Density functional theory studies of oxygen and carbonate binding to a dicopper patellamide complex

Reza Latifi, Mojtaba Bagherzadeh, Bruce F. Milne, Marcel Jaspars, Sam P. de Visser

Research output: Contribution to journalArticle

13 Citations (Scopus)

Abstract

In this work we present results of density functional theory (DFT) Calculations oil dicopper patellamides and their affinity for molecular oxygen and carbonate. Patellamides are cyclic octapeptides that are produced by a cyanobacterium, and may show promise as therapeutics. Thus, carbonate binding to a dicopper patellamide center gives a stable cyclic octapeptide with a twist of almost 90 degrees. The system exists in dose-lying open-shell singlet and triplet spin states with two Unpaired electrons in orthogonal sigma(center dot) orbitals on each metal center. Subsequently, we replaced carbonate with dioxygen and found a stable Cu-2(mu-O)(2) diamond shaped patellamide core. In this structure the original dioxygen bond is significantly weakened to essentially a single bond, which should enable the system to transfer these oxygen atoms to substrates. We predicted the IR and Raman spectra of the Cu(mu-O)(2) diamond shaped patellamide structure using density functional theory and found a considerable isotope effect on the O-O stretch vibration for O-16(2) versus O-18(2) bound structures. Our studies reveal that carbonate forms an extremely stable complex with dicopper patellamide, but that additional molecular oxygen to this system does not give a potential oxidant. Therefore, it is more likely that carbonate prepares the system for dioxygen binding by folding it into the correct configuration followed in the proposed catalytic cycle by a protonation event preceding dioxygen binding to enable the system to reorganize to form a stable Cu-2(mu-O)(2)-patellamide cluster. Alternatively, carbonate may act as an inhibitor that blocks the catalytic activity of the system. It is anticipated that the Cu2(()mu-O)(2)-patellamide structure is a potential active oxidant of the dicopper patellamide complex. Crown Copyright (C) 2008 Published by Elsevier Inc. All rights reserved.

Original languageEnglish
Pages (from-to)2171-2178
Number of pages8
JournalJournal of Inorganic Biochemistry
Volume102
Issue number12
Early online date2 Sep 2008
DOIs
Publication statusPublished - Dec 2008

Keywords

  • density functional theory
  • carbonate
  • oxygen
  • copper
  • tyrosinase
  • ascidian lissoclinum-patella
  • C-H hydroxylation
  • taurine/alpha-ketoglutarate dioxygenase
  • mononuclear nonheme iron(IV)-OXO
  • copper proteins
  • ribonucleotide reductase
  • cyclic octapeptide
  • crystal-structure
  • diiron proteins
  • reactivity

Cite this

Density functional theory studies of oxygen and carbonate binding to a dicopper patellamide complex. / Latifi, Reza; Bagherzadeh, Mojtaba; Milne, Bruce F.; Jaspars, Marcel; de Visser, Sam P.

In: Journal of Inorganic Biochemistry, Vol. 102, No. 12, 12.2008, p. 2171-2178.

Research output: Contribution to journalArticle

Latifi, Reza ; Bagherzadeh, Mojtaba ; Milne, Bruce F. ; Jaspars, Marcel ; de Visser, Sam P. / Density functional theory studies of oxygen and carbonate binding to a dicopper patellamide complex. In: Journal of Inorganic Biochemistry. 2008 ; Vol. 102, No. 12. pp. 2171-2178.
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abstract = "In this work we present results of density functional theory (DFT) Calculations oil dicopper patellamides and their affinity for molecular oxygen and carbonate. Patellamides are cyclic octapeptides that are produced by a cyanobacterium, and may show promise as therapeutics. Thus, carbonate binding to a dicopper patellamide center gives a stable cyclic octapeptide with a twist of almost 90 degrees. The system exists in dose-lying open-shell singlet and triplet spin states with two Unpaired electrons in orthogonal sigma(center dot) orbitals on each metal center. Subsequently, we replaced carbonate with dioxygen and found a stable Cu-2(mu-O)(2) diamond shaped patellamide core. In this structure the original dioxygen bond is significantly weakened to essentially a single bond, which should enable the system to transfer these oxygen atoms to substrates. We predicted the IR and Raman spectra of the Cu(mu-O)(2) diamond shaped patellamide structure using density functional theory and found a considerable isotope effect on the O-O stretch vibration for O-16(2) versus O-18(2) bound structures. Our studies reveal that carbonate forms an extremely stable complex with dicopper patellamide, but that additional molecular oxygen to this system does not give a potential oxidant. Therefore, it is more likely that carbonate prepares the system for dioxygen binding by folding it into the correct configuration followed in the proposed catalytic cycle by a protonation event preceding dioxygen binding to enable the system to reorganize to form a stable Cu-2(mu-O)(2)-patellamide cluster. Alternatively, carbonate may act as an inhibitor that blocks the catalytic activity of the system. It is anticipated that the Cu2(()mu-O)(2)-patellamide structure is a potential active oxidant of the dicopper patellamide complex. Crown Copyright (C) 2008 Published by Elsevier Inc. All rights reserved.",
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T1 - Density functional theory studies of oxygen and carbonate binding to a dicopper patellamide complex

AU - Latifi, Reza

AU - Bagherzadeh, Mojtaba

AU - Milne, Bruce F.

