The aromatic amino acid phenylalanine: a versatile tool for binding transition metal ions
Context The human body contains many different types of transition metal ions, such as Zn 2+ , Cu 2+ , which are involved in many physiological processes. An excess or deficiency of these ions can cause diseases, such as Alzheimer's disease, which is closely related to the levels of these ions...
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| Published in | Journal of molecular modeling Vol. 30; no. 11; p. 377 |
|---|---|
| Main Authors | , , , |
| Format | Journal Article |
| Language | English |
| Published |
Berlin/Heidelberg
Springer Berlin Heidelberg
01.11.2024
Springer Nature B.V |
| Subjects | |
| Online Access | Get full text |
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| Abstract | Context
The human body contains many different types of transition metal ions, such as Zn
2+
, Cu
2+
, which are involved in many physiological processes. An excess or deficiency of these ions can cause diseases, such as Alzheimer's disease, which is closely related to the levels of these ions in the body. In-depth understanding of various physiological and pathological mechanisms related to metal ions requires understanding the interaction between metal ions and nearby amino acids at the atomic level. This article selected four transition metal ions: Zn
2+
, Cu
2+
, Fe
2+
, and Mn
2+
and the aromatic amino acid Phe, known for its strong coordination capability, as study subjects, comprehensively examining their binding situations. The results show that there are multiple binding modes between them and Phe, and most of the binding modes involve benzene ring coordination. The coordination strength order of the four metal ions with benzene ring, carbonyl O, hydroxyl O and amino N is different. For the lowest energy structure formed by each ion with Phe, all four ions are bound to N, carbonyl O, and benzene ring. Zn
2+
is combined with two C’s of the benzene ring, Cu
2+
with four C’s of the benzene ring, and Fe
2+
and Mn
2+
with the benzene ring as a whole. Part of the reason for this phenomenon may be derived from the tendency of transition metal ions to reach 18e stable structures when bound to ligands. There is a strong binding force between the four ions and Phe, and the binding trend is Cu
2+
(-294.9 kcal/mol) > Zn
2+
(-261.3 kcal/mol) > Fe
2+
(-247.5 kcal/mol) > Mn
2+
(-220.2 kcal/mol). Mayer bond order analysis and molecular orbital localization analysis found that there are very strong chemical interactions between transition metal ions and surrounding atoms, especially with N and carbonyl O.
Methods
Several initial structures with different coordination modes to Phe were created according to chemical intuition for each divalent cation. Then semiempirical MD simulations at GFN2 level were run on these structures. The numerous generated structures were classified according to some criteria, then representative geometries were preliminarily optimized by TPSSh/6-31G*/LanL2DZ. To get more accurate electronic energies, high-precision quantum chemistry calculations at the level of TPSSh/def2TZVPP//TPSSh/def2QZVPP were carried out on the selected low-lying structures. All the optimized structures were confirmed to be minima without imaginary frequency by performing frequency analyses. Further electronic structure analyses such as IRI, Mayer bond order, IBSI etc. were performed to get more insights into the binding between the transition metal ions and Phe. |
|---|---|
| AbstractList | The human body contains many different types of transition metal ions, such as Zn
, Cu
, which are involved in many physiological processes. An excess or deficiency of these ions can cause diseases, such as Alzheimer's disease, which is closely related to the levels of these ions in the body. In-depth understanding of various physiological and pathological mechanisms related to metal ions requires understanding the interaction between metal ions and nearby amino acids at the atomic level. This article selected four transition metal ions: Zn
, Cu
, Fe
, and Mn
and the aromatic amino acid Phe, known for its strong coordination capability, as study subjects, comprehensively examining their binding situations. The results show that there are multiple binding modes between them and Phe, and most of the binding modes involve benzene ring coordination. The coordination strength order of the four metal ions with benzene ring, carbonyl O, hydroxyl O and amino N is different. For the lowest energy structure formed by each ion with Phe, all four ions are bound to N, carbonyl O, and benzene ring. Zn
is combined with two C's of the benzene ring, Cu
with four C's of the benzene ring, and Fe
and Mn
with the benzene ring as a whole. Part of the reason for this phenomenon may be derived from the tendency of transition metal ions to reach 18e stable structures when bound to ligands. There is a strong binding force between the four ions and Phe, and the binding trend is Cu
(-294.9 kcal/mol) > Zn
(-261.3 kcal/mol) > Fe
(-247.5 kcal/mol) > Mn
(-220.2 kcal/mol). Mayer bond order analysis and molecular orbital localization analysis found that there are very strong chemical interactions between transition metal ions and surrounding atoms, especially with N and carbonyl O.
