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Kozlyuk N, Sengupta S, Lupták A, Martin RW. In situ NMR measurement of macromolecule-bound metal ion concentrations. JOURNAL OF BIOMOLECULAR NMR 2016; 64:269-273. [PMID: 27108020 DOI: 10.1007/s10858-016-0031-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 04/15/2016] [Indexed: 06/05/2023]
Abstract
Many nucleic acids and proteins require divalent metal ions such as Mg(2+) and Ca(2+) for folding and function. The lipophilic alignment media frequently used as membrane mimetics also bind these divalent metals. Here we demonstrate the use of (31)P NMR spectrum of a metal ion chelator (deoxycytidine diphosphate) to measure the bound [Mg(2+)] and [Ca(2+)] in situ for several biological model systems at relatively high divalent ion concentrations (1-10 mM). This method represents a general approach to measuring divalent metal ion binding in NMR samples where the amount and type of metal ion added to the system is known.
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Affiliation(s)
- Natalia Kozlyuk
- Department of Chemistry, University of California, Irvine, CA, 92697, USA
| | - Suvrajit Sengupta
- Department of Chemistry, University of California, Irvine, CA, 92697, USA
| | - Andrej Lupták
- Department of Chemistry, University of California, Irvine, CA, 92697, USA.
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, 92697, USA.
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, 92697, USA.
| | - Rachel W Martin
- Department of Chemistry, University of California, Irvine, CA, 92697, USA.
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, 92697, USA.
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Hollander A, Danino D. Cochleate characterization by cryogenic electron microscopy methods: Cryo-TEM and Cryo-SEM. Colloids Surf A Physicochem Eng Asp 2015. [DOI: 10.1016/j.colsurfa.2015.07.025] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Gresh N, Cisneros GA, Darden TA, Piquemal JP. Anisotropic, Polarizable Molecular Mechanics Studies of Inter- and Intramolecular Interactions and Ligand-Macromolecule Complexes. A Bottom-Up Strategy. J Chem Theory Comput 2007; 3:1960-1986. [PMID: 18978934 PMCID: PMC2367138 DOI: 10.1021/ct700134r] [Citation(s) in RCA: 276] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
We present an overview of the SIBFA polarizable molecular mechanics procedure, which is formulated and calibrated on the basis of quantum chemistry (QC). It embodies nonclassical effects such as electrostatic penetration, exchange-polarization, and charge transfer. We address the issues of anisotropy, nonadditivity, and transferability by performing parallel QC computations on multimolecular complexes. These encompass multiply H-bonded complexes and polycoordinated complexes of divalent cations. Recent applications to the docking of inhibitors to Zn-metalloproteins are presented next, namely metallo-beta-lactamase, phosphomannoisomerase, and the nucleocapsid of the HIV-1 retrovirus. Finally, toward third-generation intermolecular potentials based on density fitting, we present the development of a novel methodology, the Gaussian electrostatic model (GEM), which relies on ab initio-derived fragment electron densities to compute the components of the total interaction energy. As GEM offers the possibility of a continuous electrostatic model going from distributed multipoles to densities, it allows an inclusion of short-range quantum effects in the molecular mechanics energies. The perspectives of an integrated SIBFA/GEM/QM procedure are discussed.
