Affiliation(s)
- Ryan E Cowley
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
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Cowley RE, Eckert NA, Vaddadi S, Figg TM, Cundari TR, Holland PL. Selectivity and Mechanism of Hydrogen Atom Transfer by an Isolable Imidoiron(III) Complex. J Am Chem Soc 2011; 133:9796-811. [DOI: 10.1021/ja2005303] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Ryan E. Cowley
- Department of Chemistry, University of Rochester, Rochester, New York, 14627, United States
| | - Nathan A. Eckert
- Department of Chemistry, University of Rochester, Rochester, New York, 14627, United States
| | - Sridhar Vaddadi
- Department of Chemistry and Center for Advanced Scientific Computing and Modeling, University of North Texas, Denton, Texas, 76203, United States
| | - Travis M. Figg
- Department of Chemistry and Center for Advanced Scientific Computing and Modeling, University of North Texas, Denton, Texas, 76203, United States
| | - Thomas R. Cundari
- Department of Chemistry and Center for Advanced Scientific Computing and Modeling, University of North Texas, Denton, Texas, 76203, United States
| | - Patrick L. Holland
- Department of Chemistry, University of Rochester, Rochester, New York, 14627, United States
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14
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Schenk WA. The coordination chemistry of small sulfur-containing molecules: a personal perspective. Dalton Trans 2011; 40:1209-19. [DOI: 10.1039/c0dt00975j] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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15
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Li F, England J, Que L. Near-stoichiometric conversion of H(2)O(2) to Fe(IV)=O at a nonheme iron(II) center. Insights into the O-O bond cleavage step. J Am Chem Soc 2010; 132:2134-5. [PMID: 20121136 DOI: 10.1021/ja9101908] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Near-quantitative formation of an oxoiron(IV) intermediate [Fe(IV)(O)(TMC)(CH(3)CN)](2+) (2) from stoichiometric H(2)O(2) was achieved with [Fe(II)(TMC)](2+) (1) (TMC = 1,4,8,11-tetramethyl-1,4,8,11-tetraaza-cyclotetradecane). This important outcome is best rationalized by invoking a direct reaction between 1 and H(2)O(2) followed by a heterolytic O-O bond cleavage facilitated by an acid-base catalyst (2,6-lutidine in our case). A sizable H/D KIE of 3.7 was observed for the formation of 2, emphasizing the importance of proton transfer in the cleavage step. Pyridines with different pK(a) values were also investigated, and less basic pyridines were found to function less effectively than 2,6-lutidine. This study demonstrates that the reaction of Fe(II) with H(2)O(2) to form Fe(IV)= O can be quite facile. Two factors promote the near-stoichiometric conversion of H(2)O(2) to Fe(IV)=O in this case: (a) the low reactivity between 1 and 2 and (b) the poor H-atom abstracting ability of 2, which inhibits subsequent reaction with residual H(2)O(2). Both factors inhibit formation of the Fe(III) byproduct commonly found in reactions of Fe(II) complexes with H(2)O(2). These results may shed light into the nature of the O-O bond cleaving step in the activation of dioxygen by nonheme iron enzymes and in the first step of the Fenton reaction.
