Biomedical subjects

Jeffrey D Evanseck

Publications and source records attributed to Jeffrey D Evanseck.

8 recordsLinked to original sources

PubMed2006

Secondary anchor substitutions in an HLA-A*0201-restricted T-cell epitope derived from Her-2/neu.

We investigated analogues of GP2 (IISAVVGIL), an HLA-A*0201-restricted T-cell epitope derived from residues 654-662 in the tumor-associated antigen (TAA) Her-2/neu. One limiting factor of GP2 is its poor affinity for HLA-A*0201. Conformational analysis revealed the P5-P7 region in GP2 appears to be linked to the stability of P9 side chain interaction with the MHC molecule. To identify variants of GP2 with enhanced presentation to HLA-A*0201, we tested V6S, V6T, V6Q, G7P, G7F, T6F7, and Q6F7 for their capacity to stabilize cell surface HLA-A*0201 molecules. Of the mono-substituted variants, V6Q and G7F exhibited superior stabilization as compared to GP2. Molecular dynamics simulations suggest the improved binding can be attributed to concerted motions in the central and C-terminal regions of the peptide. These data support the notion that amino acids in HLA-A*0201 epitopes may be inter-dependent. Priming HLA-A*0201 transgenic mice with G7F-loaded syngeneic dendritic cells stimulated mouse T cells to produce a higher level of INFgamma than mice immunized with GP2.

Amino Acid Substitution↗

PubMed2005

Generalized anomeric interpretation of the "high-energy" N-P bond in N-methyl-N'-phosphorylguanidine: importance of reinforcing stereoelectronic effects in "high-energy" phosphoester bonds.

Electronic structure calculations have been performed on a model N-phosphorylguanidine, or phosphagen, to understand the stereoelectronic factors contributing to the lability of the "high-energy" N-P bond. The lability of the N-P bond is central to the physiological role of phosphagens involving phosphoryl transfer reactions important in cellular energy buffering and metabolism. Eight protonated forms of N-methyl-N'-phosphorylguanidine have been energy minimized at levels of theory ranging up to B3LYP/6-311++G(d,p) and MP2/6-311++G(d,p) to investigate the correlation between protonation state and N-P bond length. Selected forms have also been minimized using the CCSD/6-311++G(d,p) and QCISD/6-311++G(d,p) levels of theory. Bulk solvation energies using the polarized continuum model (PCM) with B3LYP/6-311++G(d,p) test the influence of the surroundings on computed structures and energies. The N-P bond length depends on the overall protonation state where increased protonation at the phosphoryl group or deprotonation at the unsubstituted N'' nitrogen results in shorter, stronger N-P bonds. Natural bond orbital analysis shows that the protonation state affects the N-P bond length by altering the magnitude of stabilizing n(O) --> sigma*(N-P) stereoelectronic interactions and to a lesser extent the sigma(N-P) --> sigma*(C-N'') and sigma(N-P) --> sigma*(C-N) interactions. The computations do not provide evidence of a competition between the phosphoryl and guanidinium groups for the same lone pair on the bridging nitrogen, as previously suggested by opposing resonance theory. The computed n(O) --> sigma*(N-P) anomeric effect provides a novel explanation of "high-energy" N-P bond lability. This offers new mechanistic insight into phosphoryl transfer reactions involving both phosphagens and other biochemically important "high-energy" phosphoester bonds.

Guanidines↗

PubMed2005

Effect of a bound non-nucleoside RT inhibitor on the dynamics of wild-type and mutant HIV-1 reverse transcriptase.

HIV-1 reverse transcriptase (RT) is an important target for drugs used in the treatment of AIDS. Drugs known as non-nucleoside RT inhibitors (NNRTI) appear to alter the structural and dynamical properties of RT which in turn inhibit RT's ability to transcribe. Molecular dynamics (MD), principal component analysis (PCA), and binding free energy simulations are employed to explore the dynamics of RT and its interaction with the bound NNRTI nevirapine, for both wild-type and mutant (V106A, Y181C, Y188C) RT. These three mutations commonly arise in the presence of nevirapine and result in resistance to the drug. We show that a bound NNRTI hinders the motion of almost all RT amino acids. The mutations, located in the non-nucleoside RT inhibitor binding pocket, partially restore RT flexibility. The binding affinities calculated by molecular mechanics/Poisson-Boltzmann surface accessibility (MM-PBSA) show that nevirapine interacts stronger with wild-type RT than with mutant RT. The mutations cause a loss of van der Waals interactions between the drug and the binding pocket. The results from this study suggest that a good inhibitor should efficiently enter and maximally occupy the binding pocket, thereby interacting effectively with the amino acids around the binding pocket.

Amino Acid Substitution↗

PubMed2004

Density functional theory determination of an axial gateway to explain the rate and endo selectivity enhancement of Diels-Alder reactions by bis(oxazoline)-Cu(II).

A novel conceptual model and unique understanding of rate and endo selectivity enhancements delivered by bis(oxazoline)-Cu(II) Lewis acid catalysts in the Diels-Alder reaction of cyclopentadiene and acrylate imide is presented. Despite previously reported kinetic and spectroscopic studies, the physical reasons for endo selectivity and rate enhancements remain poorly understood. Large-scale density functional calculations using Becke three-parameter density functional theory with the nonlocal correlation of Lee, Yang, and Parr and the 6-31G(d) basis set have been carried out for the first time to understand the geometric and energetic consequences of C(2)-substituent variation. The unique positioning of the tert-butyl C(2)-substituent with respect to the diene, referred to as the "axial gateway", maintains the electrophilicity of the catalyst by shielding the reactive metal center from nucleophilic attack. The interplay between steric and electronic factors is crucial to understanding the observed enhanced rates and endo selectivity.

