Dynamical signature of abasic damage in DNA.

Time-dependent Stokes shift (TDSS) responses in proteins and DNA exhibit a broad range of long time scales (>10 ps) that are not present in bulk aqueous solution. The physical interpretation of the long TDSS time scales in biomolecular systems is a matter of considerable debate because of the many different components present in the sample (water, biomolecule, counterions), which have highly correlated motions and intrinsically different abilities to adapt to local perturbations. Here we use molecular dynamics (MD) simulations to show that the surprisingly slow (∼10 ns) TDSS response of coumarin 102 (C102), a base pair replacement, reflects a distinct dynamical signature for DNA damage.

Nitrile groups as vibrational probes of biomolecular structure and dynamics: an overview.

This paper presents an overview of recent experiments and theoretical developments aimed at using vibrational spectroscopy to understand the structure and dynamics of nitrile-labeled biomolecules. Nitrile groups are excellent vibrational probes of proteins and DNA because they absorb in a region of the spectrum that is relatively free of absorption due to the biomolecule, and they have high extinction coefficients. The vibrational frequency of nitrile groups is also extraordinarily sensitive to its local environment, and thus C[triple bond, length as m-dash]N bonds have been employed in both linear and 2-D infrared (IR) spectroscopy experiments and also as vibrational Stark probes of electric fields in proteins.

Effects of Long-Range Electrostatics on Time-Dependent Stokes Shift Calculations.

Molecular dynamics simulations are essential to the correct interpretation of the response measured in time-dependent Stokes shift (TDSS) experiments of fluorescent probe molecules in biological environments. Within linear response theory, the TDSS response is the time correlation function of the fluctuations of ΔE(t), the difference between the solute environment interaction energy with the probe, modeled in both its electronically excited and ground states. ΔE(t) is dominated by electrostatic interactions between the environment and the ground- and excited-state charge distributions of the probe.

The dynamics of water at DNA interfaces: computational studies of Hoechst 33258 bound to DNA.

Together, spectroscopy combined with computational studies that relate directly to the experimental measurements have the potential to provide unprecedented insight into the dynamics of important biological processes. Recent time-resolved fluorescence experiments have shown that the time scales for collective reorganization at the interface of proteins and DNA with water are more than an order of magnitude slower than in bulk aqueous solution. The molecular interpretation of this change in the collective response is somewhat controversial some attribute the slower reorganization to dramatically retarded water motion, while others describe rapid water dynamics combined with a slower biomolecular response.

Solvation dynamics of Hoechst 33258 in water: an equilibrium and nonequilibrium molecular dynamics study.

Integrated within an appropriate theoretical framework, molecular dynamics (MD) simulations are a powerful tool to complement experimental studies of solvation dynamics. Together, experiment, theory, and simulation have provided substantial insight into the dynamic behavior of polar solvents. MD investigations of solvation dynamics are especially valuable when applied to the heterogeneous environments found in biological systems, where the calculated response of the environment to the electrostatic perturbation of the probe molecule can easily be decomposed by component (e.

Molecular dynamics simulations of arachidonic acid-derived pentadienyl radical intermediate complexes with COX-1 and COX-2: insights into oxygenation regio- and stereoselectivity.

The two cyclooxygenase enzymes, COX-1 and COX-2, are responsible for the committed step in prostaglandin biosynthesis and are the targets of the nonsteroidal antiinflammatory drugs aspirin and ibuprofen and the COX-2 selective inhibitors, Celebrex, Vioxx, and Bextra. The enzymes are remarkable in that they catalyze two dioxygenations and two cyclizations of the native substrate, arachidonic acid, with near absolute regio- and stereoselectivity. Several theories have been advanced to explain the nature of enzymatic control over this series of reactions, including suggestions of steric shielding and oxygen channeling.

Molecular dynamics simulations of arachidonic acid complexes with COX-1 and COX-2: insights into equilibrium behavior.

The cyclooxygenase (COX) enzymes are responsible for the committed step in prostaglandin biosynthesis, the generation of prostaglandin H(2). As a result, these enzymes are pharmacologically important targets for nonsteroidal antiinflammatory drugs, such as aspirin and newer COX-2 selective inhibitors. The cyclooxygenases are functional homodimers, and each subunit contains both a cyclooxygenase and a peroxidase active site.

Three-dimensional models for beta-adrenergic receptor complexes with agonists and antagonists.

Molecular modeling methods have been used to construct three-dimensional models for agonist and antagonist complexes with beta-adrenergic receptors. The recent rhodopsin crystal structure was used as a template in standard homology modeling methods. The rhodopsin-based homology models were assessed for agreement with experimental results for beta-adrenergic receptors, and compared with receptor models developed using de novo modeling techniques.

Refinement of the conformation of a critical region of charge-charge interaction between cholecystokinin and its receptor.

Insight into the molecular basis of cholecystokinin (CCK) binding to its receptor has come from receptor mutagenesis and photoaffinity labeling studies, with both contributing to the current hypothesis that the acidic Tyr-sulfate-27 residue within the peptide is situated adjacent to basic Arg(197) in the second loop of the receptor. Here, we refine our understanding of this region of interaction by examining a structure-activity series of these positions within both ligand and receptor and by performing three-dimensional molecular modeling of key pairs of modified ligand and receptor constructs. The important roles of Arg(197) and Tyr-sulfate-27 were supported by the marked negative impact on binding and biological response with their natural partner molecule when the receptor residue was replaced by acidic Asp or Glu and when the peptide residue was replaced by basic Arg, Lys, p-amino-Phe, p-guanidino-Phe, or p-methylamino-Phe.