Polypeptide Conformation Research Articles

Differential effects of ganglioside lipids on the conformation and aggregation of islet amyloid polypeptide.

Despite causing over 1 million deaths annually, Type 2 Diabetes (T2D) currently has no curative treatments. Aggregation of the islet amyloid polypeptide (hIAPP) into amyloid plaques plays an important role in the pathophysiology of T2D and thus presents a target for therapeutic intervention. The mechanism by which hIAPP aggregates contribute to the development of T2D is unclear, but it is proposed to involve disruption of cellular membranes. However, nearly all research on hIAPP-lipid interactions has focused on anionic phospholipids, which are primarily present in the cytosolic face of plasma membranes. We seek here to characterize the effects of three gangliosides, the dominant anionic lipids in the outer leaflet of the plasma membrane, on the aggregation, structure, and toxicity of hIAPP. Our results show a dual behavior that depends on the molar ratio between the gangliosides and hIAPP. For each ganglioside, a low-lipid:peptide ratio enhances hIAPP aggregation and alters the morphology of hIAPP fibrils, while a high ratio eliminates aggregation and stabilizes an α-helix-rich hIAPP conformation. A more negative lipid charge more efficiently promotes aggregation, and a larger lipid headgroup improves inhibition of aggregation. hIAPP also alters the phase transitions of the lipids, favoring spherical micelles over larger tubular micelles. We discuss our results in the context of the available lipid surface area for hIAPP binding and speculate on a role for gangliosides in facilitating toxic hIAPP aggregation.

Dual-Mode Arginine Assay Based on the Conformation Switch of a Ferrocene-Grafted Polypeptide.

Both controllable regulation of the conformational structure of a polypeptide and specific recognition of an amino acid are still arduous challenges. Here, a novel dual-mode (electrochemical and colorimetric) biosensor was built for arginine (Arg) recognition based on a conformation switch, utilizing controllable and synergistic self-assembly of a ferrocene-grafted hexadecapeptide (P16Fc) with gold nanoparticles (AuNPs). Benefiting from the flexibility and unique topological structure of P16Fc formed nanospheres, the assembly and disassembly can undergo a conformation transition induced by Arg through controlling the distance and number of Fc detached from the gold surface, producing on-off electrical signals. Also, they can induce aggregation and dispersion of AuNPs in solution, causing a color change. The mechanism of Arg recognition with polypeptide conformation regulation was well explored by combining microstructure characterizations with molecular mechanics calculations. The electrochemical and colorimetric assays for Arg were successfully established in sensitive and selective manner, not only obtaining a very low detection limit, but also effectively eliminating the interference from other amino acids and overcoming the limitation of AuNP aggregation. Notably, the conformational change-based assay with the peptide regulated by the target will make a powerful tool for the amino acid biosensing and health diagnosis.

Synthetic cationic helical polypeptides for the stimulation of antitumour innate immune pathways in antigen-presenting cells.

Intracellular DNA sensors regulate innate immunity and can provide a bridge to adaptive immunogenicity. However, the activation of the sensors in antigen-presenting cells (APCs) by natural agonists such as double-stranded DNAs or cyclic nucleotides is impeded by poor intracellular delivery, serum stability, enzymatic degradation and rapid systemic clearance. Here we show that the hydrophobicity, electrostatic charge and secondary conformation of helical polypeptides can be optimized to stimulate innate immune pathways via endoplasmic reticulum stress in APCs. One of the three polypeptides that we engineered activated two major intracellular DNA-sensing pathways (cGAS-STING (for cyclic guanosine monophosphate-adenosine monophosphate synthase-stimulator of interferon genes) and Toll-like receptor 9) preferentially in APCs by promoting the release of mitochondrial DNA, which led to the efficient priming of effector T cells. In syngeneic mouse models of locally advanced and metastatic breast cancers, the polypeptides led to potent DNA-sensor-mediated antitumour responses when intravenously given as monotherapy or with immune checkpoint inhibitors. The activation of multiple innate immune pathways via engineered cationic polypeptides may offer therapeutic advantages in the generation of antitumour immune responses.

