Light induced states in MbCO denatured with Guanidine hydrochloride

We present the results of a comparative study of the binding of carbon monoxide to myoglobin in glycerol/buffer solution with different concentrations of guanidine hydrochloride, under extended illumination over the temperature range 30 – 80 K. The changes in the Soret band indicate that the folding state of the protein is a key parameter in determining the photodissociation process and the relaxation rate of the protein. Received: 30 January 1997 / Accepted: 14 August 1997     

Structures of photolyzed carboxymyoglobin

The structures of photoactivated carboxymyoglobin (Mb*CO) at temperatures to 10 K have been investigated by Fourier transform infrared (FT-IR) spectroscopy, visible spectroscopy, and near-infrared spectroscopy. Two energy states for *CO are observed by FT-IR, which are altered in frequency by 94% and 88% of the difference from the ground-state heme CO toward free CO gas [Alben, J. O., Beece, D., Bowne, S. F., Doster, W., Eisenstein, L. Frauenfelder, H., Good, D., McDonald, J. D., Marden, M. C., Moh, P. P., Reinisch, L., Reynolds, A. H., Shyamsundar, E., & Yue, K. T. (1982) Proc. Natl. Acad. Sci. U.S.A. 79, 3744-3748]. Ground-state MbCO shows no absorption in the near-infrared from 700 to 1200 nm. Conversely, Mb*CO shows an absorption near 766 nm, similar to that of ferrous myoglobin (deoxy-Mb) at 758 nm. These data are compared with M?ssbauer isomer shifts and quadrupole splitting [Spartalian, K., Lang, G., & Yonetani, T. (1976) Biochim. Biophys. Acta 428, 281-290] and magnetic susceptibility measurements [Roder, H., Berendzen, J., Bowne, S. F., Frauenfelder, H., Sauke, T. B., Shyamsunder, E., & Weissman, M. B. (1984) Proc. Natl. Acad. Sci. U.S.A. 81, 2359-2363], which clearly indicate that the iron in both Mb*CO and deoxy-Mb is in the high-spin Fe(II) state, as does the heme transition in the Soret [Iizuka, T., Yamamoto, H., Kotani, M., & Yonetani, T. (1974) Biochim. Biophys. Acta 371, 126-139]. Thus the electronic structure of iron in Mb*CO is nearly identical with that of deoxy-Mb, and *CO is only slightly perturbed from the free gas.(ABSTRACT TRUNCATED AT 250 WORDS)     

Observation of nanosecond transient states in laser-induced reactions of pyridoxal 5′-phosphate

A nanosecond laser-flash photolysis system is described. The intensity of the 5-ns resolved pulses of the analyzing flash can be digitized with 0.03% precision. As a result, the electronic absorption spectra of transients in 60-μl samples of 10^?4m enzyme have been determined.     

A high-resolution NMR study of long-lived water molecules in both oxidation states of a minimal cytochrome c

The interaction of water with oxidized and reduced cytochrome c from the Gram-positive bacterium Bacillus pasteurii (a 71-amino acid long monoheme cytochrome) is investigated through CLEANEX experiments and (15)N-edited ePHOGSY and Tr-ROESY experiments. It appears that a water molecule gives rise to dipolar cross-relaxation with the amide protons of Gly74 and Ile75, with a residence time longer than 0.4 ns, to account for a negative NOE. Such water molecule is present in both the oxidized and reduced species and in the X-ray structure. It appears to have a structural role. Other possible roles are discussed by comparison with the water molecules present in other c-type cytochromes. The amide proton of Cys35 is found to exchange rapidly with the solvent in the oxidized but not in the reduced protein, at variance with H/D exchange experiments, which probe a different time scale. The present data confirm that electron-transfer proteins evolved to minimize reorganization energy upon change of the oxidation state, even though the consequent variation of charge of the metal ion may induce some changes in the structure and/or dynamics of the protein.     

Dynamics of ligand rebinding to unfolded MbCO by guanidine HCl

Femtosecond vibrational spectroscopy was used to probe a functionally important dynamics and residual structure of myoglobin unfolded by 4 M guanidine HCl. The spectra of the dissociated CO indicated that the residual structure of unfolded myoglobin (Mb) forms a few hydrophobic cavities that could accommodate the dissociated ligand. Geminate rebinding (GR) of CO to the unfolded Mb is three-orders-of-magnitude faster and more efficient than the native Mb but similar to a model heme in a viscous solvent, suggesting that the GR of CO to heme is accelerated by the longer retention of the dissociated ligand near the Fe atom by the poorly-structured protein matrix of the unfolded Mb or viscous solvent. The inefficient GR of CO in native Mb, while dissociated CO is trapped in the primary heme pocket located near the active binding site, indicates that the tertiary structure of the pocket in native Mb plays a functionally significant role.     

