Ultraviolet resonance Raman study of side chain electrostatic control of poly-L-lysine conformation

pH-Induced Changes in Polypeptide Conformation: Force-Field Comparison with Experimental Validation

Microsecond-long all-atom molecular dynamics (MD) simulations, circular dichroism, laser Doppler velocimetry, and dynamic light-scattering techniques have been used to investigate pH-induced changes in the secondary structure, charge, and conformation of poly l-lysine (PLL) and poly l-glutamic acid (PGA). The employed combination of the experimental methods reveals for both PLL and PGA a narrow pH range at which they are charged enough to form stable colloidal suspensions, maintaining their α-helix content above 60%; an elevated charge state of the peptides required for colloidal stability promotes the peptide solvation as a random coil. To obtain a more microscopic view on the conformations and to verify the modeling performance, peptide secondary structure and conformations rising in MD simulations are also examined using three different force fields, i.e., OPLS-AA, CHARMM27, and AMBER99SB*-ILDNP. Ramachandran plots reveal that in the examined setup the α-helix content is systematically overestimated in CHARMM27, while OPLS-AA overestimates the β-sheet fraction at lower ionization degrees. At high ionization degrees, the OPLS-AA force-field-predicted secondary structure fractions match the experimentally measured distribution most closely. However, the pH-induced changes in PLL and PGA secondary structure are reasonably captured only by the AMBER99SB*-ILDNP force field, with the exception of the fully charged PGA in which the α-helix content is overestimated. The comparison to simulations results shows that the examined force fields involve significant deviations in their predictions for charged homopolypeptides. The detailed mapping of secondary structure dependency on pH for the polypeptides, especially finding the stable colloidal α-helical regime for both examined peptides, has significant potential for practical applications of the charged homopolypeptides. The findings raise attention especially to the pH fine tuning as an underappreciated control factor in surface modification and self-assembly.

Advancements of two dimensional correlation spectroscopy in protein researches

The developments of two-dimensional correlation spectroscopy (2DCOS) applications in protein studies are discussed, especially for the past two decades. The powerful utilities of 2DCOS combined with various analytical techniques in protein studies are summarized. The emphasis is on the vibration spectroscopic techniques including IR, NIR, Raman and optical activity (ROA), as well as vibration circular dichroism (VCD) and fluorescence spectroscopy. In addition, some new developments, such as hetero-spectral 2DCOS, moving-window correlation, and model based correlation, are also reviewed for their utility in the investigation of the secondary structure, denaturation, folding and unfolding changes of protein. Finally, the new possibility and challenges of 2DCOS in protein research are highlighted as well.

Two-dimensional correlation spectroscopy in protein science, a summary for past 20years

Two-dimensional correlation spectroscopy (2DCOS) has been widely used to Infrared, Raman, Near IR, Optical Activity (ROA), Vibrational Circular Dichroism (VCD) and Fluorescence spectroscopy. In addition, several new developments, such as 2D hetero-correlation analysis, moving-window two-dimensional (MW2D) correlation, model based correlation (βν and kν correlation analyses) have also well incorporated into protein research. They have been used to investigate secondary structure, denaturation, folding and unfolding changes of protein, and have contributed greatly to the field of protein science. This review provides an overview of the applications of 2DCOS in the field of protein science for the past 20 year, especially to memory our old friend, Dr. Boguslawa Czarnik-Matusewicz, for her great contribution in this research field. The powerful utility of 2DCOS combined with various analytical techniques in protein studies is summarized. The noteworthy developments and perspective of 2DCOS in this field are highlighted finally.