Sensing PEGylated Peptide Conformations Using a Protein Nanopore.

Membrane pores are exploited for the stochastic sensing of various analytes, and here, we use electrical recordings to explore the interaction of PEGylated peptides of different sizes with a protein pore, CymA. This wide-diameter natural pore comprises densely filled charged residues, facilitating electrophoretic binding of polyethylene glycol (PEG) tagged with a nonaarginine peptide. The small PEG 200 peptide conjugates produced monodisperse blockages and exhibited voltage-dependent translocation across the pores. Notably, the larger PEG 1000 and 2000 peptide conjugates yielded heterogeneous blockages, indicating a multitude of PEG conformations hindering their translocation through the pore. Furthermore, a much larger PEG 5000 peptide occludes the pore entrance, resulting in complete closure. The competitive binding of different PEGylated peptides with the same pore produced specific blockage signals reflecting their identity, size, and conformation. Our proposed model of sensing distinct polypeptide conformations corresponds to disordered protein unfolding, suggesting that this pore can find applications in proteomics.

Gold Nanoclusters Enhance the Efficacy of the Polymer-Based Chaperone in Restoring and Maintaining the Native Conformation of Human Islet Amyloid Polypeptide.

The misfolding and un-natural fibrillation of proteins/peptides are associated with many conformation diseases, such as human islet amyloid polypeptide (hIAPP) in type 2 diabetes (T2D). Inspired by molecular chaperones maintaining protein homeostasis in vivo, many polymer-based artificial chaperones were introduced to regulate protein/peptide folding and fibrillation. However, the pure polymer chaperones prefer to agglomerate into large-size micelles in the physiological environment and thus lose their chaperone functions, which greatly restricts the application of polymer-based chaperones. Here, we designed and prepared a core-shell artificial chaperone based on a dozen poly-(N-isopropylacrylamide-co-N-acryloyl-O-methylated-l-arginine) (PNAMR) anchored on a gold-nanocluster (AuNC) core. The introduction of the AuNC core significantly reduced the size and enhanced the efficacy and stability of polymer-based artificial chaperones. The PNAMR@AuNCs, with a diameter of 2.5 ± 0.5 nm, demonstrated exceptional ability in maintaining the natively unfolded conformation of protein away from the misfolding and the following fibrillation by directly binding to the natively unfolded monomolecular hIAPP and hence in preventing their conversion into toxic oligomers. More excitingly, the PNAMR@AuNCs were able to restore the natural unfolded conformation of hIAPP via dissolving the β-sheet-rich hIAPP fibrils. Considering the uniform molecular mechanism of protein misfolding and fibrillation in conformation disorders, this finding provides a generic therapeutic strategy for neurodegenerative diseases and other conformation diseases by using PNAMR@AuNC artificial chaperones to restore and maintain the native conformation of amyloid proteins.

Control of the structure and morphology of polypeptide/surfactant spread films by exploiting specific interactions.