Journal Article↗

PubMed2004

Enhanced sampling by multiple molecular dynamics trajectories: carbonmonoxy myoglobin 10 micros A0-->A(1-3) transition from ten 400 picosecond simulations.

The utility of multiple trajectories to extend the time scale of molecular dynamics simulations is reported for the spectroscopic A-states of carbonmonoxy myoglobin (MbCO). Experimentally, the A0-->A(1-3) transition has been observed to be 10 micros at 300 K, which is beyond the time scale of standard molecular dynamics simulations. To simulate this transition, 10 short (400 ps) and two longer time (1.2 ns) molecular dynamics trajectories, starting from five different crystallographic and solution phase structures with random initial velocities centered in a 37 A radius sphere of water, have been used to sample the native-fold of MbCO. Analysis of the ensemble of structures gathered over the cumulative 5.6 ns reveals two biomolecular motions involving the side chains of His64 and Arg45 to explain the spectroscopic states of MbCO. The 10 micros A0-->A(1-3) transition involves the motion of His64, where distance between His64 and CO is found to vary up to 8.8 +/- 1.0 A during the transition of His64 from the ligand (A(1-3)) to bulk solvent (A0). The His64 motion occurs within a single trajectory only once, however the multiple trajectories populate the spectroscopic A-states fully. Consequently, multiple independent molecular dynamics simulations have been found to extend biomolecular motion from 5 ns of total simulation to experimental phenomena on the microsecond time scale.

Animals↗

PubMed2003

The effect of solvent on a Lewis acid catalyzed Diels-Alder reaction, using computed and experimental kinetic isotope effects.

A new transition structure for the Diels-Alder reaction between isoprene and acrolein catalyzed by Et(2)AlCl is found to reconcile reported discrepancies between computed and observed secondary kinetic isotope effects (KIEs). Including the effect of solvent realigns the computed results with experiment demonstrating the importance of nonbond interactions at transition structures. Comparison of experimental and newly predicted KIE data reaffirms the ability of theory and experiment to probe the mechanism and transition structure geometry of organic reactions.

Journal Article↗

PubMed2003

Impact of multiple cation-pi interactions upon calix[4]arene substrate binding and specificity.

The cation-pi interaction influence on the conformation and binding of calix[4]arenes to alkali-metal cations has been studied using a dehydroxylated model. The model allows for the separation of cooperative cation-pi and electrostatic forces commonly found in the binding motifs found in calixarene complexes. Starting from the four well-known calix[4]arene conformations, six conformers for this dehydroxylated model (cone, partial cone, flattened cone, chair, 1,2-alternate, and 1,3-alternate) have been characterized by geometry optimization and frequency analysis using the Becke three-parameter exchange functional with the nonlocal correlation functional of Lee, Yang, and Parr and the 6-31G(d) basis set. Without the stabilization provided by the hydroxyl hydrogen bonds in calix[4]arene, neither the cone nor the 1,2-alternate conformation is computed to be a ground-state structure. The partial cone, flattened cone, chair, and 1,3-alternate conformers have been identified as ground-state structures in a vacuum, with the partial cone and the 1,3-alternate as the lowest energy minima in the aromatic model. The C(4)(v)() cone conformation is found to be a transition structure separating the flattened cone (C(2)(v)()) conformers. The energetic and structural preferences of the calix[4]arene model change dramatically when it is bound to Li(+), Na(+), and K(+). The number of pi-faces, the positioning of these pi-faces with respect to the cations, and the nature of the cation were studied as factors in the binding strength. A detailed study of the distances and angles between the aromatic ring centroids and the cations reveals the energetic advantages of multiple weak cation-pi interactions. The geometries are often far from the optimal cation-pi interaction in which the cation approaches in a perpendicular path the aromatic ring center, where the quadrupole moment is strongest. The results reveal that multiple weaker nonoptimal cation-pi interactions contribute significantly to the overall binding strength. This theoretical analysis underscores the importance of neighboring aromatic faces and provides new insight into the significance of cation-pi binding, not only for calix[4]arenes, but also for other supramolecular and biological systems.

Journal Article↗

PubMedDate not supplied

Computational and conformational evaluation of FTase alternative substrates: insight into a novel enzyme binding pocket.

Protein farnesyltransferase (FTase) is an important anticancer drug target. In an effort to develop isoprenoid diphosphate-based FTase inhibitors, striking variations have been observed in the ability of conservatively modified analogues to bind to the enzyme. For example, 2Z-GGPP is an alternative substrate with high binding affinity, while GGPP is not an alternative substrate. Using the availability of high-resolution FTase crystal structures, we have used pharmacophore and docking studies to elucidate a new binding pocket for isoprenoid analogues. The unique conformations between the first two isoprene units of 2Z-GGPP, but not GGPP, allows 2Z-GGPP to exploit this new binding pocket. The discovered conformation allows the molecule to adopt a reactive conformation while placing hydrophobic groups within the predominately hydrophobic binding pocket. This computational finding is supported by NMR studies on (13)C-labeled 2Z-farnesol, which confirm that the computationally predicted conformation is also favored in solution. These discoveries suggest that ligand conformational flexibility may be an important design consideration for the development of both inhibitors and alternative substrates of FTase.

Binding Sites↗