Secondary structure and dynamics study of the intrinsically disordered silica-mineralizing peptide P5 S3 during silicic acid condensation and silica decondensation

The silica forming repeat R5 of sil1 from Cylindrotheca fusiformis was the blueprint for the design of P5 S3 , a 50-residue peptide which can be produced in large amounts by recombinant bacterial expression. It contains 5 protein kinase A target sites and is highly cationic due to 10 lysine and 10 arginine residues. In the presence of supersaturated orthosilicic acid P5 S3 enhances silica-formation whereas it retards the dissolution of amorphous silica (SiO2 ) at globally undersaturated concentrations. The secondary structure of P5 S3 during these 2 processes was studied by circular dichroism (CD) spectroscopy, complemented by nuclear magnetic resonance (NMR) spectroscopy of the peptide in the absence of silicate. The NMR studies of dual-labeled (13 C, 15 N) P5 S3 revealed a disordered structure at pH 2.8 and 4.5. Within the pH range of 4.5-9.5 in the absence of silicic acid, the CD data showed a disordered structure with the suggestion of some polyproline II character. Upon silicic acid polymerization and during dissolution of preformed silica, the CD spectrum of P5 S3 indicated partial transition into an α-helical conformation which was transient during silica-dissolution. The secondary structural changes observed for P5 S3 correlate with the presence of oligomeric/polymeric silicic acid, presumably due to P5 S3 -silica interactions. These P5 S3 -silica interactions appear, at least in part, ionic in nature since negatively charged dodecylsulfate caused similar perturbations to the P5 S3 CD spectrum as observed with silica, while uncharged ß-d-dodecyl maltoside did not affect the CD spectrum of P5 S3 . Thus, with an associated increase in α-helical character, P5 S3 influences both the condensation of silicic acid into silica and its decondensation back to silicic acid.

Two-dimensional correlation spectroscopy in polymer study

This review outlines the recent works of two-dimensional correlation spectroscopy (2DCOS) in polymer study. 2DCOS is a powerful technique applicable to the in-depth analysis of various spectral data of polymers obtained under some type of perturbation. The powerful utility of 2DCOS combined with various analytical techniques in polymer studies and noteworthy developments of 2DCOS used in this field are also highlighted.

Two-dimensional Raman correlation spectroscopy reveals molecular structural changes during temperature-induced self-healing in polymers based on the Diels–Alder reaction

For the first time two-dimensional Raman correlation analysis has been used to study self-healing polymers based on the Diels–Alder reaction.

Structural attributes affecting peptide entrapment in PEO brush layers

A more quantitative understanding of peptide loading and release from polyethylene oxide (PEO) brush layers will provide direction for development of new strategies for drug storage and delivery. In this work we recorded selected effects of peptide structure and amphiphilicity on adsorption into PEO brush layers based on covalently stabilized Pluronic(®)F 108. Optical waveguide lightmode spectroscopy and circular dichroism measurements were used to characterize the adsorption of poly-l-glutamic acid, poly-l-lysine, and the cationic amphiphilic peptide WLBU2, to the brush layers. The structure of WLBU2 as well as that of the similarly-sized homopolymers was controlled between disordered and more ordered (helical) forms by varying solution conditions. Adsorption kinetic patterns were interpreted with reference to a simple model for protein adsorption, in order to evaluate rate constants for peptide adsorption and desorption from loosely and tightly bound states. While more ordered peptide structure apparently promoted faster adsorption and elution rates, resistance to elution while in the PEO layer was dependent on peptide amphiphilicity. The results presented here are compelling evidence of the potential to create anti-fouling surface coatings capable of storing and delivering therapeutics.

UV resonance Raman spectroscopy monitors polyglutamine backbone and side chain hydrogen bonding and fibrillization

