Jane Vanderkooi - Academia.edu (original) (raw)

Papers by Jane Vanderkooi

Biochemistry, 2001

Infrared and optical spectra of carbonmonoxy horseradish peroxidase were monitored as a function ... more Infrared and optical spectra of carbonmonoxy horseradish peroxidase were monitored as a function of pH and substrate binding. The analyses of experimental results together with semiempirical calculations show that the CO-porphyrin complex is sensitive to environmental changes. The electronic Q(0,0) band of the porphyrin and the CO stretching mode respond to external perturbations with different symmetry dependencies. In this way, the complex is nonisotropic, and the combined spectral analyses constitute a valuable tool for the investigation of structure. In the absence of substrate and at pH 6.0, the low-spin heme optical Q(0,0) absorption band is a single peak that narrows as the temperature decreases. Under these conditions, the CO vibrational stretch frequency is at 1903 cm -1 . Addition of the substrates benzohydroxamic acid or naphthohydroxamic acid produces a split of ∼320 cm -1 in the Q(0,0) absorption band that is clearly evident at <100 K and shifts the CO absorption to 1916 cm -1 . Increasing the pH to 9.3 also causes a split in the Q(0,0) optical band and elicits a shift in ν(CO) to a higher frequency (1936 cm -1 ). The splitting of the Q(0,0) band and the shifts in the IR spectra are both consistent with changes in the local electric field produced by the proximity of the electronegative carbonyl of the substrate near the heme or the protonation and/or deprotonation of the distal histidine, although other effects are also considered. The larger effect on the Q(0,0) band with substrate at low pH and the shift of ν(CO) at high pH can be rationalized by the directionality of the field and the orientation dependence of dipolar interactions.

Biochemistry, 1996

The cyanide complex of Fe II Mb prepared and maintained at temperatures below 0°C is sufficiently... more The cyanide complex of Fe II Mb prepared and maintained at temperatures below 0°C is sufficiently stable to permit spectroscopic characterization and allow comparison with free HCN and other ferric and ferrous CN complexes. The visible absorption spectrum of Fe II Mb-CN has a split R band maxima at 571 and 563 nm, suggesting distortion in the x-y plane of the porphyrin. Fe II Mb-CN, like the CO complex, was found to be optically active by circular dichroism. The C-N stretching frequencies for the CN-ferrous complexes are very sensitive to parameters within the heme pocket. The values are as follows: Fe II Mb at pH 8, 2057 cm -1 with a shoulder appearing at 2078 cm -1 at pH 5.6; Fe II Mp, 2034 cm -1 . In contrast, the frequencies for C-N stretch differ little among ferric heme complexes, ranging from 2123 to 2125 cm -1 for myoglobin, hemoglobin, and microperoxidase. These values compare with free HCN (2094 cm -1 ) or CN -(2080 cm -1 ). Quantum chemical modeling of the neutral ironporphyrin complex with imidazole and cyanide and of its anion was used to explain the effects of the cyanide coordination and of iron reduction on the C-N stretching frequencies. The lower νC-N for Fe II Mb-CN relative to the ferric complex is attributed to the appearance of additional electron density on all the anti-bonding CN orbitals. The extra electron density was also used to explain that the band width of C-N stretching mode was greater in the ferrous complexes than in the ferric complex. Finally, the calculation shows that σ donation weakens the Fe-C bond, in qualitative agreement with the spontaneous dissociation of CNfrom Fe II Mb at -5°C. The sensitivity of CN complexes of ferrous heme proteins to the heme pocket environment and the ability to correlate spectroscopic parameters with calculated electron density suggest that infrared spectroscopy of the CN ligand is an appropriate tool to study ferrous heme proteins.

