摘要:

Raman and transient absorption spectroscopy are employed to probe structural and kinetic changes in CO binding to myoglobin at variable pressure and temperature. The shift of the iron-histidine mode with pressure observed in Raman measurements with resonance excitation for the vibrational modes associated with the active site is consistent with a conformational change, which alters the tilt angle between the heme plane and the proximal histidine and the out-of-plane iron position. Flash photolysis experiments in the time range5×10−8to102&hthinsp;secondsmonitoring the Soret absorption band show that the multistep kinetics show significant dependence on pressure. ©1999 American Institute of Physics.

ISSN:0094-243X    

DOI:10.1063/1.59875

出版商:AIP    

年代:1999

数据来源: AIP

摘要:

Embedding myoglobin in a trehalose matrix results in a sizeable inhibition of the so called protein specific motions: this fact has been evidenced by several experimental methods, like CO rebinding after flash photolysis. Mo¨ssbauer spectroscopy, optical absorption spectroscopy and more recently, by neutron scattering. Based on this fact one expects a sizeable inhibition of substrates interconversion in proteins embedded in a trehalose matrix. In this paper we present preliminary data on the effect that embedding carbonmonoxy-myoglobin in trehalose matrices of different water content has on the interconversion among A substrates. The results indicate that the interconversion is almost fully hindered in extremely dry samples wherein, as shown by neutron diffusion measurements, the motions of the protein’s hydrogens keep being harmonic even at 300K. ©1999 American Institute of Physics.

ISSN:0094-243X    

DOI:10.1063/1.59876

出版商:AIP    

年代:1999

数据来源: AIP

摘要:

To investigate the role of the covalent linkage between the heme iron and the proximal histidine on the iron-porphyrin dynamics, we have studied the temperature dependence of the Soret band in the carbonmonoxy derivative of the human hemoglobin mutant &agr;87(F8)His→Gly.In the alpha chains of this mutant the proximal histidine is substituted with a glycine, so that the covalent linkage between the heme iron and the protein is missing. Imidazole is added as an exogenous ligand to preserve the iron sixfold coordination. For the mutant we observe; i) a Soret band peak frequency shift of about 30 cm−1, suggesting different geometry for the iron-imidazole and the iron-proximal histidine linkages; ii) a smaller spectral heterogeneity, suggesting that conformational substates of the proximal side may contribute to the spectral heterogeneity observed in native hemoglobin; iii) anharmonic contributions still present and even larger than those observed for native hemoglobin. This last result indicates that the presence of the covalent linkage between iron and proximal histidine is not necessary for anharmonicity and that the non covalent interactions between the heme and the aminoacid residues of the heme pocket provide an efficient pathway for transmitting anharmonic, protein-specific, motions to the iron-porphyrin system. ©1999 American Institute of Physics.

ISSN:0094-243X    

DOI:10.1063/1.59884

出版商:AIP    

年代:1999

数据来源: AIP

摘要:

In the last few years, numerous studies have been devoted to localized modes in nonlinear lattices because they provide examples of localization in the absence of any disorder. In DNA there are indirect observations of large amplitude, highly localized, motions of the base pairs. In order to provide a direct evidence of nonlinear localization in DNA, we propose an experiment based on a recent study of the opening of DNA with piconewton forces. An analysis of the experiment shows that thermal fluctuations, which are affected by nonlinear localization, play an important role in the opening and this is why the collective breaking of patches of base pairs are detected, similarly to what is found in thermal denaturation. Using a simple model of DNA, we show that the experiment performed with an homopolymer might provide a direct observation of nonlinear energy localization in DNA and we discuss possible implications in biology. ©1999 American Institute of Physics.

ISSN:0094-243X    

DOI:10.1063/1.59885

出版商:AIP    

年代:1999

数据来源: AIP

摘要:

The molecules of a ribonucleotide reductase enzyme of class 1 contains a stable tyrosyl radical located 35 Å from the substrate binding site. In the crystallographic structure several amino acid side chains have been identified with potential to form an array of hydrogen bonds from the tyrosyl radical to the substrate binding area. The side chains may also orient so thatpand &pgr; orbital overlaps exist along the same array. The radical is supposed to make the reduction of the substrate possible by an initial one equivalent oxidation. The model presented here shows how the oxidizing equivalent can move in both directions along the side chain array with concomitant switching of the hydrogen bonds without any charge separation occurring, and how the protein dynamics is controlling the process. The conformation(s) making radical transfer possible have appreciable probability only when substrate is bound to the complete enzyme. The model explains known properties of the enzyme, in particular the stability of the radical and the enzyme reaction kinetics. ©1999 American Institute of Physics.

