Stability and folding dynamics of polyglutamic acid

Characterization of Secondary Structures of Model Polypeptides in Solutions with Hyper-Raman Spectroscopy

Characterization of the secondary structures of two model polypeptides, poly-l-lysine and poly-l-glutamic acid in aqueous solutions has been demonstrated by hyper-Raman (HR) spectroscopy for the first time. Complementary to infrared (IR) and visible Raman spectroscopy, HR spectroscopy gives the amide I, II, and III bands originating from the polypeptide backbones and the CCH₃ symmetric bending mode, enabling us to distinguish different conformations. The α-helix gives the broad and weak amide III band, while the β-sheet and the random coil show similar spectral patterns with different relative intensities between the amide I and II bands. HR spectra from aqueous solutions of the α-helix and the random coil of poly-l-ornithine also possess these spectral features. The HR spectra are analogous to UV resonance Raman (UVRR) spectra, indicating the signal enhancement due to the electronic resonance effect via the π-π* transition. In contrast, the vibrational frequencies of the amide I band in the HR spectra are much higher than those in the IR, visible Raman, and UVRR spectra, suggesting the non-coincidence between HR, IR, and Raman bands. Our finding suggests that HR spectroscopy is promising to provide complementary information on the secondary structures of polypeptides in aqueous solutions as a spectral approach differing from existing vibrational spectroscopic methods.

Evaluation of formation and proportion of secondary structure in γ-polyglutamic acid by terahertz time-domain spectroscopy

The study of secondary structure is essential for understanding peptides and proteins. Here, we measured the terahertz (THz) spectra of γ-polyglutamic acid (γ-PGA) dominated by α-helix and random coil (RC) respectively. The α-helix has two absorption peaks in the THz region, but no absorption peak is observed in the RC conformation. We believe this is because the hydrogen bonding effect leads to a higher orientation in the helix-dominated γ-PGA. At lower pH, the absorption intensity of γ-PGA increases with the induction time. Similar changes were obtained in the Fourier infrared spectroscopy (FTIR). Through the correlation analysis of THz and IR spectroscopy, it is found that the characteristic peak at 1.2 THz can be used as a sensitive indicator of the intermediate conformation of the α-helical structure. In addition, the transformation of α-helix-RC conformation is related to the peak intensity at 1.99 THz (R² = 0.991), which preliminarily indicates that terahertz time-domain spectroscopy (THz-TDS) has the potential to become a new effective method for characterizing and evaluating secondary structure.

Modeling and Designing Particle-Regulated Amyloid-like Assembly of Synthetic Polypeptides in Aqueous Solution

In cells, actin and tubulin polymerization is regulated by nucleation factors, which promote the nucleation and subsequent growth of protein filaments in a controlled manner. Mimicking this natural mechanism to control the supramolecular polymerization of macromolecular monomers by artificially created nucleation factors remains a largely unmet challenge. Biological nucleation factors act as molecular scaffolds to boost the local concentrations of protein monomers and facilitate the required conformational changes to accelerate the nucleation and subsequent polymerization. An accelerated assembly of synthetic poly(l-glutamic acid) into amyloid fibrils catalyzed by cationic silica nanoparticle clusters (NPCs) as artificial nucleation factors is demonstrated here and modeled as supramolecular polymerization with a surface-induced heterogeneous nucleation pathway. Kinetic studies of fibril growth coupled with mechanistic analysis demonstrate that the artificial nucleators predictably accelerate the supramolecular polymerization process by orders of magnitude (e.g., shortening the assembly time by more than 10 times) when compared to the uncatalyzed reaction, under otherwise identical conditions. Amyloid-like fibrillation was supported by a variety of standard characterization methods. Nucleation followed a Michaelis-Menten-like scheme for the cationic silica NPCs, while the corresponding anionic or neutral nanoparticles had no effect on fibrillation. This approach shows the effectiveness of charge-charge interactions and surface functionalities in facilitating the conformational change of macromolecular monomers and controlling the rates of nucleation for fibril growth. Molecular design approaches like these inspire the development of novel materials via biomimetic supramolecular polymerizations.

