Computational Graphics Software for Interactive Docking and Visualization of Ligand-Protein Complementarity.

The Dockeye software is designed to complement automated docking protocols by allowing the user's chemical know-how and experience of what makes for good protein-ligand binding, knowledge that is not easily encoded into automated algorithms, to guide the docking. It allows the interactive manipulation of the ligand placement against a protein target. Real-time intuitively comprehensible feedback about the location, spatial density, and the extent of both favorable and unfavorable atomic interactions between ligand and protein is provided through a carefully designed graphical object.

DNA Conformational Changes Play a Force-Generating Role during Bacteriophage Genome Packaging.

Motors that move DNA, or that move along DNA, play essential roles in DNA replication, transcription, recombination, and chromosome segregation. The mechanisms by which these DNA translocases operate remain largely unknown. Some double-stranded DNA (dsDNA) viruses use an ATP-dependent motor to drive DNA into preformed capsids.

Water loading driven size, shape, and composition of cetyltrimethylammonium/hexanol/pentane reverse micelles.

Cetyltrimethylammonium bromide (CTAB)/hexanol reverse micelles have found a variety of applications that demand control over physical parameters. Water content or loading is among the most basic tunable components and is the major driver of the physical properties of these systems. This study uses small-angle scattering with contrast variation to characterize these systems as a function of water loading.

Companion Simulations and Modeling to NMR-Based Dynamical Studies of Proteins.

NMR-based studies of protein dynamics and molecular simulations have a synergistic relationship. Molecular simulations, in combination with interpretative theoretical models, leverage the dynamical information obtained from NMR. They provide the concrete physical schema underlying the quantities measured by NMR, and help extend the range of applications beyond the strictly dynamic properties.

Measuring Entropy in Molecular Recognition by Proteins.

Molecular recognition by proteins is fundamental to the molecular basis of biology. Dissection of the thermodynamic landscape governing protein-ligand interactions has proven difficult because determination of various entropic contributions is quite challenging. Nuclear magnetic resonance relaxation measurements, theory, and simulations suggest that conformational entropy can be accessed through a dynamical proxy.

Entropy in molecular recognition by proteins.

Molecular recognition by proteins is fundamental to molecular biology. Dissection of the thermodynamic energy terms governing protein-ligand interactions has proven difficult, with determination of entropic contributions being particularly elusive. NMR relaxation measurements have suggested that changes in protein conformational entropy can be quantitatively obtained through a dynamical proxy, but the generality of this relationship has not been shown.

On the ability of molecular dynamics force fields to recapitulate NMR derived protein side chain order parameters.

Molecular dynamics (MD) simulations have become a central tool for investigating various biophysical questions with atomistic detail. While many different proxies are used to qualify MD force fields, most are based on largely structural parameters such as the root mean square deviation from experimental coordinates or nuclear magnetic resonance (NMR) chemical shifts and residual dipolar couplings. NMR derived Lipari-Szabo squared generalized order parameter (O(2) ) values of amide NH bond vectors of the polypeptide chain were also often employed for refinement and validation.

Characterization of Cetyltrimethylammonium Bromide/Hexanol Reverse Micelles by Experimentally Benchmarked Molecular Dynamics Simulations.

Encapsulation of small molecules, proteins, and other macromolecules within the protective water core of reverse micelles is emerging as a powerful strategy for a variety of applications. The cationic surfactant cetyltrimethylammonium bromide (CTAB) in combination with hexanol as a cosurfactant is particularly useful in the context of solution NMR spectroscopy of encapsulated proteins. Small-angle X-ray and neutron scattering is employed to investigate the internal structure of the CTAB/hexanol reverse micelle particle under conditions appropriate for high-resolution NMR spectroscopy.

Regulation of brain glutamate metabolism by nitric oxide and S-nitrosylation.

Nitric oxide (NO) is a signaling intermediate during glutamatergic neurotransmission in the central nervous system (CNS). NO signaling is in part accomplished through cysteine S-nitrosylation, a posttranslational modification by which NO regulates protein function and signaling. In our investigation of the protein targets and functional impact of S-nitrosylation in the CNS under physiological conditions, we identified 269 S-nitrosocysteine residues in 136 proteins in the wild-type mouse brain.

Analysis of the size dependence of macromolecular crowding shows that smaller is better.

The aqueous milieu inside cells contains as much as 30-40% dissolved protein and RNA by volume. This large concentration of macromolecules is expected to cause significant deviations from solution ideality. In vivo biochemical reaction rates and equilibria might differ significantly from those measured in the majority of in vitro experiments that are performed at much lower macromolecule concentrations.

On the relationship between NMR-derived amide order parameters and protein backbone entropy changes.

Molecular dynamics simulations are used to analyze the relationship between NMR-derived squared generalized order parameters of amide NH groups and backbone entropy. Amide order parameters (O(2) NH ) are largely determined by the secondary structure and average values appear unrelated to the overall flexibility of the protein. However, analysis of the more flexible subset (O(2) NH  < 0.

