Structural shifts in TolC facilitate Efflux-Mediated β-lactam resistance.

Efflux-mediated β-lactam resistance is a major public health concern, reducing the effectiveness of β-lactam antibiotics against many bacteria. Structural analyses show the efflux protein TolC in Gram-negative bacteria acts as a channel for antibiotics, impacting bacterial susceptibility and virulence. This study examines β-lactam drug efflux mediated by TolC using experimental and computational methods.

Computational approaches for deciphering the equilibrium and kinetic properties of iron transport proteins.

With the advances in three-dimensional structure determination techniques, high quality structures of the iron transport proteins transferrin and the bacterial ferric binding protein (FbpA) have been deposited in the past decade. These are proteins of relatively large size, and developments in hardware and software have only recently made it possible to study their dynamics using standard computational resources. We review computational techniques towards understanding the equilibrium and kinetic properties of iron transport proteins under different environmental conditions.

Increased substrate affinity in the Escherichia coli L28R dihydrofolate reductase mutant causes trimethoprim resistance.

Dihydrofolate reductase (DHFR) is a ubiquitous enzyme with an essential role in cell metabolism. DHFR catalyzes the reduction of dihydrofolate to tetrahydrofolate, which is a precursor for purine and thymidylate synthesis. Several DHFR targeting antifolate drugs including trimethoprim, a competitive antibacterial inhibitor, have therefore been developed and are clinically used.

FbpA iron storage and release are governed by periplasmic microenvironments.

Ferric binding protein (FbpA) is part of an elaborate iron piracy mechanism evolved in Gram-negative bacteria, shuttling iron in the periplasmic space, from the outer to the cytoplasmic membrane side. We address how the dissociation process of iron is facilitated, since the binding constant of iron is on the order of 10 M at 6.5 pH and 200 mM ionic strength (IS).

Predicting long term cooperativity and specific modulators of receptor interactions in human transferrin from dynamics within a single microstate.

Transferrin (Tf) is an essential transport protein circulating iron in the blood and delivering it to tissues. It displays highly pH dependent cooperativity between the two lobes each carrying an iron, and forms a tight complex with the receptor during endocytosis and recycling back to the serum. We explore short-term dynamics within selected microstates of human Tf to identify functional information relevant to long-term dynamics.

Molecular basis for solvent dependent morphologies observed on electrosprayed surfaces.

We study the causes of the observed tunable hydrophobicity of poly(styrene-co-perfluoroalkyl ethylacrylate) electrosprayed in THF, DMF, and THF:DMF (1:1) solvents. Under the assumption that equilibrium morphologies in the solvent significantly affect the patterns observed on electrosprayed surfaces, we use atomistic and coarse-grained simulations supported by dynamic light scattering (DLS) experiments to focus on the parameters that affect the resulting morphology of superhydrophobic electrosprayed beads. The differing equilibrium chain size distributions in these solvents examined by DLS are corroborated by chain dimensions obtained via molecular dynamics simulations.

How orientational order governs collectivity of folded proteins.

The past decade has witnessed the development and success of coarse-grained network models of proteins for predicting many equilibrium properties related to collective modes of motion. Curiously, the results are usually robust toward the different cutoff distances used for constructing the residue networks from the knowledge of the experimental coordinates. In this study, we present a systematical study of network construction and their effect on the predicted properties.

Manipulation of conformational change in proteins by single-residue perturbations.

Using the perturbation-response scanning (PRS) technique, we study a set of 25 proteins that display a variety of conformational motions upon ligand binding (e.g., shear, hinge, allosteric).

Perturbation-response scanning reveals ligand entry-exit mechanisms of ferric binding protein.

We study apo and holo forms of the bacterial ferric binding protein (FBP) which exhibits the so-called ferric transport dilemma: it uptakes iron from the host with remarkable affinity, yet releases it with ease in the cytoplasm for subsequent use. The observations fit the "conformational selection" model whereby the existence of a weakly populated, higher energy conformation that is stabilized in the presence of the ligand is proposed. We introduce a new tool that we term perturbation-response scanning (PRS) for the analysis of remote control strategies utilized.

How a vicinal layer of solvent modulates the dynamics of proteins.

The dynamics of a folded protein is studied in water and glycerol at a series of temperatures below and above their respective dynamical transition. The system is modeled in two distinct states whereby the protein is decoupled from the bulk solvent at low temperatures, and communicates with it through a vicinal layer at physiological temperatures. A linear viscoelastic model elucidates the less-than-expected increase in the relaxation times observed in the backbone dynamics of the protein.

Relaxation kinetics and the glassiness of native proteins: coupling of timescales.

We provide evidence that the onset of functional dynamics of folded proteins with elevated temperatures is associated with the effective sampling of its energy landscape under physiological conditions. The analysis is based on data describing the relaxation phenomena governing the backbone dynamics of bovine pancreatic trypsin inhibitor derived from molecular dynamics simulations, previously reported by us. By representing the backbone dynamics of the folded protein by three distinct regimes, it is possible to decompose its seemingly complex dynamics, described by a stretch exponential decay of the backbone motions.

Relaxation kinetics and the glassiness of proteins: the case of bovine pancreatic trypsin inhibitor.

Folded proteins may be regarded as soft active matter under physiological conditions. The densely packed hydrophobic interior, the relatively molten hydrophilic exterior, and the spacer connecting these put together a large number of locally homogeneous regions. For the case of the bovine pancreatic trypsin inhibitor, with the aid of molecular dynamics simulations, we have demonstrated that the kinetics of the relaxation of the internal motions is highly concerted, manifesting the protein's heterogeneity, which may arise from variations in density, local packing, or the local energy landscape.

Coordination topology and stability for the native and binding conformers of chymotrypsin inhibitor 2.

We demonstrate that the stabilization of the binding region is accomplished at the expense of a loss in the stability of the rest of the protein. A novel molecular mechanics (MM) approach is introduced to distinguish residue stabilities of proteins in a given conformation. As an example, the relative stabilities of folded chymotrypsin inhibitor 2 (CI2) in unbound form, and CI2 in complex with subtilisin novo is investigated.

Elucidating the structural mechanisms for biological activity of the chemokine family.

Chemokines are a family of proteins involved in inflammatory and immune response. They share a common fold, made up of a three-stranded beta-sheet, and an overlaying alpha-helix. Chemokines are mainly categorized into two subfamilies distinguished by the presence or absence of a residue between two conserved cysteines in the N-terminus.