Light- and temperature-dependent dynamics of chromophore and protein structural changes in bathy phytochrome Agp2

Bacterial phytochromes are sensoric photoreceptors that transform light absorbed by the photosensor core module (PCM) to protein structural changes that eventually lead to the activation of the enzymatic output module. The underlying photoinduced reaction cascade in the PCM starts with the isomerization of the tetrapyrrole chromophore, followed by conformational relaxations, proton transfer steps, and a secondary structure transition of a peptide segment (tongue) that is essential for communicating the signal to the output module. In this work, we employed various static and time-resolved IR and resonance Raman spectroscopic techniques to study the structural and reaction dynamics of the Meta-F intermediate of both the PCM and the full-length (PCM and output module) variant of the bathy phytochrome Agp2 from Agrobacterium fabrum. In both cases, this intermediate represents a branching point of the phototransformation, since it opens an unproductive reaction channel back to the initial state and a productive pathway to the final active state, including the functional protein structural changes. It is shown that the functional quantum yield, i.e. the events of tongue refolding per absorbed photons, is lower by a factor of ca. two than the quantum yield of the primary photochemical process. However, the kinetic data derived from the spectroscopic experiments imply an increased formation of the final active state upon increasing photon flux or elevated temperature under photostationary conditions. Accordingly, the branching mechanism does not only account for the phytochrome's function as a light intensity sensor but may also modulate its temperature sensitivity.

Smart co-delivery of miR-34a and cytotoxic peptides (LTX-315 and melittin) by chitosan based polyelectrolyte nanocarriers for specific cancer cell death induction

A novel polyelectrolyte nanocarrier was synthesized via layer-by-layer self-assembly of polycationic and polyanionic chains. The nanocarrier is composed of polyglutamate grafted chitosan core, dextran sulfate as a complexing agent, and polyethyleneimine shell decorated with folic acid. This polyelectrolyte complex has unique physicochemical properties so that the core is considered as an efficient carrier for LTX-315 and melittin peptides, and the shell is suitable for delivery of miR-34a. The spherical nanocarriers with an average size of 123 ± 5 nm and a zeta potential of -36 ± 1 mV demonstrated controlled-release of gene and peptides ensured a synergistic effect in establishing multiple cell death pathways on chemoresistance human breast adenocarcinoma cell line, MDA-MB-231. In vitro cell viability assays also revealed no cytotoxicity for the nanocarriers, and an IC50 of 15 μg/mL and 150 μg/mL for melittin and LTX-315, respectively, after 48 h, whereas co-delivery of melittin with miR-34a increased smart death induction by 54%.

Human serum albumin-imprinted polymers with high capacity and selectivity for abundant protein depletion

Depletion of human serum albumin (HSA), the most abundant protein in human plasma, from serum/plasma is a prerequisite before their proteomic analysis. Molecularly imprinted polymers (MIPs) using HSA as a template have been designed for this purpose, but suffer from a low sorption capacity and low selectivity. Here, a new HSA-imprinted polymer was synthesized using N-isopropylacrylamide (NIPAM) as the main monomer; acrylamide (AAm), methacrylic acid (MAA), and dimethylaminoethyl methacrylate (DMAEMA) as functional monomers; and oligoglutamic acid-based peptide crosslinker (PC) as a crosslinker at pH 5.5. When pH is adjusted to 7.4, the peptide chains in the polymer change from a helical conformation to an extended coil conformation, and the polymer swells. Consequently, the template protein is removed completely. When pH is adjusted back to 5.5, the peptide chains fold back precisely to the helical conformation. Both the size and shape of the imprint cavities are restored. Therefore, the polymer rebinds the template protein selectively. Highest imprinting factor (IF) was observed at pH 5.5 at which the polymer was synthesized. The IF increases with the increasing number of glutamic acid residues in the PCs because of their increased degree of helicity at pH 5.5. No improvement in imprinting effect was observed when using a peptide crosslinker containing both L- and D-glutamic acid residues and hence incapable of folding into α-helix, further confirming the key role of the pH-induced helix-coil transition of the peptide chains. The MIP synthesized here presents a much higher affinity to HSA than the nontemplate proteins. It could be used repeatedly without evident decrease in sorption capacity. Because of the mild eluting conditions, the secondary structure of the extracted HSA protein remains unchanged. Finally, the MIP was used to deplete HSA from human serum. Because of its high sorption capacity and high selectivity, HSA was depleted completely and selectively. STATEMENT OF SIGNIFICANCE: A new molecularly imprinted polymer (MIP) using human serum albumin (HSA) as a template was synthesized using N-isopropylacrylamide (NIPAM) as the main monomer; acrylamide (AAm), methacrylic acid (MAA), and dimethylaminoethyl methacrylate (DMAEMA) as functional monomers; and oligoglutamic acid-based peptide crosslinker as a crosslinker. Because of the reversible and precise pH-induced helix-coil transition of the peptide chains, the template protein was removed facilely and completely under mild conditions. Simultaneously, a significant improvement in imprinting efficiency was obtained. The sorption capacity was as high as 648.05 mg/g and the imprinting factor was 7.9. Because of its high selectivity and high binding capacity, the MIP synthesized here is highly promising for the depletion of HSA, the most abundant protein in serum, which is a prerequisite for its proteomic analysis. For the first time, complete and selective depletion of HSA from human serum was achieved using a protein-imprinted polymer.

