1
|
Application of Heteronuclear NMR Spectroscopy to Bioinorganic and Medicinal Chemistry ☆. REFERENCE MODULE IN CHEMISTRY, MOLECULAR SCIENCES AND CHEMICAL ENGINEERING 2018. [PMCID: PMC7157447 DOI: 10.1016/b978-0-12-409547-2.10947-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
2
|
Haddadi H, Alizadeh N, Shamsipur M, Asfari Z, Lippolis V, Bazzicalupi C. Cation−π Interaction in Complex Formation Between Tl+ Ion and Calix[4]crown-6 and Some Calix[4]biscrown-6 Derivatives: Thallium-203 NMR, Proton NMR, and X-ray Evidence. Inorg Chem 2010; 49:6874-82. [DOI: 10.1021/ic100097v] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hedayat Haddadi
- Department of Chemistry, Faculty of Basic Sciences, Tarbiat Modares University, P.O. Box 14115-175, Tehran, Iran
| | - Naader Alizadeh
- Department of Chemistry, Faculty of Basic Sciences, Tarbiat Modares University, P.O. Box 14115-175, Tehran, Iran
| | | | - Zouhair Asfari
- Laboratoire de Chimie Analytique et Sciences Séparatives, UMR 7178 IPHC-DSA, ECPM, 25 Rue Becquerel, 67087, Strasbourg Cedex, France
| | - Vito Lippolis
- Dipartimento di Chimica Inorganica ed Analitica, Università degli Studi di Cagliari, S.S. 554 Bivio per Sestu, 09042 Monserrato (CA), Italy
| | - Carla Bazzicalupi
- Dipartimento di Chimica “Ugo Schiff”, Università degli Studi di Firenze, Polo Scientifico, Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
| |
Collapse
|
3
|
Abstract
Experimental designs used to monitor the magnitude of an allosteric response can greatly influence observed values. We report here the impact of buffer, monovalent cation, divalent cation, and anion on the magnitude of the allosteric regulation of the affinity of human liver pyruvate kinase (hL-PYK) for substrate, phosphoenolpyruvate (PEP). The magnitudes of the allosteric activation by fructose-1,6-bisphosphate (Fru-1,6-BP) and the allosteric inhibition by alanine are independent of most, but not all buffers tested. However, these magnitudes are dependent on whether Mg(2+) or Mn(2+) is included as the divalent cation. In the presence of Mn(2+), any change in K(app-PEP) caused by Fru-1,6-BP is minimal. hL-PYK activity does not appear to require monovalent cation. Monovalent cation binding in the active site impacts PEP affinity with minimum influence on the magnitude of allosteric coupling. However, Na(+) and Li(+) reduce the magnitude of the allosteric response to Fru-1,6-BP, likely due to mechanisms outside of the active site. Which anion is used to maintain a constant monovalent cation concentration also influences the magnitude of the allosteric response. The value of determining the impact of ions on allosteric function can be appreciated by considering that representative structures used in comparative studies have often been determined using protein crystals grown in diverse buffer and salt conditions.
Collapse
|
4
|
Ronconi L, Sadler PJ. Applications of heteronuclear NMR spectroscopy in biological and medicinal inorganic chemistry. Coord Chem Rev 2008; 252:2239-2277. [PMID: 32226090 PMCID: PMC7094630 DOI: 10.1016/j.ccr.2008.01.016] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2007] [Accepted: 01/15/2008] [Indexed: 11/30/2022]
Abstract
There is a wide range of potential applications of inorganic compounds, and metal coordination complexes in particular, in medicine but progress is hampered by a lack of methods to study their speciation. The biological activity of metal complexes is determined by the metal itself, its oxidation state, the types and number of coordinated ligands and their strength of binding, the geometry of the complex, redox potential and ligand exchange rates. For organic drugs a variety of readily observed spin I = 1/2 nuclei can be used (1H, 13C, 15N, 19F, 31P), but only a few metals fall into this category. Most are quadrupolar nuclei giving rise to broad lines with low detection sensitivity (for biological systems). However we show that, in some cases, heteronuclear NMR studies can provide new insights into the biological and medicinal chemistry of a range of elements and these data will stimulate further advances in this area.
