The effect of salt and temperature on the conformational changes of P1LEA-22, a repeat unit of plant Late Embryogenesis Abundant proteins.

The effect of choline chloride on the conformational dynamics of the 11-mer repeat unit P1LEA-22 of group 3 Late Embryogenesis Abundant (G3LEA) proteins was studied. Circular dichroism data of aqueous solutions of P1LEA-22 revealed that the peptide favors a polyproline II (PPII) helix structure at low temperature, with increasing temperature promoting a gain of unstructured conformations. Furthermore, increases in sample FeCl or choline chloride concentrations causes a gain in PPII helical structure at low temperature.

The effect of neat ionic liquid on the folding of short peptides.

Using circular dichroism spectroscopy, we show evidence of unusual folding behaviour for several designed peptides in neat ionic liquid. Helical peptides, AKA(2) and Trp-cage, exhibit heat-induced folding, with stable helical structure persisting to 96 °C, whereas the β-hairpin Trpzip4 is destabilized by the neat [C(4)mpy][Tf(2)N].

Probing the folding transition state structure of the villin headpiece subdomain via side chain and backbone mutagenesis.

Backbone-backbone hydrogen bonds are a common feature of native protein structures, yet their thermodynamic and kinetic influence on folding has long been debated. This is reflected by the disparity between current protein folding models, which place hydrogen bond formation at different stages along the folding trajectory. For example, previous studies have suggested that the denatured state of the villin headpiece subdomain contains a residual helical structure that may provide a bias toward the folded state by confining the conformational search associated with its folding.

Folding kinetics of a naturally occurring helical peptide: implication of the folding speed limit of helical proteins.

The folding mechanism and dynamics of a helical protein may strongly depend on how quickly its constituent alpha-helices can fold independently. Thus, our understanding of the protein folding problem may be greatly enhanced by a systematic survey of the folding rates of individual alpha-helical segments derived from their parent proteins. As a first step, we have studied the relaxation kinetics of the central helix (L9:41-74) of the ribosomal protein L9 from the bacterium Bacillus stearothermophilus , in response to a temperature-jump ( T-jump) using infrared spectroscopy.

Probing the kinetic cooperativity of beta-sheet folding perpendicular to the strand direction.

In an attempt to determine how the folding dynamics of multistranded beta-sheets vary with the strand number, we have studied the temperature-induced relaxation kinetics of a four-stranded beta-sheet, DPDPDP. Our results show that the thermally induced relaxation of DPDPDP occurs on the nanosecond time scale; however, a comparison of the current results with those obtained on a sequence-related, three-stranded beta-sheet suggests that increasing the strand number from three to four increases the folding free energy barrier by a minimum of 0.8 kcal/mol, depending on the folding mechanism.

The effect of charge-charge interactions on the kinetics of alpha-helix formation.

The formation of the monomeric alpha-helix represents one of the simplest scenarios in protein folding; however, our current understanding of the folding dynamics of the alpha-helix motif is mainly based on studies of alanine-rich model peptides. To examine the effect of peptide sequence on the folding kinetics of alpha-helices, we studied the relaxation kinetics of a 21-residue helical peptide, Conantokin-T (Con-T), using time-resolved infrared spectroscopy in conjunction with a laser-induced temperature jump technique. Con-T is a neuroactive peptide containing a large number of charged residues that is found in the venom of the piscivorous cone snail Conus tulipa .

Probing the folding intermediate of Rd-apocyt b562 by protein engineering and infrared T-jump.

Small proteins often fold in an apparent two-state manner with the absence of detectable early-folding intermediates. Recently, using native-state hydrogen exchange, intermediates that exist after the rate-limiting transition state have been identified for several proteins. However, little is known about the folding kinetics from these post-transition intermediates to their corresponding native states.

Fluorescence correlation spectroscopic study of serpin depolymerization by computationally designed peptides.

Members of the serine proteinase inhibitor (serpin) family play important roles in the inflammatory and coagulation cascades. Interaction of a serpin with its target proteinase induces a large conformational change, resulting in insertion of its reactive center loop (RCL) into the main body of the protein as a new strand within beta-sheet A. Intermolecular insertion of the RCL of one serpin molecule into the beta-sheet A of another leads to polymerization, a widespread phenomenon associated with a general class of diseases known as serpinopathies.

Truncation of a cross-linked GCN4-p1 coiled coil leads to ultrafast folding.

Structural perturbation has been extensively used in protein folding studies because it yields valuable conformational information regarding the folding process. Here we have used N-terminal truncation on a cross-linked variant of the GCN4-p1 leucine zipper, aiming to develop a better understanding of the folding mechanism of the coiled-coil motif. Our results indicate that removing the first heptad repeat in this cross-linked GCN4-p1 coiled coil significantly decreases the folding free energy barrier and results in a maximum folding rate of (2.

Microviscosity in multiple regions of complex aqueous solutions of poly(ethylene oxide)-poly(propylene oxide)-poly(ethylene oxide).

Aqueous poly(ethylene oxide)-poly(propylene oxide)-poly(ethylene oxide) (PEO109-PPO41-PEO109) copolymers are nonionic surfactants that self-organize to form aggregate structures with increasing temperature or concentration. We have studied two concentrations over a range of temperatures so that the copolymers are in one of three microphases: unimers, micelles, or hydrogels formed from body centered cubic aggregates of micelles. Three different coumarin dyes were chosen based on their hydrophobicity so that different aggregate regions could be probed independently-water insoluble coumarin 153 (C153), hydrophobic coumarin 102 (C102), and the hydrophilic sodium carboxylate form of coumarin 343 (C343-).

Ultrafast folding of a computationally designed Trp-cage mutant: Trp2-cage.

Miniproteins provide useful model systems for understanding the principles of protein folding and design. These proteins also serve as useful test cases for theories of protein folding, and their small size and ultrafast folding kinetics put them in a regime of size and time scales that is now becoming accessible to molecular dynamics simulations. Previous estimates have suggested the "speed limit" for folding is on the order of 1 mus.