Tuning uracil derivatives for the AIE-based detection of pyrene at a nano-molar level: single-crystal X-ray structure and DFT support

Single crystal X-ray structurally characterized azo-uracil derivative (L) is explored for the selective detection of pyrene via aggregation-induced emission (AIE) with 99-fold fluorescence enhancement.

Uncovering the Early Stages of Domain Melting in Calmodulin with Ultrafast Temperature-Jump Infrared Spectroscopy

The signaling protein calmodulin (CaM) undergoes a well-known change in secondary structure upon binding Ca²⁺, but the structural plasticity of the Ca²⁺-free apo state is linked to CaM functionality. Variable temperature studies of apo-CaM indicate two structural transitions at 46 and 58 °C that are assigned to melting of the C- and N-terminal domains, respectively, but the molecular mechanism of domain unfolding is unknown. We report temperature-jump time-resolved infrared (IR) spectroscopy experiments designed to target the first steps in the C-terminal domain melting transition of human apo-CaM. A comparison of the nonequilibrium relaxation of apo-CaM with the more thermodynamically stable holo-CaM, with 4 equiv of Ca²⁺ bound, shows that domain melting of apo-CaM begins on microsecond time scales with α-helix destabilization. These observations enable the assignment of previously reported dynamics of CaM on hundreds of microsecond time scales to thermally activated melting, producing a complete mechanism for thermal unfolding of CaM.

Structural basis for inhibition of a response regulator of σS stability by a ClpXP antiadaptor

Dorich et al. present the first crystal structure of RssB bound to an antiadaptor, the DNA damage-inducible IraD. The structural data, together with mechanistic studies, suggest that RssB plasticity is critical for regulation of σ^S degradation.

The stationary phase promoter specificity subunit σ^S (RpoS) is delivered to the ClpXP machinery for degradation dependent on the adaptor RssB. This adaptor-specific degradation of σ^S provides a major point for regulation and transcriptional reprogramming during the general stress response. RssB is an atypical response regulator and the only known ClpXP adaptor that is inhibited by multiple but dissimilar antiadaptors (IraD, IraP, and IraM). These are induced by distinct stress signals and bind to RssB in poorly understood manners to achieve stress-specific inhibition of σ^S turnover. Here we present the first crystal structure of RssB bound to an antiadaptor, the DNA damage-inducible IraD. The structure reveals that RssB adopts a compact closed architecture with extensive interactions between its N-terminal and C-terminal domains. The structural data, together with mechanistic studies, suggest that RssB plasticity, conferred by an interdomain glutamate-rich flexible linker, is critical for regulation of σ^S degradation. Structural modulation of interdomain linkers may thus constitute a general strategy for tuning response regulators.