We demonstrate control of the structure and morphology of polypeptide/surfactant films at the air/water interface as a function of the maximum compression ratio of the surface area, exploiting a recently developed film formation mechanism that requires minimal quantities of materials involving the dissociation of aggregates. The systems studied are poly(L-lysine) (PLL) or poly(L-arginine) (PLA) with sodium dodecyl sulfate (SDS), chosen because the surfactant (i) interacts more strongly with the latter polypeptide due to the formation of hydrogen bonds between the guanidinium group and its oxygen atoms, and (ii) induces bulk β-sheet and α-helix conformations of the respective polypeptides. The working hypothesis is that such different interactions may be used to tune the film properties when compressed to form extended structures (ESs). Neutron reflectometry reveals that application of a high compression ratio (4.5 : 1) results in the nanoscale self-assembly of ESs containing up to two PLL-wrapped SDS bilayers. Brewster angle microscopy provides images of the PLL/SDS ESs as discrete regions on the micrometre scale while additional linear regions of PLA/SDS ESs mark macroscopic film folding. Ellipsometry demonstrates high stability of the different ESs formed. The collapse of PLL/SDS films upon compression to a very high ratio (10 : 1) is irreversible due to the formation of solid domains that remain embedded in the film upon expansion while that of PLA/SDS films is reversible. These findings demonstrate that differences in the side group of a polypeptide can have a major influence on controlling the film properties, marking a key step in the development of this new film formation mechanism for the design of biocompatible and/or biodegradable films with tailored properties for applications in tissue engineering, biosensors and antimicrobial coatings.

Molecular weight and molecular weight distribution of sericin protein extracted from cocoon waste of <i>Bombyx mori</i>

Silk sericin comprises a globular water-soluble protein that surrounds silk fibres, sticking them together and providing cocoon adhesion. Sericin was isolated from the extract solution in two ways: the first sample was obtained by concentrating the filtered extract at low pressure (SLP); the second sample was obtained by ultrafiltration (SUF) using a membrane. In this work, the size exclusion-high-performance liquid chromatography involving viscometry and refractive index detectors was used to determine the molecular weight and conformation of sericin polypeptides obtained from cocoons of the Bombyx mori silkworm. The aggregation processes of silk sericin protein under various isolation conditions from the solution were considered. It was shown that sericin macromolecules are present as a monodisperse polypeptide at low concentrations, which aggregates at concentrations greater than 1–2 mg/ml. The obtained data indicate that, along with the parameters of the extraction process, the conditions for its isolation from the solution, including temperature, pressure and degree of concentration, affect the molecular weight and aggregative behaviour of the protein. The results confirm and complement previously obtained data on the influence of various factors on the association of protein macromolecules in solution. The resulting sericin fractions can find many applications, including materials for tissue engineering, coatings for surface modification, cell culture media, cosmetics, as well as food additives and medical biomaterials.

Conformation of Light-Harvesting Complex II Trimer Depends upon Its Binding Site.

The light-harvesting complex II (LHCII) trimer in plants functions as a major antenna complex and a quencher to protect it from photooxidative damage. Theoretical studies on the structure of an LHCII trimer have demonstrated that excitation energy transfer between chlorophylls (Chls) in LHCII can be modulated by its exquisite conformational fluctuation. However, conformational changes depending on its binding location have not yet been investigated, even though reorganization of protein complexes occurs by physiological regulations. In this study, we investigated conformational differences in LHCII by comparing published structures of an identical LHCII trimer in the three different photosystem supercomplexes from the green alga Chlamydomonas reinhardtii. Our results revealed distinct differences in Chl configurations as well as polypeptide conformations of the LHCII trimers depending on its binding location. We propose that these configurational differences readily modulate the function of LHCII and possibly lead to a change in excitation-energy flow over the photosynthetic supercomplex.

Paramagnetic relaxation enhancement NMR reveals the structures and ribosome interactions of nascent chains during biosynthesis

The crucial process of protein folding begins co-translationally on the ribosome. Emerging evidence is demonstrating that the ribosome itself is an active player in regulating the folding of nascent chains, a process that is vital for proteostasis. However, surprisingly little is known structurally about the conformations of nascent polypeptides on their parent ribosome during vectorial emergence and how the ribosome modulates co-translational folding.

Native state of natural proteins optimizes local entropy.

The differing ability of polypeptide conformations to act as the native state of proteins has long been rationalized in terms of differing kinetic accessibility or thermodynamic stability. Building on the successful applications of physical concepts and sampling algorithms recently introduced in the study of disordered systems, in particular artificial neural networks, we quantitatively explore how well a quantity known as the local entropy describes the native state of model proteins. In lattice models and all-atom representations of proteins, we are able to efficiently sample high local entropy states and to provide a proof of concept of enhanced stability and folding rate. Our methods are based on simple and general statistical-mechanics arguments, and thus we expect that they are of very general use.