AU - Jaspars, Marcel

AU - de Visser, Sam P.

PY - 2008/12

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N2 - In this work we present results of density functional theory (DFT) Calculations oil dicopper patellamides and their affinity for molecular oxygen and carbonate. Patellamides are cyclic octapeptides that are produced by a cyanobacterium, and may show promise as therapeutics. Thus, carbonate binding to a dicopper patellamide center gives a stable cyclic octapeptide with a twist of almost 90 degrees. The system exists in dose-lying open-shell singlet and triplet spin states with two Unpaired electrons in orthogonal sigma(center dot) orbitals on each metal center. Subsequently, we replaced carbonate with dioxygen and found a stable Cu-2(mu-O)(2) diamond shaped patellamide core. In this structure the original dioxygen bond is significantly weakened to essentially a single bond, which should enable the system to transfer these oxygen atoms to substrates. We predicted the IR and Raman spectra of the Cu(mu-O)(2) diamond shaped patellamide structure using density functional theory and found a considerable isotope effect on the O-O stretch vibration for O-16(2) versus O-18(2) bound structures. Our studies reveal that carbonate forms an extremely stable complex with dicopper patellamide, but that additional molecular oxygen to this system does not give a potential oxidant. Therefore, it is more likely that carbonate prepares the system for dioxygen binding by folding it into the correct configuration followed in the proposed catalytic cycle by a protonation event preceding dioxygen binding to enable the system to reorganize to form a stable Cu-2(mu-O)(2)-patellamide cluster. Alternatively, carbonate may act as an inhibitor that blocks the catalytic activity of the system. It is anticipated that the Cu2(()mu-O)(2)-patellamide structure is a potential active oxidant of the dicopper patellamide complex. Crown Copyright (C) 2008 Published by Elsevier Inc. All rights reserved.

AB - In this work we present results of density functional theory (DFT) Calculations oil dicopper patellamides and their affinity for molecular oxygen and carbonate. Patellamides are cyclic octapeptides that are produced by a cyanobacterium, and may show promise as therapeutics. Thus, carbonate binding to a dicopper patellamide center gives a stable cyclic octapeptide with a twist of almost 90 degrees. The system exists in dose-lying open-shell singlet and triplet spin states with two Unpaired electrons in orthogonal sigma(center dot) orbitals on each metal center. Subsequently, we replaced carbonate with dioxygen and found a stable Cu-2(mu-O)(2) diamond shaped patellamide core. In this structure the original dioxygen bond is significantly weakened to essentially a single bond, which should enable the system to transfer these oxygen atoms to substrates. We predicted the IR and Raman spectra of the Cu(mu-O)(2) diamond shaped patellamide structure using density functional theory and found a considerable isotope effect on the O-O stretch vibration for O-16(2) versus O-18(2) bound structures. Our studies reveal that carbonate forms an extremely stable complex with dicopper patellamide, but that additional molecular oxygen to this system does not give a potential oxidant. Therefore, it is more likely that carbonate prepares the system for dioxygen binding by folding it into the correct configuration followed in the proposed catalytic cycle by a protonation event preceding dioxygen binding to enable the system to reorganize to form a stable Cu-2(mu-O)(2)-patellamide cluster. Alternatively, carbonate may act as an inhibitor that blocks the catalytic activity of the system. It is anticipated that the Cu2(()mu-O)(2)-patellamide structure is a potential active oxidant of the dicopper patellamide complex. Crown Copyright (C) 2008 Published by Elsevier Inc. All rights reserved.

KW - density functional theory

KW - carbonate

KW - oxygen

KW - copper

KW - tyrosinase

KW - ascidian lissoclinum-patella

KW - C-H hydroxylation

KW - taurine/alpha-ketoglutarate dioxygenase

KW - mononuclear nonheme iron(IV)-OXO

KW - copper proteins

KW - ribonucleotide reductase

KW - cyclic octapeptide

KW - crystal-structure

KW - diiron proteins

KW - reactivity

U2 - 10.1016/j.jinorgbio.2008.08.009

DO - 10.1016/j.jinorgbio.2008.08.009

M3 - Article

VL - 102

SP - 2171

EP - 2178

JO - Journal of Inorganic Biochemistry

JF - Journal of Inorganic Biochemistry

SN - 0162-0134

IS - 12

ER -