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Type 2 diabetes is characterized by elevated blood glucose levels resulting from a pancreatic β-cell secretory insufficiency combined with insulin resistance, most significantly manifested in skeletal muscle and liver (1). If untreated, diabetic complications develop that cause loss of vision, peripheral neuropathy, impaired kidney function, heart disease, and stroke. The disease has a polygenic basis because numerous genes (the latest count exceeding 20) participate in its pathogenesis, but modern lifestyle characterized by limited physical activity and excessive caloric intake are critical precipitating factors for the current epidemic of type 2 diabetes worldwide (2). It appears that available treatments, including attempts at lifestyle alterations and drug therapies including insulin, are insufficient to stem the tide. Therefore, new approaches, including the development of therapeutic agents with novel mechanisms of action, are needed. Selection of new drug targets to treat type 2 diabetes has to be guided primarily by consideration of established physiological chemistry of glucose homeostasis and of prevailing views about the pathophysiology of type 2 diabetes because the genetics of the disease that could serve as another guiding principle remain prohibitively perplexing. The glucose-phosphorylating enzyme glucokinase (GK) was identified as an outstanding drug target for developing antidiabetic medicines because it has an exceptionally high impact on glucose homeostasis because of its glucose sensor role in pancreatic β-cells and as a rate-controlling enzyme for hepatic glucose clearance and glycogen synthesis, both processes that are impaired in type 2 diabetes (3). Milestones in the 45-year history of GK research are listed in Supplementary Table 1 (Supplementary References S1–S27). In the mid-1990s, Hoffmann La-Roche scientists conducted a high-throughput screen in search of small molecules that could reverse the inhibition of GK by its regulatory protein (GKRP, see further discussion below) and identified a hit molecule that reversed GKRP inhibition by directly stimulating GK (4 …

The OH stretch mode from water and organic hydroxyl groups have strong infrared absorption, the position of the band going to lower frequency with increased H-bonding. This band was used to study water in trehalose and glycerol solutions and in genetically modified yeast cells containing varying amounts of trehalose. Concentration-dependent changes in water structure induced by trehalose and glycerol in solution were detected, consistent with an increase of lower-energy H-bonds and interactions at the expense of higher-energy interactions. This result suggests that these molecules disrupt the water H-bond network in such a way as to strengthen molecule-water interactions while perturbing water-water interactions. The molecule-induced changes in the water H-bond network seen in solution do not translate to observable differences in yeast cells that are trehalose-deficient and trehalose-rich. Although comparison of yeast with low and high trehalose showed no observable effect on intracellular water structure, the structure of water in cells is different from that in bulk water. Cellular water exhibits a larger preference for lower-energy H-bonds or interactions over higher-energy interactions relative to that shown in bulk water. This effect is likely the result of the high concentration of biological molecules present in the cell. The ability of water to interact directly with polar groups on biological molecules may cause the preference seen for lower-energy interactions.

The heme in horseradish peroxidase (HRP) was replaced by phosphorescent Pt-mesoporphyrin IX (PtMP), which acted as a phosphorescent marker of oxygen quenching and allowed comparison with another probe, Pd-mesoporphyrin IX (Khajehpour et al. (2003) Proteins 53, 656-666). Benzohydroxamic acid (BHA), a competitive inhibitor of the enzyme, was also used to monitor its effects on phosphorescence quenching. With the addition of BHA, in the presence of oxygen, the phosphorescence intensity of the protein increased. In contrast, the addition of BHA, in the absence of oxygen, reduced the phosphorescence intensity of the protein. K(d) = 18 microM when BHA binds to PtMP-HRP. The effect of BHA can be explained by two factors: (1) BHA reduces the accessibility of O(2) to the protein interior and (2) BHA itself quenches the phosphorescence. Consistent with this, the oxygen quenching of the phosphorescence of PtMP-HRP gave a quenching constant of k(q) = 234 mm Hg(-1) s(-1) in the absence of BHA and k(q) = 28.7 mm Hg(-1) s(-1) in the presence of BHA. The quenching rate of BHA is 4000 s(-1). The relative quantum yield of the phosphorescence of the Pt derivative is about six times that of the Pd derivative, whereas the phosphorescence lifetime is approximately eight times shorter. The high quantum yield and suitable lifetime make Pt-porphyrins appropriate as sensors of O(2) diffusion and flexibility in heme proteins.

Infrared (IR) spectroscopy is used for studying the carbohydrate moieties of glycosylated proteins. IR spectra of mono- and disaccharides in the fingerprint region are specific to each sugar and to the environment of the sugar molecules (i.e., aqueous solution or anhydrous glass phase). The IR spectra of glycosylated proteins (mucin, soybean peroxidase, collagen IV, and avidin) were compared with those of the constituent sugars and cytochrome c (a protein with no glycosylation). Our results demonstrate that the IR absorption spectra of glycosylated proteins show distinct absorption bands for the sugar moiety, the protein amide group, and water. Therefore, IR can be used to detect glycosylation.

Phosphorescence of single protein molecules has been directly observed by laser confocal microscopy. The native horseradish peroxidase (HRP) has been converted into a phosphorescent analog (Pt-HRP) by replacing the heme prosthetic group with platinum mesoporphyrin IX (Pt-MP). Oxygen quenching of the triplet state emission of single Pt-HRP molecules has been directly detected and the oxygen quenching constant could be estimated at the single molecule level. The method lays a foundation for experimental studies of the pathways of oxygen diffusion in proteins.

