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A purified thermostable gellan lyase, produced by a thermophilic bacterium, Geobacillus stearothermophilus 98, was characterized in relation to its physicochemical properties. The gellan lyase was established to have a molecular weight of 216 kDa, defined by capillary gel electrophoresis. Amino acid analysis revealed high quantities of Lys, His, Ala, Val, Ile, Glx, and Pro residues. The circular dichroism revealed 45% β-structure and practically lack of α-spiral domains. Kinetic studies showed high affinity of the enzyme to gellan as a substrate (Km = 0.21 μM). The thermal denaturation investigated by cicular dichroism showed a highly cooperative transition with a midpoint (Tm) at about 75 °C. A single product was identified after enzyme action on gellan. Large exothermic aggregation near Tm was observed by differential scanning calorimetry. Two types of gellan lyase crystals were reproducibly isolated.

An improved four-stage isolation and purification procedure for preparing poplar isoplastocyanins is described in detail. Absorbance (UV-VIS) spectroscopy and isoelectric focusing (IEF) are used to determine the protein purity and identity. The present procedure increases twice the total plastocyanin (PC) yield. Four PC isoform fractions are consecutively isolated at the third chromatographic step: oxidized PCa(II) and PCb(II) and reduced PCb(I) and PCa(I). PCa(II) and PCb(II) obtained at the fourth chromatographic step are highly purified PC isoforms which show the purity index (p.i.) A278/A597 ≤ 0.85. Isoelectric points (pI values) of the PC isoforms are found to be at pH 3.92 ± 0.04 for PCa and at pH 3.85 ± 0.02 for PCb. The results of appropriate biological experiments that include the highly purified poplar PC isoforms could give answers to the questions about the physiological significance of PC dimorphism for photosynthesis.

The redox potentials of poplar plastocyanins a and b (PCa, PCb) were determined by spectro photometric titrations of their reduced forms with [Fe(CN)6]3-. It was found that the two isoforms have the following millimolar extinction coefficients ε597, equilibrium constants Keq of one-electron exchange with [Fe(CN)6]4-/[Fe(CN)6]3-, and standard electron potentials E0′: PCa: ε597 = (4.72 ± 0.08) mM-1 cm-1, Keq = 0.133 ± 0.009, E0′ = (354 ± 11) mV; PCb: ε597 = (5.23 ± 0.16) mM-1 cm-1, Keq = 0.175 ± 0.010, E0′ = (363 ± 12) mV. The pH dependence of the redox potential of PCb was studied too. It was found, that the value of E0′ for PCb is constant in the pH range 6.5 - 9.5, but decreases in the range 4.8 - 6.5. On the whole, the dependence resembles that of PC from some well-known plant species, including poplar PCa. The changes of E0′ in the pH-dependent region for poplar PCb, however, are smaller and are 13 mV per pH unit, whereas in the other well-known plant species the changes are about 50 - 60 mV per pH unit. It has been assumed that the weaker pH dependence of E0′ of PCb accounts for some structural differences between PCa and PCb

In this study, we address the issue of performing meaningful pKa calculations using homology modeled three-dimensional (3D) structures and analyze the possibility of using the calculated pKa values to detect structural defects in the models. For this purpose, the 3D structure of each member of five large protein families of a bacterial nucleoside monophosphate kinases (NMPK) have been modeled by means of homology-based approach. Further, we performed pKa calculations for the each model and for the template X-ray structures. Each bacterial NMPK family used in the study comprised on average 100 members providing a pool of sequences and 3D models large enough for reliable statistical analysis. It was shown that pKa values of titratable groups, which are highly conserved within a family, tend to be conserved among the models too. We demonstrated that homology modeled structures with sequence identity larger than 35% and gap percentile smaller than 10% can be used for meaningful pKa calculations. In addition, it was found that some highly conserved titratable groups either exhibit large pKa fluctuations among the models or have pKa values shifted by several pH units with respect to the pKa calculated for the X-ray structure. We demonstrated that such case usually indicates structural errors associated with the model. Thus, we argue that pKa calculations can be used for assessing the quality of the 3D models by monitoring fluctuations of the pKa values for highly conserved titratable residues within large sets of homologous proteins.

We performed an investigation of the pH-dependent quenching of the fluorescence of tryptophan residues of TEM-1 β-lactamase from E. coli by uncharged and charged quenchers. pH-dependent Stern-Volmer constants (KSV/pH) of tryptophan residues allowed us to determine subtle but discrete structurally and functionally important processes.

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 p K 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 p K a 's of amino acids in the neighboring acidic clusters.

Centrins are highly conserved calcium-binding proteins involved in the nucleotide-excision repair pathway as a subunit of the heterotrimer including the XPC and hHR23B proteins. A complex formed by a Ca2+-bound human centrin 2 construct (the wild type lacking the first 25 amino acids) with a 17-mer peptide derived from the XPC sequence (residues Asn847-Arg863) was crystallized. Data were collected to 1.65 angstroms resolution from crystals grown in 30% monomethyl polyethylene glycol (MPEG) 500, 100 mM NaCl and 100 mM Bicine pH 9.0. Crystals are monoclinic and belong to space group C2, with two molecules in the asymmetric unit. The unit-cell parameters are a = 60.28, b = 59.42, c = 105.14 angstroms, alpha = gamma = 90, beta = 94.67 degrees. A heavy-atom derivative was obtained by co-crystallization with Sr2+. The substitution was rationalized by calorimetry experiments, which indicate a binding constant for Sr2+ of 4.0 x 10(4) M(-1).

