Inhibition of bacterial IF2 binding to fMet-tRNA((fMet)) by aminoglycosides.

Screening for inhibitors of bacterial protein synthesis Initiation Factor 2 (IF2) binding to N-formyl-Methionyl-transfer RNA (fMet-tRNA((fMet))) identified a series of aminoglycosides, that included amikacin and kanamycin A1, as inhibitors of this interaction. Subsequent testing revealed that aminoglycosides displayed a wide range of inhibitory activity. However, the failure of these compounds to completely inhibit binding of IF2 to fMet-tRNA((fMet)), the known ability of aminoglycosides to bind RNA, and the ability of the aminoglycosides to displace PicoGreen bound to fMet-tRNA((fMet)) suggest these compounds act by binding fMet-tRNA((fMet)). This hypothesis is further supported by isothermal denaturation experiments that failed to show any interaction between the IF2 protein and the aminoglycosides.

The ligand affinity of proteins measured by isothermal denaturation kinetics.

An isothermal denaturation kinetic method was developed for identifying potential ligands of proteins and measuring their affinity. The method is suitable for finding ligands specific toward proteins of unknown function and for large-scale drug screening. It consists of analyzing the kinetics of isothermal denaturation of the protein-with and without the presence of potential specific ligands-as measured by long-wavelength fluorescent dyes whose quantum yield increases when bound to hydrophobic regions exposed upon unfolding of the proteins. The experimental procedure was developed using thymidylate kinase and stromelysin as target proteins. The kinetics of thermal unfolding of both of these enzymes were consistent with a pathway of two consecutive first-order rate-limiting steps. Reflecting the stabilizing effect of protein/ligand complexes, the presence of specific ligands decreased the value of the rate constants of both steps in a dose-dependent manner. The dependence of the rate constants on ligand concentration obeyed a simple binding isotherm, the analysis of which yielded an accurate equilibrium constant for ligand binding. The method was validated by comparing its results with those obtained under the same conditions by steady-state fluorescence spectroscopy, circular dichroism, and uv spectrophotometry: The corresponding rate constants were comparable for each of the analytical detection methods.

Thermodynamic and circular dichroism studies differentiate inhibitor interactions with the stromelysin S(1)-S(3) and S(')(1)-S(')(3) subsites.

Interactions of stromelysin with a series of inhibitors representative of three chemical templates with distinct binding modes were examined. Unfolding temperatures for inhibitor complexes were 10 degrees C to 15 degrees C greater than for apo stromelysin. Minor changes in ellipticity in the far-UV CD spectra of complexes indicated that ligand-induced conformational changes were localized to the binding site and did not involve gross changes in protein folding. Isothermal titrating calorimetry of thiadiazole-containing inhibitors, which bind in the S(1)-S(3) subsites of stromelysin, indicated that the binding interaction was exothermic and only slightly favorable entropically. Near-UV CD spectra showed large positive ellipticity increases from 250 to 300 nm, consistent with an interaction between the benzene ring of the inhibitor and stromelysin residues Tyr155 and Tyr168. Interactions between stromelysin and amide-hydroxamate ligands, which bind in the S(')(1)-S(')(3) subsites, were found to be both enthalpically and entropically driven. Binding of this class of ligands resulted in modest negative ellipticity changes at 260-285 nm and positive increases at 292 nm. Stromelysin complexed to a lactam-hydroxamate inhibitor with structure extending into both the S(1)-S(3) and S(')(1)-S(')(3) subsites showed increased ellipticity at 245 nm and negative changes at 260-285 and 295 nm.

Cation binding to the integrin CD11b I domain and activation model assessment.