We utilize 198 and 204 nm excited UV resonance Raman spectroscopy (UVRR) and circular dichroism spectroscopy (CD) to monitor the backbone conformation and the Gln side chain hydrogen bonding (HB) of a short, mainly polyGln peptide with a D(2)Q(10)K(2) sequence (Q10). We measured the UVRR spectra of valeramide to determine the dependence of the primary amide vibrations on amide HB. We observe that a nondisaggregated Q10 (NDQ10) solution (prepared by directly dissolving the original synthesized peptide in pure water) exists in a β-sheet conformation, where the Gln side chains form hydrogen bonds to either the backbone or other Gln side chains. At 60 °C, these solutions readily form amyloid fibrils. We used the polyGln disaggregation protocol of Wetzel et al. [Wetzel, R., et al. (2006) Methods Enzymol.413, 34-74] to dissolve the Q10 β-sheet aggregates. We observe that the disaggregated Q10 (DQ10) solutions adopt PPII-like and 2.5(1)-helix conformations where the Gln side chains form hydrogen bonds with water. In contrast, these samples do not form fibrils. The NDQ10 β-sheet solution structure is essentially identical to that found in the NDQ10 solid formed upon evaporation of the solution. The DQ10 PPII and 2.5(1)-helix solution structure is essentially identical to that in the DQ10 solid. Although the NDQ10 solution readily forms fibrils when heated, the DQ10 solution does not form fibrils unless seeded with the NDQ10 solution. This result demonstrates very high activation barriers between these solution conformations. The NDQ10 fibril secondary structure is essentially identical to that of the NDQ10 solution, except that the NDQ10 fibril backbone conformational distribution is narrower than in the dissolved species. The NDQ10 fibril Gln side chain geometry is more constrained than when NDQ10 is in solution. The NDQ10 fibril structure is identical to that of the DQ10 fibril seeded by the NDQ10 solution.

UV resonance Raman studies of the NaClO4 dependence of poly-L-lysine conformation and hydrogen exchange kinetics

We used 204 nm excitation UV Resonance Raman (UVRR) spectroscopy to examine the effects of NaClO(4) on the conformation of poly-L-lysine (PLL). The presence of NaClO(4) induces the formation of α-helix, π-helix/bulge, and turn conformations. The dependence of the AmIII(3) frequency on the peptide Ψ Ramachandran angle allows us to experimentally determine the conformational population distributions and the energy landscape of PLL along the Ramachandran Ψ angle. We also used UVRR to measure the NaClO(4) concentration dependence of PLL amide hydrogen exchange kinetics. Exchange rates were determined by fitting the D(2)O exchanging PLL UVRR AmII' band time evolution. Hydrogen exchange is slowed at high NaClO(4) concentrations. The PLL AmII' band exchange kinetics at 0.0, 0.2, and 0.35 M NaClO(4) can be fit by single exponentials, but the AmII' band kinetics of PLL at 0.8 M NaClO(4) requires a double exponential fit. The exchange rates for the extended conformations were monitored by measuring the C(α)-H band kinetics. These kinetics are identical to those of the AmII' band until 0.8 M NaClO(4) whereupon the extended conformation exchange becomes clearly faster than that of the α-helix-like conformations. Our results indicate that ClO(4)(-) binds to the PLL backbone to protect it from OH(-) exchange catalysis. In addition, ClO(4)(-) binding also slows the conformational exchange between the extended and α-helix-like conformations, probably by increasing the activation barriers for conformational interchanges.

Effects of two solvent conditions on the free energy landscape of the BBL peripheral subunit binding domain

BBL is a small independently folding domain with two main parallel helices. The experiment of C(α) secondary shifts has shown that changing the pH from ~7 to ~5 results in the reduced helicity at the C-terminus of helix 2. Combining constant pH molecular dynamics with replica exchange, we sampled the protein conformation space and protonation states extensively under a neutral pH condition and an acidic condition. Our results reveal that the solvent conditions influence the free energy landscape. Under the neutral pH condition, the denatured state and the native state are well separated. The condition of the acidic pH reshapes the free energy surface, leading to a broadly populated denatured-state basin and a low free energy barrier between the denatured state and the native state. The acidic pH shifts the equilibrium between the denatured state and the native state in favor of the denatured state. Caution must be used to interpret experimental data under the acidic condition because the contribution of the denatured state is significant. Our simulation results are supported by the fact that the calculated chemical shifts are in good agreement with the experiment data.

Conformation of poly-L-glutamate is independent of ionic strength

CD and UV resonance Raman measurements surprisingly find that the charge screening of even 2 M concentrations of NaCl and KCl does not alter the unfolded PPII and 2.5(1)-helix conformations of poly-L-glutamate. These salts appear to be excluded from the region between the side chain charges and the peptide backbone. Furthermore, no direct ion pairing occurs between these salts and the side chain carboxylates.