FT-Raman and QM/MM study of the interaction between histamine and DNA

The interaction between histamine and highly polymerized calf-thymus DNA has been investigated using FT-Raman spectroscopy and the hybrid QM/MM (quantum mechanics/molecular mechanics) methodology. Raman spectra of solutions containing histamine and calf-thymus DNA, at different molar ratios, were recorded. Solutions were prepared at physiological settings of pH and ionic strength, using both natural and heavy water as the solvent. The analysis of the spectral changes on the DNA Raman spectra when adding different concentrations of histamine allowed us to identify the reactive sites of DNA and histamine, which were used to built two minor groove and one intercalated binding models. They were further used as starting points of the QM/MM theoretical study. However, minimal energy points were only reached for the two minor groove models. For each optimized structure, we calculated analytical force constants of histamine molecule in order to perform the vibrational dynamics. Normal mode descriptions allowed us to compare calculated wavenumbers for DNA-interacting histamine to those measured in the Raman spectra of DNA–histamine solutions. � 2005 Elsevier B.V. All rights reserved.

[1]  C. Junghans,et al.  DNA immunisation with minimalistic expression constructs. , 2004, Vaccine.

[2]  Thomas G. Spiro,et al.  Biological applications of Raman spectroscopy , 1987 .

[3]  U. Chatterjee,et al.  Effect of unconventional feeds on production cost, growth performance and expression of quantitative genes in growing pigs , 2022, Journal of the Indonesian Tropical Animal Agriculture.

[4]  W. L. Jorgensen,et al.  Comparison of simple potential functions for simulating liquid water , 1983 .

[5]  F. Sánchez-Jiménez,et al.  Chlorpheniramine inhibits the synthesis of ornithine decarboxylase and the proliferation of human breast cancer cell lines , 1995, Breast Cancer Research and Treatment.

[6]  Fritz Eckstein,et al.  Nucleic acids and molecular biology , 1987 .

[7]  J. Yager,et al.  The role of polyamine catabolism in polyamine analogue-induced programmed cell death. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[8]  N. Pattabiraman,et al.  Molecular mechanics of the interactions of spermine with DNA: DNA bending as a result of ligand binding. , 1990, Nucleic acids research.

[9]  Marek Jutel,et al.  Histamine regulates T-cell and antibody responses by differential expression of H1 and H2 receptors , 2001, Nature.

[10]  Peter Pulay,et al.  Systematic AB Initio Gradient Calculation of Molecular Geometries, Force Constants, and Dipole Moment Derivatives , 1979 .

[11]  Igor P. Ivanov,et al.  Conservation of polyamine regulation by translational frameshifting from yeast to mammals , 2000, The EMBO journal.

[12]  K. Speranskiy,et al.  Accurate theoretical prediction of vibrational frequencies in an inhomogeneous dynamic environment: a case study of a glutamate molecule in water solution and in a protein-bound form. , 2004, The Journal of chemical physics.

[13]  F. Sánchez-Jiménez,et al.  DNA-chlorpheniramine interaction studied by spectroscopic techniques. , 1998, Biochimica et biophysica acta.

[14]  Eamonn F. Healy,et al.  Development and use of quantum mechanical molecular models. 76. AM1: a new general purpose quantum mechanical molecular model , 1985 .

[15]  H. Ohtsu,et al.  New functions of histamine found in histidine decarboxylase gene knockout mice. , 2003, Biochemical and biophysical research communications.

[16]  K. Matsushima,et al.  Swine Toll-like receptor 9(1) recognizes CpG motifs of human cell stimulant. , 2003, Biochimica et Biophysica Acta.

[17]  F. Monsma,et al.  Molecular modeling and site-specific mutagenesis of the histamine-binding site of the histamine H4 receptor. , 2002, Molecular pharmacology.

[18]  R. Casero,et al.  Structural specificity of polyamines and polyamine analogues in the protection of DNA from strand breaks induced by reactive oxygen species. , 1998, Biochemical and biophysical research communications.

