pH-dependent secondary conformation of bovine lens alpha-crystallin: ATR infrared spectroscopic study with second-derivative analysis

The mechanism for thermal-enhanced chaperone-like activity of α-crystallin against UV irradiation-induced aggregation of γD-crystallin

Exposure to solar UV irradiation damages γ-crystallin, leading to cataract formation via aggregation. α-Crystallin, as a small heat-shock protein (sHsps), efficiently suppresses this irreversible aggregation by selectively binding the denatured γ-crystallin monomer. In this study, liquid chromatography tandem mass spectrometry (LC-MS) was used to evaluate UV-325 nm irradiation-induced photodamage of human γD-crystallin in the presence of bovine α-crystallin, atomic force microscope (AFM) and dynamic light scattering (DLS) techniques were used to detect the quaternary structure changes of α-crystallin oligomer, and Fourier transform infrared (FTIR) spectroscopy and temperature-jump (T-jump) nanosecond time-resolved IR absorbance difference spectroscopy were used to probe the secondary structure changes of bovine α-crystallin. We find that the thermal-induced subunit dissociation of α-crystallin oligomer involves the breaking of hydrogen bonds at the dimeric interface, leading to three different spectral components at varied temperature regions as resolved from temperature-dependent IR spectra. Under UV-325 nm irradiation, unfolded γD-crystallin binds to the dissociated α-crystallin subunit to form αγ-complex, then follows the reassociation of αγ-complex to the partially dissociated α-crystallin oligomer. This prevents the aggregation of denatured γD-crystallin. The formation of the γD-bound α-crystallin oligomer is further confirmed by AFM and DLS analysis, which reveals an obvious size expansion in the reassociated αγ-oligomers. In addition, UV-325 nm irradiation causes a peptide bond cleavage of γD-crystallin at Ala158 in presence of α-crystallin. Our results suggest a very effective protection mechanism for subunits dissociated from α-crystallin oligomers against UV irradiation-induced aggregation of γD-crystallin, at an expense of a loss of a short C-terminal peptide in γD-crystallin.

Analysis of conformational variation in macromolecular structural models

Experimental conditions or the presence of interacting components can lead to variations in the structural models of macromolecules. However, the role of these factors in conformational selection is often omitted by in silico methods to extract dynamic information from protein structural models. Structures of small peptides, considered building blocks for larger macromolecular structural models, can substantially differ in the context of a larger protein. This limitation is more evident in the case of modeling large multi-subunit macromolecular complexes using structures of the individual protein components. Here we report an analysis of variations in structural models of proteins with high sequence similarity. These models were analyzed for sequence features of the protein, the role of scaffolding segments including interacting proteins or affinity tags and the chemical components in the experimental conditions. Conformational features in these structural models could be rationalized by conformational selection events, perhaps induced by experimental conditions. This analysis was performed on a non-redundant dataset of protein structures from different SCOP classes. The sequence-conformation correlations that we note here suggest additional features that could be incorporated by in silico methods to extract dynamic information from protein structural models.

ATR-IR spectroscopy as applied to nucleic acid films

For the first time the ATR technique was applied to obtain IR absorption spectra of DNA and RNA dry films. There was worked out procedure of the nucleic acid removal from germanium plate, which obviously was a main obstacle to application of ATR-IR spectroscopy to nucleic acids. This technique of IR spectroscopy was applied to confirmation of RNA tropism of aurin tricarboxylic acid observed by molecular biological methods.

PH-dependent coordination of metal-lisinopril complex investigated by attenuated total reflection/Fourier transform infrared spectroscopy

In order to simulate the in vivo binding behavior of angiotensin-converting enzyme (ACE) inhibitors to the zinc-containing active center of ACE, the in vitro interaction between lisinopril and zinc or nickel ions was investigated in aqueous solutions of different pH by using attenuated total reflection (ATR)/Fourier transform infrared (FT-IR) spectroscopy with second-derivative IR spectral analysis. The results indicated that the lisinopril dissociation process occurred in a stepwise fashion during increase in pH. The IR peaks at 1642 cm(-1) (carbonyl stretching of tertiary amide) and at 1582 cm(-1) (asymmetric COO- stretching) for lisinopril in solution at pH 3.5 shifted to 1606 and 1586 cm(-1) after addition of Ni2+ ions, respectively, but there was no marked changes in IR spectra of lisinopril after addition of Zn2+ ions. When the Zn2+ ions were added to lisinopril solution at pH 5.0, the peak at 1642 cm(-1) also shifted to 1604 cm(-1) and the peak at 1582 cm(-1) shifted to 1586 cm(-1), similar to the changes at pH 3.5 after adding Ni2+ ions. However, the peaks at 1582 and 1642 cm(-1) both shifted to 1599 cm(-1) after addition of Ni2+ ions at pH 5.0 or at pH 7.3. The peak at 1576 cm(-1) also shifted to 1599 cm(-1) after addition of Zn2+ ions to lisinopril solution at pH 7.3. Different coordination sites or types (chelating, bridging or pseudounidentate complex) between lisinopril and Zn2+ or Ni2+ ions were proposed, based on the separation value between v(as) (COO-) and v(s) (COO-), and the shifting of carbonyl groups. Coordination of the secondary amine in lisinopril to metal ions was also evidenced.