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Hahn MB, Solomun T, Wellhausen R, Hermann S, Seitz H, Meyer S, Kunte HJ, Zeman J, Uhlig F, Smiatek J, Sturm H. Influence of the Compatible Solute Ectoine on the Local Water Structure: Implications for the Binding of the Protein G5P to DNA. J Phys Chem B 2015; 119:15212-20. [PMID: 26555929 DOI: 10.1021/acs.jpcb.5b09506] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Microorganisms accumulate molar concentrations of compatible solutes like ectoine to prevent proteins from denaturation. Direct structural or spectroscopic information on the mechanism and about the hydration shell around ectoine are scarce. We combined surface plasmon resonance (SPR), confocal Raman spectroscopy, molecular dynamics simulations, and density functional theory (DFT) calculations to study the local hydration shell around ectoine and its influence on the binding of a gene-5-protein (G5P) to a single-stranded DNA (dT25). Due to the very high hygroscopicity of ectoine, it was possible to analyze the highly stable hydration shell by confocal Raman spectroscopy. Corresponding molecular dynamics simulation results revealed a significant change of the water dielectric constant in the presence of a high molar ectoine concentration as compared to pure water. The SPR data showed that the amount of protein bound to DNA decreases in the presence of ectoine, and hence, the protein-DNA dissociation constant increases in a concentration-dependent manner. Concomitantly, the Raman spectra in terms of the amide I region revealed large changes in the protein secondary structure. Our results indicate that ectoine strongly affects the molecular recognition between the protein and the oligonucleotide, which has important consequences for osmotic regulation mechanisms.
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Affiliation(s)
- Marc Benjamin Hahn
- Federal Institute for Materials Research and Testing , D-12205 Berlin, Germany.,Department of Physics, Free University Berlin , D-14195 Berlin, Germany
| | - Tihomir Solomun
- Federal Institute for Materials Research and Testing , D-12205 Berlin, Germany
| | - Robert Wellhausen
- Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytic and Bioprocesses , D-14476 Potsdam-Golm, Germany
| | - Sabrina Hermann
- Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytic and Bioprocesses , D-14476 Potsdam-Golm, Germany
| | - Harald Seitz
- Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytic and Bioprocesses , D-14476 Potsdam-Golm, Germany
| | - Susann Meyer
- Federal Institute for Materials Research and Testing , D-12205 Berlin, Germany.,Institute of Biochemistry and Biology, University of Potsdam , D-14476 Potsdam, Germany
| | - Hans-Jörg Kunte
- Federal Institute for Materials Research and Testing , D-12205 Berlin, Germany
| | - Johannes Zeman
- Institute for Computational Physics, University of Stuttgart , D-70569 Stuttgart, Germany
| | - Frank Uhlig
- Institute for Computational Physics, University of Stuttgart , D-70569 Stuttgart, Germany
| | - Jens Smiatek
- Institute for Computational Physics, University of Stuttgart , D-70569 Stuttgart, Germany
| | - Heinz Sturm
- Federal Institute for Materials Research and Testing , D-12205 Berlin, Germany.,Technical University Berlin , D-10587 Berlin, Germany
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Manor D, Callender R, Noy N. The interactions of retinoids with retinol-binding protein. A resonance Raman spectroscopic study. EUROPEAN JOURNAL OF BIOCHEMISTRY 1993; 213:413-8. [PMID: 8477713 DOI: 10.1111/j.1432-1033.1993.tb17776.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We have measured the pre-resonance Raman spectrum of retinal, retinoic acid and retinol in dilute CCl4 solutions and when bound to the bovine-serum retinol-binding protein. The comparison reveals that the binding interaction does not involve any specific interactions of the head group and/or the polyene chain with a particular protein residue. The data indicate hydrogen bonding of bound retinal's head-group oxygen to water, as well as some torsional angle change of its polyene chain upon binding.
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Affiliation(s)
- D Manor
- Department of Physics, City College of the City University of New York, NY
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3
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Chikishev AY, Lucassen GW, Koroteev NI, Otto C, Greve J. Polarization sensitive coherent anti-Stokes Raman scattering spectroscopy of the amide I band of proteins in solutions. Biophys J 1992; 63:976-85. [PMID: 1330043 PMCID: PMC1262235 DOI: 10.1016/s0006-3495(92)81691-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Polarization sensitive coherent anti-Stokes Raman scattering (PCARS) spectroscopy is a fruitful technique to study Raman vibrations of diluted molecules under off-electron resonant conditions. We apply PCARS as a direct spectroscopic method to investigate the broad amide I band of proteins in heavy water. In spontaneous Raman spectroscopy, this band is not well resolved. We fit a number of spectra taken of each protein under different polarization conditions, with a single set of parameters. It then appears that some substructure is observed in the amide I band. From this substructure, we determine the percentage of alpha-helix, beta-sheet, and random coil for the proteins lysozyme, albumin, ribonuclease A, and alpha-chymotrypsin.