The heme of horseradish peroxidase is buried in the protein, but a channel from the protein surface connects the aqueous solution to the heme site. Ferric horseradish peroxidase has an absorption band at 640 nm that is attributed to a charge-transfer (CT) transition between the a 2u HOMO of ﷿ electrons of the porphyrin ring and the dxy/dyz orbital of the ferric ion. Because the water channel extends to the Fe, it seems likely that the CT band will be sensitive to the hydration of the protein. To study this premise, the protein was incorporated into trehalose/sucrose glasses and the hydration of the sugar glasses was varied. Absorption spectra of HRP in sugar glasses and in glycerol/water were taken in the range 10-300 K. The CT absorption band shows vibronic fine structure. The peak positions are the same in hydrated sugar and glycerol/water but the peak positions change in desiccated sugar glass. The data suggest that in hydrated, but not desiccated, sugar glass, water is retained in the heme pocket. Binding of the competitive inhibitor benzohydroxamic acid to the protein increases the CT absorption and resolution. The effect of benzohydroxamic acid on the Fe as calculated using a combination of density functional theory and molecular mechanics is to stabilize the spin state 3 /2 with respect to 5 /2. At low temperature the widths of the lines in the CT band are narrower for the protein in glycerol/water (glass transition at 150 K) than in trehalose/sucrose (glass formation at 65 °C). This indicates that the CT band is inhomogeneously broadened and sensitive to the solvent. The spectral narrowing of the CT absorption occurs as the temperature decreases over the temperature range studied. Water, as indicated by the OH stretch, also shifts in this range. The findings are discussed in terms of how buried water and nearby charges can modulate the activity of the heme.

Oxygen and other molecules of similar size take part in a variety of protein reactions. Therefore, it is critical to understand how these small molecules penetrate the protein matrix. The protein system studied in this case is horseradish peroxidase (HRP). We have converted the native HRP into a phosphorescent analog by replacing the heme prosthetic group by Pd-mesoporphyrin. Oxygen readily quenches the phosphorescence of Pd porphyrins, and this can be used to characterize oxygen diffusion through the protein matrix. Our measurements indicate that solvent viscosity and pH modulate the accessibility of the heme pocket relative to small molecules. The binding of the substrate benzohydroxamic acid (BHA) to the protein drastically impedes oxygen access to the heme pocket. These results indicate that, first, the penetration of small molecules through the protein matrix is a function of protein dynamics, and second, there are specific pathways for the diffusion of these molecules. The effect of substrate and pH on protein dynamics has been investigated with the use of molecular dynamics calculations. We demonstrate that the model of a "fluctuating entry point," as suggested by Zwanzig (J Chem Phys 1992;97:3587-3589), properly describes the diffusion of oxygen through the protein matrix.

The reactive site structure and CO IR spectral signature of horseradish peroxidase complexed with CO were studied using a combination of density functional theory and molecular modeling. The quantum chemical model used included the proximal His170, the distal amino acids His42 and Arg38, and the crystallographic water molecule that interacts with CO, His42, and Arg38. The mutant H42L was simulated by removing distal histidine from the cluster and the mutant R38L by removing the arginine. In the models where the Arg38 is present a hydrogen bond interaction is found between the He of Arg and the oxygen of adduct -CO. When both His42 and Arg38 are present they interact with the CO moiety, but they also interact with each other so their effect is not simply additive. The effect of a change in pH was modeled by removing potentially titratable hydrogen atoms identified by molecular mechanics and Poisson-Boltzmann pK a calculations on the active site. Previously observed IR spectral features of CO as a function of pH and active site mutations could be interpreted primarily in terms of changes in CO and Fe-CO bond lengths produced by changes in active site composition and charge state. The effect of the charge relay due to the possible second deprotonation (assuming that the first deprotonation took place in the His42) from the Arg38 or H Φ in the proximal His170 gives a decrease of the CO stretching frequency.

The effects of nitroprusside and S-nitrosocysteine, compounds that generate nitric oxide (NO), on synaptosomal energy-producing pathways and energy level were investigated. The decrease in respiration was much faster and more pronounced with S-nitrosocysteine than with nitroprusside. S-Nitrosocysteine, at 10 microM, inhibited by 80% respiration with glucose and succinate (plus rotenone) in intact synaptosomes and with ascorbate/cytochrome c in broken preparations. Oxygenated hemoglobin reversed and/or prevented the inhibition, whereas glutathione (GSH) prolonged it. Under aerobic conditions, the synaptosomal energy level (creatine phosphate/creatine and ATP/ADP ratios) was reduced by the presence of S-nitrosocysteine, whereas lactate generation was enhanced. The effects on energy parameters were greater at 5 min than at 15 min of incubation and were more pronounced in the presence of GSH. Under strictly anaerobic conditions, lactate production was reduced by the NO-generating compounds in a concentration-dependent manner. It is concluded that (a) inhibition of oxidative phosphorylation by NO leads to a fall in the synaptosomal energy level, which in turn stimulates glycolysis; (b) glycolysis can be inhibited by higher concentrations of the radical; and (c) inhibitory effects on the energy-generating pathway and ATP level could contribute to NO toxicity under some in vivo situations.

The spectral diffusion dynamics of free base cytochrome c (H2-Cc) in a dry trehalose film is tremendously enhanced as compared to a glycerol/water glass. We show that relaxation as well as fluctuation processes contribute to the spectral diffusion dynamics. Relaxation shows up in aging phenomena which can be measured in a separate fashion. In both solvents, the spectral diffusion as well as the aging dynamics follow power laws in time. The respective exponents are quite different, yet the influence of the solvent on them is only marginal. The large difference in the magnitude of the spectral diffusion dynamics in the two solvents can be traced back to a correspondingly large difference in the inhomogeneous width which itself seems to come from the much higher glass transition temperature in trehalose, which is close to the unfolding temperature of cytochrome c.

Porphyrin electronic transitions in heme proteins provide a useful tool for probing the protein environment, since the surrounding protein affects the porphyrin π-electron cloud. Perturbations can arise from structural distortions of the porphyrin ring, from the internal electric field generated by charged and polar groups, or from axial ligation to the heme iron. In this work, cytochrome c in aqueous solution or in glasses of trehalose or glycerol/water was examined as a function of temperature to evaluate the effect of fluctuations on the heme. The amide I band of cytochrome c in trehalose remains constant over a wide temperature excursion, indicating that interactions between the protein and the matrix do not change with temperature. The width of the Q(0,0) optical transition measured at low temperature (i.e.

