Biomedical subjects

P X Qi

Publications and source records attributed to P X Qi.

6 recordsLinked to original sources

PubMed2002

Secondary structural studies of bovine caseins: structure and temperature dependence of beta-casein phosphopeptide (1-25) as analyzed by circular dichroism, FTIR spectroscopy, and analytical ultracentrifugation.

The defining structural feature of all of the caseins is their common phosphorylation sequence. In milk, these phosphoserine residues combine with inorganic calcium and phosphate to form colloidal complexes. In addition, nutritional benefits have been ascribed to the phosphopeptides from casein. To obtain a molecular basis for the functional, chemical, and biochemical properties of these casein peptides, the secondary structure of the phosphopeptide of bovine beta-casein (1-25) was reexamined using Fourier transform infrared (FTIR) and circular dichroism (CD) spectroscopies. Both methods predict secondary structures for the peptide which include polyproline II elements as well as beta-extended sheet and turn-like elements. These structural elements were highly stable from 5 degrees to 70 degrees C. Reexamination of previously published 1H NMR data using chemical shift indices suggests structures in accord with the CD and FTIR data. Dephosphorylation showed little or no secondary structural changes, as monitored by CD and FTIR, but the modified peptide demonstrated pronounced self-association. The polymers formed were not highly temperature sensitive, but were pressure sensitive as judged by analytical ultracentrifugation at selected rotor speeds. Molecular dynamics (MD) simulations demonstrated relatively large volume changes for the dephosphorylated peptide, in accord with the pressure dependent aggregation observed in the analytical ultracentrifuge data. In contrast the native peptide in MD remained relatively rigid. The physical properties of the peptide suggest how phosphorylation can alter its biochemical and physiological properties.

Amino Acid Sequence↗

PubMed2002

Molten globule structures in milk proteins: implications for potential new structure-function relationships.

Recent advances in the field of protein chemistry have significantly enhanced our understanding of the possible intermediates that may occur during protein folding and unfolding. In particular, studies on alpha-lactalbumin have led to the theory that the molten globule state may be a possible intermediate in the folding of many proteins. The molten globule state is characterized by a somewhat compact structure, a higher degree of hydration and side chain flexibility, a significant amount of native secondary structure but little tertiary folds, and the ability to react with chaperones. Purified alpha(s1)- and kappa-caseins share many of these same properties; these caseins may thus occur naturally in a molten globule-like state with defined, persistent structures. The caseins appear to have defined secondary structures and to proceed to quaternary structures without tertiary folds. This process may be explained, in part, by comparison with the architectural concepts of tensegrity. By taking advantage of this "new view" of protein folding, and applying these concepts to dairy proteins, it may be possible to generate new and useful forms of proteins for the food ingredient market.

Animals↗

PubMed1998

The burst phase in ribonuclease A folding and solvent dependence of the unfolded state.

Submillisecond burst phase signals measured in kinetic protein folding experiments have been widely interpreted in terms of the fast formation of productive folding intermediates. Experimental comparisons with non-folding polypeptide chains show that, for ribonuclease A and cytochrome c, these signals in fact reflect a shift from one biased ensemble of the unfolded state to another as a function of change in denaturant concentration.

Animals↗

PubMed1996

Solution structure of horse heart ferricytochrome c and detection of redox-related structural changes by high-resolution 1H NMR.

A model for the solution structure of horse heart ferricytochrome c has been determined by nuclear magnetic resonance spectroscopy combined with hybrid distance geometry-simulated annealing calculations. Forty-four highly refined structures were obtained using a total of 1671 distance constraints based on the observed magnitude of nuclear Overhauser effects and 58 torsion angle restrains based on the magnitude of determined J-coupling constants. The model incorporates six long-lived water molecules detected by pseudo-two-dimensional NOESY-TOCSY spectra. The all-residue root mean square deviation about the average structure is 0.33 +/- 0.04 A for the backbone N, C alpha, and C' atoms and 0.83 +/- 0.05 A for all heavy atoms. The overall topology of the model for solution structure is very similar to that seen in previously reported models for crystal structures of homologous c-type cytochromes though there are a number of significant differences in detailed aspects of the structure. Two of the three main helices display localized irregularities in helical hydrogen bonding resulting in bifurcation of main chain hydrogen bond acceptor carbonyls. The N- and C-terminal helices are tightly packed and display several interhelical interactions not seen in reported crystal models. To provide an independent measure of the accuracy of the model for the oxidized protein, the expected pseudocontact shifts induced by the spin 1/2 iron were compared to the observed redox-dependent chemical shift changes. These comparisons confirm the general accuracy of the model for the oxidized protein and its observed differences with the structure of the reduced protein. The structures of the reduced and oxidized states of the protein provide a template to explain a range of physical and biological data spanning the redox properties, folding, molecular recognition, and stability of the cytochrome c molecule. For example, a redox-dependent reorganization of surface residues at the heme edge can be directly related to the redox behavior of the protein and thereby provides a previously undocumented linkage between structural change potentially associated with molecular recognition of redox partners and the fundamental parameters governing electron transfer.

Animals↗

PubMed1994

Solution structure of horse heart ferrocytochrome c determined by high-resolution NMR and restrained simulated annealing.

A model for the solution structure of horse heart ferrocytochrome c has been determined by nuclear magnetic resonance spectroscopy combined with hybrid distance geometry-simulated annealing calculations. Forty-four highly refined structures were obtained using a total of 1940 distance constraints based on the observed magnitude of nuclear Overhauser effects and 85 torsional angle restraints based on the magnitude of determined J-coupling constants. The all-residue root mean square deviation about the average structure is 0.47 +/- 0.09 A for the backbone N, C alpha, and C' atoms and 0.91 +/- 0.07 A for all heavy atoms. The overall topology of the model for solution structure is very similar to that seen in previously reported models for crystal structures of homologous c-type cytochromes. However, a detailed comparison between the model for the solution structure and the available model for the crystal structure of tuna ferrocytochrome c indicates significant differences in a number of secondary and tertiary structural features. For example, two of the three main helices display 3(10) to alpha-helical transitions resulting in bifurcation of main-chain hydrogen bond acceptor carbonyls. The N- and C-terminal helices are tightly packed and display several interhelical interactions not seen in previously reported models. The geometry of heme ligation is well-defined and completely consistent with the crystal structures of homologous cytochromes c as are the locations of four of six structural water molecules. Though the total solvent-accessible surface area of the protoporphyrin ring is similar to that seen in crystal studies of tuna ferrocytochrome c, the distribution is somewhat different. This is mainly due to a difference in packing of residues Phe-82 and Ile-81 such that Ile-81 crosses the edge of the heme in the solution structure. These and other observations help to explain a range of physical and biological data spanning the redox properties, folding, molecular recognition, and stability of the protein.

Animals↗

PubMed1994

Structural water in oxidized and reduced horse heart cytochrome c.

The existence of structural water in the interior of both oxidized and reduced horse-heart cytochrome c in solution is demonstrated using nuclear magnetic resonance spectroscopy. Six water molecules have been located in ferrocytochrome c and five in ferricytochrome c, with residence times greater than a few hundred picoseconds. Two water molecules are located in the haem crevice, one of which is found to undergo a large change in position with a change of oxidation state. Both of these observations indicate that buried structural waters in the haem crevice have, by microscopic dielectric effects, significant roles in the setting of the solvent reorganization energy associated with electron transfer.

Animals↗