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Affiliation(s)
- Nohad Gresh
- Laboratoire de Pharmacochimie Moléculaire et Cellulaire, U648 INSERM, UFR Biomédicale, Université René-Descartes, 45, rue des Saints-Pères, 75006 Paris, France, Laboratory of Structural Biology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, and Laboratoire de Chimie Théorique, Université Pierre-et-Marie-Curie, UMR 7616 CNRS, case courrier 137, 4, place Jussieu, 75252 Paris, France
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Piquemal JP, Williams-Hubbard B, Fey N, Deeth RJ, Gresh N, Giessner-Prettre C. Inclusion of the ligand field contribution in a polarizable molecular mechanics: SIBFA-LF. J Comput Chem 2003; 24:1963-70. [PMID: 14531050 DOI: 10.1002/jcc.10354] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
To account for the distortion of the coordination sphere that takes place in complexes containing open-shell metal cations such as Cu(II), we implemented, in sum of interactions between fragments ab initio computed (SIBFA) molecular mechanics, an additional contribution to take into account the ligand field splitting of the metal d orbitals. This term, based on the angular overlap model, has been parameterized for Cu(II) coordinated to oxygen and nitrogen ligands. The comparison of the results obtained from density functional theory computations on the one hand and SIBFA or SIBFA-LF on the other shows that SIBFA-LF gives geometric arrangements similar to those obtained from quantum mechanical computations. Moreover, the geometric improvement takes place without downgrading the energetic agreement obtained from SIBFA. The systems considered are Cu(II) interacting with six water molecules, four ammonia or four imidazoles, and four water plus two formate anions.
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Affiliation(s)
- Jean-Philip Piquemal
- Laboratoire de Chimie Théorique, UMR 7616, Université P. & M. Curie, Case Courrier 137, 4, place Jussieu, 75252 Paris, Cedex 05, France
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Langlet J, Gresh N, Giessner-Prettre C. A molecular mechanics/continuum reaction field investigation of the interactions between polar amino acid side chains in water and organic solvents. Biopolymers 1995. [DOI: 10.1002/bip.360360609] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Kakiuchi T, Kondo T, Senda M. Divalent Cation-Induced Phase Transition of Phosphatidylserine Monolayer at the Polarized Oil–Water Interface and Its Influence on the Ion-Transfer Processes. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 1990. [DOI: 10.1246/bcsj.63.3270] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Abstract
In conclusion, charged membrane together with their adjacent electrolyte solution form a thermodynamic and physico-chemical entity. Their surfaces represent an exceptionally complicated interfacial system owing to intrinsic membrane complexity, as well as to the polarity and often large thickness of the interfacial region. Despite this, charged membranes can be described reasonably accurately within the framework of available theoretical models, provided that the latter are chosen on the basis of suitable criteria, which are briefly discussed in Section A. Interion correlations are likely to be important for the regular and/or rigid, thin membrane-solution interfaces. Lateral distribution of the structural membrane charge is seldom and charge distribution perpendicular to the membranes is nearly always electrostatically important. So is the interfacial hydration, which to a large extent determines the properties of the innermost part of the interfacial region, with a thickness of 2-3 nm. Fine structure of the ion double-layer and the interfacial smearing of the structural membrane charge decrease whilst the surface hydration increases the calculated value of the electrostatic membrane potential relative to the result of common Gouy-Chapman approximation. In some cases these effects partly cancel-out; simple electrostatic models are then fairly accurate. Notwithstanding this, it is at present difficult to draw detailed molecular conclusions from a large part of the published data, mainly owing to the lack of really stringent controls or calibrations. Ion binding to the membrane surface is a complicated process which involves charge-charge as well as charge-solvent interactions. Its efficiency normally increases with the ion valency and with the membrane charge density, but it is also strongly dependent on the physico-chemical and thermodynamic state of the membrane. Except in the case of the stereospecific ion binding to a membrane, the relatively easily accessible phosphate and carboxylic groups on lipids and integral membrane proteins are the main cation binding sites. Anions bind preferentially to the amine groups, even on zwitterionic molecules. Membrane structure is apt to change upon ion binding but not always in the same direction: membranes with bound ions can either expand or become more condensed, depending on the final hydrophilicity (polarity) of the membrane surface. The more polar membranes, as a rule, are less tightly packed and more fluid. Diffusive ion flow across a membrane depends on the transmembrane potential and concentration gradients, but also on the coulombic and hydration potentials at the membrane surface.(ABSTRACT TRUNCATED AT 400 WORDS)