Several initial structures with different coordination modes to Phe were created according to chemical intuition for each divalent cation. Then semiempirical MD simulations at GFN2 level were run on these structures. The numerous generated structures were classified according to some criteria, then representative geometries were preliminarily optimized by TPSSh/6-31G*/LanL2DZ. To get more accurate electronic energies, high-precision quantum chemistry calculations at the level of TPSSh/def2TZVPP//TPSSh/def2QZVPP were carried out on the selected low-lying structures. All the optimized structures were confirmed to be minima without imaginary frequency by performing frequency analyses. Further electronic structure analyses such as IRI, Mayer bond order, IBSI etc. were performed to get more insights into the binding between the transition metal ions and Phe. ContextThe human body contains many different types of transition metal ions, such as Zn2+, Cu2+, which are involved in many physiological processes. An excess or deficiency of these ions can cause diseases, such as Alzheimer's disease, which is closely related to the levels of these ions in the body. In-depth understanding of various physiological and pathological mechanisms related to metal ions requires understanding the interaction between metal ions and nearby amino acids at the atomic level. This article selected four transition metal ions: Zn2+, Cu2+, Fe2+, and Mn2+ and the aromatic amino acid Phe, known for its strong coordination capability, as study subjects, comprehensively examining their binding situations. The results show that there are multiple binding modes between them and Phe, and most of the binding modes involve benzene ring coordination. The coordination strength order of the four metal ions with benzene ring, carbonyl O, hydroxyl O and amino N is different. For the lowest energy structure formed by each ion with Phe, all four ions are bound to N, carbonyl O, and benzene ring. Zn2+ is combined with two C’s of the benzene ring, Cu2+ with four C’s of the benzene ring, and Fe2+ and Mn2+ with the benzene ring as a whole. Part of the reason for this phenomenon may be derived from the tendency of transition metal ions to reach 18e stable structures when bound to ligands. There is a strong binding force between the four ions and Phe, and the binding trend is Cu2+(-294.9 kcal/mol) > Zn2+(-261.3 kcal/mol) > Fe2+(-247.5 kcal/mol) > Mn2+(-220.2 kcal/mol). Mayer bond order analysis and molecular orbital localization analysis found that there are very strong chemical interactions between transition metal ions and surrounding atoms, especially with N and carbonyl O.MethodsSeveral initial structures with different coordination modes to Phe were created according to chemical intuition for each divalent cation. Then semiempirical MD simulations at GFN2 level were run on these structures. The numerous generated structures were classified according to some criteria, then representative geometries were preliminarily optimized by TPSSh/6-31G*/LanL2DZ. To get more accurate electronic energies, high-precision quantum chemistry calculations at the level of TPSSh/def2TZVPP//TPSSh/def2QZVPP were carried out on the selected low-lying structures. All the optimized structures were confirmed to be minima without imaginary frequency by performing frequency analyses. Further electronic structure analyses such as IRI, Mayer bond order, IBSI etc. were performed to get more insights into the binding between the transition metal ions and Phe. The human body contains many different types of transition metal ions, such as Zn2+, Cu2+, which are involved in many physiological processes. An excess or deficiency of these ions can cause diseases, such as Alzheimer's disease, which is closely related to the levels of these ions in the body. In-depth understanding of various physiological and pathological mechanisms related to metal ions requires understanding the interaction between metal ions and nearby amino acids at the atomic level. This article selected four transition metal ions: Zn2+, Cu2+, Fe2+, and Mn2+ and the aromatic amino acid Phe, known for its strong coordination capability, as study subjects, comprehensively examining their binding situations. The results show that there are multiple binding modes between them and Phe, and most of the binding modes involve benzene ring coordination. The coordination strength order of the