Biophysical Chemistry, 2003

The role of the solvent matrix in affecting CO bound to ferrous horseradish peroxidase was examin... more The role of the solvent matrix in affecting CO bound to ferrous horseradish peroxidase was examined by comparing band-widths of νCO for the protein in aqueous solutions and in trehalose/sucrose glasses. We have previously observed that the optical absorption band and the CO stretching mode respond to the glass transition of glycerol/water in ways that depend upon the presence of substrate (Biochemistry 40 (2001) 3483). It is now demonstrated that the CO group band-width for the protein with bound inhibitor benzhydroxamic acid is relatively insensitive to temperature or the glass transition of the solvent. In contrast, in the absence of inhibitor, the band-width varies with the temperature that the glass is formed. The results show that solvent dependent and independent motions can be distinguished, and that the presence of substrate changes the protein such that the Fe–CO site is occluded from the solvent conditions. Molecular dynamic calculations, based upon X-ray structures, showed that the presence of benzhydroxamic acid decreases the distance between His42 and Arg38 and this leads for closer distances to the O of the CO from these residues. These results are invoked to account for the observed line width changes of the CO band.

Biophysical Journal, 2001

Spectroscopy of horseradish peroxidase with and without the substrate analog, benzohydroxamic aci... more Spectroscopy of horseradish peroxidase with and without the substrate analog, benzohydroxamic acid, was monitored in a glycerol/water solvent as a function of temperature. It was determined from the water infrared (IR) absorption that the solvent has a glass transition at 170 -180 K. In the absence of substrate, both the heme optical Q(0,0) absorption band and the IR absorption band of CO bound to heme broaden markedly upon heating from 10 -300 K. The Q(0,0) band broadens smoothly in the whole temperature interval, whereas the IR bandwidth is constant in the glassy matrix and increases from 7 to 16 cm Ϫ1 upon heating above the glass transition. Binding of substrate strongly diminishes temperature broadening of both the bands. The results are consistent with the view that the substrate strongly reduces the amplitude of motions of amino acids forming the heme pocket. The main contribution to the Q(0,0) bandwidth arises from the heme vibrations that are not affected by the phase transition. The CO band thermal broadening stems from the anharmonic coupling with motions of the heme environment, which, in the glassy state, are frozen in. Unusually strong temperature broadening of the CO band is interpreted to be caused by thermal population of a very flexible excited conformational substrate. Analysis of literature data on the thermal broadening of the A 0 band of Mb(CO) (Ansari et al., 1987. Biophys. Chem. 26:337-355) shows that such a state presents itself also in myoglobin.

The Journal of Physical Chemistry, 1993

... Andras D. Kaposi,t Judit Fidy,+ Solomon S. Stavrov,* and Jane M. Vanderkooi' Institu... more ... Andras D. Kaposi,t Judit Fidy,+ Solomon S. Stavrov,* and Jane M. Vanderkooi' Institute of Biophysics, Semmelweis Medical University, Budapest HI 444, PO ... whereZ,,is theexcitation intensity,Akis the0,O-1,kabsorption transition probability, vk is related to the l,k - 1,0 vibrational ...

Biopolymers, 2002

The spectroscopy of horseradish peroxidase with and without the substrate analogue benzohydroxami... more The spectroscopy of horseradish peroxidase with and without the substrate analogue benzohydroxamic acid (BHA) was monitored in different solvents as a function of the temperature in the interval from 10 to 300 K. Thermal broadening of the Q(0,0) optical absorption band arises mainly from interaction of the electronic π → π transition with the heme vibrations. In contrast, the width of the IR absorption band of CO bound to heme is controlled by the coupling of the CO transition moment to the electric field of the protein matrix. The IR bandwidth of the substrate free enzyme in the glycerol/H2O solvent hardly changes in the glassy matrix and strongly increases upon heating above the glass transition. Heating of the same enzyme in the trehalose/H2O glass considerably broadens the band. The binding of the substrate strongly diminishes the temperature broadening of the CO band. This result is consistent with the view that the BHA strongly reduces the amplitude of vibrations of the heme pocket environment. Unusually strong thermal broadening of the CO band above the glass transition is interpreted to be caused by thermal population of a very flexible excited conformational substate. The thermal broadening of the same band in the trehalose glass is caused by an increase of the protein vibrational amplitude in each of the conformational substates, their population being independent of the temperature in the glassy matrix. © 2002 Wiley Periodicals, Inc. Biopolymers (Biospectroscopy) 67: 255–258, 2002

