Biomedical subjects

E Alexov

Publications and source records attributed to E Alexov.

9 recordsLinked to original sources

PubMed2005

Comparative study of the stability of poplar plastocyanin isoforms.

The stability of the two isoforms of poplar plastocyanin (PCa and PCb) was studied with differential scanning calorimetry (DSC) technique. It was shown that the thermal unfolding of both isoforms is an irreversible process with two endothermic and one exothermic peaks. The melting temperature of PCb was found to be 1.3+/-0.2 K degrees higher than of PCa, which indicates that PCb is more stable. The enthalpy of unfolding was estimated from the heat capacity curves and was found to be significantly higher for PCb at salt concentration I=0.1 M. In addition, PCb unfolding enthalpy and melting temperature are much more sensitive to the changes in the salt concentration as found in the experiments done at different ionic strength. The experiments were complemented with numerical calculations. The salt effect on the stability was modeled using the X-ray structure of PCa and a homology modeled structure of PCb. It was found, in agreement with the experimental data, that the stability of PCb changes by 4.7 kJ more than PCa, as the salt concentration increases from zero to 0.1 M. Thus, the differences in only 12 amino acid positions between "a" and "b" isoforms result in a measurable difference in the folding enthalpy and a significant difference in the salt dependence. The optimization of the electrostatic energies of PCa and PCb were studied and it was shown that PCb is better electrostatically optimized.

Plastocyanin↗

PubMed2004

Experimental and numerical study of the poplar plastocyanin isoforms using Tyr as a probe for electrostatic similarity and dissimilarity.

A detailed study of the tyrosine spectral characteristics was carried out in a broad range of pHs for both isoforms of plastocyanin from poplar. It was found that Tyr 80 is always protonated while Tyr 83 can form a tirosinate at high pHs. The pK(a) of Tyr 83 is practically identical in plastocyanin a and b, but the quenching of its spectrum is different in the isoforms. This provides insights that the acidic patches surrounding Tyr 83 have different electrostatic properties in plastocyanin a and b. The protonation states and the electrostatic interactions were numerically modeled on the existing plastocyanin a structure and on a homology model of plastocyanin b. The results of numerical calculations agree with the experimental findings and identify several differences in the titration behavior of the acidic patches. The difference of the tyrosine quenching pH profiles of the isoforms is rationalized by the differences in the calculated pK(a)'s of amino acids in the neighboring acidic clusters.

Acrylamide↗

PubMed2002

Key role of proline L209 in connecting the distant quinone pockets in the reaction center of Rhodobacter sphaeroides.

Photosynthetic bacterial reaction centers convert light excitation into chemical free energy. The initial electron transfer leads to the consecutive semireductions of the primary (Q(A)) and secondary (Q(B)) quinone acceptors. The Q(A)(-) and Q(B)(-) formations induce proton uptake from the bulk. Their magnitudes (H(+)/Q(A)(-) and H(+)/Q(B)(-), respectively) probe the electrostatic interactions within the complex. The pH dependence of H(+)/Q(A)(-) and H(+)/Q(B)(-) were studied in five single mutants modified at the L209 site (L209P-->F,Y,W,E,T). This residue is situated at the border of a continuous chain of water molecules connecting Q(B) to the bulk. In the wild type (WT), a proton uptake band is present at high pH in the H(+)/Q(A)(-) and H(+)/Q(B)(-) curves and is commonly attributed to a cluster of acidic groups situated nearby Q(B). In the H(+)/Q(A)(-) curves of the L209 variants, this band is systematically absent but remains in the H(+)/Q(B)(-) curves. Moreover, notable increase of H(+)/Q(B)(-) is observed in the L209 mutants at neutral pH as compared with the WT. The large effects observed in all L209 mutants are not associated with significant structural changes (Kuglstatter, A., Ermler, U., Michel, H., Baciou, L. & Fritzsch, G. Biochemistry (2001) 40, 4253-4260). Our data suggest that, in the L209 mutants, the Q(B) cluster does not respond to the Q(A)(-) formation as observed in the WT. We propose that, in the mutants, removal of the rigid proline L209 breaks a necessary hydrogen bonding connection between the quinone sites. These findings suggest an important role for structural rigidity in ensuring a functional interaction between quinone binding sites.

Benzoquinones↗

PubMed2001

Revealing the involvement of extended hydrogen bond networks in the cooperative function between distant sites in bacterial reaction centers.

In reaction center proteins of photosynthetic bacteria, the amplitude of proton uptake induced by the one-electron reduction of either of the two quinone electron acceptors (Q(A) and Q(B)) is an intrinsic observable of the electrostatic interactions associated with the redox function of the complex. We report here that, in Rhodobacter capsulatus, complete restoration of proton uptake (upon formation of Q(A)(-) and Q(B)(-)) to the level found in the wild type is observed in a mutant reaction center in which a tyrosine substitution in the Q(A) environment (Ala(M274) --> Tyr) is coupled with mutations of acidic residues near Q(B) (Glu(L212) --> Ala/Asp(L213) --> Ala) that initially cancel the proton uptake above pH 8. This result demonstrates that proton uptake occurs by strong cooperation between structural motifs, such as hydrogen-bonded networks, that span the 18 A distance between the two quinone acceptors.