four metal ions with benzene ring, carbonyl O, hydroxyl O and amino N is different. For the lowest energy structure formed by each ion with Phe, all four ions are bound to N, carbonyl O, and benzene ring. Zn2+ is combined with two C's of the benzene ring, Cu2+ with four C's of the benzene ring, and Fe2+ and Mn2+ with the benzene ring as a whole. Part of the reason for this phenomenon may be derived from the tendency of transition metal ions to reach 18e stable structures when bound to ligands. There is a strong binding force between the four ions and Phe, and the binding trend is Cu2+(-294.9 kcal/mol) > Zn2+(-261.3 kcal/mol) > Fe2+(-247.5 kcal/mol) > Mn2+(-220.2 kcal/mol). Mayer bond order analysis and molecular orbital localization analysis found that there are very strong chemical interactions between transition metal ions and surrounding atoms, especially with N and carbonyl O.CONTEXTThe human body contains many different types of transition metal ions, such as Zn2+, Cu2+, which are involved in many physiological processes. An excess or deficiency of these ions can cause diseases, such as Alzheimer's disease, which is closely related to the levels of these ions in the body. In-depth understanding of various physiological and pathological mechanisms related to metal ions requires understanding the interaction between metal ions and nearby amino acids at the atomic level. This article selected four transition metal ions: Zn2+, Cu2+, Fe2+, and Mn2+ and the aromatic amino acid Phe, known for its strong coordination capability, as study subjects, comprehensively examining their binding situations. The results show that there are multiple binding modes between them and Phe, and most of the binding modes involve benzene ring coordination. The coordination strength order of the four metal ions with benzene ring, carbonyl O, hydroxyl O and amino N is different. For the lowest energy structure formed by each ion with Phe, all four ions are bound to N, carbonyl O, and benzene ring. Zn2+ is combined with two C's of the benzene ring, Cu2+ with four C's of the benzene ring, and Fe2+ and Mn2+ with the benzene ring as a whole. Part of the reason for this phenomenon may be derived from the tendency of transition metal ions to reach 18e stable structures when bound to ligands. There is a strong binding force between the four ions and Phe, and the binding trend is Cu2+(-294.9 kcal/mol) > Zn2+(-261.3 kcal/mol) > Fe2+(-247.5 kcal/mol) > Mn2+(-220.2 kcal/mol). Mayer bond order analysis and molecular orbital localization analysis found that there are very strong chemical interactions between transition metal ions and surrounding atoms, especially with N and carbonyl O.Several initial structures with different coordination modes to Phe were created according to chemical intuition for each divalent cation. Then semiempirical MD simulations at GFN2 level were run on these structures. The numerous generated structures were classified according to some criteria, then representative geometries were preliminarily optimized by TPSSh/6-31G*/LanL2DZ. To get more accurate electronic energies, high-precision quantum chemistry calculations at the level of TPSSh/def2TZVPP//TPSSh/def2QZVPP were carried out on the selected low-lying structures. All the optimized structures were confirmed to be minima without imaginary frequency by performing frequency analyses. Further electronic structure analyses such as IRI, Mayer bond order, IBSI etc. were performed to get more insights into the binding between the transition metal ions and Phe.METHODSSeveral initial structures with different coordination modes to Phe were created according to chemical intuition for each divalent cation. Then semiempirical MD simulations at GFN2 level were run on these structures. The numerous generated structures were classified according to some criteria, then representative geometries were preliminarily optimized by TPSSh/6-31G*/LanL2DZ. To get more accurate electronic energies, high-precision quantum chemistry calculations at the level of TPSSh/def2TZVPP//TPSSh/def2QZVPP were carried out on the selected low-lying structures. All the optimized structures were confirmed to be minima without imaginary frequency by performing frequency analyses. Further electronic structure analyses such as IRI, Mayer bond order, IBSI etc. were performed to get more insights into the binding between the transition metal ions and Phe. Context The