Biophysical Journal, 2006

The temperature dependencies of the infrared absorption CO bands of carboxy complexes of horserad... more The temperature dependencies of the infrared absorption CO bands of carboxy complexes of horseradish peroxidase (HRP(CO)) in glycerol/water mixture at pH 6.0 and 9.3 are interpreted using the theory of optical absorption bandshape. The bands’ anharmonic behavior is explained assuming that there is a higher-energy set of conformational substates (CSSh), which are populated upon heating and correspond to the protein substates with disordered water molecules in the heme pocket. Analysis of the second moments of the CO bands of the carboxy complexes of myoglobin (Mb(CO)) and hemoglobin (Hb(CO)), and of HRP(CO) with benzohydroxamic acid (HRP(CO)+BHA), shows that the low energy CSSh exists also in the open conformation of Mb(CO), where the heme pocket is spacious enough to accommodate a water molecule. In the HRP(CO)+BHA and closed conformations of Mb(CO) and Hb(CO), the heme pocket is packed with BHA and different amino acids, the CSSh has much higher energy and is hardly populated even at the highest temperatures. Therefore only motions of these amino acids contribute to the band broadening. These motions are linked to the protein surface and frozen in the glassy matrix, whereas in the liquid solvent they are harmonic. Thus the second moment of the CO band is temperature-independent in glass and is proportional to the temperature in liquid. The temperature dependence of the second moment of the CO peak of HRP(CO) in the trehalose glass exhibits linear coupling to an oscillator. This oscillator can be a moving water molecule locked in the heme pocket in the whole interval of temperatures or a trehalose molecule located in the heme pocket.

European Journal of Biochemistry, Feb 1, 2001

We have recently demonstrated that metalloporphyrins are potent inhibitors of both human immunode... more We have recently demonstrated that metalloporphyrins are potent inhibitors of both human immunodeficiency virus type 1 (HIV-1) and human immunodeficiency virus type 2 (HIV-2) reverse transcriptases (RTs) [Argyris, E.G., Vanderkooi, J.M., Venkateswaran, P.S., Kay, B.K., and Paterson, Y. (1999) J. Biol. Chem. 274, 1549±1556]. In addition, by screening a phage peptide library we discovered that a peptide with sequence similarity to residues 398±407 from the connection subdomain of HIV RTs binds heme. These findings suggested that this highly conserved region may be the binding site for metalloporphyrins and a novel site for inhibition of enzymatic activity. Our most recent data presented here confirm this suggestion. Screening of HIV-1 RT 398±407 peptide analogs by fluorescence assays demonstrates that Trp residues at positions 401 and 402 are important for heme binding. Furthermore, site-directed mutagenesis of these residues verified these findings and indicated that heme inhibits HIV-1 RT by binding on the connection subdomain of the p66 subunit of the enzyme but not on the p51 subunit. This was also confirmed by analyzing the binding affinities of heme for mutant HIV-1 RT heterodimers, using intrinsic fluorescence assays. The clear identification of the connection domain as a novel inhibition site is crucial in understanding the mechanism of heme binding and enzymatic inhibition and will facilitate the generation of novel porphyrin-based inhibitors of RT.

Biochemistry Usa, 1996

... The same phenomenon has been observed in metalloporphyrin coordination compounds in crystalli... more ... The same phenomenon has been observed in metalloporphyrin coordination compounds in crystalline host matrices (Canters et al., 1976; Kim & Bohandy, 1977; Jansen et al., 1978;Platenkamp & Canters, 1981). ... MgTBP, n-octane, 15 962, 30, 4.2, Platenkamp & Canters, 1981. ...

Journal of the American Chemical Society, Apr 1, 2003

The fluorescence intensity-time records of individual metal-free porphyrin cytochrome-c and Zn po... more The fluorescence intensity-time records of individual metal-free porphyrin cytochrome-c and Zn porphyrin cytochrome-c molecules whose translational motions are restricted by encapsulation in trehalose are examined by single-molecule spectroscopy by means of a two-channel confocal microscope that records transient fluorescence signals in two orthogonal polarization directions. Large angular motions often occur on time scales ranging to many seconds. Measurements of the photobleaching time distributions indicate that the trehalose glass restricts the accessibilty of the fluorescent molecules to oxygen.

