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Vibrational spectroscopy and computer modeling of proteins: solving structure of α1-acid glycoprotein

Vladimír Kopecký, Rüdiger Ettrich, Kateřina Hofbauerová, Vladimír Baumruk
2004 Spectroscopy (Ottawa)  
This work introduces a new approach connecting vibrational spectroscopy with homology and energetic molecular modeling of proteins. Combination of both methods can compensate their disadvantages and result in realistic three-dimensional protein models. The approach is most powerful for membrane proteins or glycoproteins with high carbohydrate content where X-ray or NMR analysis is not always successful. Nevertheless, it can also serve as a tool of preliminary analysis of any protein with
more » ... structure. Power of the approach is demonstrated on human α1-acid glycoprotein. Its predicted structure published in [V. Kopecký Jr. et al.,Biochem. Biophys. Res. Commun.300(2003), 41–46] is discussed in detail with respect to the approach and its general employment.
doi:10.1155/2004/747828 fatcat:tb7z65k44behjdguvgxgboj6zu

Anharmonic effects in IR, Raman, and Raman optical activity spectra of alanine and proline zwitterions

Petr Daněček, Josef Kapitán, Vladimír Baumruk, Lucie Bednárová, Vladimír Kopecký, Petr Bouř
2007 Journal of Chemical Physics  
The difference spectroscopy of the Raman optical activity ͑ROA͒ provides extended information about molecular structure. However, interpretation of the spectra is based on complex and often inaccurate simulations. Previously, the authors attempted to make the calculations more robust by including the solvent and exploring the role of molecular flexibility for alanine and proline zwitterions. In the current study, they analyze the IR, Raman, and ROA spectra of these molecules with the emphasis
more » ... the force field modeling. Vibrational harmonic frequencies obtained with 25 ab initio methods are compared to experimental band positions. The role of anharmonic terms in the potential and intensity tensors is also systematically explored using the vibrational self-consistent field, vibrational configuration interaction ͑VCI͒, and degeneracy-corrected perturbation calculations. The harmonic approach appeared satisfactory for most of the lower-wavelength ͑200-1800 cm −1 ͒ vibrations. Modern generalized gradient approximation and hybrid density functionals, such as the common B3LYP method, provided a very good statistical agreement with the experiment. Although the inclusion of the anharmonic corrections still did not lead to complete agreement between the simulations and the experiment, occasional enhancements were achieved across the entire region of wave numbers. Not only the transitional frequencies of the C-H stretching modes were significantly improved but also Raman and ROA spectral profiles including N-H and C-H lower-frequency bending modes were more realistic after application of the VCI correction. A limited Boltzmann averaging for the lowest-frequency modes that could not be included directly in the anharmonic calculus provided a realistic inhomogeneous band broadening. The anharmonic parts of the intensity tensors ͑second dipole and polarizability derivatives͒ were found less important for the entire spectral profiles than the force field anharmonicities ͑third and fourth energy derivatives͒, except for a few weak combination bands which were dominated by the anharmonic tensor contributions.
doi:10.1063/1.2738065 pmid:17581069 fatcat:ksf4degwmjfz5csnkv45xsajue

Electronic and vibrational optical activity of several peptides related to neurohypophyseal hormones: Disulfide group conformation

Markéta Pazderková, Lucie Bednárová, Helena Dlouhá, Martin Flegel, Michal Lebl, Jan Hlaváček, Vladimír Setnička, Marie Urbanová, Sixtus Hynie, Věra Klenerová, Vladimír Baumruk, Petr Maloň
2012 Biopolymers  
doi:10.1002/bip.22105 pmid:22899367 fatcat:izcqe4feufaa5gd6whxfbi2p7y

Changes in Na+,K+-ATPase structure induced by cation binding Approach by Raman spectroscopy