human body contains many different types of transition metal ions, such as Zn 2+ , Cu 2+ , which are involved in many physiological processes. An excess or deficiency of these ions can cause diseases, such as Alzheimer's disease, which is closely related to the levels of these ions in the body. In-depth understanding of various physiological and pathological mechanisms related to metal ions requires understanding the interaction between metal ions and nearby amino acids at the atomic level. This article selected four transition metal ions: Zn 2+ , Cu 2+ , Fe 2+ , and Mn 2+ and the aromatic amino acid Phe, known for its strong coordination capability, as study subjects, comprehensively examining their binding situations. The results show that there are multiple binding modes between them and Phe, and most of the binding modes involve benzene ring coordination. The coordination strength order of the four metal ions with benzene ring, carbonyl O, hydroxyl O and amino N is different. For the lowest energy structure formed by each ion with Phe, all four ions are bound to N, carbonyl O, and benzene ring. Zn 2+ is combined with two C’s of the benzene ring, Cu 2+ with four C’s of the benzene ring, and Fe 2+ and Mn 2+ with the benzene ring as a whole. Part of the reason for this phenomenon may be derived from the tendency of transition metal ions to reach 18e stable structures when bound to ligands. There is a strong binding force between the four ions and Phe, and the binding trend is Cu 2+ (-294.9 kcal/mol) > Zn 2+ (-261.3 kcal/mol) > Fe 2+ (-247.5 kcal/mol) > Mn 2+ (-220.2 kcal/mol). Mayer bond order analysis and molecular orbital localization analysis found that there are very strong chemical interactions between transition metal ions and surrounding atoms, especially with N and carbonyl O. Methods Several initial structures with different coordination modes to Phe were created according to chemical intuition for each divalent cation. Then semiempirical MD simulations at GFN2 level were run on these structures. The numerous generated structures were classified according to some criteria, then representative geometries were preliminarily optimized by TPSSh/6-31G*/LanL2DZ. To get more accurate electronic energies, high-precision quantum chemistry calculations at the level of TPSSh/def2TZVPP//TPSSh/def2QZVPP were carried out on the selected low-lying structures. All the optimized structures were confirmed to be minima without imaginary frequency by performing frequency analyses. Further electronic structure analyses such as IRI, Mayer bond order, IBSI etc. were performed to get more insights into the binding between the transition metal ions and Phe. CONTEXT: The human body contains many different types of transition metal ions, such as Zn²⁺, Cu²⁺, which are involved in many physiological processes. An excess or deficiency of these ions can cause diseases, such as Alzheimer's disease, which is closely related to the levels of these ions in the body. In-depth understanding of various physiological and pathological mechanisms related to metal ions requires understanding the interaction between metal ions and nearby amino acids at the atomic level. This article selected four transition metal ions: Zn²⁺, Cu²⁺, Fe²⁺, and Mn²⁺ and the aromatic amino acid Phe, known for its strong coordination capability, as study subjects, comprehensively examining their binding situations. The results show that there are multiple binding modes between them and Phe, and most of the binding modes involve benzene ring coordination. The coordination strength order of the four metal ions with benzene ring, carbonyl O, hydroxyl O and amino N is different. For the lowest energy structure formed by each ion with Phe, all four ions are bound to N, carbonyl O, and benzene ring. Zn²⁺ is combined with two C’s of the benzene ring, Cu²⁺ with four C’s of the benzene ring, and Fe²⁺ and Mn²⁺ with the benzene ring as a whole. Part of the reason for this phenomenon may be derived from the tendency of transition metal ions to reach 18e stable structures when bound to ligands. There is a strong binding force between the four ions and Phe, and the binding trend is Cu²⁺(-294.9 kcal/mol) > Zn²⁺(-261.3 kcal/mol) > Fe²⁺(-247.5 kcal/mol) > Mn²⁺(-220.2 kcal/mol). Mayer bond order analysis and molecular orbital localization analysis found that there are very strong chemical interactions between transition metal ions and