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.

We present in this work low-temperature visible absorption spectra for recombinant Thermus thermophilus cytochrome c552. The Q-band presents a remarkable splitting at low temperature. We performed quantum chemical calculations to evaluate quantitatively the effect of heme conformation, axial ligand, peripheral substituents and local electric fields on the electronic spectra. In an attempt to find correlation between protein structure and spectral splitting, we carried out the same calculations on three other cytochrome c's: horse heart, tuna heart, and yeast. The quantum chemical calculations were performed at the INDO level with extensive configuration interaction. The electric field at the heme pocket was included in the calculations through a set of point charges fitting the actual electric field. The results obtained show clearly that all mentioned effects contribute to the observed spectral splitting in a complex nonadditive way.

Low-temperature UV−vis absorption and Stark-effect hole-burning spectra of Zn substituted cytochrome c are studied experimentally and theoretically using quantum mechanical and Poisson−Boltzmann el...

Resonance Raman and UV-visible absorption spectra show that nickel(II) microperoxidase-11 (NiMP-11) is four-coordinate in aqueous solution in the pH range from 1.0 to 13.0. In aqueous solutions of NiMP-11 in the absence of cetyltrimethylammonium bromide (CTAB), NiMP-11 is aggregated. In CTAB micellar solutions, where aggregation of NiMP-11 does not occur, the Raman spectra of NiMP-11 are similar to that of nickel(II) cytochrome c (NiCyt-c). The presence of the peptide segment shifts the equilibrium heavily in favor of the nonplanar form, just as does the entire protein component in the case of NiCyt-c. This further elucidates the structural mechanism by which the protein segment ruffles the heme, most likely modulating the redox potential as indicated for the cytochromes c3 [Ma, J.-G., et al. (1998) Biochemistry 37, 12431-12442]. Furthermore, the hydrophobic environment that is provided by the CTAB micelle is found to be crucial to the native folding of the pentapeptide and formation of two hydrogen bonds in the peptide backbone. These two H-bonds act to contract the peptide segment exerting the force on the macrocycle that causes the ruffling and makes the redox potential more negative than if the heme were to remain planar. The structure of the heme and pentapeptide may also be associated with redox-linked triggering of the formation and release of cytochrome-protein complexes.

Spectral diffusion waiting time experiments at 100 mK combined with aging time experiments are used to shed light on the features of the energy landscape of a cytochrome c-type protein and the respective conformational dynamics. The energy landscape shows features of a hierarchical organization. The time law which governs the dynamics in conformational phase space is a power law. The respective processes seem to be related to generalized diffusive-like motions.

Resonance Raman spectra with Q-band excitation are reported for microperoxidase-11, the cytochrome c analog. Spectra were acquired in the mid-frequency range for the oxidized, and reduced forms of the undecapeptide, as well as for the imidazole and carbonyl complexes. Oxidation and spin state marker bands of the undecapeptides are consistent with a six-coordinate, low spin iron in both oxidation states. Porphyrin core size correlations yield a porphyrin-centre to pyrrole-nitrogen distance of 2.00 A for MP11, suggestive of a six-coordinate species in a distorted heme environment. Molecular dynamics results show that the non-planarity of the heme of the parent cytochrome is conserved in the microperoxidase and its carbonmonoxy analog.

We performed hole burning Stark effect experiments on a cytochrome c type protein. From the behavior of the holes in an external electric field conclusions on local electric fields in the heme pocket can be drawn. We varied the pH value in order to study the influence of different groups on the pocket field: (a) titratable amino acid residues, (b) the porphyrin side chains (especially the propionates) and (c) the two axial ligands His18 and Met80. Surprisingly, a variation of the pH between 4.1 and 12.7 has no influence on the Stark effect. However, at a pH-level

The photoactivated metastable triplate states of the porphyrin (free-base, i.e., metal-free) zinc and tin derivatives of horse cytochrome c were investigated using electron paramagnetic resonance. Zero-field splitting parameters, line shape, and Jahn-Teller distortion in the temperature range 3.8-150 K are discussed in terms of porphyrin-protein interactions. The zero-field splitting parameters D for the free-base, Zn and Sn derivatives are 465 x 10(-4), 342 x 10(-4) and 353 x 10(-4) cm-1, respectively, and are temperature invariant over the temperature ranges studied. AN E value at 4 K of 73 x 10(-4) cm-1 was obtained for Zn cytochrome c, larger than any previously found for Zn porphyrins derivatives of hemeproteins, showing that the heme site of cytochrome c imposes an asymmetric field. Though the E value for Zn cytochrome c is large, the geometry of the site appears quite constrained, as indicated by a spectral line shape showing a single species. Intersystem crossing occurred predominantly to the T2 > zero-field spin sublevel. EPR line shape changes with respect to temperature of Zn cyt c are interpreted in terms of vibronic coupling, and a maximum Jahn-Teller crystal-field splitting of approximately 180 cm-1 is obtained. Sn cytochrome c in comparison with the Zn protein exhibits a photoactivated triplet line shape that is less well resolved in the X-Y region. The magnitude of E value is approximately 60 x 10(-4) cm-1 at 4 K; its value rapidly tends toward zero with increasing temperature, from which a value for the Jahn-Teller crystal-field splitting of > or = 40 cm-1 is estimated. In contrast to those for the metal cytochromes, the magnitude of E value for the free-base derivative was essentially zero at all temperatures studied. This finding is discussed as a consequence of an excited-state tautomerization process that occurs even at 4 K.