[19]  M. Record,et al.  Equilibrium dialysis studies of polyamine binding to DNA , 1982, Biopolymers.

[20]  T. Thomas,et al.  Polyamines in cell growth and cell death: molecular mechanisms and therapeutic applications , 2001, Cellular and Molecular Life Sciences CMLS.

[21]  G. Thomas,et al.  Structure and interactions of the single-stranded DNA genome of filamentous virus fd: investigation by ultraviolet resonance raman spectroscopy. , 1997, Biochemistry.

[22]  Bernhard Schrader,et al.  Infrared and Raman spectroscopy : methods and applications , 1995 .

[23]  K. Kashiwagi,et al.  Polyamines: mysterious modulators of cellular functions. , 2000, Biochemical and biophysical research communications.

[24]  F. Sánchez-Jiménez,et al.  Fourier transform Raman study of the structural specificities on the interaction between DNA and biogenic polyamines. , 2001, Biophysical journal.

[25]  S. Matsufuji,et al.  Ornithine decarboxylase antizyme: a novel type of regulatory protein. , 1996, Trends in biochemical sciences.

[26]  Z. Hall.  Cancer , 1906, The Hospital.

[27]  F. Sánchez-Jiménez,et al.  On the interpretation of Raman spectra of 1-aminooxy-spermine/DNA complexes. , 2004, Nucleic acids research.

[28]  A. Turner,et al.  Transition-state structural refinement with GRACE and CHARMM: Realistic modelling of lactate dehydrogenase using a combined quantum/classical method , 1997 .

[29]  Carlos Rodríguez-Caso,et al.  Biogenic Amines and Polyamines: Similar Biochemistry for Different Physiological Missions and Biomedical Applications , 2003, Critical reviews in biochemistry and molecular biology.

[30]  A. Paiva,et al.  Ionization of histamine, N-acetylhistamine, and their iodinated derivatives. , 1970, Journal of medicinal chemistry.

[31]  F. Sánchez-Jiménez,et al.  Raman study of the interaction between polyamines and a GC oligonucleotide. , 2001, Biochemical and biophysical research communications.

[32]  E. B. Wilson,et al.  A Method of Obtaining the Expanded Secular Equation for the Vibration Frequencies of a Molecule , 1939 .

[33]  C. Savoye,et al.  Radioprotection of DNA by spermine: a molecular modelling approach. , 1999, International journal of radiation biology.

[34]  B. Feuerstein,et al.  Implications and concepts of polyamine‐nucleic acid interactions , 1991, Journal of cellular biochemistry.

[35]  Miguel Angel Medina,et al.  Mammalian histidine decarboxylase: from structure to function , 2005, BioEssays : news and reviews in molecular, cellular and developmental biology.

[36]  I. Tuñón,et al.  Structural and vibrational study of the tautomerism of histamine free-base in solution. , 2003, Journal of the American Chemical Society.

[37]  Alexander D. MacKerell,et al.  All‐atom empirical force field for nucleic acids: II. Application to molecular dynamics simulations of DNA and RNA in solution , 2000 .

[38]  M. Karplus,et al.  CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .

[39]  Seymour S. Cohen.  A Guide to the Polyamines , 1998 .

[40]  T. Thomas,et al.  Polyamine structural effects on the induction and stabilization of liquid crystalline DNA: potential applications to DNA packaging, gene therapy and polyamine therapeutics. , 2002, Nucleic acids research.

[41]  E. Taillandier,et al.  Interpretation of DNA vibrational spectra by normal coordinate analysis. , 1990, The International journal of biochemistry.

[42]  G. Ciccotti,et al.  Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes , 1977 .

[43]  F. LaBella,et al.  Potent interaction of histamine and polyamines at microsomal cytochrome P450, nuclei, and chromatin from rat hepatocytes , 1998, Journal of cellular biochemistry.