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Affiliation(s)
- G Cevc
- Medizinische Biophysik, Technischen Universität München, F.R.G
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Ion binding to charged lipid monolayers: The role of double layer and ion binding models. J Colloid Interface Sci 1990. [DOI: 10.1016/0021-9797(90)90004-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Tocanne JF, Teissié J. Ionization of phospholipids and phospholipid-supported interfacial lateral diffusion of protons in membrane model systems. BIOCHIMICA ET BIOPHYSICA ACTA 1990; 1031:111-42. [PMID: 2155023 DOI: 10.1016/0304-4157(90)90005-w] [Citation(s) in RCA: 299] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- J F Tocanne
- Centre de Recherche de Biochimie et Génétique Cellulaires du C.N.R.S., Toulouse, France
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Dluhy RA, Cameron DG, Manisch HH. Infrared spectroscopic evidence for intermolecular hydrogen bonding in. ACTA ACUST UNITED AC 1984. [DOI: 10.1016/0005-2760(84)90220-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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A theoretical study of the relative affinities of an aliphatic and an aromatic bisguanylhydrazone for the minor groove of double-stranded (dA-dT) n oligomers. ACTA ACUST UNITED AC 1984. [DOI: 10.1007/bf00548948] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Frank AW. Synthesis and properties of N-, O-, and S-phospho derivatives of amino acids, peptides, and proteins. CRC CRITICAL REVIEWS IN BIOCHEMISTRY 1984; 16:51-101. [PMID: 6325089 DOI: 10.3109/10409238409102806] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The literature on chemical (i.e., nonenzymic) phosphorylation of amino acids, peptides, and proteins is reviewed through 1982. The review covers synthetic methods, chemical reactions, and physical properties, with emphasis on the techniques used for separation and characterization of the products. Synthetic methods are classified by reagent rather than product, and are illustrated by experimental procedures for the most important methods. Chemical reactions are classified into four groups depending on whether the reaction site is the phospho group, the amino group, the carboxyl group, or in the case of serine the hydroxyl group. Physical data are given for all of the known N-, O-, and S-phospho derivatives of the amino acids, peptides, and proteins, within certain limitations, and are discussed in detail in the section on physical properties. Emphasis is given to the techniques used for separation of the products, such as chromatography and electrophoresis, and for characterization of the products, particularly spectroscopy. Medical and other uses of the products are mentioned.
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Theoretical studies of molecular conformation. Derivation of an additive procedure for the computation of intramolecular interaction energies. Comparison withab initio SCF computations. ACTA ACUST UNITED AC 1984. [DOI: 10.1007/bf00577135] [Citation(s) in RCA: 132] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Schlieper P, Steiner R. Drug-induced surface potential changes of lipid vesicles and the role of calcium. Biochem Pharmacol 1983; 32:799-804. [PMID: 6838628 DOI: 10.1016/0006-2952(83)90579-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The effects of four different drugs with local anesthetic properties were investigated on the surface potential of phospholipid vesicles composed of electrostatically neutral lipids (phosphatidylcholine), negatively charged lipids (phosphatidylserine) and a mixture of acidic and neutral lipids (soy bean lipids). Propranolol, tetracaine, lidocaine and procaine decrease the negative surface potential of phosphatidylserine and soy bean liposomes and increase that of phosphatidylcholine liposomes. The drugs interact with the liposomes in such a way that the protonated amine groups point towards the polar head groups of the phospholipids and the rest of the molecule is probably incorporated into the hydrophobic core of the lipid bilayer. The same sequence in drug activity normally measured in biological tissues (propranolol greater than tetracaine greater than lidocaine greater than procaine) is found for the surface potential change of the phospholipids. Calcium prevents the binding of the drugs to phosphatidylserine, especially the binding of lidocaine and procaine. Because of its high affinity for negative surface charges, Ca2+ chelates with phosphatidylserine and blocks the incorporation of the drug molecule. Vice versa, when incorporated into the liposomal bilayer, the drug blocks the interaction of calcium. These antagonistic effects are only observed in liposomes made from acidic phospholipids and not in those made from pure electrostatically neutral lipids like phosphatidylcholine.