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Affiliation(s)
- A Y Chikishev
- International Laser Center, Moscow State University, Russia
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4
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Brahms S, Fritsch V, Brahms JG, Westhof E. Investigations on the dynamic structures of adenine- and thymine-containing DNA. J Mol Biol 1992; 223:455-76. [PMID: 1738158 DOI: 10.1016/0022-2836(92)90664-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The structures of poly(dA-dT), poly(dA-dBr5U) and of poly(dA).poly(dT) have been investigated in solution and in fibers, by Raman spectroscopy. Both the alternating poly(dA-dT), poly(dA-dBr5U) and non-alternating poly(dA).poly(dT) exhibit, in the region of sugar phosphate backbone vibrations, two bands of almost equal intensity at about 841 cm-1 and 817 cm-1. The analysis of the characteristic bands of thymine residues that are sensitive to sugar puckers gives indication of a significant displacement from the C(2')-endo conformer suggesting the adoption of alternative conformers such as O(4')-endo. In contrast, the diagnostic Raman bands for the sugar pucker of adenine residues suggest, instead, predominant adoption of C(2')-endo conformations. These Raman results are compatible with rapid dynamic changes of sugar puckers between C(2')-endo and O(4')-endo for the thymidine (and uridine) residues, whereas in adenine residues the sugar puckers fluctuate around the C(2')-endo pucker in all synthetic DNA molecules studied. Molecular dynamics simulations, performed on six different starting models using two distance-dependent dielectric functions epsilon(r) = 4 r and a sigmoidal dependence), all gave similar dynamic behavior in agreement with these Raman data and their interpretation. The mean calculated pseudorotation phases of the adenine residues are systematically higher (around C(2')-endo) than those of the thymine residues (close to O(4')-endo-C(1')-exo). Besides, the mean lifetimes of the thymine residues are 1.5 to 2.0-fold higher in the O(4')-endo than in the C(2')-endo domain, while those of the adenine residues are two to threefold higher in the C(2')-endo than in the O(4')-endo domain. In the Raman spectra of the alternating poly(dA-dBr5U), the splitting of a band into two components arising from the two contributions of ApBr5U and Br5UpA provides strong evidence for a repeating dinucleotide structure in solution. The calculated twist values averaged over the simulation runs are also systematically higher in the 5'T-A3' step (39 degrees) than in the 5'A-T3' step (33 degrees). Simultaneously, the calculated roll values are positive in the 5'T-A3' step (6 degrees) and negative in the 5'A-T3' step (-9 degrees), while the propeller twist values are about the same (-11 degrees to -16 degrees). On the other hand, in the homopolymer, the average twist value is close to 36 degrees with the roll angle close to 0 degrees and large propeller twist values (-20 degrees).
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Affiliation(s)
- S Brahms
- Institut Jacques Monod, Université Paris VII, France
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5
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Puppels GJ, de Mul FF, Otto C, Greve J, Robert-Nicoud M, Arndt-Jovin DJ, Jovin TM. Studying single living cells and chromosomes by confocal Raman microspectroscopy. Nature 1990; 347:301-3. [PMID: 2205805 DOI: 10.1038/347301a0] [Citation(s) in RCA: 507] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Many indirect methods have been developed to study the constitution and conformation of macromolecules inside the living cell. Direct analysis by Raman spectroscopy is an ideal complement to techniques using directly labelled fluorescent probes or of indirect labelling with mono- and polyclonal antibodies. The high information content of Raman spectra can characterize biological macromolecules both in solution and in crystals. The positions, intensities and linewidths of the Raman lines (corresponding to vibrational energy levels) in spectra of DNA-protein complexes yield information about the composition, secondary structure and interactions of these molecules, including the chemical microenvironment of molecular subgroups. The main drawback of the method is the low Raman scattering cross-section of biological macromolecules, which until now has prohibited studies at the level of the single cell with the exception of (salmon) sperm heads, in which the DNA is condensed to an exceptionally high degree. Ultraviolet-resonance Raman spectroscopy has been used to obtain single cell spectra (and F. Sureau and P. Y. Turpin, personal communication), but in this method absorption of laser light may impair the integrity of the sample. We have avoided this problem in developing a novel, highly sensitive confocal Raman microspectrometer for nonresonant Raman spectroscopy. Our instrument makes it possible to study single cells and chromosomes with a high spatial resolution (approximately less than 1 micron 3).