Isotopically Site-Selected Dynamics of a Three-Stranded β-Sheet Peptide Detected with Temperature-Jump Infrared-Spectroscopy

Infrared detected temperature-jump (T-jump) spectroscopy and site-specific isotopic labeling were applied to study a model three-stranded β-sheet peptide with the goal of individually probing the dynamics of strand and turn structural elements. This peptide had two ^DPro-Gly (pG) turn sequences to stabilize the two component hairpins, which were labeled with ¹³C═O on each of the Gly residues to resolve them spectroscopically. Labeling the second turn on the amide preceding the ^DPro (Xxx-^DPro amide) provided an alternate turn label as a control. Placing ¹³C═O labels on specific in-strand residues gave shifted modes that overlap the Xxx-^DPro amide I' modes. Their impact could be separated from the turn dynamics by a novel difference transient analysis approach. Fourier-transform infrared spectra were modeled with density functional theory-computations which showed the local, isotope-selected vibrations were effectively uncoupled from the other amide I modes. Our T-jump dynamics results, combined with nuclear magnetic resonance structures and equilibrium spectral measurements, showed the first turn to be most stable and best formed with the slowest dynamics, whereas the second turn and first strand (N-terminus) had similar dynamics, and the third strand (C-terminus) had the fastest dynamics and was the least structured. The relative dynamics of the strands, Xxx-^DPro amides, and ¹³C-labeled Gly residues on the turns also qualitatively corresponded to molecular dynamics (MD) simulations of turn and strand fluctuations. MD trajectories indicated the turns to be bistable, with the first turn being Type I' and the second turn flipping from I' to II'. The differences in relaxation times for each turn and the separate strands revealed that the folding process of this turn-stabilized β-sheet structure proceeds in a multistep process.

Transient two-dimensional vibrational spectroscopy of an operating molecular machine

Synthetic molecular machines are promising building blocks for future nanoscopic devices. However, the details of their mechanical behaviour are in many cases still largely unknown. A deeper understanding of mechanics at the molecular level is essential for the design and construction of complex nanodevices. Here, we show that transient two-dimensional infrared (T2DIR) spectroscopy makes it possible to monitor the conformational changes of a translational molecular machine during its operation. Translation of a macrocyclic ring from one station to another on a molecular thread is initiated by a UV pulse. The arrival of the shuttling macrocycle at the final station is visible from a newly appearing cross peak between these two moieties. To eliminate spectral congestion in the T2DIR spectra, we use a subtraction method applicable to many other complex molecular systems. The T2DIR spectra indicate that the macrocycle adopts a boat-like conformation at the final station, which contrasts with the chair-like conformation at the initial station.

A deeper understanding of the mechanics of molecular machines is limited by the fast motions which are in the nanosecond or picosecond timescale. Here the authors present a real-time observation of structural changes in a rotaxane-based molecular shuttle by transient two-dimensional infrared spectroscopy.

Influence of Glu/Arg, Asp/Arg, and Glu/Lys Salt Bridges on α-Helical Stability and Folding Kinetics

Using a combination of ultraviolet circular dichroism, temperature-jump transient-infrared spectroscopy, and molecular dynamics simulations, we investigate the effect of salt bridges between different types of charged amino-acid residue pairs on α-helix folding. We determine the stability and the folding and unfolding rates of 12 alanine-based α-helical peptides, each of which has a nearly identical composition containing three pairs of positively and negatively charged residues (either Glu(-)/Arg(+), Asp(-)/Arg(+), or Glu(-)/Lys(+)). Within each set of peptides, the distance and order of the oppositely charged residues in the peptide sequence differ, such that they have different capabilities of forming salt bridges. Our results indicate that stabilizing salt bridges (in which the interacting residues are spaced and ordered such that they favor helix formation) speed up α-helix formation by up to 50% and slow down the unfolding of the α-helix, whereas salt bridges with an unfavorable geometry have the opposite effect. Comparing the peptides with different types of charge pairs, we observe that salt bridges between side chains of Glu(-) and Arg(+) are most favorable for the speed of folding, probably because of the larger conformational space of the salt-bridging Glu(-)/Arg(+) rotamer pairs compared to Asp(-)/Arg(+) and Glu(-)/Lys(+). We speculate that the observed impact of salt bridges on the folding kinetics might explain why some proteins contain salt bridges that do not stabilize the final, folded conformation.

