The free energy landscapes governing conformational changes in a glutamate receptor ligand-binding domain.

Ionotropic glutamate receptors are ligand-gated transmembrane ion channels activated by the binding of glutamate. The free energy landscapes governing the opening/closing of the GluR2 S1S2 ligand-binding domain in the apo, DNQX-, and glutamate-bound forms are computed by using all-atom molecular dynamics simulations with explicit solvent, in conjunction with an umbrella sampling strategy. The apo S1S2 easily accesses low-energy conformations that are more open than observed in X-ray crystal structures.

In vivo measurement of intramolecular distances using genetically encoded reporters.

The function of membrane proteins occurs in the context of the cell membrane in living cells acting in concert with various cell components such as other proteins, cofactors, etc. The understanding of the function at the molecular level requires structural techniques, but high resolution structural studies are normally obtained in vitro and in artificial membranes or detergent. Ideally the correlation of structure and function should be carried out in the native environment but most of the techniques applicable in vivo lack the high resolution necessary to track conformational changes on a molecular level.

Dynamics of the Kv1.2 voltage-gated K+ channel in a membrane environment.

All-atom molecular dynamics simulations are used to better understand the dynamic environment experienced by the Kv1.2 channel in a lipid membrane. The structure of the channel is stable during the trajectories.

Folding time predictions from all-atom replica exchange simulations.

We present an approach to predicting the folding time distribution from all-atom replica exchange simulations. This is accomplished by approximating the multidimensional folding process as stochastic reaction-coordinate dynamics for which effective drift velocities and diffusion coefficients are determined from the short-time replica exchange simulations. Our approach is applied to the folding of the second beta-hairpin of the B domain of protein G.

Total synthesis by modern chemical ligation methods and high resolution (1.1 A) X-ray structure of ribonuclease A.

The total chemical synthesis of RNase A using modern chemical ligation methods is described, illustrating the significant advances that have been made in chemical protein synthesis since Gutte and Merrifield's pioneering preparation of RNase A in 1969. The identity of the synthetic product was confirmed through rigorous characterization, including the determination of the X-ray crystal structure to 1.1 Angstrom resolution.

Characterization of conformational equilibria through Hamiltonian and temperature replica-exchange simulations: assessing entropic and environmental effects.

Molecular dynamics simulations based on the replica-exchange framework (REMD) are emerging as a useful tool to characterize the conformational variability that is intrinsic to most chemical and biological systems. In this work, it is shown that a simple extension of the replica-exchange method, known as Hamiltonian REMD, greatly facilitates the characterization of conformational equilibria across large energetic barriers, or in the presence of substantial entropic effects, overcoming some of the difficulties of REMD based on temperature alone. In particular, a comparative assessment of the HREMD and TREMD approaches was made, through computation of the gas-phase free-energy difference between the so-called D(2d) and S(4) states of tetrabutylammonium (TBA), an ionic compound of frequently used in biophysical studies of ion channels.

Selective desulfurization of cysteine in the presence of Cys(Acm) in polypeptides obtained by native chemical ligation.

Increased versatility for the synthesis of proteins and peptides by native chemical ligation requires the ability to ligate at positions other than Cys. Here, we report that Raney nickel can be used under standard conditions for the selective desulfurization of Cys in the presence of Cys(Acm). This simple and practical tactic enables the more common Xaa-Ala junctions to be used as ligation sites for the chemical synthesis of Cys-containing peptides and proteins.

Atomic Level Anisotropy in the Electrostatic Modeling of Lone Pairs for a Polarizable Force Field Based on the Classical Drude Oscillator.

Electron pairs in the valence shell of an atom that do not participate in the bonding of a molecule ("lone pairs") give rise to a concentrated electron density away from the atom center. To account for the asymmetry in the electron charge density that arises from lone pairs, an electrostatic model is developed that is parametrically anisotropic at the atomic level. The model uses virtual interaction sites with partial charges that are associated but not coincident with the nuclei.

Applied reaction dynamics: efficient synthesis gas production via single collision partial oxidation of methane to CO on Rh111.

Supersonic molecular beams have been used to determine the yield of CO from the partial oxidation of CH4 on a Rh111 catalytic substrate, CH4+12O2-->CO+2H2, as a function of beam kinetic energy. These experiments were done under ultrahigh vacuum conditions with concurrent molecular beams of O2 and CH4, ensuring that there was only a single collision for the CH4 to react with the surface. The fraction of CH4 converted is strongly dependent on the normal component of the incident beam's translational energy, and approaches unity for energies greater than approximately 1.

Absolute binding free energy calculations using molecular dynamics simulations with restraining potentials.

The absolute (standard) binding free energy of eight FK506-related ligands to FKBP12 is calculated using free energy perturbation molecular dynamics (FEP/MD) simulations with explicit solvent. A number of features are implemented to improve the accuracy and enhance the convergence of the calculations. First, the absolute binding free energy is decomposed into sequential steps during which the ligand-surrounding interactions as well as various biasing potentials restraining the translation, orientation, and conformation of the ligand are turned "on" and "off.