Collapse
Key Words
- ADP, adenosine diphosphate
- AES, atomic emission spectroscopy
- AMP, adenosine monophosphate
- ATP, adenosine triphosphate
- BNCT, boron neutron capture therapy
- BPG, 2,3-bisphosphoglycerate
- BSA, bovine serum albumin
- BSH, sodium borocaptate
- Bioinorganic chemistry
- Biological systems
- DNA, deoxyribonucleic acid
- EDTA-N4, ethylenediaminetetraacetamide
- EFG, electric field gradient
- GMP, guanosine monophosphate
- HMQC, heteronuclear multiple quantum correlation
- Heteronuclear NMR spectroscopy
- Im, imidazole
- In, indazole
- MQF, multiple quantum filtered
- MRI, magnetic resonance imaging
- Medicinal inorganic chemistry
- Metallopharmaceuticals
- NOE, nuclear Overhauser effect
- PET, positron emission tomography
- Quadrupolar nuclei
- RBC, red blood cell
- RNA, ribonucleic acid
- SDS, sodium dodecyl sulfate
- rRNA, ribosomal ribonucleic acid
- tRNA, transfer ribonucleic acid
Collapse
Affiliation(s)
- Luca Ronconi
- School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, UK
| | - Peter J Sadler
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| |
Collapse
|
5
|
Hsiao C, Tannenbaum E, VanDeusen H, Hershkovitz E, Perng G, Tannenbaum AR, Williams LD. Complexes of Nucleic Acids with Group I and II Cations. NUCLEIC ACID–METAL ION INTERACTIONS 2008. [DOI: 10.1039/9781847558763-00001] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Chiaolong Hsiao
- School of Chemistry and Biochemistry Georgia Institute of Technology Atlanta GA 30332-0400 USA
| | | | - Halena VanDeusen
- School of Chemistry and Biochemistry Georgia Institute of Technology Atlanta GA 30332-0400 USA
| | - Eli Hershkovitz
- School of Electrical and Computer Engineering Georgia Institute of Technology Atlanta GA 30332–0250 USA
- School of Biomedical Engineering Georgia Institute of Technology Atlanta, GA 30332–0250 USA
| | - Ginger Perng
- School of Electrical and Computer Engineering Georgia Institute of Technology Atlanta GA 30332–0250 USA
| | - Allen R. Tannenbaum
- School of Electrical and Computer Engineering Georgia Institute of Technology Atlanta GA 30332–0250 USA
- School of Biomedical Engineering Georgia Institute of Technology Atlanta, GA 30332–0250 USA
| | - Loren Dean Williams
- School of Chemistry and Biochemistry Georgia Institute of Technology Atlanta GA 30332-0400 USA
| |
Collapse
|
6
|
Gold B, Marky LM, Stone MP, Williams LD. A review of the role of the sequence-dependent electrostatic landscape in DNA alkylation patterns. Chem Res Toxicol 2007; 19:1402-14. [PMID: 17112226 PMCID: PMC2532758 DOI: 10.1021/tx060127n] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Alkylating agents, including environmental and endogenous carcinogens and DNA targeting antineoplastic agents, that adduct DNA via intermediates with significant cationic charge show a sequence selectively in their covalent bonding to nucleobases. The resulting patterns of alkylation eventually contribute to the agent-dependent distributions and types of mutations. The origin of the regioselective modification of DNA by electrophiles has been attributed to steric and/or electronic factors, but attempts to mechanistically model and predict alkylation patterns have had limited success. In this review, we present data consistent with the role of the intrinsic sequence-dependent electrostatic landscape (SDEL) in DNA that modulates the equilibrium binding of cations and the bonding of reactive charged alkylating agents to atoms that line the floor of the major groove of DNA.
Collapse
Affiliation(s)
- Barry Gold
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA.