surrounding atoms, especially with N and carbonyl O. METHODS: Several initial structures with different coordination modes to Phe were created according to chemical intuition for each divalent cation. Then semiempirical MD simulations at GFN2 level were run on these structures. The numerous generated structures were classified according to some criteria, then representative geometries were preliminarily optimized by TPSSh/6-31G*/LanL2DZ. To get more accurate electronic energies, high-precision quantum chemistry calculations at the level of TPSSh/def2TZVPP//TPSSh/def2QZVPP were carried out on the selected low-lying structures. All the optimized structures were confirmed to be minima without imaginary frequency by performing frequency analyses. Further electronic structure analyses such as IRI, Mayer bond order, IBSI etc. were performed to get more insights into the binding between the transition metal ions and Phe. |
| ArticleNumber | 377 |
| Author | Wang, Changying Jiang, Xiankai Miao, Junjian Wang, Zishuo |
| Author_xml | – sequence: 1 givenname: Xiankai surname: Jiang fullname: Jiang, Xiankai organization: School of Sciences, Changzhou Institute of Technology – sequence: 2 givenname: Zishuo surname: Wang fullname: Wang, Zishuo organization: College of Food Science and Technology, Shanghai Ocean University – sequence: 3 givenname: Changying surname: Wang fullname: Wang, Changying organization: School of Sciences, Changzhou Institute of Technology – sequence: 4 givenname: Junjian surname: Miao fullname: Miao, Junjian email: jjmiao@shou.edu.cn organization: College of Food Science and Technology, Shanghai Ocean University, Engineering Research Center of Food Thermal-Processing Technology, Shanghai Ocean University |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/39404766$$D View this record in MEDLINE/PubMed |
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| Keywords | Conformational search DFT calculation Transition metal ion Coordination mode Phenylalanine |
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Bloino J, Janesko BG, Gomperts R, Mennucci B, Hratchian HP, Ortiz JV, Izmaylov AF, Sonnenberg JL, Williams-Young D, Ding F, Lipparini F, Egidi F, Goings J, Peng B, Petrone A, Henderson T, Ranasinghe D, Zakrzewski VG, Gao J, Rega N, Zheng G, Liang W, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Vreven T, Throssell K, Montgomery JA, Jr, Peralta JE, Ogliaro F, Bearpark MJ, Heyd JJ, Brothers EN,Kudin KN, Staroverov VN, Keith TA, Kobayashi R, Normand J, Raghavachari K, Rendell AP, Burant JC, Iyengar SS, Tomasi J, Cossi M, Millam JM, Klene M, Adamo C, Cammi R, Ochterski JW, Martin RL, MorokumaK, Farkas O, Foresman JB,Fox DJ (2016) Gaussian 16 Revision C.01 Gaussian Inc [software] CostanzoFDella ValleRGBaroneVMD simulation of the Na+-phenylalanine complex in water: competition between cation-pi interaction and aqueous solvationJ Phys Chem B200510923016230231:CAS:528:DC%2BD2MXhtF2rtbnP10.1021/jp055271g16853999 PipekJMezeyPGA fast intrinsic localization procedure applicable for ab initio and semiempirical linear combination of atomic orbital wave functionsJ Chem Phys198990491649261:CAS:528:DyaL1MXks1Cht7w%3D10.1063/1.456588 RimolaARodriguez-SantiagoLSodupeMCation−π interactions and oxidative effects on Cu+ and Cu2+ binding to Phe, Tyr, Trp, and his amino acids in the gas phase. Insights from first-principles calculationsJ Phys Chem B200611024189241991:CAS:528:DC%2BD28XhtFKjs7zJ10.1021/jp064957l17125391 KhaliliBAn insight into the interaction of L-proline with the transition metal cations Fe2+, Co2+, Ni2+: a gas phase theoretical studyJ Mol Model201622111:CAS:528:DC%2BC2MXitVClt73O10.1007/s00894-015-2865-026676722 RuanCRodgersMTCation-pi interactions: structures and energetics of complexation of Na+ and K+ with the aromatic amino acids, phenylalanine, tyrosine, and tryptophanJ Am Chem Soc200412614600146101:CAS:528:DC%2BD2cXos1WgtLg%3D10.1021/ja048297e15521780 BoopathiSKolandaivelPFe2+ binding on amyloid β-peptide promotes aggregationProteins201684125712741:CAS:528:DC%2BC28XptVGnsb8%3D10.1002/prot.2507527214008 KhodabandehMHReisiHDavariMDZareKZahediMOhanessianGInteraction modes and absolute affinities of α-amino acids for Mn2+: a comprehensive pictureChemPhysChem201314173317451:CAS:528:DC%2BC3sXlvFahurs%3D10.1002/cphc.20120096423589411 TaoJPerdewJPStaroverovVNScuseriaGEClimbing the density functional ladder: nonempirical meta-generalized gradient