[44]  F. Sánchez-Jiménez,et al.  Histamine, polyamines, and cancer. , 1999, Biochemical pharmacology.

[45]  Siegfried Wartewig,et al.  IR and Raman Spectroscopy: Fundamental Processing , 2003 .

[46]  T. James,et al.  High-resolution NMR structure of an AT-rich DNA sequence , 2002, Journal of biomolecular NMR.

[47]  I. Haworth,et al.  Multiple DNA binding modes of anthracene-9-carbonyl-N1-spermine. , 1995, Bioorganic & medicinal chemistry.

[48]  T. Thomas,et al.  Effects of aminooxy analogues of biogenic polyamines on aggregation and stability of calf thymus DNA. , 2002, Biopolymers.

[49]  M. Olvera de la Cruz,et al.  Precipitation of DNA by polyamines: a polyelectrolyte behavior. , 1998, Biophysical journal.

[50]  J. Davie,et al.  Intracellular histamine and liver regeneration: high affinity binding of histamine to chromatin, low affinity binding to matrix, and depletion of a nuclear storage pool following partial hepatectomy. , 1992, Biochemical and Biophysical Research Communications - BBRC.

[51]  A. Lyubartsev,et al.  Spermine: an "invisible" component in the crystals of B-DNA. A grand canonical Monte Carlo and molecular dynamics simulation study. , 2001, Journal of molecular biology.

[52]  H. Matsue,et al.  TLR3-, TLR7-, and TLR9-Mediated Production of Proinflammatory Cytokines and Chemokines from Murine Connective Tissue Type Skin-Derived Mast Cells but Not from Bone Marrow-Derived Mast Cells 1 , 2004, The Journal of Immunology.

[53]  F. LaBella,et al.  Interaction of histamine and other bioamines with cytochromes P450: implications for cell growth modulation and chemopotentiation by drugs. , 2000, Seminars in cancer biology.

[54]  M. Morris,et al.  Infrared and Raman Spectroscopy , 2000 .

[55]  Alexander D. MacKerell,et al.  All‐atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data , 2000 .

[56]  W. C. Swope,et al.  A computer simulation method for the calculation of equilibrium constants for the formation of physi , 1981 .

[57]  F. J. Ramírez,et al.  Vibrational spectra and assignments of histamine dication in the solid state and in solution , 2000 .

[58]  M. Arock,et al.  Trends in histamine research: new functions during immune responses and hematopoiesis. , 2002, Trends in immunology.

[59]  Carl Nathan,et al.  Points of control in inflammation , 2002, Nature.

[60]  T. Thomas,et al.  Ionic and structural effects on the thermal helix‐coil transition of DNA complexed with natural and synthetic polyamines , 1984, Biopolymers.

[61]  Ian H. Williams,et al.  Transition-state structural refinement with GRACE and CHARMM: Flexible QM/MM modelling for lactate dehydrogenase , 1999 .

[62]  G. G. Stokes.  "J." , 1890, The New Yale Book of Quotations.

[63]  G. Barone,et al.  Interactions with Natural Polyamines and Thermal Stability of DNA. A DSC Study and a Theoretical Reconsideration , 1997 .

[64]  Miguel Ángel Medina,et al.  Characterization by Raman spectroscopy of conformational changes on guanine–cytosine and adenine–thymine oligonucleotides induced by aminooxy analogues of spermidine , 2004 .

[65]  I. Tuñón,et al.  Vibrational Dynamics of Histamine Monocation in Solution: an Experimental (FT-IR, FT-Raman) and Theoretical (SCRF-DFT) Study , 2000 .

[66]  W. C. Johnson,et al.  Principles of physical biochemistry , 1998 .

[67]  C. Akdis,et al.  Immune regulation by histamine. , 2002, Current opinion in immunology.

[68]  H. Wallace,et al.  Insufficiently charged isosteric analogue of spermine: interaction with polyamine uptake, and effect on Caco-2 cell growth. , 2002, Biochemical pharmacology.