The remarkable hydration of the antifreeze protein Maxi: a computational study.

The long four-helix bundle antifreeze protein Maxi contains an unusual core for a globular protein. More than 400 ordered waters between the helices form a nano-pore of internal water about 150 Å long. Molecular dynamics simulations of hydrated Maxi were carried out using the CHARMM27 protein forcefield and the TIP3P water model.

A sharp thermal transition of fast aromatic-ring dynamics in ubiquitin.

Aromatic amino acid side chains have a rich role within proteins and are often central to their structure and function. Suitable isotopic-labelling strategies enable studies of sub-nanosecond aromatic-ring dynamics using solution NMR relaxation methods. Surprisingly, it was found that the three aromatic side chains in human ubiquitin show a sharp thermal dynamical transition at approximately 312 K.

TCR triggering by pMHC ligands tethered on surfaces via poly(ethylene glycol) depends on polymer length.

Antigen recognition by T cells relies on the interaction between T cell receptor (TCR) and peptide-major histocompatibility complex (pMHC) at the interface between the T cell and the antigen presenting cell (APC). The pMHC-TCR interaction is two-dimensional (2D), in that both the ligand and receptor are membrane-anchored and their movement is limited to 2D diffusion. The 2D nature of the interaction is critical for the ability of pMHC ligands to trigger TCR.

Banding of NMR-derived methyl order parameters: implications for protein dynamics.

Our understanding of protein folding, stability, and function has begun to more explicitly incorporate dynamical aspects. Nuclear magnetic resonance has emerged as a powerful experimental method for obtaining comprehensive site-resolved insight into protein motion. It has been observed that methyl-group motion tends to cluster into three "classes" when expressed in terms of the popular Lipari-Szabo model-free squared generalized order parameter.

Microscopic insights into the NMR relaxation-based protein conformational entropy meter.

Conformational entropy is a potentially important thermodynamic parameter contributing to protein function. Quantitative measures of conformational entropy are necessary for an understanding of its role but have been difficult to obtain. An empirical method that utilizes changes in conformational dynamics as a proxy for changes in conformational entropy has recently been introduced.

Calculation of configurational entropy with a Boltzmann-quasiharmonic model: the origin of high-affinity protein-ligand binding.

Accurate assessment of configurational entropy remains a large challenge in biology. While many methods exist to calculate configurational entropy, there is a balance between accuracy and computational demands. Here we calculate ligand and protein conformational entropies using the Boltzmann-quasiharmonic (BQH) method, which treats the first-order entropy term by the Boltzmann expression for entropy while determining correlations using the quasiharmonic model.

Allostery in the lac operon: population selection or induced dissociation?

Allostery, the modulation of function of a protein at one site by the binding of a ligand at a different site, is a property of many proteins. Two kinetically distinct models have been proposed: i) The induced fit model in which the ligand binds to the protein and then induces the conformational change. ii) The population selection model, in which the protein spontaneously undergoes a conformational change, which is then 'captured' by the ligand.

Improved method of preparation of supported planar lipid bilayers as artificial membranes for antigen presentation.

T cell activation is the result of direct cell-cell contact between T cells and antigen presenting cells (APCs), and of interactions between membrane-bound ligands and receptors at the contact interface, the "immunological synapse." Model APCs based upon supported fluid lipid bilayers have been used to dissect these complex molecular interactions and to facilitate real-time microscopic observations. Nearly all studies have used liposome fusion-based methods to make supported bilayers, and the biophysical properties of these membranes were not characterized in detail.

Intrinsic linear heterogeneity of amyloid β protein fibrils revealed by higher resolution mass-per-length determinations.

Amyloid β proteins spontaneously form fibrils in vitro that vary in their thermodynamic stability and in morphological characteristics such as length, width, shape, longitudinal twist, and the number of component filaments. It is vitally important to determine which variant best represents the type of fibril that accumulates in Alzheimer disease. In the present study, the nature of morphological variation was examined by dark-field and transmission electron microscopy in a preparation of seeded amyloid β protein fibrils that formed at relatively low protein concentrations and exhibited remarkably high thermodynamic stability.

Differential scanning calorimetry and fluorescence study of lactoperoxidase as a function of guanidinium-HCl, urea, and pH.

The stability of bovine lactoperoxidase to denaturation by guanidinium-HCl, urea, or high temperature was examined by differential scanning calorimetry (DSC) and tryptophan fluorescence. The calorimetric scans were observed to be dependent on the heating scan rate, indicating that lactoperoxidase stability at temperatures near Tm is controlled by kinetics. The values for the thermal transition, Tm, at slow heating scan rate were 66.

Protein pockets: inventory, shape, and comparison.

The shape of the protein surface dictates what interactions are possible with other macromolecules, but defining discrete pockets or possible interaction sites remains difficult. First, there is the problem of defining the extent of the pocket. Second, one has to characterize the shape of each pocket.