| | | | | | | |
Collapse
|
7
|
Oria-Hernández J, Riveros-Rosas H, Ramírez-Sílva L. Dichotomic Phylogenetic Tree of the Pyruvate Kinase Family. J Biol Chem 2006; 281:30717-24. [PMID: 16905543 DOI: 10.1074/jbc.m605310200] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
K+ dependence was assumed to be a feature of all pyruvate kinases until it was discovered that some enzymes express K+ -independent activity. Almost all the K+ -independent pyruvate kinases have Lys at position 117, instead of the Glu present in the K+ -dependent muscle enzyme. Mutagenesis studies show that the internal positive charge substitutes for the K+ requirement (Laughlin, L. T. & Reed, G. H. (1997) Arch. Biochem. Biophys. 348, 262-267). In this work a phylogenetic analysis of pyruvate kinase was performed to ascertain the abundance of K+ -independent activities and to explore whether the K+ activating effect is related to the evolutionary history of the enzyme. Of the 230 studied sequences, 46% have Lys at position 117, and the rest have Glu. Pyruvate kinases with Lys117 and Glu117 are separated in two clusters. All of the enzymes of the Glu117 cluster that have been characterized are K+ -dependent, whereas those of the Lys117 cluster are K+ -independent. Thus, there is a strict correlation between the dichotomy of the tree and the dependence of activity on K+. 77% of the pyruvate kinases that possess Lys117 have Lys113/Gln114; they also have Ile, Val, or Leu at position 120. These residues are replaced by Glu117 and Thr113/Lys114/Thr120 in 80% of K+ -dependent pyruvate kinases. Structural analysis indicates that these residues are in a hinge region involved in the acquisition of the catalytic conformation of the enzyme. The route of conversion from K+ -independent to K+ -dependent pyruvate kinases is described. A plausible explanation of how enzymes developed K+ dependence is put forth.
Collapse
Affiliation(s)
- Jesús Oria-Hernández
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, 04510 México, D. F., México
| | | | | |
Collapse
|
8
|
Gill ML, Strobel SA, Loria JP. 205Tl NMR Methods for the Characterization of Monovalent Cation Binding to Nucleic Acids. J Am Chem Soc 2005; 127:16723-32. [PMID: 16305263 DOI: 10.1021/ja055358f] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Monovalent cations play an important role in many biological functions. The guanine rich sequence, d(G4T4G4), requires monovalent cations for formation of the G-quadruplex, d(G4T4G4)2. This requirement can be satisfied by thallium (Tl+), a potassium (K+) surrogate. To verify that the structure of d(G4T4G4)2 in the presence of Tl+ is similar to the K+-form of the G-quadruplex, the solution structure of the Tl+-form of d(G4T4G4)2 was determined. The 10 lowest energy structures have an all atom RMSD of 0.76 +/- 0.16 A. Comparison of this structure to the identical G-quadruplex formed in the presence of K+ validates the isomorphous nature of Tl+ and K+. Using a 1H-205Tl spin-echo difference experiment we show that, in the Tl+-form of d(G4T4G4)2, small scalar couplings (<1 Hz) exist between 205Tl and protons in the G-quadruplex. These data comprise the first 1H-205Tl scalar couplings observed in a biological system and have the potential to provide important constraints for structure determination. These experiments can be applied to any system in which the substituted Tl+ cations are in slow exchange with the bulk ions in solution.
Collapse
Affiliation(s)
- Michelle L Gill
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
| | | | | |
Collapse
|
9
|
Abstract
In spite of the fact that Group 13 metal ions (Al(3+), Ga(3+), In(3+) and Tl(+/3+)) show no main biological role, they are NMR-active nuclides which can be used in magnetic resonance spectroscopy of biologically relevant systems. The fact that these metal ions are quadrupolar (with the exception of thallium) means that they are particularly sensitive to ligand type and coordination geometry. The line width of the NMR signals of their complexes shows a strong dependence on the symmetry of coordination, which constitutes an effective tool in the elucidation of structures. Here we report published NMR studies of this family of elements, applied to systems of biological importance. Special emphasis is given to binding studies of these cations to biological molecules, such as proteins, and to chelating agents of radiopharmaceutical interest. The possibility of in vivo NMR studies is also stressed, with extension to (27)Al-based MRI (magnetic resonance imaging) experiments.
Collapse
Affiliation(s)
- J P André
- Centro de Química, Universidade do Minho, Campus de Gualtar, 4710, Braga, Portugal.