Pavel Anzenbacher, Peter Mojzes, Vladimir Baumruk, Evžen Amler
1992 FEBS Letters  
Roman analysis of Na*,K*-ATPasc structural changes induced by cation binding reveals a slight decrease (< 10%) of the a-helical content upon E,-E2 transition. Pronounced conformational clxu~ges ol'the enzyme are unlikely as the character of the onv'iconment of tyrosinc residues remains unaltered. However, local changes can take place as evidenced by changes in tryptophan vibration at about 880 cm-l.
doi:10.1016/0014-5793(92)81414-h pmid:1330684 fatcat:stegoqhm5ffbzdhxbxq4wb6o5i

Measurement and Calculation of the Raman Optical Activity of α-Pinene and trans-Pinane

Petr Bouř, Vladimír Baumruk, Jana Hanzlíková
1997 Collection of Czechoslovak Chemical Communications  
(Vol. 62) (1997) Bour, Baumruk, Hanzlikova: Collect. Czech. Chem. Commun. (Vol. 62) (1997)  ... 
doi:10.1135/cccc19971384 fatcat:yye3mb3swjawdoywr53tjjd57e

Structure of the dimeric N-glycosylated form of fungal β-N-acetylhexosaminidase revealed by computer modeling, vibrational spectroscopy, and biochemical studies

Rüdiger Ettrich, Vladimír Kopecký, Kateřina Hofbauerová, Vladimír Baumruk, Petr Novák, Petr Pompach, Petr Man, Ondřej Plíhal, Michal Kutý, Natallia Kulik, Jan Sklenář, Helena Ryšlavá (+2 others)
2007 BMC Structural Biology  
Fungal β-N-acetylhexosaminidases catalyze the hydrolysis of chitobiose into its constituent monosaccharides. These enzymes are physiologically important during the life cycle of the fungus for the formation of septa, germ tubes and fruit-bodies. Crystal structures are known for two monomeric bacterial enzymes and the dimeric human lysosomal β-Nacetylhexosaminidase. The fungal β-N-acetylhexosaminidases are robust enzymes commonly used in chemoenzymatic syntheses of oligosaccharides. The enzyme
more » ... om Aspergillus oryzae was purified and its sequence was determined. Results: The complete primary structure of the fungal β-N-acetylhexosaminidase from Aspergillus oryzae CCF1066 was used to construct molecular models of the catalytic subunit of the enzyme, the enzyme dimer, and the N-glycosylated dimer. Experimental data were obtained from infrared and Raman spectroscopy, and biochemical studies of the native and deglycosylated enzyme, and are in good agreement with the models. Enzyme deglycosylated under native conditions displays identical kinetic parameters but is significantly less stable in acidic conditions, consistent with model predictions. The molecular model of the deglycosylated enzyme was solvated and a molecular dynamics simulation was run over 20 ns. The molecular model is able to bind the natural substrate -chitobiose with a stable value of binding energy during the molecular dynamics simulation. Conclusion: Whereas the intracellular bacterial β-N-acetylhexosaminidases are monomeric, the extracellular secreted enzymes of fungi and humans occur as dimers. Dimerization of the fungal β-
doi:10.1186/1472-6807-7-32 pmid:17509134 pmcid:PMC1885261 fatcat:rpxvontv2jdpffrq453kjuedce

Chiroptical Properties and Conformation of Four Lasiocepsin-Related Antimicrobial Peptides: Structural Role of Disulfide Bridges