Biomolecular dynamics studied with IR-spectroscopy using quantum cascade lasers combined with nanosecond perturbation techniques

Early events of protein folding can be studied with fast perturbation techniques triggering non-equilibrium relaxation dynamics. A nanosecond laser-excited pH-jump or temperature-jump (T-jump) was applied to initiate helix folding or unfolding of poly-l-glutamic acid (PGA). PGA is a homopolypeptide with titratable carboxyl side-chains whose protonation degree determines the PGA conformation. A pH-jump was realized by the photochemical release of protons and induces PGA folding due to protonation of the side-chains. Otherwise, the helical conformation can be unfolded by a T-jump. We operated under conditions where PGA does not aggregate and temperature and pH are the regulatory properties of its conformation. The experiments were performed in such a manner that the folding/unfolding jump proceeded to the same PGA conformation. We quantified the increase/decrease in helicity induced by the pH-/T-jump and demonstrated that the T-jump results in a relatively small change in helical content in contrast to the pH-jump. This is caused by the strong pH-dependence of the PGA conformation. The conformational changes were detected by time-resolved single wavelength IR-spectroscopy using quantum cascade lasers (QCL). We could independently observe the kinetics for α-helix folding and unfolding in PGA by using different perturbation techniques and demonstrate the high sensitivity of time-resolved IR-spectroscopy to study protein folding mechanisms.

Feasible protein aggregation of phosphorylated poly-γ-glutamic acid derivative from Bacillus subtilis (natto)

Poly-γ-glutamic acid (PGA) was modified with phosphorylating agents such as sodium metaphosphate and potassium metaphosphate in the culture medium of Bacillus subtilis (natto). The highly phosphorylated PGA derivatives were prepared and investigated for their chemical and physicochemical properties. The PGA derivatives had approximately 7% (W/W) inorganic phosphorus and characteristic absorbance PO₂^- bands at 1082cm^-1 and 1260cm^-1 by Fourier Transform Infrared Spectroscopy. The derivative modified by sodium metaphosphate (J-5) was easily hydrated in water and had extremely low viscosity. The shear rate-induced transition leading to the decrease of viscosity was not observed in J-5 whereas the derivative modified by potassium metaphosphate (J-6) as well as unmodified PGA (J-1) showed the typical decrease of viscosity. In circular dichroism (CD) measurement of J-5, there was a significant loss of the negative chirality CD signal, implying that protein aggregation occured at decreasing pH from 6.2 to 4.4. The thioflavin T fluorescence intensity of the aqueous solution in the J-5 was extremely high despite the absence of heat-treatment. The results indicate that the J-5 is the likeliest type of aggregation by β-sheet cross-linking which is relevant to protein diseases like Alzheimer's disease.

Effect of polymer topology on non-covalent polymer–protein complexation: miktoarm versus linear mPEG-poly(glutamic acid) copolymers

We report the design of mPEG-(poly(glutamic acid)) with different macromolecular topology – linear and miktoarm – for reversible non-covalent protein complexation.

Smart metallopoly(l-glutamic acid) polymers: reversible helix-to-coil transition at neutral pH

Coordination to Zn species can be reversibly used to control the helix-to-coil transition of synthetic poly(l-glutamic acid) polymers at a neutral pH of 7.

Amyloidogenic Properties of Short α-L-Glutamic Acid Oligomers

Poly-L-glutamic acid (PLGA) forms amyloid-like β2-fibrils with the main spectral component of vibrational amide I' band unusually shifted below 1600 cm(-1). This distinct infrared feature has been attributed to the presence of bifurcated hydrogen bonds coupling C═O and N-D (N-H) groups of the main chains to glutamate side chains. Here, we investigate how decreasing the chain length of PLGA affects its capacity to form β2-fibrils. A series of acidified aqueous solutions of synthetic (l-Glu)n peptides (n ≈ 200, 10, 6, 5, 4, and 3) were incubated at high temperature. We observed that n = 4 is the critical chain length for which formation of aggregates with the β2-like infrared features is still observed under such conditions. Interestingly, according to atomic force microscopy (AFM), the self-assembly of (L-Glu)n chains varying vastly in length produces fibrils with rather uniform diameters of approximately 4-6 nm. Kinetic experiments on (L-Glu)5 and (L-Glu)200 peptides indicate that the fibrillation is significantly accelerated not only in the presence of homologous seeds but also upon cross-seeding, suggesting thereby a common self-assembly theme for (L-Glu)n chains of various lengths. Our results are discussed in the context of mechanisms of amyloidogenic fibrillation of homopolypeptides.