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Gresh N. A theoretical study of the interaction of monomethylammonium with double-stranded oligonucleotides. J Comput Chem 1983. [DOI: 10.1002/jcc.540040314] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Abstract
Exposure in vitro of various mammalian retroviruses to the chelating agents EDTA or EGTA in millimolar concentrations resulted in partial disintegration of viral membranes as measured by accessibility or even release of reverse transcriptase, an internal viral protein, without any other treatment usually required. Among the viruses responding to chelators were mammalian type C viruses, primate type D viruses and bovine leukemia virus. The effect was dose-dependent. The avian type C virus AMV, however, was found to be not susceptible to the agents. Rauscher mouse leukemia virus treated in vitro with EDTA or EGTA showed reduced infectivity in mice. The results are considered as evidence for some association of divalent cations with membranes of mammalian retroviruses. The disintegrating activity of EGTA suggests that Ca2+ is an integral constituent of viruses but Mg2+ may also be involved. These cations seem to be responsible for maintaining integrity of retroviral membranes which, after chelation of ions, are either disrupted or become permeable for the exogenous template of reverse transcriptase. In addition, the disintegrating activity of trifluoperazine may indicate that a calmodulin-like protein occurs in retroviral membranes.
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Bruni A, Palatini P. Biological and pharmacological properties of phospholipids. PROGRESS IN MEDICINAL CHEMISTRY 1982; 19:111-203. [PMID: 6758038 DOI: 10.1016/s0079-6468(08)70329-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Wilschut J, Düzgüneş N, Papahadjopoulos D. Calcium/magnesium specificity in membrane fusion: kinetics of aggregation and fusion of phosphatidylserine vesicles and the role of bilayer curvature. Biochemistry 1981; 20:3126-33. [PMID: 7248275 DOI: 10.1021/bi00514a022] [Citation(s) in RCA: 208] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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Düzgünes N, Nir S, Wilschut J, Bentz J, Newton C, Portis A, Papahadjopoulos D. Calcium- and magnesium-induced fusion of mixed phosphatidylserine/phosphatidylcholine vesicles: effect of ion binding. J Membr Biol 1981; 59:115-25. [PMID: 7241577 DOI: 10.1007/bf01875709] [Citation(s) in RCA: 110] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The aggregation, leakage, and fusion of pure PS (phosphatidylserine) and mixed PS/PC (phosphatidylcholine) sonicated vesicles were studied by light scattering, the release of encapsulated carboxyfluorescein, and a new fusion assay which monitors the mixing of the internal compartments of fusing vesicles. On a time scale of 1 min the extent of fusion was considerably greater than leakage. The Ca2+ and Mg2+ concentrations required to induce fusion increased when the PS content of the vesicles was decreased, and/or when the NaCl concentration was increased. Calculations employing a modified Gouy-Chapman equation and experimentally determined intrinsic binding constants of Na+ and Ca2+ to PS were shown to predict correctly the amount of Ca2+ bound in mixed PS/PC vesicles. For vesicles composed of either pure PS or of mixtures with PC in 100 mM NaCl (4:1 and 2:1 PS/PC); the induction of fusion (on a time scale of minutes) occurred when the amount of Ca or Mg bound/PS molecule exceeded 0.35-0.39. The induction of fusion for both pure PS and PS/PC mixed vesicles (with PS exceeding 50%) can be explained by assuming that destabilization of these vesicles requires a critical binding ratio of divalent cations to PS.
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Berthod H, Pullman A. Molecular potential, cation binding, and hydration properties of the carboxylate anion.Ab initio studies with an extended polarized basis set. J Comput Chem 1981. [DOI: 10.1002/jcc.540020115] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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