BACKGROUND: The integrin family of cell-surface receptors mediate cell adhesion through interactions with the extracellular matrix or other cell-surface receptors. The alpha chain of some integrin heterodimers includes an inserted 'I domain' of about 200 amino acids which binds divalent metal ions and is essential for integrin function. Lee et al. proposed that the I domain of the integrin CD11b adopts a unique 'active' conformation when bound to its counter receptor. In addition, they proposed that the lack of adhesion in the presence of Ca2+ ion reflected the stabilization of an 'inactive' I-domain conformation. We set out to independently determine the structure of the CD11 b I domain and to evaluate the structural effects of divalent ion binding to this protein. RESULTS: We have determined the X-ray structure of a new crystal form of the CD11 b I domain in the absence of added metal ions by multiple isomorphous replacement (MIR). Metal ions were easily introduced into this crystal form allowing the straight-forward assessment of the structural effects of divalent cation binding at the metal ion dependent adhesion site (MIDAS). The equilibrium binding constants for these ions were determined by titration calorimetry. The overall protein conformation and metal-ion coordination of the I domain is the same as that observed for all previously reported CD11 a I-domain structures and a CD11 b I-domain complex with Mn2+. These structures define a majority conformation. CONCLUSIONS: Addition of the cations Mg2+, Mn2+ and Cd2+ to the metal-free I domain does not induce conformational changes in the crystalline environment. Moreover, we find that Ca2+ binds poorly to the I domain which serves to explain its failure to support adhesion. We show that the active conformation proposed by Lee et al, is likely to be a construct artifact and we propose that the currently available data do not support a dramatic structural transition for the I domain during counter-receptor binding.

Spectroscopic studies on the conformational transitions of a bovine growth hormone releasing factor analog.

The secondary structure of the bovine growth hormone releasing factor analog, [Ile2, Ser8.28, Ala15, Leu27, Hse30] bGRF(1-30)-NH-Ethyl, acetate salt (U-90699F) was studied in solution by Fourier transform infrared and Raman spectroscopies. Spectroscopic studies revealed that concentrated aqueous solutions of U-90699F (100 mg ml-1) undergo a secondary structure transition from disordered coil/alpha-helix to intermolecular beta-sheet. Disordered coil and alpha-helical structure were grouped together in the infrared and Raman studies since the amide I vibrations are close in frequency and overlap in assignments was possible. Before the conformational transition, the facile exchange of the peptide's amide hydrogens for deuterium indicated that the majority of amide hydrogens were readily accessible to solvent. The kinetics of the conformational transition coincided with an increase in solution viscosity and turbidity. An initiation phase preceded the conformational transition during which only minor spectral changes were observed by infrared spectroscopy. The initiation phase and reaction kinetics were consistent with a highly cooperative nucleation ultimately leading to a network of intermolecular beta-sheet structure and gel formation. Increased temperature accelerated the conformational transition. The conformational transition was thermally irreversible but the beta-sheet structure of aggregated or gelled peptide could be disrupted by dilution and agitation.

Solid phases of delavirdine mesylate.

Delavirdine mesylate was recrystallized from solution under a variety of conditions. Seven crystal forms and a stable amorphous phase were isolated from solution. Two of these crystal forms were polymorphic anhydrates: from XI (U-90152T) and form VIII (U-90152S). Two hydrates (forms VI and XIV), an ethanol solvate (form VII), an acetonitrile solvate (form XIII), and a solvate from methanol/acetone (from XII) were also identified. Six additional phases were identified as the products of solid-state transformations of the hydrated and solvated phases. The solid phases were differentiated by infrared spectroscopy and X-ray powder diffraction. Several of the solid-state phase transformations were mediated by atmospheric moisture. These transformations were studied as a function of relative humidity with dynamic moisture sorption gravimetry (DMSG). DMSG also provided useful measurements of hygroscopicity.

Preparation, characterization, and in vivo evaluation of an oil suspension of a bovine growth hormone releasing factor analog.

Pharmacia & Upjohn Inc. has discovered a superior bovine growth hormone releasing factor analog, [IIe2,Ser8,28,Ala15,Leu27,Hse30] bGRF (1-30)-NH-ethyl, acetate salt (U-90699F), for enhancement of animal growth. This report delineates the preparation, characterization, and in vivo evaluation of a U-90699F oil suspension. The oil suspension formulation was selected because of its simplicity, inexpensiveness, and ability to produce sustained U-90699F release. 40% U-90699F monomers were incorporated into Miglyol oil with acceptable injectability. Both reversed-phase-high-pressure liquid chromatography (RP-HPLC) and Fourier transform infrared spectroscopy (FTIR) were utilized to evaluate its chemical and structural stability. This suspension formulation demonstrated no significant changes in concentration as determined by RP-HPLC for 10 weeks at both 25 and 39 degrees C. The U-90699F dispersed in oil also showed no signs of structural conversion from alpha-helix to beta-sheet as monitored by FTIR. However, there was an increase in alpha-helix/disordered coil structure after initial drug incorporation. The suspension was subcutaneously administered to Holstein steers. Areas under the serum somatotropin concentration curve were used to determine the duration of action. It was found that the suspension was able to effectively elevate serum somatotropin for at least 14 days.