Structural Assignment of Spectra by Characterization of Conformational Substates in Bound MbCO

Residue motions of the distal heme pocket and bound CO ligand of carbonmonoxy Myoglobin are studied using a combination of molecular dynamics simulations and quantum chemical methods. Using mixed quantum mechanics/molecular mechanics calculations together with sampling from molecular dynamics simulations (QM/MM(MD)), the experimentally observed spectroscopic A₀ and A₁ substates of the bound CO ligand are assigned to the open and closed conformation of His⁶⁴ and the His_ɛ⁶⁴ tautomer, respectively. Several previously proposed origins of the A₃ substate, including rotamers of the doubly protonated His⁶⁴H⁺ side chain, His⁶⁴H⁺ inside the distal pocket, and cooperative motions with Arg⁴⁵, are investigated with QM/MM(MD). However, the signatures of the calculated infrared spectra do not agree with the experimentally observed ones. For additional insight on this, extensive molecular dynamics simulations are used together with improved electrostatics for the bound ligand. A CO fluctuating charge model is developed to describe the ab initio dipole and quadrupole moments of the bound ligand. CO absorption spectra are then obtained directly from the dynamics simulations. Finally, the electrostatics of the heme pocket is examined in detail in an attempt to determine the structural origins of the observed spectroscopic A-states from MD simulations. However, contrary to related simulations for unbound CO in myoglobin, the shifts and splittings for carbonmonoxy Myoglobin are generally small and difficult to relate to structural change. This suggests that coupling of the CO motion to other degrees of freedom, such as the Fe-CO stretching and bending, is important to correctly describe the dynamics of bound CO in myoglobin.     

Functional equivalence of metarhodopsin II and the Gt-activating form of photolyzed bovine rhodopsin

Absorption of a photon by the visual pigment rhodopsin leads to the formation of an activated conformational state, denoted rho*, which is capable of activating the visual G-protein, Gt. The bleaching of rhodopsin can be resolved into a series of spectrally distinct photointermediates. Previous studies suggest that the photointermediate metarhodopsin II (meta II, lambda max of 380 nm) corresponds to the physiologically active form rho*. In the studies reported herein, spectral and enzymological data were analyzed and compared so as to evaluate the temporal correspondence between meta II and rho*. This information was obtained by direct observation of the meta II and rho* decay times in parallel experiments utilizing identical preparations of urea-stripped, bovine retinal rod outer segment disk membranes at pH 8.0, 20 degrees C. Postflash spectra were deconvolved to resolve the meta II absorbance at 380 nm, and a decay time for the loss of meta II of 8.2 min (SD = 0.5 min) was obtained from fitting these data to a single-exponential decay process. The diminishing ability of bleached rhodopsin to activate Gt was measured by monitoring the level of catalyzed exchange of Gt-bound GDP for a nonhydrolyzable GTP analogue. Analysis of the decrease in the initial velocity of nucleotide exchange, measured at various postflash incubation times, yielded a rho* decay time of 7.7 min (SD = 0.5 min) when analyzed as a single-exponential process. The similarity of these decay times provides direct evidence that meta II and rho* are present over the same time regime, and further supports the equivalence of these two forms of photoactivated rhodopsin.(ABSTRACT TRUNCATED AT 250 WORDS)     

Single-crystal electron paramagnetic resonance studies of photolyzed oxy- and nitric oxide-cobalt myoglobins

Low-temperature photodissociation of oxygen from oxy-cobalt myoglobin was studied by single-crystal electron paramagnetic resonance (EPR) spectroscopy at 5 K. The photolyzed oxy-cobalt myoglobin exhibited an EPR spectrum consisting of two nonequivalent sets (species I and II) of the principal values and eigenvectors of the g tensors: g1I = 3.55, g2I = 3.47, and g3I = 2.26 for species I, and g1II = 2.04, g2II = 1.93, and g3II = 1.86 for species II, which resembled neither the deoxy nor the oxy form. Possible models of the photodissociated state of oxy-cobalt myoglobin are proposed by comparison with cobalt porphyrin complexes. The photolyzed product of nitric oxide-cobalt myoglobin exhibited new EPR signals at g = 4.3 and a very broad signal at around g = 2. The principal g values have been determined from the single-crystal EPR measurements: g1 = 4.39, g2 = 4.27, and g3 = 4.00. Analysis of another EPR signal around g = 2 was difficult due to its broadness. Magnetic interactions were observed. An isotropic EPR signal at g = 4.3 suggested a weakly spin-coupled system between cobaltous spin (S = 1/2 or 3/2) and nitric oxide spin (S = 1/2).     

Nanosecond optical rotatory dispersion spectroscopy: application to photolyzed hemoglobin-CO kinetics.