The interaction of spermine, spermidine and putrescine with the Ca(2+)-binding protein, parvalbumin, was studied at pH 6 and 7, with the help of the intrinsic fluorescence properties of tryptophan and circular dichroic spectroscopy of the protein in the ultraviolet region. Polyamines bind to parvalbumin that is either Ca(2+)-free or partially saturated with Ca2+, as indicated by a change in the emission maximum and intensity of tryptophan fluorescence. The binding affinities for the interactions are about 4 mM, 8 mM and > 20 mM for spermine, spermidine and putrescine, respectively. No alterations in fluorescence properties were detected when the polyamines were added to fully Ca(2+)-bound parvalbumin. An increase in the ellipticity of the circular dichroic spectrum in the region where tryptophan absorbs was observed when polyamines were added to Ca(2+)-free parvalbumin. This finding indicates that polyamine binding affects the segment of the protein where tryptophan is located. Based on these results it is postulated that polyamines bind to the Ca(2+)-free or partially saturated parvalbumin and stabilize its structure.

Optical and proton nuclear magnetic resonance (NMR) studies were carried out to assess the structure of the polypeptide chain and metal ligation in zinc-substituted horse heart cytochrome c (Zn Cyt c). The 1D- and 2D-NMR (COSY, TOCSY, and NOESY) spectra allowed the assignment of proton resonances in 67 amino acid residues. These residues arose from all structural elements of the protein, alpha-helices, beta-turns, and segments of the protein with no defined secondary structure. Small deviations of the chemical shifts of Zn Cyt c proton resonances from native Fe(II) Cyt c of less than 0.1 ppm are due to not fully matching solvent conditions. Differences in the chemical shifts between the two proteins in the range 0.10-0.20 ppm are not clustered and are observed not only in the vicinity of the Zn porphyrin but also on distant surface locations of the cytochrome. The resonance positions of the bridge protons, from the thioether bonds of the porphyrin with Cys 14 and Cys 17, were conserved in Zn Cyt c. Similarly, the Met 80 and His 18 protons had chemical shifts supporting the proposal that His 18 and Met 80, as for Fe(II) Cyt c, may provide the axial ligation in the Zn protein and that zinc may be in an unusual hexacoordinated geometry. Chemical shifts from proton resonances of alternative axial ligands of misfolded cytochrome like His 33, Lys 79, and Phe 82 were found to be the same as in the Fe(II) protein, excluding the possibility of their axial ligation to Zn. The His 18-Zn-Met 80 ligation was also consistent with data from absorption and luminescence studies. We conclude that Zn Cyt c is an adequate structural model for Fe(II) Cyt c as both share the same overall structure, including axial ligands, environment in the porphyrin vicinity, and the same binding interface with redox partners.

Fluorescence-line-narrowing (FLN) spectra are presented for Sn cytochrome c (Snc) obtained under Q0-0 and Q0-1 excitation and for Zn cytochrome c (Znc) under Q0-1 excitation. Vibrational frequencies of the ground and first excited states are reported for Snc. Additional excited-state Znc frequencies are also presented, thus contributing to a previous FLN Znc investigation. The spectra of Snc shows more phonon broadening than for Znc, but vibrational frequencies of the S0 and S1 states could be obtained and the distribution function of the 0, 0 transition was determined. Snc and Znc showed good agreement in their excited-state vibrational frequencies. Some S1 vibrational frequencies of Znc are seen to downshift with respect to ground-state vibrations, suggesting that the porphyrin S0 to S1 expansion observed in other porphyrin systems also occurs in cytochrome c derivatives. © 1995 John Wiley & Sons, Inc.

The optical absorption spectrum of mesoporphyrin-IX-substituted horseradish peroxidase shows a series of electronic origins with a typical spacing on the order of 100 cm -1 . These origins correspond with different tautomer states of mesoporphyrin-IX. A change in the pH from 8 to 5 induces severe changes in structure as well as in the intensity distribution of the tautomer origins. In addition, the pattern of photochemical tautomer transformation changes significantly. The straightforward interpretation is that a change in pH leads to a structural accommodation of the apoprotein. This structural rearrangement influences the energy hypersurface of the prosthetic group leading to the change in the origin spectrum observed

Glucokinase (GK ; EC 2.7.1.1.) phosphorylates and regulates glucose metabolism in insulin-producing pancreatic beta-cells, hepatocytes, and certain cells of the endocrine and nervous systems allowing it to play a central role in glucose homeostasis . Most importantly, it serves as glucose sensor in pancreatic beta-cells mediating glucose-stimulated insulin biosynthesis and release and it governs the capacity of the liver to convert glucose to glycogen. Activating and inactivating mutations of the glucokinase gene cause autosomal dominant hyperinsulinemic hypoglycemia and hypoinsulinemic hyperglycemia in humans, respectively, illustrating the preeminent role of glucokinase in the regulation of blood glucose and also identifying the enzyme as a potential target for developing antidiabetic drugs . Small molecules called glucokinase activators (GKAs) which bind to an allosteric activator site of the enzyme have indeed been discovered and hold great promise as new antidiabetic agents. GKAs increase the enzyme’s affinity for glucose and also its maximal catalytic rate. Consequently, they stimulate insulin biosynthesis and secretion, enhance hepatic glucose uptake, and augment glucose metabolism and related processes in other glucokinase-expressing cells. Manifestations of these effects, most prominently a lowering of blood glucose, are observed in normal laboratory animals and man but also in animal models of diabetes and patients with type 2 diabetes mellitus (T2DM ) . These compelling concepts and results sustain a strong R&D effort by many pharmaceutical companies to generate GKAs with characteristics allowing for a novel drug treatment of T2DM.