Infrared investigation on the conformation of proteins deposited on polyethylene films.

Aqueous protein solutions deposited and dried on thin polyethylene sheets were analyzed by Fourier transform infrared spectroscopy. This convenient sampling method produced reliable estimates of protein secondary structure on relatively small quantities of protein. The total amount of protein deposited and examined by infrared spectroscopy ranged from 200 to 80 micrograms. To estimate secondary structure, principal component regression and partial least squares (PLS) analyses were applied to the infrared spectra from 12 different deposited proteins. Principal component regression with five principal components provided the fractions of helix, beta-sheet, turn, and other or random structure present in the proteins with standard deviations of 6.3, 7.3, 7.0, and 6.3%, respectively, compared to a reference data set of X-ray structures. Similar results were achieved through PLS analysis. Factor analysis provided reliable estimates of helix and beta-sheet structure with prediction errors similar to those obtained by other infrared methods. Analysis of various types of turn structure grouped together was unsuccessful.

An infrared and circular dichroism combined approach to the analysis of protein secondary structure.

Selected regions of infarred (ir) and circular dichroism (CD) spectral data from 10 proteins were combined and analyzed by a factor analysis method. The regions consisted of the area normalized amide I region from 1700 to 1600 cm-1 for the ir spectra and from 178 to 240 nm for the CD spectra. Each CD spectrum was scaled by a factor of 0.5 before appending the data to the ir spectral data. The scaling factor was deemed necessary to account for relative intensity differences between the ir and CD data and provided nearly optimum agreement between secondary structure estimated by the combined approach to secondary structure determined by X-ray crystallography. The ir/CD combined approach to estimation of helix, beta-sheet, beta-turn, and other or undefined secondary structure agreed with X-ray crystallographic determined structure better than estimation using data from either method alone. Correlation coefficients between X-ray and ir/CD combined secondary structure determinations were 0.99 for helix, 0.90 for beta-sheet, 0.70 for beta-turn, and 0.78 for other structure. The four most significant eigenvectors or basis spectra from eigenanalysis of the ir/CD data are presented as well as generalized inverse spectra for four secondary structures.

Protein secondary structure from Fourier transform infrared spectroscopy: a data base analysis.

An infrared (ir) method to determine the secondary structure of proteins in solution using the amide I region of the spectrum has been devised. The method is based on the circular dichroism (CD) matrix method for secondary structure analysis given by Compton and Johnson (L. A. Compton and W. C. Johnson, 1986, Anal. Biochem. 155, 155-167). The infrared data matrix was constructed from the normalized Fourier transform infrared spectra from 1700 to 1600 cm-1 of 17 commercially available proteins. The secondary structure matrix was constructed from the X-ray data of the seventeen proteins with secondary structure elements of helix, beta-sheet, beta-turn, and other (random). The CD and ir methods were compared by analyzing the proteins of the CD and ir databases as unknowns. Both methods produce similar results compared to structures obtained by X-ray crystallographic means with the CD slightly better for helix conformation, and the ir slightly better for beta-sheet. The relatively good ir analysis for concanavalin A and alpha-chymotrypsin indicate that the ir method is less affected by the presence of aromatic groups. The concentration of the protein and the cell path length need not be known for the ir analysis since the spectra can be normalized to the total ir intensity in the amide I region. The ir spectra for helix, beta-sheet, beta-turn, and other, as extracted from the data-base, agree with the literature band assignments. The ir data matrix and the inverse matrix necessary to analyze unknown proteins are presented.