approximation designed for molecules and solidsPhys Rev Lett2003911464011:CAS:528:DC%2BD3sXnvVKmur4%3D10.1103/PhysRevLett.91.14640114611541 WarmlanderSTiimanAAbeleinALuoJJarvetJSoderbergKLDanielssonJGraslundABiophysical studies of the amyloid β-Peptide: interactions with metal ions and small moleculesChemBioChem201314169217041:CAS:528:DC%2BC3sXhtlWkurjN10.1002/cbic.20130026223983094 Tian L (2023) Molclus program, Version 1.12. http://www.keinsci.com/research/molclus.html. Accessed 23 August 2023 PolferNCOomensJMooreDTvon HeldenGMeijerGDunbarRCInfrared spectroscopy of phenylalanine Ag(I) and Zn(II) complexes in the gas phaseJ Am Chem Soc20061285175251:CAS:528:DC%2BD28XntFCntA%3D%3D10.1021/ja054929116402839 MayerICharge, bond order and valence in the AB initio SCF theoryChem Phys Lett1983972702741:CAS:528:DyaL3sXksVeltL0%3D10.1016/0009-2614(83)80005-0 BoopathiSKolandaivelPRole of zinc and copper metal ions in amyloid β-peptides Aβ1–40 and Aβ1–42 aggregationRSC Adv2014438951389651:CAS:528:DC%2BC2cXhtlGmurvF10.1039/C4RA05390G O'BrienJTPrellJSSteillJDOomensJWilliamsERInteractions of mono- and divalent metal ions with aspartic and glutamic acid investigated with IR photodissociation spectroscopy and theoryJ Phys Chem A200811210823108301:CAS:528:DC%2BD1cXhtF2ju7fP10.1021/jp805787e18828579 RyzhovVDunbarRCCerdaBWesdemiotisCCation-π effects in the complexation of Na+ and K+ with Phe, Tyr, and Trp in the gas phaseJ Am Soc Mass Spectrom200011103710461:CAS:528:DC%2BD3cXot1Onsr4%3D10.1016/S1044-0305(00)00181-111118110 SiuFMMaNLTsangCWCation−π interactions in sodiated phenylalanine complexes: is phenylalanine in the charge-solvated or Zwitterionic form?J Am Chem Soc2001123339733981:CAS:528:DC%2BD3MXhvVOru7s%3D10.1021/ja005687211457088 CreightonTEProteins: structures and molecular properties1993LondonMacmillan RimolaASodupeMTortajadaJRodriguez-SantiagoLGas phase reactivity of Cu+-aromatic amino acids: an experimental and theoretical studyInt J Mass spectrom200625760691:CAS:528:DC%2BD28XhtVOnurvJ10.1016/j.ijms.2006.06.017 KapotaCLemaireJMaitrePOhanessianGVibrational signature of charge solvation vs salt bridge isomers of sodiated amino acids in the gas phaseJ Am Chem Soc2004126183618421:CAS:528:DC%2BD2cXmtFWgtg%3D%3D10.1021/ja036932v14871116 GrimmeSExploration of chemical compound, conformer, and reaction space with meta-dynamics simulations based on tight-binding quantum chemical calculationsJ Chem Theory Comput201915284728621:CAS:528:DC%2BC1MXms1ahs7Y%3D10.1021/acs.jctc.9b0014330943025 LarruceaJRezabalEMarinoTRussoNUgaldeJMAb initio study of microsolvated Al3+−aromatic amino acid complexesJ Phys Chem B201014901790221:CAS:528:DC%2BC3cXns1Cmu7s%3D10.1021/jp101874p VerkerkUHZhaoJSaminathanISLauJKOomensJHopkinsonACSiuKWInfrared multiple-photon dissociation spectroscopy of tripositive ions: lanthanum-tryptophan complexesInorg Chem201251470747101:CAS:528:DC%2BC38Xks1Ciu7c%3D10.1021/ic202697322455512 PrachtPBohleFGSAutomated exploration of the low-energy chemical space with fast quantum chemical methodsPhys Chem Chem Phys202022716971921:CAS:528:DC%2BB3cXjsVSmtr0%3D10.1039/C9CP06869D32073075 KleinJKhartabilHBoissonJCContreras-GarciaJPiquemalJPHenonENew way for probing bond strengthJ Phys Chem A2020124185018601:CAS:528:DC%2BB3cXisFKksLY%3D10.1021/acs.jpca.9b0984532039597 BergJMPrinciples of bioinorganic chemistry1994SausalitoUniversity Science Books Gallivan JP, Dougherty DA (1999) Cation-π interactions in structural biology. Proc Natl Acad Sci USA 96:9459-9464.https://doi.org/10.1073/pnas.96.17.9459 RemkoMFitzDBroerRRodeBMEffect of metal Ions (Ni2+, Cu2+ and Zn2+) and water coordination on the structure of L-phenylalanine, L-tyrosine, L-tryptophan and their zwitterionic formsJ Mol Model201117311731281:CAS:528:DC%2BC3MXhsFKgsr3O10.1007/s00894-011-1000-0213601873224218 MaJCDoughertyDAThe Cation−π interactionChem Rev199797130313241:CAS:528:DyaK2sXksV2kurk%3D10.1021/cr960374411851453 SiuFMMaNLTsangCWCompetition between π and Non-π cation-binding sites in aromatic amino acids: a theoretical study of alkali metal Cation (Li+, Na+, K+)–phenylalanine complexesChemistry200410196619761:CAS:528:DC%2BD2cXjs1yhsrs%3D10.1002/chem.20030551915079836 GanesanADreyerJWangFAkolaJLarruceaJDensity functional study of Cu2+-phenylalanine complex under micro-solvation environmentJ Mol Graph Model2013451801911:CAS:528:DC%2BC3sXhs1Wlu7fE10.1016/j.jmgm.2013.08.01524056305 BannwarthCEhlertSGrimmeSGFN2-xTB—an accurate