Parvalbumin, aldolase and liver alcohol dehydrogenase (ADH), proteins exhibiting long-lived phosphorescence lifetimes at room temperature, were examined for their reactivity with ferricytochrome c (cytochrome c Fe3+) as an external electron acceptor. Illumination of a reaction mixture containing protein and cytochrome c in the absence of oxygen brought about reduction of cytochrome c in relation to the duration of light. The largest portion of reduced cytochrome c was found with a sample containing ADH, where a 50% reduction of cytochrome c was reached after 5 min of illumination with a xenon lamp. Parvalbumin and aldolase were about half as effective under the same conditions. Several lines of evidence support the idea that the reaction of cytochrome c occurred by a long-range electron transfer from the excited triplet state of tryptophan. First, cytochrome c quenches the tryptophan phosphorescence and with parvalbumin, its bimolecular quenching rate constant, kq, was 2.9 x 10(6) M-1 s-1. Second, when the illuminated reaction mixture was supplied with 0.2 mM to 1 mM nitrite, a concentration range of nitrite which quenches the tryptophan phosphorescence but not the fluorescence, the amount of reduced cytochrome c on illumination markedly decreased. Finally, for all illuminated protein samples, the extent of cytochrome c reduction occurred parallel to a decrease in tryptophan content as judged from a decrease in fluorescence intensity and/or a decrease in tryptophan absorption at 280 nm.

From the pressure induced frequency shift of photochemical holes burnt into mesomorphyrin substituted horseradish peroxidase, we determined the compressibility of the protein and the vacuum frequency of the chromophore. From the compressibility, an estimation of the volume fluctuations of the biomolecule is possible.

The effect of binding the aromatic hydrogen donor naphthohydroxamic acid (NHA) to Zn mesoporphyrin substituted horseradish peroxidase was studied by conventional and laser-excited steady-state and time-resolved luminescence spectroscopy. The free enzyme is characterized by a Soret band at 418 nm and a 0-0 bond at 587 nm, determined by fluorescence line narrowing. The fluorescence and phosphorescence maxima at 77 K are at 585 and 721 nm, respectively. At 20 K the fluorescence decay of the 0-0 band using vibronic excitation could be fit by using two components, 1.15-1.18 (A{sub 1} = 0.91-0.92) and 3.3-3.6 ns, in the entire energy range of the 0-0 emissions; this leads to a mean value of 1.4 ns. The phosphorescence lifetime at 77 K was 22 ms, using a single-exponential fit, while at room temperature the lifetime decreases due to thermal enhancement of delayed fluorescence. The inhomogeneous distribution of 0-0 energies at cryogenic temperatures is narrow, with a width of 35 cm{sup {minus}1}. The spectral parameters are consistent with the view that, in the free enzyme, the Zn atom is out-of-place and 5-coordinated. Upon addition of substrate, the ligation is changed in the direction of less coordination. The spectra are incompatible with the formation ofmore » a complex between NHA and the porphyrin, which means that it is unlikely that the aromatic substrate lies parallel and face to face with the heme. The two species for the protein-substrate complex were interpreted as being deformed structures that arise through vibronic interactions of the quasi-planar Zn mesoporphyrin. Following this interpretation, the loss of resolution in the line narrowed spectra upon substrate binding could be caused by either rapid interconversion between the deformed Zn mesoporphyrin structures or interaction with a close molecule above the plane. Finally, the results are contrasted with the literature data for Zn cytochrome c.« less

We have previously shown that cytochrome c can be electrostatically bound to an ultrathin multilayer film having a negatively charged hydrophilic surface; furthermore, x-ray diffraction and absorption spectroscopy techniques indicated that the cytochrome c was bound to the surface of these ultrathin multilayer films as a molecular monolayer. The ultrathin fatty acid multilayers were formed on alkylated glass, using the Langmuir-Blodgett method. In this study, optical linear dichroism was used to determine the average orientation of the heme group within cytochrome c relative to the multilayer surface plane. The cytochrome c was either electrostatically or covalently bound to the surface of an ultrathin multilayer film. Horse heart cytochrome c was electrostatically bound to the hydrophilic surface of fatty acid multilayer films having an odd number of monolayers. Ultrathin multilayer films having an even number of monolayers would not bind cytochrome c, as expected for such hydrophobic surfaces. Yeast cytochrome c was covalently bound to the surface of a multilayer film having an even number of fatty acid monolayers plus a surface monolayer of thioethyl stearate. After washing extensively with buffer, the multilayer films with either electrostatically or covalently bound cytochrome c were analyzed for bound protein by optical absorption spectroscopy; the orientation of the cytochrome c heme was then investigated via optical linear dichroism. Polarized optical absorption spectra were measured from 450 to 600 nm at angles of 0 degrees, 30 degrees, and 45 degrees between the incident light beam and the normal to the surface plane of the multilayer. The dichroic ratio for the heme alpha-band at 550 nm as a function of incidence angle indicated that the heme of the electrostatically-bound monolayer of cytochrome c lies, on average, nearly parallel to the surface plane of the ultrathin multilayer. Similar results were obtained for the covalently-bound yeast cytochrome c. Furthermore, fluorescence recovery after photobleaching (FRAP) was used to characterize the lateral mobility of the electrostatically bound cytochrome c over the monolayer plane. The optical linear dichroism and these initial FRAP studies have indicated that cytochrome c electrostatically bound to a lipid surface maintains a well-defined orientation relative to the membrane surface while exhibiting measurable, but highly restricted, lateral motion in the plane of the surface.

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.

In this work the active site of trypsin has been probed with the dye rose bengal. The dye binds competitively to the enzyme, and it can be used as a probe of the active site of the enzyme. On the basis of the emission wavelength, the binding site of trypsin is relatively polar and is similar to that of acetone in its polarity. The triplet state of rose bengal is quenched by trypsin. This quenching may be caused by the tryptophan and tyrosine residues that are in the near vicinity of the trypsin active site. This quenching can compete with the formation of singlet oxygen from the excited triplet state of rose bengal. We demonstrate that the singlet oxygen involved in the photoinactivation of trypsin is produced by the free rose bengal in solution and the bound dye is incapable of producing singlet oxygen. This explains the lack of correlation between photoinactivation efficiency and sensitizer binding capability previously reported by Wade and Spikes.