Effects of Glycine on the Local Conformation and Internal Backbone Dynamics of Polypeptides

The effects, that glycine (Gly) has on the local chain conformation and internal backbone dynamics (IBD) of polypeptides, were investigated by comparing the fluorescence response of a series of pyr...

The first resolution revolution in protein structure analysis: X-ray diffraction of polypeptide conformations and globular protein folds in 1950s and 1960s

The first resolution revolution in protein structure analysis: X-ray diffraction of polypeptide conformations and globular protein folds in 1950s and 1960s

Nanoengineered polypeptides from tetraphenylethylene-functionalized N-carboxyanhydride: Synthesis, self-assembly and intrinsic aggregation-induced emission

Ring-opening polymerization of N-carboxyanhydrides (NCAs) bearing pendant groups creates functional polypeptides. In this paper, we report the design, synthesis and polymerization of tetraphenylethylene (TPE)-modified NCA, which is used to incorporate aggregation-induced emission (AIE)-active segments into polypeptides. Specifically, we attempted the synthesis of amphiphilic methoxy poly(ethyleneglycol)-block-poly(γ-benzyl-l-glutamate)-block-poly(γ-4-(1,2,2-triphenylvinyl)benzyl-l-glutamate) (PEG-PBLG-PTPELG), which had well-controlled molecular weight and narrow polydispersity. The hydrophilic PEG and hydrophobic PBLG-PTPELG assembled into micelles in aqueous solution with diameter around 70 ​nm, displaying AIE at 480 ​nm. Our work demonstrates that the TPE-modified NCA is applicable for the preparation of the AIE-active polypeptides, integrating the AIE luminogens into the polypeptides which may offer unique opportunities for tuning AIE properties by adjusting the composition and conformation of polypeptides. We preliminarily explored the use of the amphiphilic polypeptides for the formulation of doxorubicin-containing micelles that can potentially be used for real-time monitoring of the nanomedicine distribution.

Antioxidant activity of linear and star-shaped polypeptides modified with dopamine and glutathione

The aim of this study was to investigate the effect of topology on the antioxidative activities of antioxidant-grafted polypeptides. The linear and star-shaped poly(L-glutamic acid) (PLG) polypeptides were synthesized by N-carboxyanhydrides (NCAs) ring opening polymerization (ROP) using primary amine and polyols as initiators, followed by deprotection. Graft copolypeptides (PLG-Dopa, PLG-GSH and PLG-Dopa-GSH) were obtained by EDC/NHS coupling chemistry using dopamine (Dopa) and glutathione (GSH). Successful synthesis of these polypeptides was confirmed by 1H NMR, MALDI TOF, GPC, UV–vis and IR spectra analyses. The conformation of polypeptides was investigated by circular dichroism (CD) spectroscopy, demonstrating the grafting of Dopa and GSH onto PLG was accompanied by a conformational change from a random coil to α-helical structure. The results showed that the antioxidant activities of PLG-Dopa and PLG-Dopa-GSH were mainly ascribed to Dopa. It was found that the conjugation of Dopa resulted in the decrease in its antioxidant activity and the antioxidant-grafted polypeptides exhibited comparable antioxidant activity regardless the polypeptide arm number. The conjugation of GSH could prolong polypeptide antioxidant activity by preventing Dopa from oxidation. It was found that both PLG-Dopa and PLG-Dopa-GSH exhibited good hemocompatibility and biocompatibility.