Biochemistry Usa, 1992

Page 1. 6538 Biochemistry 1992, 31, 6538-6544 Kalnin, NN, Baikalov, I. A., & Venyaminov, S. Y... more Page 1. 6538 Biochemistry 1992, 31, 6538-6544 Kalnin, NN, Baikalov, I. A., & Venyaminov, S. Yu. (1990) Kauppinen, JK, Moffat, DJ, Mantsch, HH, & Cameron, Kennedy, DF, Crisma, M., Toniolo, C., & Chapman, D. Krimm, S., & Bandekar, J. (1986) Adu. Protein Chem. 38, ...

Arch Biochem Biophys, 1969

J Phys Chem B, 2004

Spectral diffusion broadening of cytochrome c carrying the free-base analogue of heme is investig... more Spectral diffusion broadening of cytochrome c carrying the free-base analogue of heme is investigated in its unfolded state and compared with the corresponding broadening in the native state. Spectral diffusion is much larger in the unfolded state, in comparison to the native state. Interestingly, the time law that governs spectral diffusion changes as the aging time increases, from a power-law behavior in the native state to an apparent logarithmic behavior in the unfolded state.

Biophysical Journal, Jul 31, 1996

We performed hole-burning Stark effect experiments on cytochrome c in which the iron of the heme ... more We performed hole-burning Stark effect experiments on cytochrome c in which the iron of the heme was either removed or replaced by Zn. According to the experiments, the free-base compound has an effective inversion center, even in the protein. The Zn compound, on the other hand, shows quite peculiar features: in the low-frequency range of the inhomogeneous band, it definitely has a dipole moment, as indicated by a splitting of the hole in the external field. However, in the maximum of the inhomogeneous band, a severe charge redistribution occurs, as the experiments show. In addition to the Stark experiments, we performed calculations of the electrostatic fields at the pyrrole rings and at the metal site of the heme group. We interpret our findings with a model based on structural hierarchies: the protein can exist in a few subconformations, which can be distinguished through the structure of the heme pocket. The different pocket structures support different structures of the chromophore, which, in turn, can be distinguished through their behavior in an external field. These distinct structures, in turn, correspond to a rather broad distribution of protein structures, which leave, however, the pocket structure largely unchanged. These structures show up in inhomogeneous broadening.

J Am Chem Soc, 1995

Page 1. 12514 J. Am. Chem. SOC. 1995, 117, 12514-12527 EPR Spectroscopy and Photophysics of the L... more Page 1. 12514 J. Am. Chem. SOC. 1995, 117, 12514-12527 EPR Spectroscopy and Photophysics of the Lowest Photoactivated Triplet State of a Series of Highly Conjugated (Porphinato)Zn Arrays PJ Angiolillo,t Victor SPY. Lin? J. M. Vanderkooi,*J and Michael J. Theden**' ...

Time-Resolved Laser Spectroscopy in Biochemistry IV, 1994

ABSTRACT Mesoporphyrin IX was used as a fluorescent analogue of heme in cytochrome c peroxidase (... more ABSTRACT Mesoporphyrin IX was used as a fluorescent analogue of heme in cytochrome c peroxidase (CcP). Details of the fluorescence spectra of CcP obtained under conditions of energy selection revealed interactions of the porphyrin with the heme pocket. It was shown that the energy of a 0,0 transition shifted with pH in parallel with changes in the electric field of the protein.

Biochimica Et Biophysica Acta Protein Structure and Molecular Enzymology, Aug 18, 1998

Three ways are generally used to visualize proteins : (1) a static model in which the atomic posi... more Three ways are generally used to visualize proteins : (1) a static model in which the atomic positions are defined, (2) a dynamic model taking into account fluctuations, and (3) a reactive model that reflects the internal and external electric fields of the molecule. The properties of chromophoric prosthetic groups can be probed by optical spectroscopy, and when high resolution techniques are used, the results reveal information about the local electric fields in proteins, as influenced and determined by atomic positions and dynamics. ß

Photochem Photobiol, 1990

ABSTRACT