The role of the solvent matrix in affecting CO bound to ferrous horseradish peroxidase was examined by comparing band-widths of n for the protein in aqueous solutions and in trehalose ysucrose glasses. We have previously CO observed that the optical absorption band and the CO stretching mode respond to the glass transition of glycerol y 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. 2003 Elsevier Science B.V. All rights reserved.

Free base and Pd porphyrin derivatives of horseradish peroxidase show long-lived excited states that are quenched by the presence of the peroxidase inhibitor, benzhydroxamic acid. The relaxation times of the excited-state luminescence and the rates of the quenching reaction for these derivatives of peroxidase were monitored as a function of pH, temperature, and viscosity with the view of examining how protein dynamics affect the quenching reaction. As solvent viscosity increases, the rate decreases, but at the limit of very high viscosity (i.e., high glycerol or sugar glass) the quenching still occurs. A model is presented that is consistent with the known structure of the enzyme-inhibitor complex. It is considered that the inhibitor is held at an established position but that solvent-dependent and independent motions allow a limited diffusion of the two reactants. Since there is a steep dependence upon distance and orientation, the diffusion toward the favorable position for reaction enhances the reaction rate. The solvent viscosity dependent and independent effects were separated and analyzed. The importance of internal reaction dynamics is demonstrated in the observation that rigidity of solvent imposed by incorporating the protein into glass at room temperature allows the reaction to occur, while the reaction is inhibited at low temperature. The results emphasize that protein dynamics plays a role in determining reaction rates.

We compare the spectral diffusion broadening of mesoporphyrin substituted horseradish peroxidase with the chromophore doped host glass. Whereas the broadening in the glass is smooth and follows a power law with an exponent close to (3)/(2), there is a a steplike broadening in the protein which occurs around 14 K. The observed phenomena are interpreted on the basis of a two domain interaction of the chromophore with its environment.

We have shown that heme and zinc protoporphyrin inhibit both human immunodeficiency virus type 1 (HIV-1) and type 2 (HIV-2) reverse transcriptases (RTs) and, in combination with other nucleoside and non-nucleoside inhibitors, exert an additive effect on HIV-1 RT inhibition. Screening of a phage peptide library against heme resulted in the isolation of a peptide with sequence similarity to sequence 398–407 from the connection subdomain of both HIV-1 and HIV-2 RTs, suggesting that this highly conserved region of HIV RTs corresponds to the binding site for metalloporphyrins and a new site for inhibition of enzyme activity. Inclusion of a synthetic peptide corresponding to the exact sequence 398–407 of HIV-1 RT in RT inhibition assays had a protective effect on metalloporphyrin inhibition, as it was able to reverse the inhibitory effect of both metalloporphyrins on HIV-1 RT activity. Furthermore, intrinsic fluorescence assays indicated that these metalloporphyrins bind to synthetic peptide 398–407 as well as to intact dimeric HIV-1 RT. The identification of this novel inhibition site will help to expand our understanding of the mode of action of metalloporphyrins in RT inhibition and will assist in the design and development of more potent metalloporphyrin RT inhibitors for the management of HIV infection.

The FTIR spectra of the asymmetric carboxylate absorption region of three c -type cytochromes—namely horse heart, yeast and bonito cytochromes c —as well as continuum electrostatic calculations performed on their respective protein matrices, show that these combined methods can target specific protein regions and yield pertinent protein charge information that correlates with the observed spectral data. Deconvolution of the IR carboxylate stretch frequency region (1525–1675 cm −1 ) in the three cytochromes yield different ν oco a distributions. In the case of the bonito cytochrome c carboxylates, two ν oco a populations are clearly distinguishable in the deconvoluted spectra—which is not the case for the more complex ν oco a deconvolutions of the other two cytochromes. The frequency distributions of the calculated potentials are consistent with the experimental observations and we conclude that the IR carboxylate absorption in proteins can be modified by the electrostatic environment.

The carboxylate groups of organic acids give strong absorption in the infrared between approximately 1550 and 1650 cm-1. For acetate and chloroacetate derivatives, the infrared (IR) frequency of the carboxylate antisymmetric stretching mode (v(a)OCO) is related to the square root of the pK of the acid, with a shift of approximately 20 cm-1 to higher frequency for a pK drop in the range 5-3. It follows that v(a)OCO may respond to conditions on the protein surface. In this paper, the IR amide I' and carboxylate absorptions of cytochrome c from horse, yeast, and tuna are compared with model compounds such as Val-Glu and microperoxidase-11, the 11 amino acid fragment of horse cytochrome c containing the covalently bound heme. For microperoxidase-11, the contribution from all four carboxylates can be accounted for and the 1567 cm-1 absorption is assigned to the heme propionates. For the proteins, the carboxylate absorption band is inhomogeneous, i.e., there is a distribution of frequencies. Both the amide I' and carboxylate bands are sensitive to protein conformation as shown by their different pH, salt, and redox dependence.