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Affiliation(s)
- G J Puppels
- University of Twente, Department of Applied Physics, Enschede, The Netherlands
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DeGrazia H, Harman JG, Tan GS, Wartell RM. Investigation of the cAMP receptor protein secondary structure by Raman spectroscopy. Biochemistry 1990; 29:3557-62. [PMID: 2162197 DOI: 10.1021/bi00466a019] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Raman spectroscopy was employed to examine the secondary structure of the cAMP receptor protein (CRP). Spectra were obtained over the range 400-1900 cm-1 from solutions of CRP and from CRP-cAMP cocrystals. The spectra of CRP dissolved in 30 mM sodium phosphate and 0.15 M NaCl buffered at either pH 6 or pH 8 or dissolved in 0.15-0.2 M NaCl at protein concentrations of 5, 15, and 30 mg/mL were examined. Estimates of the secondary structure distribution were made by analyzing the amide I region of the spectra (1630-1700 cm-1). CRP secondary structure distributions were essentially the same in either pH and at all protein concentrations examined. The amide I analyses indicated a structural distribution of 44% alpha-helix, 28% beta-strand, 18% turn, and 10% undefined for CRP in solution. Raman spectra of CRP-cAMP cocrystals differed from the spectra of CRP in solution. Some differences were assigned to interfering background bands, whereas other spectral differences were attributed to changes in CRP structure. Differences in the amide III region and in the intensity at 935 cm-1 were consistent with alterations in secondary structure. Analysis of the amide I region of the CRP-cAMP cocrystal spectrum indicated a secondary structure distribution of 37% alpha-helix, 33% beta-strand, 17% turn, and 12% undefined. This result is in agreement with a published secondary structure distribution derived from X-ray analysis of CRP-cAMP cocrystals (37% alpha-helix and 36% beta-strand).(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- H DeGrazia
- School of Physics, Georgia Institute of Technology, Atlanta 30332
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7
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Himmler HJ, Eysel HH. Raman study on a model system for the interaction of proteins with nucleic acids: lysine—tyrosine—lysine and polyriboadenylic acid. J Mol Struct 1989. [DOI: 10.1016/0022-2860(89)80016-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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8
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Dick LR, Geraldes CF, Sherry AD, Gray CW, Gray DM. 13C NMR of methylated lysines of fd gene 5 protein: evidence for a conformational change involving lysine 24 upon binding of a negatively charged lanthanide chelate. Biochemistry 1989; 28:7896-904. [PMID: 2514796 DOI: 10.1021/bi00445a052] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Helical complexes formed between fd DNA and reductively methylated fd gene 5 protein were indistinguishable by electron microscopy from complexes formed with the nonmethylated protein. 13C NMR spectroscopy of 13C-enriched N epsilon, N epsilon-dimethyllsyl residues of the protein showed that three of these residues (Lys-24, Lys-46, and Lys-69) were selectively perturbed by binding of the oligomer d(pA)7. These were the same lysyl residues that we previously found to be most protected from methylation by binding of the protein to poly[r(U)] [Dick, L. R., Sherry, A. D., Newkirk, M. M., & Gray D. M. (1988) J. Biol. Chem. 263, 18864-18872]. Thus, these lysines are probably directly involved in the nucleic acid binding function of the protein. Negatively charged chelates of lanthanide ions were used to perturb the 13C NMR resonances of labeled lysyl and amino-terminal residues of the gene 5 protein. The terbium chelate was found to bind tightly (Ka approximately 10(5) M-1) to the protein with a stoichiometry of 1 chelate molecule per protein dimer. 13C resonances of Lys-24, Lys-46, and Lys-69 were maximally shifted by the terbium chelate and were maximally relaxed by the gadolinium chelate. Also, the terbium chelate was excluded by the oligomer d(pA)7. Computer fits of the induced chemical shifts of 13C resonances with those expected for various positions of the terbium chelate failed to yield a possible chelate binding site unless the chemical shift for Lys-24 was excluded from the fitting process.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- L R Dick
- Program in Molecular and Cell Biology, University of Texas at Dallas, Richardson 75083-0688
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Dick LR, Sherry AD, Newkirk MM, Gray DM. Reductive methylation and 13C NMR studies of the lysyl residues of fd gene 5 protein. Lysines 24, 46, and 69 may be involved in nucleic acid binding. J Biol Chem 1988. [DOI: 10.1016/s0021-9258(18)37362-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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