ISSN:0094-243X    

DOI:10.1063/1.59887

出版商:AIP    

年代:1999

数据来源: AIP

摘要:

We present a general framework for analyzing how molecular structure and dynamics control the effective tunneling coupling in electron transfer reactions. Using combined molecular dynamics and electronic structure calculations, we explore four principal issues that could not be quantitatively addressed at thePathwayslevel: sensitivity to the choice of the electronic Hamiltonian, interference among pathways, sensitivity to the electron transfer bridge conformation and modulation by the dynamical motion of the bridge. To be able to categorize the electronic orbital interactions, to identify the most relevant ones and to investigate their sensitivity to the bridge structure and dynamics, we introduce the dynamic overlap-coupling (S–H) maps. Using this framework, we identify dominant pathways mediated by these interactions and analyze the effects of the interference among them on the effective coupling. This approach provides a clear view of how the bridge structure and dynamics controls the effective coupling, allowing for a more quantitative understanding of biological ET reactions, guiding detailed calculations andde novodesign of ET proteins. ©1999 American Institute of Physics.

ISSN:0094-243X    

DOI:10.1063/1.59877

出版商:AIP    

年代:1999

数据来源: AIP

摘要:

Proton transport across lipid membranes is a fundamental aspect of biological energy transduction (metabolism). This function is believed to be mediated by a Grotthuss mechanism involving proton hopping along hydrogen-bonded networks embedded in membrane-spanning proteins. Using molecular simulations, we have explored the structural, dynamic, and thermodynamic properties giving rise to long-range proton translocation in hydrogen-bonded networks involving water molecules, or ‘water wires,’ which are emerging as ubiquitousH+-transport devices in biological systems. ©1999 American Institute of Physics.

ISSN:0094-243X    

DOI:10.1063/1.59878

出版商:AIP    

年代:1999

数据来源: AIP

摘要:

Dynamic self-organization effects in proteins under non-equilibrium conditions of photoinduced charge separation are discussed. Successive charge transfer turnover events induce cumulative structural rearrangements with long relaxation times. Perturbations by the modified macromolecular structure on the turnover rate result in an autocatalytic feedback mechanism and may lead to formation of new conformational states. Under such conditions, the efficiency of charge separation and transfer may change by several orders of magnitude, stabilizing the charge-separated state and facilitating charge flow through the molecule. Experimental results on bacterial photosynthetic reaction centers indicate that dynamic self-organization effects determine the function of these macromolecules, favoring stabilization of the charge-separated state over the non-functional recombination event. The protein-cofactor system of reaction centers may be described as a molecular machine that functions under non-equilibrium conditions of electron flow to promote a charge-separated state. ©1999 American Institute of Physics.

ISSN:0094-243X    

DOI:10.1063/1.59888

出版商:AIP    

年代:1999

数据来源: AIP

摘要:

The optical absorption hysteresis of reaction centers from purple bacteriaRb. sphaeroideswas studied at temperatures from −20&hthinsp;°C to +20&hthinsp;°C with actinic light intensity variation. For experiments over low excitation intensity ranges (<0.1 mW/cm2), we obtained optical absorption hysteresis loops, atT=+20&hthinsp;°C,that were similar to those previously reported. However, at lower temperatures, there was a gradual decrease in the hysteresis gap, and it vanished for temperatures below −10&hthinsp;°C. At room temperature but for higher excitation intensity ranges closer to saturation(Imax∼1&hthinsp;mW/cm2),the hysteresis gap became much wider—more than 50&percent; of the total bleaching amplitude. For these intensity ranges, the gapincreasesat lower temperatures. Theoretical modeling shows that the hysteresis of light-induced optical absorbance changes can be ascribed to a non-equilibrium effect of transitions between stable states of a double-well potential. This model predicts a decrease of the hysteresis gap with a decrease in temperature for low actinic light intensity ranges. For higher light-intensity ranges, an increase in the hysteresis gap with temperature decrease arises due to a narrowing of the reaction center distribution function at low temperatures. ©1999 American Institute of Physics.

ISSN:0094-243X    

DOI:10.1063/1.59879

出版商:AIP    

年代:1999

数据来源: AIP

摘要:

Great advances have been made in quantifying biochemical and physiological activities in cultured cells. It has, however, been difficult to quantify changes of cell morphology. A method has now been developed that can continuously and non-invasively track morphological changes of adherent cells and provide quantitative data from both sparse and confluent cultures. The method is based on electrical detection of cellsin vitroand can follow both motion and morphology of cells in real time. ©1999 American Institute of Physics.

ISSN:0094-243X    

DOI:10.1063/1.59880

出版商:AIP    

年代:1999

数据来源: AIP