A standard technique for static optical rotatory dispersion (ORD) measurements is adapted to the measurement of ORD changes on a nanosecond (ns) time scale, giving approximately a million-fold improvement in time-resolution over conventional instrumentation. The technique described here is similar in principle to a technique recently developed for ns time-resolved circular dichroism (TRCD) spectroscopy, although the time-resolved optical rotatory dispersion (TRORD) technique requires fewer optical components. As with static ORD, TRORD measurements may be interpreted by empirical comparisons or may be transformed, via the Kramers-Kronig relations, to more easily interpreted TRCD spectra. TRORD can offer experimental advantages over TRCD in studying kinetic processes effecting changes in the chiral structures of biological molecules. In particular, the wider dispersion of ORD bands compared with the corresponding CD bands means that ORD information may often be obtained outside of absorption bands, a signal-to-noise advantage for multichannel measurements. Demonstration of the technique by its application to ns TRORD and the transform-calculated TRCD of carboxy-hemoglobin (Hb-CO) after laser photolysis is presented.     

Coumarin-caged glycine that can be photolyzed within 3 microseconds by visible light

The synthesis and characterization of a new photolabile precursor of glycine (coumarin-caged glycine) are reported. The new compound is suitable for rapid chemical kinetic investigations of the membrane-bound neurotransmitter receptor activated by glycine. Unlike previously used caging groups for glycine, this precursor can be photolyzed rapidly and efficiently in the visible wavelength region. This allows the use of a relatively inexpensive light source. The alpha-carboxyl group of glycine was covalently coupled to the 7-(diethylamino)coumarin (DECM) caging group. The caged compound has a major absorption band with a maximum at 390 nm (epsilon390 = 13,900 M-1 cm-1). Photolysis was performed at wavelengths of >or=400 nm (epsilon400 = 12,400 M-1 cm-1). Under physiological conditions, DECM-caged glycine is water soluble and stable. In the visible wavelength region, it photolyzes rapidly to release glycine with a half-life of approximately 2.5 micrometers and a quantum yield of 0.12 +/- 0.01. The experimental results demonstrated that neither DECM-caged glycine nor its byproduct inhibits or activates human alpha1 glycine receptors expressed on the surface of HEK 293 cells.     

Effect of solvent viscosity on the heme-pocket dynamics of photolyzed (carbonmonoxy)hemoglobin

The heme-pocket dynamics subsequent to carbon monoxide photolysis from human hemoglobin have been monitored as a function of glycerol-water solvent composition with time-resolved resonance Raman spectroscopy. Prompt (geminate) ligand recombination rates and the transient heme-pocket geometry established within 10 ns after photolysis appear to be largely independent of solvent composition. The rate of relaxation of the transient geometry to an equilibrium deoxy configuration is, however, quite sensitive to solvent composition. These observations suggest that the former processes result from local, internal motions of the protein, while the relaxation dynamics of the proximal heme pocket are predicated upon more global protein motions that are dependent upon solvent viscosity.     

Light-induced protein-matrix uncoupling and protein relaxation in dry samples of trehalose-coated MbCO at room temperature

In humid samples of trehalose-coated carboxy-myoglobin (MbCO), thermally driven conformational relaxation takes place after photodissociation of the carbon monoxide (CO) molecule at room temperature. In such samples, because of the extreme viscosity of the external matrix, photodissociated CO cannot diffuse out of the protein and explores the whole (proximal and distal side) heme pocket, experiencing averaged protein heme pocket structures, as a results of the presence of Brownian motions. At variance, in very dry samples, a lower portion of the photodissociated CO diffuses from the distal to the proximal heme pocket side probing in nonaveraged structures. We revisit here the flash photolysis data by Librizzi et al. (2002) and report on new, room temperature experiments in MbCO-trehalose samples, shortly illuminated prior the laser pulse. In dry samples, pre-illumination increased the diffusion of CO from the distal to the proximal heme pocket side, which resulted in less structure than in non-pre-illuminated samples. Such an effect, which is absent in humid samples, stems from a decoupling of the protein internal degrees of freedom from those of the external water-sugar matrix. We suggest that such a decoupling can be brought about by the continuous attempts performed by the protein during pre-illumination to undergo relaxation toward the photodissociated deoxy state. This, in turn, causes a collapse in the hydrogen bond network, which connects the protein surface to the water-sugar matrix, as reported by Cottone et al. (2002) and Giuffrida et al. (2003). In the conclusion section, we discuss the possible involvement of the processes invoked to rationalize the present data, in the function of macromolecules and interactions in living cells.     

