Biomedical subjects

C C Lester

Publications and source records attributed to C C Lester.

10 recordsLinked to original sources

PubMed1999

New general approach for determining the solution structure of a ligand bound weakly to a receptor: structure of a fibrinogen Aalpha-like peptide bound to thrombin (S195A) obtained using NOE distance constraints and an ECEPP/3 flexible docking program.

A new approach incorporating flexible docking simulations and NMR data is presented for calculating the bound conformation of a ligand that interacts weakly with an enzyme. This approach consists of sampling directly the conformation of a flexible ligand inside a receptor active site containing surrounding flexible loops. To make this sampling efficient, a ligand-growing procedure has been adopted. Optimization of the ECEPP/3-plus-NOE constraint function is carried out by using a collective variable Monte Carlo minimization technique. Numerous energy minimizations are made possible for such a large system by using a Bezier splines energy grid technique. This new flexible docking approach was applied to determine the structure of a fibrinogen Aalpha-like peptide (7DFLAEGGGVRGPRV20) bound to an active site mutant of thrombin [thrombin(S195A)]. Structure calculations of the bound ligand, using 2D-transferred NOESY distance constraints in the DIANA program, showed that the N-terminal portion of the peptide (D7-R16) involves a chain reversal, whereas the C-terminal portion (G17-V20) adopts a fold that exists in several different orientations. In addition, the ECEPP/3 flexible docking package was used to assess the conformational variability of the ligand and surrounding 60D-insertion loop of thrombin. Amino acid residues (17-20) of the peptide interact with a region of the enzyme that exhibits broad specificity, with a preferred direction between the 60D-insertion loop and Pro37 of thrombin.

Animals↗

PubMed1997

Structural characterization of an analog of the major rate-determining disulfide folding intermediate of bovine pancreatic ribonuclease A.

The major rate-determining step in the oxidative regeneration of bovine pancreatic ribonuclease A (RNase A) proceeds through des-[40-95] RNase A, a three-disulfide intermediate lacking the Cys40-Cys95 disulfide bond. An analog of this intermediate, [C40A, C95A] RNase A, has been characterized in terms of regular backbone structure and thermodynamic stability at pH 4.6. Nearly complete backbone 1H, 15N, and 13C resonances, and most 13Cbeta side-chain resonances have been assigned for the mutant RNase A using triple-resonance NMR data and a computer program, AUTOASSIGN, for automated analysis of resonance assignments. Comparisons of chemical shift data, 3J(1HN-1Halpha) coupling constants, and NOE data for the mutant and wild-type proteins reveal that the overall chain folds of the two proteins are very similar, with localized structural perturbations in the regions spatially adjacent to the mutation sites in [C40A, C95A] RNase A. More significantly, 1H/2H amide exchange and thermodynamic data reveal a global destabilization of the mutant protein characterized by a significant difference in the midpoint of the thermal transition curves (DeltaTm of 21.8 degrees C) and a significant increase in the slowest exchanging backbone amide 1H/2H exchange rates (10(2)-10(6)-fold faster in the hydrophobic core of [C40A, C95 A] RNase A). Comparisons of the entropy DeltaS degrees (T) and enthalpy DeltaH degrees (T) of unfolding between wild-type and [C40A, C95A] RNase A reveal that some of the global destabilization of the mutant protein arises from entropic and enthalpic changes in the folded state. Implications of these observations for understanding the role of des-[40-95] in the folding pathway of RNase A are discussed.

Amino Acid Sequence↗

PubMed1997

Regeneration studies of an analog of ribonuclease A missing disulfide bonds 65-72 and 40-95.