Plastocyanin (PC) from poplar leaves is present in two isoforms, PCa and PCb, which differ in sequence by amino acid replacements at locations remote from the copper center and simultaneously act in the photosynthetic electron-transport chain. We describe ultra-high resolution structures of PCa and high-resolution structures of PCb, both under oxidizing and reducing conditions at pH 4, 6 and 8. The docking on cytochrome f and photosystem I, respectively, has been modeled for both isoforms. PCa and PCb exhibit closely similar overall and active-site structures, except for a difference in the relative orientation of the acidic patches. The isoforms exhibit substantial differences in the dependence of the reduced (CuI) geometry on pH. In PCa, the decrease in pH causes a gradual dissociation of His87 from CuI at low pH, probably adopting a neutral tautomeric state. In PCb, the histidine remains covalently bound to CuI and may adopt a doubly protonated state at low pH. The fact that both isoforms have similar although not identical functions in photosynthetic electron flows suggests that the His87 imidazole does not play a crucial role for the pathway of electron transport from cytochrome f to oxidized PC.

International audience; Human centrin 2 (HsCen2), an EF-hand calcium binding protein, plays a regulatory role in the DNA damage recognition during the first steps of the nucleotide excision repair. This biological action is mediated by the binding to a short fragment (N847-R863) from the C-terminal region of xeroderma pigmentosum group C (XPC) protein. This work presents a detailed structural and energetic characterization of the HsCen2/XPC interaction. Using a truncated form of HsCen2 we obtained a high resolution (1.8 A) X-ray structure of the complex with the peptide N847-R863 from XPC. Structural and thermodynamic analysis of the interface revealed the existence of both electrostatic and apolar inter-molecular interactions, but the binding energy is mainly determined by the burial of apolar bulky side-chains into the hydrophobic pocket of the HsCen2 C-terminal domain. Binding studies with various peptide variants showed that XPC residues W848 and L851 constitute the critical anchoring side-chains. This enabled us to define a minimal centrin binding peptide variant of five residues, which accounts for about 75% of the total free energy of interaction between the two proteins. Immunofluorescence imaging in HeLa cells demonstrated that HsCen2 binding to the integral XPC protein may be observed in living cells, and is determined by the same interface residues identified in the X-ray structure of the complex. Overexpression of XPC perturbs the cellular distribution of HsCen2, by inducing a translocation of centrin molecules from the cytoplasm to the nucleus. The present data confirm that the in vitro structural features of the centrin/XPC peptide complex are highly relevant to the cellular context.

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.

An experimental-theoretical approach for the elucidation of protein stability is proposed. The theoretical prediction of pH-dependent protein stability is based on the macroscopic electrostatic model for calculation of the pH-dependent electrostatic free energy of proteins. As a test of the method we have considered the pH-dependent stability of sperm whale metmyoglobin. Two theoretical methods for evaluation of the electrostatic free energy and p K values are applied: the finite-difference Poisson-Boltzmann method and the semiempirical approach based on the modified Tanford-Kirkwood theory. The theoretical results for electrostatic free energy of unfolding are compared with the experimental data for guanidine hydrochloride unfolding under equilibrium conditions over a wide pH range. Using the optical parameters of the Soret absorbance to monitor conformational equilibrium and Tanford's method to estimate the resulting data, it was found that the conformational free energy of unfolding of metmyoglobin is 16.3 kcal mol(-1) at neutral pH values. The total unfolding free energies were calculated on the basis of the theoretically predicted electrostatic unfolding free energies and the experimentally measured midpoints (pH(1/2)) of acidic and alkaline denaturation transitions. Experimental data for alkaline denaturation were used for the first time in theoretical analysis of the pH-dependent unfolding of myoglobin. The present results demonstrate that the simultaneous application of appropriate theoretical and experimental methods permits a more complete analysis of the pH-dependent and pH-independent properties and stability of globular proteins.

A simple theoretical model is proposed for evaluation of the optical titration behaviour of tyrosyl and carboxyl residues in proteins. The pK values involved in the model are computed using the semi-empirical method. The titration curves are calculated using the values of the molar absorption differences for tyrosyl residues in the ultraviolet (UV) region at 245 and 295 nm, and for carboxyl residues in the infrared (IR) region at 1565 and 1707 cm(-1), respectively. The theoretical tyrosyl titration curves are compared with the experimental data for lysozyme, myoglobin and chymotrypsinogen (available in the literature). This approach provides a good tool for distinguishing between the ionisation and the conformational changes in the alkaline range. The quantitative evaluation of the change of molar extinction coefficients as a function of pH in the case of carboxyl titration for lysozyme, trypsin and cytochrome c shows a good agreement with the experimental titration data.

The conformational stability of gamma-II crystallin at pH 7.0 was estimated by studying its urea denaturation at isothermal conditions. The conformational states were monitored by far UV-CD and fluorescence measurements. Gamma-II crystallin shows sigmoidal order-disorder transition curves by both methods. The presence of more than one intermediate was confirmed but at neutral pH. The experiment results were critically analyzed in terms of both linear extrapolation and Tanford's models. The Gibbs free energy of unfolding delta G u,H2O = -36 kcal mol-1 was obtained. This value corresponds to the high conformational stability of the protein predicted qualitatively by its crystal structure.

The electron transfer between the excited triplet state of zinc-substituted sperm whale myoglobin and Cu 2+ has been studied by following the decay rate of delayed fluorescence. The Cu 2+ bound on the surface of the myoglobin molecule are efficient quenchers of the excited electron state of Zn-myoglobin. Two bimolecular rate constants of quenching ( K Q ) for every pH investigated have been calculated. The pH-dependence of K Q1 indicates that the protonation of one amino acid residue (His-GH1 (119)) is important for the process. Our results support the idea of the common nature of the mechanism of quenching by Cu 2+ and oxidation of oxymyoglobin by Cu 2+ .