The alpha or Q0,0 absorption band of horse iron(II) cytochrome c splits and shifts to the blue as temperature decreases over the temperature range of 290-10 K. At room temperature, its maximum is at 18 150 cm-1 and the spectral width is 273 cm-1, whereas at 10 K, the two bands of the Q0,0 transition occur at 18 364 and 18 253 cm-1 and the width of the lowest-energy band is 96 cm-1. Temperature dependent splitting also occurs for zinc cytochrome c, a derivative in which Fe has been replaced by Zn; at 10 K, the peaks in the Q0,0 band region occur at 17 106 and 16 996 cm-1. The peak positions are independent of the cryosolvent (aqueous ethylene glycol or glycerol mixtures). The splitting of the Q0,0 band seen in the protein (approximately 110 cm-1 for iron and zinc cytochrome c) is comparable to the crystal field splitting observed for metalloporphyrins in mixed crystals. In contrast, the Q0,0 band of zinc coproporphyrin III in a glassy solvent (dimethylformamide/ethylene glycol) or in poly(vinyl chloride) shows a blue shift with temperature decrease but no evidence of Q0,0 splitting. Available spectral data show that the Q0,0 band is composed of two nearly degenerate electronic transitions and the split is due to the asymmetry in the heme pocket of the protein that arises from the surrounding polypeptide chain. This asymmetry results in the stabilization of one form of the excited state over the other, according to a Jahn-Teller mechanism.

Electronic spectra of mesoporphyrin-substituted yeast cytochrome c peroxidase (MP-CcP) were measured as a function of pH, ionic strength, and binding of cytochrome c (cyt c) by fluorescence line narrowing (FLN) spectroscopy at 5 K. The FLN spectra provided information about the vibrational structure of the first excited singlet state of MP-CcP, the various tautomeric forms of mesoporphyrin, and the positions and widths of their 0,0 bands. The composite 0,0 band of MP-CcP at pH 6 could be resolved into three components with peak positions at 16,046, 16,103, and 16,203 cm-1. MP-CcP at pH 8 could be analyzed using two components with peak positions at 16,048 and 16,193 cm-1. The disappearance of the 16,103-cm-1 component at alkaline pH suggests that it is due to a "chemical substate" arising from protonation of His52 in the distal side of the porphyrin. Computer simulations of the electrostatic field that CcP imposes on its porphyrin show that, in the presence of charged axial histidines His52 and His175, the electrostatic field at porphyrin nitrogens increases, especially along the normal to the heme by about 200 mV/A. Electric field effects may account for pH-dependent spectral shifts of the 0,0 positions of the resolved components, although hydrogen bonding may also affect these positions. On the other hand, the peak position of the components was not affected by ionic strength or binding of cyt c, implying that the electrostatic field of the heme pocket of MP-CcP remains unchanged. Indeed, computed changes in ionic strength of the solvent show no modification of the electrostatic field at the porphyrin. The only detectable effect of ionic strength and binding of cyt c to MP-CcP is on the relative contributions of the components, suggesting some rearrangements in the vicinity of the heme. Finally, shifts in the position of the vibrational lines for MP-CcP components indicate either that the tautomers have different vibrational frequencies due to the nonsymmetry of the porphyrin and/or that tautomers experience various distortions. Comparison of the vibrational spectrum of the first excited singlet state of mesoporphyrin in CcP and horseradish peroxidase also suggests that the heme pocket in the two peroxidases provides different steric restrictions.

We investigated spectral holes burnt at 1.5 K into the origins of several tautomeric forms of mesoporphyrin IX-substituted horseradish peroxidase at pH 8 under pressures up to 2 MPa. From the pressure-induced lineshift the compressibility of the apoprotein could be determined. We found that the compressibility changed significantly when measured at different tautomer origins. It was concluded that there must be a correlation between the tautomer configurations of the chromophore and the actual structures of the apoprotein. As a consequence, specific conformational substates of the protein can be selected by optical selection of the associated tautomers.

Fluorescence line narrowing (FLN) spectroscopy was used to study the role of the polypeptide chain in influencing the spectrum of Zn-substituted cytochrome c (Zn cyt c) and metal-free cyt c (porphyrin cyt c). For both derivatives the spectra show characteristics of relaxed fluorescence from an inhomogeneously broadened sample. Zero phonon lines and phonon wings can be clearly distinguished, and vibrational frequencies of the ground and excited states were identified. The inhomogeneous distribution width for porphyrin cyt c is slightly wider than that of Zn cyt c and a second population of molecules was apparent in the porphyrin cyt c. The phonon coupling was greater for Zn cyt c than for porphyrin cyt c, which may be due to the extra coupling to the polypeptide chain by metal ligation.

The purified ATPase of sarcoplasmic reticulum was covalently labeled with N-iodoacetyl-N'-(5-sulfo-1-naphthyl)ethylenediamine (1,5-IAEDANS) or with iodoacetamidofluorescein (IAF). In reconstituted vesicles containing both types of ATPase molecules fluorescence energy transfer was observed from the IAEDANS (donor) to the IAF (acceptor) fluorophore as determined by the ratio of donor and acceptor fluorescence intensities, and by nanosecond decay measurements of donor fluorescence in the presence or absence of the acceptor. The observed energy transfer may arise by random collisions between ATPase molecules due to Brownian motion or by formation of complexes containing several ATPase molecules. Experimental distinction between these two models of energy transfer is possible based on predictions derived from mathematical models. Up to tenfold dilution of the lipid phase of reconstituted vesicles with egg lecithin had no measurable effect upon the energy transfer, suggesting that random collision between ATPase molecules in the lipid phase is not the principal cause of the observed effect. Addition of unlabeled ATPase in five- to tenfold molar excess over the labeled molecules abolished energy transfer. These observations together with electron microscopic and chemical cross-linking studies support the existence of ATPase oligomers in the membrane with sufficiently long lifetimes for energy transfer to occur. A hypothetical equilibrium between monomeric and tetrameric forms of the ATPase governed by the membrane potential is proposed as the structural basis of the regulation of Ca uptake and release by sarcoplasmic reticulum membranes during muscle contraction and relaxation.

The fluorescence emission of iron-free cytochrome c (0Cyt c) in a glassy matrix was investigated under conditions of very low temperature (4.2 K.) and narrow bandwidth laser excitation. Excitation into the vibronic band, Qx(1,0) resulted in highly resolved emission spectra of linewidth 10-20 cm−1. Using the model of selective excitation developed by Abram el al. (1975) and McColgan et al. (1978), the emission spectra of vibronic excitation afforded a method to investigate excited state vibrational structure. Furthermore, emission profiles have shown that in 0Cyt c, the site distribution (inhomogeneous broadening) has a width in the order of 200cm−1.