Mutants of bovine pancreatic ribonuclease A (RNase A) that contain four of the eight cysteine residues found in the wild-type protein were prepared. Cysteine residues 40, 65, 72, and 95 were replaced by serine to form [C40S,C65S,C72S,C95S] RNase A or by alanine to form [C40A,C65A,C72A,C95A] RNase A, which contain the following four cysteine residues: 26, 58, 84, and 110. The substitutions resulted in deletion of wild-type disulfide bonds, 65-72 and 40-95. These mutants were prepared to investigate interactions that may be important for the folding and unfolding of the wild-type protein. The mutant protein was expressed and purified in an unfolded sulfonated form. Upon regeneration of the native form from the reduced mutant with DTTox, all three of the possible two-disulfide pairings, including the native one, formed. One-dimensional 1H NMR spectra demonstrated that the conformations of these three species are similar and are predominantly disordered; however, there is evidence of local structure in the vicinity of one histidine residue. It was also shown that disulfide pairing is not completely random and that both entropic factors and enthalpic interactions contribute to the formation of the native-disulfide bonds. The presence of more than a statistical population of native-disulfide pairings indicates that specific local interactions present in the reduced protein direct the preferential formation of native-disulfide bonds in the two-disulfide mutant.

Animals↗

PubMed1997

Water translational motion at the bilayer interface: an NMR relaxation dispersion measurement.

Nuclear magnetic relaxation rates for water protons in aqueous palmitoyloleoylphosphatidylcholine vesicle suspensions containing different nitroxide free radical spin labels are reported as a function of magnetic field strength corresponding to proton Larmor frequencies from 10 kHz to 30 MHz. Under these conditions the water proton relaxation rate is determined by the magnetic coupling between the water protons and the paramagnetic nitroxide fixed on the phospholipid. This coupling is made time-dependent by the relative translational motion of the water proton spins past the nitroxide radical. Using theories developed by Freed and others, we interpret the NMR relaxation data in terms of localized water translational motion and find that the translational diffusion constant for water within approximately 10 A of the phospholipid surface is 6 x 10(-10) m2 s(-1) at 298 K. Similar results are obtained for three different nitroxide labels positioned at different points on the lipid. The diffusion is a thermally activated process with an activation energy only slightly higher than that for bulk water.

Cyclic N-Oxides↗

PubMed1995

Structure-function studies of mEGF: probing the type I beta-turn between residues 25 and 26.

The interaction between epidermal growth factor (EGF) and its receptor molecule is not completely understood and has received much attention recently. Studies combining site-directed mutagenesis and NMR spectroscopy have identified a number of EGF residues that are required for activity and are believed to interact directly with the receptor. Instead of focusing on these residues, this study combines site-directed mutagenesis and NMR spectroscopy to probe the role of the type I beta-bend located between residues 25 and 26 of the N-terminal subdomain of the protein. Ser25 of murine EGF is replaced by Pro in an attempt to stabilize this turn conformation to produce a variant of mEGF with increased activity relative to that for the native protein. Ser25 is also replaced by Ala, which is found at position 25 in human EGF (hEGF), as a more conservative replacement. Receptor binding studies demonstrate that both mutations produce about a 30% reduction in binding affinity, which is shown to result from local changes within the loop or minor perturbations of residues neighboring the loop rather than from long-range perturbations of the beta-sheet of the N-terminal subdomain. The type I beta-turn appears to remain intact in both mutants; however, replacement with Pro seems to introduce more flexibility into this region of the protein. These results demonstrate that perturbation of this beta-turn has little effect on EGF-receptor interactions.

Animals↗

PubMed1993

Structural characterization of an N-acetyl-2-aminofluorene (AAF) modified DNA oligomer by NMR, energy minimization, and molecular dynamics.