| | | |
Collapse
|
10
|
Susan-Resiga D, Nowak T. Monitoring active site alterations upon mutation of yeast pyruvate kinase using 205Tl+ NMR. J Biol Chem 2003; 278:40943-52. [PMID: 12882975 DOI: 10.1074/jbc.m306068200] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The interaction of the monovalent cation with wild type (WT) yeast pyruvate kinase (YPK) and with the T298S, T298C, and T298A mutants was investigated by 205Tl+ NMR to monitor possible structural alterations at the active site by Thr-298 mutation. TlNO3 activates WT YPK with a kcat value similar to that obtained with KCl and an apparent Ka of 0.96 +/- 0.07 mm in the presence of Mn2+ and fructose 1,6-bisphosphate. With the three mutants, Tl+ is a better activator than is K+ based on kcat values. Tl+ activation and inhibition of YPK is affected by mutation of the active site Thr-298. The effect of Mn2+ on the 1/T value of 205Tl+1 in the presence of the WT and mutant YPK complexes was determined at 173 MHz (300 MHz, 1H) and 346 MHz (600 MHz, 1H). For each complex studied, 1/pT2p >> 1/pT1p and 1/pT1p is frequency-dependent suggesting fast exchange conditions. The values of 1/pT1p differ for each mutant. A correlation time of 0.65 +/- 0.35 ns was estimated for the Mn2+-205Tl+ interaction. The Tl+-Mn2+ distances at the active site of YPK were calculated from the paramagnetic contribution of Mn2+ to 1/T1M of YPK-bound 205Tl+. The calculated Tl+-Mn2+ distance for the Thr-298 mutants is decreased by about 1 A from 6.0 +/- 0.2 A observed with WT. The results suggest conformational alterations at the active site of YPK where phosphoryl transfer occurs upon mutation of Thr-298. These conformational changes may, in part, explain the alteration in kcat and kcat/Km,PEP observed with the Thr-298 mutants.
Collapse
Affiliation(s)
- Delia Susan-Resiga
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | | |
Collapse
|
11
|
Howerton SB, Nagpal A, Williams LD. Surprising roles of electrostatic interactions in DNA-ligand complexes. Biopolymers 2003; 69:87-99. [PMID: 12717724 DOI: 10.1002/bip.10319] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The positions of cations in x-ray structures are modulated by sequence, conformation, and ligand interactions. The goal here is to use x-ray diffraction to help resolve structural and thermodynamic roles of specifically localized cations in DNA-anthracycline complexes. We describe a 1.34 A resolution structure of a CGATCG(2)-adriamycin(2) complex obtained from crystals grown in the presence of thallium (I) ions. Tl(+) can substitute for biological monovalent cations, but is readily detected by distinctive x-ray scattering, obviating analysis of subtle differences in coordination geometry and x-ray scattering of water, sodium, potassium, and ammonium. Six localized Tl(+) sites are observable adjacent to each CGATCG(2)-adriamycin(2) complex. Each of these localized monovalent cations are found within the G-tract major groove of the intercalated DNA-drug complex. Adriamycin appears to be designed by nature to interact favorably with the electrostatic landscape of DNA, and to conserve the distribution of localized cationic charge. Localized inorganic cations in the major groove are conserved upon binding of adriamycin. In the minor groove, inorganic cations are substituted by a cationic functional group of adriamycin. This partitioning of cationic charge by adriamycin into the major groove of CG base pairs and the minor groove of AT base pairs may be a general feature of sequence-specific DNA-small molecule interactions and a potentially useful important factor in ligand design.
Collapse
Affiliation(s)
- Shelley B Howerton
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta 30332-0400, USA
| | | | | |
Collapse
|
12
|
Abstract
Many RNAs, including the ribosome, RNase P, and the group II intron, explicitly require monovalent cations for activity in vitro. Although the necessity of monovalent cations for RNA function has been known for more than a quarter of a century, the characterization of specific monovalent metal sites within large RNAs has been elusive. Here we describe a biochemical approach to identify functionally important monovalent cations in nucleic acids. This method uses thallium (Tl+), a soft Lewis acid heavy metal cation with chemical properties similar to those of the physiological alkaline earth metal potassium (K+). Nucleotide analog interference mapping (NAIM) with the sulfur-substituted nucleotide 6-thioguanosine in combination with selective metal rescue of the interference with Tl+ provides a distinct biochemical signature for monovalent metal ion binding. This approach has identified a K+ binding site within the P4-P6 domain of the Tetrahymena group I intron that is also present within the X-ray crystal structure. The technique also predicted a similar binding site within the Azoarcus group I intron where the structure is not known. The approach is applicable to any RNA molecule that can be transcribed in vitro and whose function can be assayed.
Collapse
Affiliation(s)
- S Basu
- Department of Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Avenue, New Haven, Connecticut 06520-8114, USA
| | | |
Collapse
|
13
|
Metzler DE, Metzler CM, Sauke DJ. Transferring Groups by Displacement Reactions. Biochemistry 2001. [DOI: 10.1016/b978-012492543-4/50015-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|