and broadly parametrized self-consistent tight-binding quantum chemical method with multipole electrostatics and density-dependent dispersion contributionsJ Chem Theory Comput201915165216711:CAS:528:DC%2BC1MXis1entL0%3D10.1021/acs.jctc.8b0117630741547 LuTChenFMultiwfn: a multifunctional wavefunction analyzerJ Comput Chem2012335805921:CAS:528:DC%2BC3MXhsFykurjN10.1002/jcc.2288522162017 ParthasarathySLongFMillerYXiaoYMolecular-level examination of Cu2+ binding structure for amyloid fibrils of 40-residue Alzheimer’s β by solid-state NMR spectroscopyJ Am Chem Soc2011133339034001:CAS:528:DC%2BC3MXitlanu7c%3D10.1021/ja1072178213416653074258 Lu T, Chen Q (2021) Interaction region indicator (IRI): a very simple real space function clearly revealing both chemical bonds and weak interactions. Chem–Methods 1:231–239. https://doi.org/10.26434/chemrxiv.13591142.v1 BannwarthCCaldeweyherEEhlertSHansenAPrachtPSeibertJSpicherSGrimmeSExtended tight-binding quantum chemistry methodsWIREs Comput Mol Sci202011181:CAS:528:DC%2BB3MXnt1aru74%3D10.1002/wcms.1493 WangPOhanessianGWesdemiotisCThe sodium ion affinities of asparagine, glutamine, histidine and arginineInt J Mass Spectrom200826934451:CAS:528:DC%2BD2sXhsVSjsbbP10.1016/j.ijms.2007.09.008 6175_CR7 A Rimola (6175_CR9) 2006; 110 A Ganesan (6175_CR25) 2013; 45 TE Creighton (6175_CR1) 1993 S Parthasarathy (6175_CR4) 2011; 133 J Klein (6175_CR35) 2020; 124 S Boopathi (6175_CR22) 2016; 84 C Kapota (6175_CR16) 2004; 126 P Pracht (6175_CR28) 2020; 22 P Wang (6175_CR17) 2008; 269 JM Berg (6175_CR2) 1994 C Bannwarth (6175_CR26) 2020; 11 FM Siu (6175_CR23) 2001; 123 J Pipek (6175_CR36) 1989; 90 C Ruan (6175_CR24) 2004; 126 S Boopathi (6175_CR3) 2014; 4 MH Khodabandeh (6175_CR21) 2013; 14 NC Polfer (6175_CR38) 2006; 128 S Warmlander (6175_CR5) 2013; 14 V Ryzhov (6175_CR11) 2000; 11 A Rimola (6175_CR10) 2006; 257 B Khalili (6175_CR15) 2016; 22 M Remko (6175_CR20) 2011; 17 J Larrucea (6175_CR8) 2010; 14 C Bannwarth (6175_CR27) 2019; 15 J Tao (6175_CR31) 2003; 91 FM Siu (6175_CR12) 2004; 10 T Lu (6175_CR37) 2012; 33 6175_CR30 I Mayer (6175_CR34) 1983; 97 JC Ma (6175_CR14) 1997; 97 JT O'Brien (6175_CR18) 2008; 112 S Grimme (6175_CR29) 2019; 15 F Costanzo (6175_CR6) 2005; 109 6175_CR13 UH Verkerk (6175_CR19) 2012; 51 6175_CR32 6175_CR33 |
| References_xml | – reference: KhaliliBAn insight into the interaction of L-proline with the transition metal cations Fe2+, Co2+, Ni2+: a gas phase theoretical studyJ Mol Model201622111:CAS:528:DC%2BC2MXitVClt73O10.1007/s00894-015-2865-026676722 – reference: SiuFMMaNLTsangCWCompetition between π and Non-π cation-binding sites in aromatic amino acids: a theoretical study of alkali metal Cation (Li+, Na+, K+)–phenylalanine complexesChemistry200410196619761:CAS:528:DC%2BD2cXjs1yhsrs%3D10.1002/chem.20030551915079836 – reference: BannwarthCCaldeweyherEEhlertSHansenAPrachtPSeibertJSpicherSGrimmeSExtended tight-binding quantum chemistry methodsWIREs Comput Mol Sci202011181:CAS:528:DC%2BB3MXnt1aru74%3D10.1002/wcms.1493 – reference: KleinJKhartabilHBoissonJCContreras-GarciaJPiquemalJPHenonENew way for probing bond strengthJ Phys Chem A2020124185018601:CAS:528:DC%2BB3cXisFKksLY%3D10.1021/acs.jpca.9b0984532039597 – reference: Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Scalmani G, Barone V, Petersson GA, Nakatsuji H, Li X, Caricato M, Marenich AV, J. Bloino J, Janesko BG, Gomperts R, Mennucci B, Hratchian HP, Ortiz JV, Izmaylov AF, Sonnenberg JL, Williams-Young D, Ding F, Lipparini F, Egidi F, Goings J, Peng B, Petrone A, Henderson T, Ranasinghe D, Zakrzewski VG, Gao J, Rega N, Zheng G, Liang W, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Vreven T, Throssell K, Montgomery JA, Jr, Peralta JE, Ogliaro F, Bearpark MJ, Heyd JJ, Brothers EN,Kudin KN, Staroverov VN, Keith TA, Kobayashi R, Normand J, Raghavachari K, Rendell AP, Burant JC, Iyengar SS, Tomasi J, Cossi M, Millam JM, Klene M, Adamo C, Cammi R, Ochterski JW, Martin RL, MorokumaK, Farkas O, Foresman JB,Fox DJ (2016) Gaussian 16 Revision C.01 Gaussian Inc [software] – reference: RimolaASodupeMTortajadaJRodriguez-SantiagoLGas phase reactivity of Cu+-aromatic amino acids: an experimental and theoretical studyInt J Mass spectrom200625760691:CAS:528:DC%2BD28XhtVOnurvJ10.1016/j.ijms.2006.06.017 – reference: MaJCDoughertyDAThe Cation−π interactionChem Rev199797130313241:CAS:528:DyaK2sXksV2kurk%3D10.1021/cr960374411851453 – reference: RuanCRodgersMTCation-pi