A protecting group for carboxylic acids that can be photolyzed by visible light

We report on a photolabile protecting (caging) group that is new for carboxylic acids. Unlike previously used caging groups for carboxylic acids, it can be photolyzed rapidly and efficiently in the visible wavelength region. The caging group 7-N,N-diethyl aminocoumarin (DECM) was used to cage the gamma-carboxyl group of glutamic acid, which is also a neurotransmitter. The caged compound has a major absorption band with a maximum at 390 nm (epsilon(390) = 13651 M(-)(1) cm(-)(1)). Experiments are performed at 400 nm (epsilon(400) = 12232 M(-)(1) cm(-)(1)) and longer wavelengths. DECM-caged glutamate is water soluble and stable at pH 7.4 and 22 degrees C. It photolyzes rapidly in aqueous solution to release glutamic acid within 3 micros with a quantum yield of 0.11 +/- 0.008 in the visible region. In whole-cell current-recording experiments, using HEK-293 cells expressing glutamate receptors and visible light for photolysis, DECM-caged glutamate and its photolytic byproducts were found to be biologically inert. Neurotransmitter receptors that are activated by various carboxyl-group-containing compounds play a central role in signal transmission between approximately 10(12) neurons of the nervous system. Caged neurotransmitters have become an essential tool in transient kinetic investigations of the mechanism of action of neurotransmitter receptors. Previously uncaging the compounds suitable for transient kinetic investigations required ultraviolet light and expensive lasers, and, therefore, special precautions. The availability of caged neurotransmitters suitable for transient kinetic investigations that can be photolyzed by visible light allows the use of simple-to-use, readily available inexpensive light sources, thereby opening up this important field to an increasing number of investigators.     

长寿型啮齿类动物的抗肿瘤机制

啮齿类动物是广泛应用于生物医学的重要模式动物,包括先天性胸腺缺陷型的裸鼠、不患癌的裸鼹鼠(Heterocephalus glaber)和盲鼹鼠(Spalax galili)等。哺乳动物的衰老过程与癌症发生率有关,衰老的程度与患癌机率呈正相关。由于啮齿类动物约占哺乳动物的40%,因此研究长寿型啮齿类动物抗肿瘤机制对于抗癌机制的研究具有十分重要的作用。复制性衰老是啮齿类动物中普遍存在的抗肿瘤机制,但在裸鼹鼠和盲鼹鼠体内发现了独特的抗肿瘤机制：盲鼹鼠主要的抗肿瘤机制是由细胞释放IFN-β,激活p53和Rb信号通路,进而导致细胞集中性死亡;裸鼹鼠的抗肿瘤机制是由高分子量透明质酸引起的早期接触性抑制介导。此外,裸鼹鼠和盲鼹鼠的基因组中还含有高表达与调节细胞死亡和抗炎机制相关的基因。本文对裸鼹鼠和盲鼹鼠的独特抗肿瘤机制进行了综述,以期为该领域的相关研究提供参考。     

Ecology and evolution of long-lived semelparous plants

One of the more dramatic life histories in the natural world is that characterized by a single, massive, fatal reproductive episode ('semelparity'). A wealth of increasingly sophisticated theoretical models on differential life history evolution have been produced over the last two decades. In recent years, empirical studies of the ecology of semelparous plants (and their iteroparous relatives) have begun to address many aspects of the biology of these species, and to test the assumptions and predictions of theoretical models. Semelparity in long-lived plants is one of the few natural phenomena that has yielded specific quantitative tests of mathematical evolutionary theory.     

A study of vibrational relaxation of B-state carbon monoxide in the heme pocket of photolyzed carboxymyoglobin.

The vibrational energy relaxation of dissociated carbon monoxide in the heme pocket of sperm whale myoglobin has been studied using equilibrium molecular dynamics simulation and normal mode analysis methods. Molecular dynamics trajectories of solvated myoglobin were run at 300 K for both the delta- and epsilon-tautomers of the distal histidine, His64. Vibrational population relaxation times were estimated using the Landau-Teller model. For carbon monoxide (CO) in the myoglobin epsilon-tautomer, for a frequency of omega0 = 2131 cm-1 corresponding to the B1 state, T1epsilon(B1) = 640 +/- 185 ps, and for a frequency of omega0 = 2119 cm-1 corresponding to the B2 state, T1epsilon(B2) = 590 +/- 175 ps. Although the CO relaxation rates in both the epsilon- and delta-tautomers are similar in magnitude, the simulations predict that the vibrational relaxation of the CO is faster in the delta-tautomer. For CO in the myoglobin delta-tautomer, it was found that the relaxation times were identical within error for the two CO substate frequencies, T1delta(B1) = 335 +/- 115 ps and T1delta(B2) = 330 +/- 145 ps. These simulation results are in reasonable agreement with experimental results of Anfinrud and coworkers (unpublished results). Normal mode calculations were used to identify the dominant coupling between the protein and CO molecules. The calculations suggest that the residues of the myoglobin pocket, acting as a first solvation shell to the CO molecule, contribute the primary "doorway" modes in the vibrational relaxation of the oscillator.