An N-acetyl-2-aminofluorene (AAF) modified deoxyoligonucleotide duplex, d(C1-C2-A3-C4-[AAF-G5]-C6-A7-C8-C9).d(G10-G11-T12-G13-C14-++ +G15-T16-G17-G18), was studied by one- and two-dimensional NMR spectroscopy. Eight of the nine complementary nucleotides form Watson-Crick base pairs, as shown by NOEs between the guanine imino proton and cytosine amino protons for G.C base pairs or by an NOE between the thymine imino proton and adenine H2 proton for A.T base pairs. The AAF-G5 and C14 bases show no evidence of complementary hydrogen bond formation to each other. The AAF-G5 base adopts a syn conformation, as indicated by NOEs between the G5 imino proton and the A3-H3' and A3-H2'/H2" protons and by NOEs between the fluorene-H1 proton of AAF and the G5-H1' or C6-H1' proton. The NOEs from the C4-H6 proton to C4 sugar protons are weak, and thus the glycosidic torsion angle in this nucleotide is not well defined by these NMR data. The remaining bases are in the anti conformation, as depicted by the relative magnitude of the H8/H6 to H2' NOEs when compared to the H8/H6 to H1' NOEs. The three base pairs on each end of the duplex exhibit NOEs characteristic of right-handed B-form DNA. Distance restraints obtained from NOESY data recorded at 32 degrees C using a 100-ms mixing time were used in conformational searches by molecular mechanics energy minimization studies. The final, unrestrained, minimum-energy conformation was then used as input for an unrestrained molecular dynamics simulation. Chemical exchange cross peaks are observed, and thus the AAF-9-mer exists in more than a single conformation on the NMR time scale. The NMR data, however, indicate the presence of a predominant conformation (> or = 70%). The structure of the predominant conformation of the AAF-9-mer shows stacking of the fluorene moiety on an adjacent base pair, exhibiting features of the base-displacement [Grunberger, D., Nelson, J. H., et al. (1970) Proc. Natl. Acad. Sci. U.S.A. 66, 488-494] and insertion-denaturation models [Fuchs, R.P.P., & Daune, M. (1971) FEBS Lett. 14, 206-208], while the distal ring of the fluorene moiety protrudes into the minor groove.

2-Acetylaminofluorene↗

PubMed1992

Magnetically coupled paramagnetic relaxation agents.

Measurements of the spin-lattice relaxation rates of water protons made over a wide frequency range have demonstrated that the effects of paramagnetic relaxation agents may be considerably enhanced when the paramagnetic center is incorporated into a compact structure macromolecule such as a protein that is rotationally constrained. The immobilization of the macromolecule profoundly changes the nature of the magnetic field dependence of the relaxation rate for both the diamagnetic and the paramagnetic samples. The immobilization also amplifies the effect of the paramagnetic center as a water-proton relaxation agent. The direct exchange of labile water molecules or protons is not a requirement for the high efficiency of this class of magnetic relaxation agents.

Animals↗

PubMed1991

The magnetic field dependence of proton spin relaxation in tissues.

The magnetic field dependence of water-proton relaxation is reported for a simple protein solution, a cross-linked protein solution, and a series of rat tissues, fresh, dried and rehydrated. The shape of the magnetic field dependence associated with water proton relaxation in tissues is accounted for by magnetic dipole-dipole interactions between the mobile water spins and the immobile spin populations of the nonrotating components of the tissue coupling the behavior of the immobilized spin system to that of the mobile water spin system. The effect of this coupling is to impart the field dependence of the relaxation associated with the immobilized spin population to that of the mobile water spins that are observed in most relaxation and imaging experiments.

Animals↗

PubMed1991

Water-proton nuclear magnetic relaxation in heterogeneous systems: hydrated lysozyme results.

Spin-lattice relaxation rates of water protons in hydrated immobilized lysozyme are measured as a function of magnetic field strength. The dependence of water relaxation versus hydration is presented from 35 to 55% by weight water content. The water-proton relaxation is directly coupled to that of the protein and the coupling exists in the absence of chemical exchange. A model is applied where relaxation within the two proton phases is coupled through a dipolar cross-relaxation mechanism as well as chemical exchange. The observed amplitudes of the water-proton relaxation profiles scale with the ratio of protein to water protons as well as the protein-proton relaxation rate. The field dependence of the protein-proton spin-lattice relaxation is presented in the presence of D2O where a cross-relaxation coupling is absent. The coupled relaxation model accounts well for the NMR relaxation data as a function of magnetic field strength which is similar to measurements on other heterogeneous systems such as tissues.

Magnetic Resonance Spectroscopy↗

PubMed1991

Comparison of agarose and cross-linked protein gels as magnetic resonance imaging phantoms.

Measurements of the magnetic field dependence of spin-lattice relaxation rates and the response of the water-proton signal intensity to off-resonance radio frequency fields show that the commonly used agarose phantom provides a less faithful representation for the magnetic response of tissue than does a cross-linked protein system. The origin of these differences lies in the structure and intramolecular dynamics of the macromolecular system used to make the gel. These distinctions will also cause differences in the magnetic response of the water spin system when paramagnetic relaxation agents or contrast agents are incorporated. Use of a thermally cross-linked bovine serum albumin phantom is suggested.

Animals↗