Hydrogen Bonding↗

PubMed2000

Modeling the effects of mutations on the free energy of the first electron transfer from QA- to QB in photosynthetic reaction centers.

Numerical calculations of the free energy of the first electron transfer in genetically modified reaction centers from Rhodobacter (Rb.) sphaeroides and Rb. capsulatus were carried out from pH 5 to 11. The multiconformation continuum electrostatics (MCCE) method allows side chain, ligand, and water reorientation to be embedded in the calculations of the Boltzmann distribution of cofactor and amino acid ionization states. The mutation sites whose effects have been modeled are L212 and L213 (the L polypeptide) and two in the M polypeptide, M43(44) and M231(233) in Rb. capsulatus (Rb. sphaeroides). The results of the calculations were compared to the experimental data, and very good agreement was found especially at neutral pH. Each mutation removes or introduces ionizable residues, but the protein maintains a net charge close to that in native RCs through ionization changes in nearby residues. This reduces the effect of mutation and makes the changes in state free energy smaller than would be found in a rigid protein. The state energy of QA-QB and QAQB- states have contributions from interactions among the residues as well as with the quinone which is ionized. For example, removing L213Asp, located in the QB pocket, predominantly changes the free energy of the QA-QB state, where the Asp is ionized in native RCs rather than the QAQB- state, where it is neutral. Side chain, hydroxyl, and water rearrangements due to each of the mutations have also been calculated showing water occupancy changes during the QA- to QB electron transfer.

Alanine↗

PubMed2000

A pragmatic approach to structure based calculation of coupled proton and electron transfer in proteins.

The coupled motion of electrons and protons occurs in many proteins. Using appropriate tools for calculation, the three-dimensional protein structure can show how each protein modulates the observed electron and proton transfer reactions. Some of the assumptions and limitations involved in calculations that rely on continuum electrostatics to calculate the energy of charges in proteins are outlined. Approaches that mix molecular mechanics and continuum electrostatics are described. Three examples of the analysis of reactions in photosynthetic reaction centers are given: comparison of the electrochemistry of hemes in different sites; analysis of the role of the protein in stabilizing the early charge separated state in photosynthesis; and calculation of the proton uptake and protein motion coupled to the electron transfer from the primary (Q(A)) to secondary (Q(B)) quinone. Different mechanisms for stabilizing intra-protein charged cofactors are highlighted in each reaction.

Electrochemistry↗

PubMed1996

Electrostatic interaction between two charged spherical molecules.

An explicit analytic expression is obtained for the electrostatic energy of the interaction between two ion-impenetrable space-charged hard spheres as a model for spherical molecules in an electrolyte solution on the basis of the linearized Poisson-Boltzmann equation. An explicit expression for the potential distribution in a 3D-space is also found. The polarization effects due to the mutual influence between the spheres are taken into account. The analysis is done by assuming different dielectric permittivities of the respective spheres and of the solution as well. It is shown that the correction terms in the expression for the total energy of interaction arising from the polarization effects always correspond to forces of attraction between the spheres. The contribution of these terms to the total energy of interaction depends on the distance between the two spheres and the dielectric permittivities of the spheres and the solution as well as on the electrolyte concentration in the solution. A numerical simulation of the potential field topography is carried out at several values of the Debye-Hückel parameter. It is shown that the polarization effect can produce significant changes in the potential distribution in the case of strong interacting spheres.

Journal Article↗

PubMed1995

Selective absorption of radio frequency energy due to collective motion of charged domains: case of lysozyme crystal.

A new aspect of the internal protein motion is pointed-- the electrostatic charges of the titratable groups fixed on the protein structure are combined with the hinge binding motion of lysozyme domain. Then the lysozyme molecule is examined as a system having charges that oscillate with the parameters of the mechanical motion. So, from such point of view, the lysozyme molecule becomes infrared and radiofrequency active. This model is applied for the case of a triclinic lysozyme crystal and the direction of the external electromagnetic flux in respect to the main crystal axes is found that corresponds to the best conditions for maximal absorption. For the purpose of the experimental measurement of the space dependence of the absorption, the direction of the incident wave and its polarization are calculated in respect to the main crystal planes in case of maximal efficiency of the absorption.

Absorption↗

PubMed1994

Analysis of electrostatic interactions in ribonuclease A monoclinic crystal.

The electrostatic field in ribonuclease A monoclinic crystal is computed. A calculation of the electrostatic free energy of interaction between one molecule and its neighbours in the crystal lattice is performed in three crystal planes. It is shown that at the pH value of crystallization for the polymorphic form under investigation the total electrostatic free energy in the monoclinic crystal of ribonuclease A already crystallized is equal to zero. However, the electrostatic free energy along the crystal axis has different values. Electrostatic forces play a negative role for the crystal stability along the alpha-axis while along the other axis the electrostatic interaction supports the crystal state. The electrostatic potential distribution of a ribonuclease A monoclinic crystal at pH 6 is plotted and it is demonstrated that these interactions have a different character in each crystallographic plane.

Crystallography↗