Markéta Pazderková, Václav Profant, Petr Maloň, Rina K. Dukor, Václav Čeřovský, Vladimír Baumruk, Lucie Bednárová
2020 Symmetry  
We report an investigation of the role of disulfide bridges in the 27-residue antimicrobial peptide lasiocepsin (I) containing two disulfide groups (Cys8–Cys25, Cys17–Cys27) and three its analogs lacking one (II, III) or both (IV) native disulfides. Selective alternate incorporation of one or both disulfide bridges influences symmetry, conformation and biological properties of these peptides as demonstrated in their chiroptical (particularly Raman) properties. The effect of modifying the
more » ... de bridge pattern on the peptide secondary structure is investigated in water and in the presence of 2,2,2-trifluoroethanol and sodium dodecyl sulphate. A combination of experimental electronic and vibrational chiroptical data shows that both disulfide groups are necessary for stabilizing lasiocepsin secondary structure. While the Cys8–Cys25 disulfide group is important for sustaining lasiocepsin tertiary structure and maintaining its biological activity, the Cys17–Cys27 disulfide bridge has a supporting function consisting in reducing peptide flexibility.
doi:10.3390/sym12050812 fatcat:jcrk56m4a5gizb5ybipr4whxpu

Comparison between CUUG and UUCG tetraloops: thermodynamic stability and structural features analyzed by UV absorption and vibrational spectroscopy

Vladimir Baumruk, Catherine Gouyette, Tam Huynh-Dinh, Jian-Sheng Sun, Mahmoud Ghomi
2001 Nucleic Acids Research  
CUUG loop is one of the most frequently occurring tetraloops in bacterial 16S rRNA. This tetraloop has a high thermodynamic stability as proved by previous UV absorption and NMR experiments. Here, we present our results concerning the thermodynamic and structural features of the 10mer 5′-r(GCG-CUUG-CGC)-3′, forming a highly stable CUUG tetraloop hairpin in aqueous solution, by means of several optical techniques (UV and FT-IR absorption, Raman scattering). UV melting profile of this decamer
more » ... ides a high melting temperature (60.7°C). A set of Raman spectra recorded at different temperatures allowed us to analyze the order-to-disorder (hairpinto-random coil) transition. Assignment of vibrational markers led us to confirm the particular nucleoside conformation, and to get information on the base stacking and base pairing in the hairpin structure. Moreover, comparison of the data obtained from two highly stable CUUG and UUCG tetraloops containing the same nucleotides but in a different order permitted an overall discussion of their structural features on the basis of Raman marker evidences.
doi:10.1093/nar/29.19.4089 pmid:11574692 pmcid:PMC60239 fatcat:4arj4dpv75gbxd7kwbwjwuoywa

IR and Raman Spectra, Conformational Flexibility, and Scaled Quantum Mechanical Force Fields of Sodium Dimethyl Phosphate and Dimethyl Phosphate Anion†

Jan Florián, Vladimír Baumruk, Marek Štrajbl, Lucie Bednárová, Josef Štěpánek
1996 The Journal of Physical Chemistry  
Quantum chemical calculations, involving Hartree-Fock (HF), perturbation (MP2), and density functional (DFT) theories, are carried out for the dimethyl phosphate anion (DMP) and sodium dimethyl phosphate (NaDMP), model systems for the DNA phosphate group. Energies, geometries, and harmonic force fields of different conformations of DMP and NaDMP are compared. In addition, atomic charges derived from the HF/6-31G* and MP2/6-31+G* electrostatic potential of DMP and NaDMP are calculated in order
more » ... determine the effects of counterions upon the charge distribution. Finally, IR and Raman spectra of solid and aqueous NaDMP, recorded here in the 80-4000 cm -1 (IR) and 150-3100 cm -1 (Raman) spectral regions, are assigned using differentially scaled Hartree-Fock, MP2, and B3-LYP force fields of DMP and NaDMP. Our interpretation of the individual vibrational bands confirms the results of the previous empirical normal-coordinate analysis of DMP of Thomas et al. (Biophys. J. 1994, 66, 225). Also, the predicted frequencies, IR and Raman intensities, depolarization ratios, and 13 C isotopic frequency shifts agree well with the experimental data. Among the computational methods, the best results are obtained using the B3-LYP gradient corrected density functional. The proposed scale factors for the HF/3-21G(*), HF/6-31G*, MP2/6-31+G*, and B3-LYP/6-31G* force fields of DMP or NaDMP are transferable to larger systems involving phosphodiester moiety, for example to nucleotides or phospholipids. † This paper is the seventh in the series "Scaled quantum mechanical force fields and vibrational spectra of solid state nucleic acid constituents".
doi:10.1021/jp9520299 fatcat:kt3k5fhjvnbuzfhuomm3ahkwqa