pH-jump induced leucine zipper folding beyond the diffusion limit

The folding of a pH-sensitive leucine zipper, that is, a GCN4 mutant containing eight glutamic acid residues, has been investigated. A pH-jump induced by a caged proton (o-nitrobenzaldehyde, oNBA) is employed to initiate the process, and time-resolved IR spectroscopy of the amide I band is used to probe it. The experiment has been carefully designed to minimize the buffer capacity of the sample solution so that a large pH jump can be achieved, leading to a transition from a completely unfolded to a completely folded state with a single laser shot. In order to eliminate the otherwise rate-limiting diffusion-controlled step of the association of two peptides, they have been covalently linked. The results for the folding kinetics of the cross-linked peptide are compared with those of an unlinked peptide, which reveals a detailed picture of the folding mechanism. That is, folding occurs in two steps, one on an ∼1-2 μs time scale leading to a partially folded α-helix even in the monomeric case and a second one leading to the final coiled-coil structure on distinctively different time scales of ∼30 μs for the cross-linked peptide and ∼200 μs for the unlinked peptide. By varying the initial pH, it is found that the folding mechanism is consistent with a thermodynamic two-state model, despite the fact that a transient intermediate is observed in the kinetic experiment.

Covalent defects restrict supramolecular self-assembly of homopolypeptides: case study of β2-fibrils of poly-L-glutamic acid

Poly-L-glutamic acid (PLGA) often serves as a model in studies on amyloid fibrils and conformational transitions in proteins, and as a precursor for synthetic biomaterials. Aggregation of PLGA chains and formation of amyloid-like fibrils was shown to continue on higher levels of superstructural self-assembly coinciding with the appearance of so-called β2-sheet conformation manifesting in dramatic redshift of infrared amide I' band below 1600 cm(-1). This spectral hallmark has been attributed to network of bifurcated hydrogen bonds coupling C = O and N-D (N-H) groups of the main chains to glutamate side chains. However, other authors reported that, under essentially identical conditions, PLGA forms the conventional in terms of infrared characteristics β1-sheet structure (exciton-split amide I' band with peaks at ca. 1616 and 1683 cm(-1)). Here we attempt to shed light on this discrepancy by studying the effect of increasing concentration of intentionally induced defects in PLGA on the tendency to form β1/β2-type aggregates using infrared spectroscopy. We have employed carbodiimide-mediated covalent modification of Glu side chains with n-butylamine (NBA), as well as electrostatics-driven inclusion of polylysine chains, as two different ways to trigger structural defects in PLGA. Our study depicts a clear correlation between concentration of defects in PLGA and increasing tendency to depart from the β2-structure toward the one less demanding in terms of chemical uniformity of side chains: β1-structure. The varying predisposition to form β1- or β2-type aggregates assessed by infrared absorption was compared with the degree of morphological order observed in electron microscopy images. Our results are discussed in the context of latent covalent defects in homopolypeptides (especially with side chains capable of hydrogen-bonding) that could obscure their actual propensities to adopt different conformations, and limit applications in the field of synthetic biomaterials.

Solvent-Exposed Salt Bridges Influence the Kinetics of α-Helix Folding and Unfolding

Salt bridges are known to play an essential role in the thermodynamic stability of the folded conformation of many proteins, but their influence on the kinetics of folding remains largely unknown. Here, we investigate the effect of Glu-Arg salt bridges on the kinetics of α-helix folding using temperature-jump transient-infrared spectroscopy and steady-state UV circular dichroism. We find that geometrically optimized salt bridges (Glu^- and Arg⁺ are spaced four peptide units apart, and the Glu/Arg order is such that the side-chain rotameric preferences favor salt-bridge formation) significantly speed up folding and slow down unfolding, whereas salt bridges with unfavorable geometry slow down folding and slightly speed up unfolding. Our observations suggest a possible explanation for the surprising fact that many biologically active proteins contain salt bridges that do not stabilize the native conformation: these salt bridges might have a kinetic rather than a thermodynamic function.