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Affiliation(s)
- Feifei Li
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, USA
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The Oniom Method and its Applications to Enzymatic Reactions. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2009. [DOI: 10.1007/978-1-4020-9956-4_2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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Lundberg M, Kawatsu T, Vreven T, Frisch MJ, Morokuma K. Transition States in a Protein Environment − ONIOM QM:MM Modeling of Isopenicillin N Synthesis. J Chem Theory Comput 2008; 5:222-34. [DOI: 10.1021/ct800457g] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marcus Lundberg
- Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo-ku, Kyoto 606-8103, Japan, and Gaussian, Inc., 340 Quinnipiac Street, Building 40, Wallingford, Connecticut 06492
| | - Tsutomu Kawatsu
- Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo-ku, Kyoto 606-8103, Japan, and Gaussian, Inc., 340 Quinnipiac Street, Building 40, Wallingford, Connecticut 06492
| | - Thom Vreven
- Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo-ku, Kyoto 606-8103, Japan, and Gaussian, Inc., 340 Quinnipiac Street, Building 40, Wallingford, Connecticut 06492
| | - Michael J. Frisch
- Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo-ku, Kyoto 606-8103, Japan, and Gaussian, Inc., 340 Quinnipiac Street, Building 40, Wallingford, Connecticut 06492
| | - Keiji Morokuma
- Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo-ku, Kyoto 606-8103, Japan, and Gaussian, Inc., 340 Quinnipiac Street, Building 40, Wallingford, Connecticut 06492
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Lundberg M, Morokuma K. Protein Environment Facilitates O2 Binding in Non-Heme Iron Enzyme. An Insight from ONIOM Calculations on Isopenicillin N Synthase (IPNS). J Phys Chem B 2007; 111:9380-9. [PMID: 17637052 DOI: 10.1021/jp071878g] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Binding of dioxygen to a non-heme enzyme has been modeled using the ONIOM combined quantum mechanical/molecular mechanical (QM/MM) method. For the present system, isopenicillin N synthase (IPNS), binding of dioxygen is stabilized by 8-10 kcal/mol for a QM:MM (B3LYP:Amber) protein model compared to a quantum mechanical model of the active site only. In the protein system, the free energy change of O2 binding is close to zero. Two major factors consistently stabilize O2 binding. The first effect, evaluated at the QM level, originates from a change in coordination geometry of the iron center. The active-site model artificially favors the deoxy state (O2 not bound) because it allows too-large rearrangements of the five-coordinate iron site. This error is corrected when the protein is included. The corresponding effect on binding energies is 3-6 kcal/mol, depending on the coordination mode of O2 (side-on or end-on). The second major factor that stabilizes O2 binding is van der Waals interactions between dioxygen and the surrounding enzyme. These interactions, 3-4 kcal/mol at the MM level, are neglected in models that include only the active site. Polarization of the active site by surrounding amino acids does not have a significant effect on the binding energy in the present system.
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Affiliation(s)
- Marcus Lundberg
- Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
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19
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Zhang Y, Oldfield E. On the Mössbauer Spectra of IsopenicillinNSynthase and a Model {FeNO}7(S=3/2) System. J Am Chem Soc 2004; 126:9494-5. [PMID: 15291525 DOI: 10.1021/ja0401242] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have carried out a series of density functional theory (DFT) calculations to predict the 57Fe Mössbauer quadrupole splittings (DeltaEQ) and isomer shifts (deltaFe) for the nitrosyl complex of isopenicillin N synthase with the substrate delta-(l-alpha-aminoadipoyl)-l-cysteinyl-d-valine (IPNS.ACV.NO) and an {FeNO}7 (S = 3/2) model system, FeL(NO)(N3)2 (L = N,N',N' '-trimethyl-1,4,7-triazacyclononane). B3LYP predictions on the model compound are in almost exact agreement with experiment. The same DFT methods did not enable the prediction of the experimental DeltaEQ and deltaFe results for IPNS.ACV.NO when using the experimental protein crystal structure but did permit good predictions of DeltaEQ, deltaFe, and the asymmetry parameter (eta) when using a fully optimized structure. This optimized structure also enabled good predictions of the Mössbauer spectra of the photodissociation product of IPNS.ACV.NO. Mulliken and natural bonding orbital (NBO) spin density analyses indicate an electronic configuration of FeII (S = 2) anti-ferromagnetically coupled to NO (S = 1/2) in the protein as well as in the model system and the geometry optimized structure helps explain part of the enzyme reaction.
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Affiliation(s)
- Yong Zhang
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
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20
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Costas M, Mehn MP, Jensen MP, Que L. Dioxygen Activation at Mononuclear Nonheme Iron Active Sites: Enzymes, Models, and Intermediates. Chem Rev 2004; 104:939-86. [PMID: 14871146 DOI: 10.1021/cr020628n] [Citation(s) in RCA: 2014] [Impact Index Per Article: 100.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Miquel Costas
- Departament de Quimica, Universitat de Girona, 17071, Girona, Spain
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Fontecave M, Ollagnier-de-Choudens S, Mulliez E. Biological radical sulfur insertion reactions. Chem Rev 2003; 103:2149-66. [PMID: 12797827 DOI: 10.1021/cr020427j] [Citation(s) in RCA: 153] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Marc Fontecave
- Laboratoire de Chimie et Biochimie des Centres Rédox Biologiques, DRDC-CB, CEA/CNRS/Université Joseph Fourier, UMR 5047, 17, Avenue des Martyrs, 38054 Grenoble Cedex 09, France.
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