Macromolecules and Materials

2013 Chemistry International  
Baumruk, Czech Republic (Vibrational optical activity of (bio)polymers), Daniele Cangialosi, Spain (Dielectric and calorimetric spectroscopy to unravel dynamics and physical aging in nano-structured polymers  ...  spectroscopy on nitroxides: a simple method to elucidate molecular and nanoscale processes in thermoresponsive polymers)  Isao Noda, USA (Two-dimensional correlation spectroscopy study of polymers)  Vladimír  ... 
doi:10.1515/ci.2013.35.6.29b fatcat:dvnoxlv3yvf45cnpkggrtvo23a

Ab initio modeling of fused silica, crystal quartz, and water Raman spectra

Martin Dračínský, Ladislav Benda, Petr Bouř
2011 Chemical Physics Letters  
Vladimír Baumruk for providing us with the water Raman spectrum.  ... 
doi:10.1016/j.cplett.2011.06.077 fatcat:uas3xiezozeffaw2f56v4j63na

STRUKTURA 2005-PROGRAM Øešení struktur

Hašek, P Vojtíšek
2005 Ó Krystalografická spoleènost Materials Structure   unpublished
Baumruk (MFF UK, Praha) IÈ a Ramanova spektroskopie -co nám mohou vibrace øíci o (bio)molekulách L9 -str. 118 9:20 Jiøí Brus (Ústav makromolekulární chemie AV ÈR, Praha) Studium struktury materiálù  ...  František Laufek (Èeská geologická služba, Praha) Krystalochemie systému Sb-Te-Ni S21 -str. 153 19.30 Veèeøe 20.00 Shromáždìní èlenù Krystalografické spoleènosti Støeda 22. 6. 7.30 Snídanì 8:30 Vladimír  ... 

Raman Spectroscopy of Proteins, DNA and Their Complexes [article]

Lubomír Dostál, Universitätsbibliothek Der FU Berlin, Universitätsbibliothek Der FU Berlin
I was fortunate to have nice friends in Prague like Vladimír Baumruk and Vladimír Kopecký who provided many valuable advices.  ... 
doi:10.17169/refubium-15762 fatcat:zl47yiwoq5hstjlxra4ee4j6u4

Inspecting chiral molecules by Raman optical activity spectroscopy

Václav Parchaňský, Josef Kapitán, Petr Bouř
2014 RSC Advances  
Josef Kapitán received his PhD from the Charles University in Prague in 2006 such as in the eld of Raman optical activity (ROA), with Petr Bouř and Vladimír Baumruk.  ... 
doi:10.1039/c4ra10416a fatcat:7s3kgd6ohrgtpgbw5hxcbuafrm

Association of CD147 and Calcium Exporter PMCA4 Uncouples IL-2 Expression from Early TCR Signaling

Verena Supper, Herbert B. Schiller, Wolfgang Paster, Florian Forster, Cyril Boulègue, Goran Mitulovic, Vladimir Leksa, Anna Ohradanova-Repic, Christian Machacek, Philipp Schatzlmaier, Gerhard J. Zlabinger, Hannes Stockinger
2016 Journal of Immunology  
The Jurkat T cell clone IL-2-Luc stably transfected with an IL-2 promoter luciferase reporter construct was the kind gift of Thomas Baumruker (Novartis Institutes for BioMedical Research, Vienna, Austria  ... 
doi:10.4049/jimmunol.1501889 pmid:26729804 fatcat:h27c2wzbqbe6jb52umud3zrhyy
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