Nanosecond T-jump experiment in poly(glutamic acid): a circular dichroism study

Poly(glutamic acid) has been studied with a nanosecond T-jump experiment. A new experimental set-up based on the frequency-quadrupling of an 82 MHz Titanium-Sapphire laser allows rapid CD measurements to be performed. Combining time-resolved absorption and circular dichroism at 204 and 220 nm, we are able to measure precisely the unfolding relaxation time as well as the helical fraction evolution. We show that only CD at 220 nm is relevant to observe the unfolding of an alpha helix whereas no change is observed for CD at 204 nm. Conversely, both absorptions yield information on the dynamics of the process.

Impact ofβ-Turn Sequence onβ-Hairpin Dynamics Studied with Infrared-Detected Temperature Jump

Folding dynamics forβ-structure loss and disordered structure gain were studied in a modelβ-hairpin peptide based on Cochran’s tryptophan zipper peptide Trpzip2, but with an altered Thr-Gly (TG) turn sequence, that is, SWTWETGKWTWK, using laser-induced temperature-jump (T-jump) kinetics with IR detection. As has been shown previously, the TG turn sequence reduces the thermodynamicβ-hairpin stability as compared to the Asn-Gly sequence used in Trpzip2 (TZ2-NG). In this study, we found that the TG-turn slows down the overall relaxation dynamics as compared to TZ2-NG, which were studied at higher temperatures where the time constants show little difference between relaxation of theβ-strand and the disordered conformation. These time constants become equivalent at lower temperatures for TZ2-TG than was seen for TZ2-NG. The correlation of thermodynamic stability and rates of relaxation suggests that the change from NG to TG turn results in a slowing of folding, lowerkf, with less change of the unfolding rate,ku, assuming two state behavior at higher temperatures.

Polypeptide conjugates of D-penicillamine and idarubicin for anticancer therapy

We investigated anticancer therapy with a novel combination of D-penicillamine (D-pen) and Idarubicin (Ida) in a synthetic dual drug conjugate (DDC). D-pen and Ida were covalently linked to poly(α)-L-glutamic acid (PGA) via reducible disulfide and acid-sensitive hydrazone bonds, respectively. The DDCs showed cell uptake and sustained release of the bound drugs in conditions mimicking the intracellular release media (10mM glutathione and pH 5.2). The in-vitro cytotoxicity of DDCs was comparable to unconjugated Ida in several sensitive and resistant cancer cell lines and correlated with the rate of cell uptake. In a single equivalent-dose pharmacokinetic study, DDCs enhanced the drug exposure by 7-fold and prolonged the plasma circulation half-life (t(1/2)) by 5-fold over unconjugated Ida. The therapeutic index of DDCs was 2-3-fold higher than unconjugated drugs. DDCs caused 89% tumor growth inhibition compared to 60% by unconjugated Ida alone and led to significant enhancement in the median survival (17%) of athymic nu/nu mice bearing NCI-H460 tumor xenografts.

Time-resolved vibrational spectroscopy of a molecular shuttle

Time-resolved vibrational spectroscopy is used to investigate the inter-component motion of an ultraviolet-triggered two-station molecular shuttle. The operation cycle of this molecular shuttle involves several intermediate species, which are observable in the amide I and amide II regions of the mid-IR spectrum. Using ab initio calculations on specific parts of the rotaxane, and by comparing the transient spectra of the normal rotaxane with that of the N-deuterated version, we can assign the observed vibrational modes of each species occurring during the shuttling cycle in an unambiguous way. The complete time- and frequency-dependent data set is analyzed using singular value decomposition (SVD). Using a kinetic model to describe the time-dependent concentrations of the transient species, we derive the absorption spectra associated with each stage in the operation cycle of the molecular shuttle, including the recombination of the charged species.

Measurement of circular dichroism dynamics in a nanosecond temperature-jump experiment

The use of a fast temperature jump (T-jump) is a very powerful experiment aiming at studying protein denaturation dynamics. However, probing the secondary structure is a difficult challenge and rarely yields quantitative values. We present the technical implementation of far-UV circular dichroism in a nanosecond T-jump experiment and show that this experiment allows us to follow quantitatively the change in the helical fraction of a poly(glutamic acid) peptide during its thermal denaturation with 12 ns time resolution.