Biomedical subjects

Bernard Alpert

Publications and source records attributed to Bernard Alpert.

4 recordsLinked to original sources

PubMed2005

Mechanism of binding of serum response factor to serum response element.

Serum response factor (SRF) is a MADS transcription factor that binds to the CArG box sequence of the serum response element (SRE). Through its binding to CArG sequences, SRF activates several muscle-specific genes as well as genes that respond to mitogens. The thermodynamic parameters of the interaction of core-SRF (the 124-245 fragment of serum response factor) with specific oligonucleotides from c-fos and desmin promoters, were determined by spectroscopy. The rotational correlation time of core-SRF labeled with bis-ANS showed that the protein is monomeric at low concentration (10(-7) m). The titration curves for the fluorescence anisotropy of fluorescein-labeled oligonucleotide revealed that under equilibrium conditions, the core-SRF monomers were bound sequentially to SRE at very low concentration (10(-9) m). Curve-fitting data showed also major differences between the wild-type sequence and the oligonucleotide sequences mutated within the CArG box. The fluorescence of the core-SRF tyrosines was quenched by the SRE oligonucleotide. This quenching indicated that under stoichiometric conditions, core-SRF was bound as a dimer to the wild-type oligonucleotide, and as a monomer or a tetramer to the mutant oligonucleotides. Far-UV CD spectra indicated that the flexibility of core-SRF changed profoundly upon its binding to its specific target SRE. Lastly, the rotational correlation time of fluorescein-labeled SRE revealed that formation of the specific complex was accompanied by a change in the SRE internal dynamics. These results indicated that the flexibility of the two partners is crucial for the DNA-protein interaction.

Amino Acid Sequence↗

PubMed2003

Protein matrix elasticity determined by fluorescence anisotropy of its tryptophan residues.

Rotational motions of Trp residues embedded within human hemoglobin matrix have been measured by using their steady-state fluorescence anisotropy. The mean square angular displacement theta2 of Trp residues, depending on the temperature, can be expressed by W = 1/2Ctheta2 where W is the thermal energy acting on the Trp residues and C the resilient torque constant of the protein matrix. To study the external medium influencing the protein dynamics, comparative experiments were made with protein in aqueous buffer and in the presence of 32% glycerol. The data show that between 5 degrees C and 25 degrees C, external medium acts on the protein matrix elasticity.

Elasticity↗

PubMed2002

Effect of solvent diffusion on the apomyoglobin-water interface.

Few techniques can identify interactions between proteins and individual water molecules when the protein is in solution. The present work has sought to bridge the gap between the molecular level studies and the search for a physical property of the solution (bathing the proteins) that would regulate the protein hydration level. The properties of the solution were varied by adding nondenaturing solutes and solvents to the protein solutions and then studying their effect on the intrinsic fluorescence of apomyoglobin. The resolution of the tryptophan emission into the two component spectra corresponding to tryptophans W7 (accessible to the solvent) and W14 (buried in the protein matrix) has allowed us to probe two specific parts of the protein. Whereas W14 is not affected when the medium is altered, the analysis of W7 fluorescence has shown that cosolvent diffusion plays a dominant role in the mobility of water molecules near the protein surface.

Ampholyte Mixtures↗

PubMed2002

Kinetics of precursor cleavage at the dibasic sites. Involvement of peptide dynamics.

The presence in the P'1 position relative to the LysArg doublet of either Phe, Tyr or Trp residues affects only pro-OT/Np(7-15) flexibility. This has a measurable effect on the dynamics of the peptide. Since the same modifications have a major influence on the K(m) and V(max) values of the peptide cleavage, these kinetic parameters should depend on the peptide substrate motions. Therefore, the primary kinetic contribution of substrate cleavage should arise from substrate dynamics rather than from the enzyme.

Amino Acid Sequence↗