interactions: structures and energetics of complexation of Na+ and K+ with the aromatic amino acids, phenylalanine, tyrosine, and tryptophanJ Am Chem Soc200412614600146101:CAS:528:DC%2BD2cXos1WgtLg%3D10.1021/ja048297e15521780 – reference: GanesanADreyerJWangFAkolaJLarruceaJDensity functional study of Cu2+-phenylalanine complex under micro-solvation environmentJ Mol Graph Model2013451801911:CAS:528:DC%2BC3sXhs1Wlu7fE10.1016/j.jmgm.2013.08.01524056305 – reference: ParthasarathySLongFMillerYXiaoYMolecular-level examination of Cu2+ binding structure for amyloid fibrils of 40-residue Alzheimer’s β by solid-state NMR spectroscopyJ Am Chem Soc2011133339034001:CAS:528:DC%2BC3MXitlanu7c%3D10.1021/ja1072178213416653074258 – reference: RemkoMFitzDBroerRRodeBMEffect of metal Ions (Ni2+, Cu2+ and Zn2+) and water coordination on the structure of L-phenylalanine, L-tyrosine, L-tryptophan and their zwitterionic formsJ Mol Model201117311731281:CAS:528:DC%2BC3MXhsFKgsr3O10.1007/s00894-011-1000-0213601873224218 – reference: BoopathiSKolandaivelPFe2+ binding on amyloid β-peptide promotes aggregationProteins201684125712741:CAS:528:DC%2BC28XptVGnsb8%3D10.1002/prot.2507527214008 – reference: KapotaCLemaireJMaitrePOhanessianGVibrational signature of charge solvation vs salt bridge isomers of sodiated amino acids in the gas phaseJ Am Chem Soc2004126183618421:CAS:528:DC%2BD2cXmtFWgtg%3D%3D10.1021/ja036932v14871116 – reference: VerkerkUHZhaoJSaminathanISLauJKOomensJHopkinsonACSiuKWInfrared multiple-photon dissociation spectroscopy of tripositive ions: lanthanum-tryptophan complexesInorg Chem201251470747101:CAS:528:DC%2BC38Xks1Ciu7c%3D10.1021/ic202697322455512 – reference: WarmlanderSTiimanAAbeleinALuoJJarvetJSoderbergKLDanielssonJGraslundABiophysical studies of the amyloid β-Peptide: interactions with metal ions and small moleculesChemBioChem201314169217041:CAS:528:DC%2BC3sXhtlWkurjN10.1002/cbic.20130026223983094 – reference: CreightonTEProteins: structures and molecular properties1993LondonMacmillan – reference: BergJMPrinciples of bioinorganic chemistry1994SausalitoUniversity Science Books – reference: RimolaARodriguez-SantiagoLSodupeMCation−π interactions and oxidative effects on Cu+ and Cu2+ binding to Phe, Tyr, Trp, and his amino acids in the gas phase. Insights from first-principles calculationsJ Phys Chem B200611024189241991:CAS:528:DC%2BD28XhtFKjs7zJ10.1021/jp064957l17125391 – reference: Gallivan JP, Dougherty DA (1999) Cation-π interactions in structural biology. 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| SSID | ssj0001256522 |
| Score | 2.3799286 |
| Snippet | Context
The human body contains many different types of transition metal ions, such as Zn
2+
, Cu
2+
, which are involved in many physiological processes. An... The human body contains many different types of transition metal ions, such as Zn , Cu , which are involved in many physiological processes. An excess or... ContextThe human body contains many different types of transition metal ions, such as Zn2+, Cu2+, which are involved in many physiological processes. An excess... The human body contains many different types of transition metal ions, such as Zn2+, Cu2+, which are involved in many physiological processes. An excess or... CONTEXT: The human body contains many different types of transition metal ions, such as Zn²⁺, Cu²⁺, which are involved in many physiological processes. An... |
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| SubjectTerms | Alzheimer disease Alzheimer's disease Amino acids Atomic structure Benzene Binding Carbonyls cations Characterization and Evaluation of Materials Chemical bonds Chemistry Chemistry and Materials Science Computer Appl. in Life Sciences Computer Applications in Chemistry Coordination Copper Divalent cations Electronic structure Electrons energy Ferrous ions Frequency analysis humans Hydrocarbons ligands Manganese ions Molecular Medicine Molecular orbitals Original Paper Phenylalanine Physiology Quantum chemistry Theoretical and Computational Chemistry Transition metals |
| Title | The aromatic amino acid phenylalanine: a versatile tool for binding transition metal ions |
| URI | https://link.springer.com/article/10.1007/s00894-024-06175-w https://www.ncbi.nlm.nih.gov/pubmed/39404766 https://www.proquest.com/docview/3117048762 https://www.proquest.com/docview/3116678119 https://www.proquest.com/docview/3154183435 |
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