Fluorescent derivatives of cytochrome c were prepared by replacing the heme iron with closed-shell metals such as zinc or tin. The iron-free derivatives of cytochrome c bind to yeast lactate dehydrogenase (cytochrome b2) stoichiometrically and with high affinity. Spectral overlap exists between the fluorescence of porphyrin, Zn(II) or Sn(IV) cytochrome c and the absorption of the heme of cytochrome b; therefore dipole-dipole interaction is possible as predicted by Förster's theory of energy transfer. Changes in the fluorescence yield and the fluorescent decay profile of the cytochrome c derivatives are consistent with the view that the heme distance is sufficiently close for dipolar interactions. The distance calculated from the data depends upon assumptions in the theory for energy transfer and uncertainties in the experiment. It can be argued that due to the symmetry of the metalloporphyrins the relative orientations of the two hemes do not introduce a significant uncertainty in the calculation. However the decay profiles of the iron-free cytochromes are complex, possibly reflecting structural rearrangement of the polypeptide chain during the fluorescent lifetime. The steady-state fluorescent yields would indicate that the mean distance is around 1.8 nm.

The midpoint redox potential of cytochrome c and the electron paramagnetic resonance spectra of nitroxide labeled cytochromes c were measured as a function of binding to purified cytochrome c oxidase, cytochrome c peroxidase, cytochrome b 5 and succinate—cytochrome c reductase. The midpoint redox potential of horse heart cytochrome c is lowered in the presence of cytochrome c oxidase and succinate-cytochrome c reductase, but is unchanged in the presence of cytochrome c peroxidase or cytochrome b 5 . Further evidence of binding is afforded by an increase in correlation time, T c , of the spin-labeled cytochrome c at methionine 65 upon binding to cytochrome c peroxidase, cytochrome c oxidase and succinate—cytochrome c reductase. The changes in midpoint redox potential and electron paramagnetic resonance spectrum of the spin-labeled derivative upon binding can either be the consequence of specific interaction leading to formation of ES complexes, or it can be due to nonspecific electrostatic interaction between positively charged groups on cytochrome c and negatively charged groups on the isolated cytochrome preparations.

Oxygen-dependent quenching of phosphorescence has been used to measure the dependence of mitochondrial oxidative phosphorylation on oxygen concentration in suspensions of isolated rat liver mitochondria. An instrument has been designed which simultaneously monitors the phosphorescence lifetime of a fluorophor and the reduction of cytochrome c by dual wavelength spectrophotometry. The phosphorescence lifetime method gives very rapid (less than 100 ms) measure of the oxygen concentration (Vanderkooi, J. M., Maniara, G., Green, T. J., and Wilson, D. F. (1987) J. Biol. Chem. 262, 5476-5482) from concentrations characteristic of air-saturated media to as low as 2 x 10(-8) M. The results may be summarized as follows. For well coupled rat liver mitochondria at pH 7.0 and in the presence of ATP, as the oxygen concentration was lowered, increased cytochrome c reduction was observed to begin at oxygen concentrations greater than 20 microM. For mitochondria in the presence of uncoupler, cytochrome c reduction began at oxygen concentrations less than 1.0 microM. The oxygen dependence of reduction of cytochrome c in well coupled mitochondria treated with ATP was strongly dependent on the pH of the suspending medium. Reduction of cytochrome c began at higher oxygen concentrations as the pH was made more alkaline. The oxygen concentration for half-maximal respiratory rates was much larger for well coupled mitochondria treated with ATP (approximately 0.7 microM) than for mitochondria treated with uncoupler (less than 0.1 microM). It is concluded that the oxygen dependence of mitochondrial oxidative phosphorylation is such that mitochondria could function in their proposed role of tissue oxygen sensors for regulation of such diverse functions as local blood flow and electrical activity in the carotid body.

A cytochrome c derivative from which iron is removed has been prepared and characterized. Several lines of evidence indicate that native and porphyrin cytochrome c have similar conformations: they have similar elution characteristics on Sephadex gel chromatography; in both proteins the tryptophan fluorescence is quenched and the pK values of protonation of the porphyrin are identical. Porphyrin cytochrome c does not substitute for native cytochrome c in either the oxidase reaction or in restoring electron transport in cytochrome-c-depleted mitochondria. It does however competitively inhibit native cytochrome c in these reactions, the Ki for inhibition being larger than the Km for reaction. The absorption and emission spectra, and the polarized excitation spectrum of the porphyrin cytochrome c are characteristic of free base porphyrin. The absence of fluorescence quenching of porphyrin cytochrome c when the protein is bound to cytochrome oxidase suggests that heme to heme distance between these proteins is larger than 0.5 to 0.9 nm depending upon orientation. Binding of the porphyrin cytochrome c to phospholipids or to mitochondria increases the fluorescence polarization of a positively polarized absorption band, which indicates that the bound form of the protein does not rotate freely within the time scale of relaxation from the excited state.

Fluorescence site selection spectra of Zn‐substituted cytochrome c and Zn‐mesoporphyrin were measured as a function of excitation energy and temperature within 5–60 K. The emission energies determined for Zn‐cytochrome c were comparable with those of Zn‐mesoporphyrin and mesoporphyrin in polar glassy matrices and with resonance Raman spectra of heme proteins. In the site selection spectra of both Zn‐cytochrome c and Zn‐mesoporphyrin in polar organic glass an increase in the intensity of zero phonon emission lines was observed with an increase of temperature between 5 and 30 K. The irregular spectral changes were interpreted on the basis of the temperature dependence of the linewidth as well as possible hole‐burning phenomena.