Oligomers, fibrils and aggregates formed by alpha-synuclein: role of solution conditions

The classical Hofmeister series orders ions into kosmotropes and chaotropes, based on their interaction with the solvent, water. The role of protein is mostly ignored probably because most of the proteins studied are natively folded and broadly follow this classification pattern. Recent reports suggest that the interaction of ions is different with solvent molecules of proximal layer and bulk. Intrinsically disordered proteins (IDPs) differ from globular proteins in the fraction of polar vis-à-vis hydrophobic amino acids and the absence of distinct secondary and tertiary structures. The kosmotrope, ammonium sulphate, increases the compactness of the polypeptide conformation, with differing effects for globular proteins and IDPs. For globular proteins, lowered flexibility corresponds to a more stable native structure. Using oligomer-specific and aggregation-specific antibodies and comparing with fibrillation results, we show for alpha-synuclein, an IDP, ammonium sulphate-induced compaction results in the formation of the aggregation-prone hydrophobic core, which combines with other similar moieties to form the fibrillar ‘seed’. SEC-HPLC and SAXS analysis show the presence of the threshold oligomers. In the presence of the aggregation suppressor, arginine too, an oligomer is formed. This oligomer, however, is ‘dead’, and does not move further along the aggregation pathway. Thus, alpha-synuclein undergoes compaction in the presence of protein stabilisers, with differing consequences. In case of the chaotropes, KSCN and urea, aggregation of alpha-synuclein is partially inhibited. However, the amounts and types of aggregates formed are different in the two cases. Thus, the classical catalogue of molecules into protein stabilisers and destabilisers requires a relook for IDPs. Communicated by Ramaswamy H. Sarma

Effect of surface chemistry on islet amyloid polypeptide conformation.

The formation of dense, linear arrays (fibrils) by biomolecules is the hallmark of a number of degenerative diseases, such as Alzheimer's and type-2 diabetes. Protein fibrils have also attracted interest as building blocks for new materials. It has long been recognized that surfaces can affect the fibrillation process. Recent work on the model fibril forming protein human islet amyloid polypeptide (hIAPP) has shown that while the protein concentration is highest at hydrophobic surfaces, the rate of fibril formation is lower than on other surfaces. To understand this, replica exchange molecular dynamics simulations were used to investigate the conformations that hIAPP adopts on surfaces of different hydrophobicities. The hydrophobic surface stabilizes α-helical structures which are significantly different to those found on the hydrophilic surface and in bulk solution. There is also a greatly reduced conformational ensemble on the hydrophobic surface due to long-lived contacts between hydrophobic residues on the protein and the surface. This new microscopic information will help us determine the mechanism of the enhancement of fibril formation on surfaces and provides new insight into the effect of nanointerfaces and protein conformation.

Effect of Like Charges on the Conformation and Internal Dynamics of Polypeptides Probed by Pyrene Excimer Fluorescence

Three series of pyrene-labeled polypeptides, namely, poly(l-lysine) (Py-PLL), poly(l-glutamic acid) (Py-PLGA), and poly(d,l-glutamic acid) (Py-PDLGA), were studied in dimethyl sulfoxide (DMSO) by m...

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.

SPECS: Integration of side-chain orientation and global distance-based measures for improved evaluation of protein structural models.

Significant advancements in the field of protein structure prediction have necessitated the need for objective and robust evaluation of protein structural models by comparing predicted models against the experimentally determined native structures to quantitate their structural similarities. Existing protein model versus native similarity metrics either consider the distances between alpha carbon (Cα) or side-chain atoms for computing the similarity. However, side-chain orientation of a protein plays a critical role in defining its conformation at the atomic-level. Despite its importance, inclusion of side-chain orientation in structural similarity evaluation has not yet been addressed. Here, we present SPECS, a side-chain-orientation-included protein model-native similarity metric for improved evaluation of protein structural models. SPECS combines side-chain orientation and global distance based measures in an integrated framework using the united-residue model of polypeptide conformation for computing model-native similarity. Experimental results demonstrate that SPECS is a reliable measure for evaluating structural similarity at the global level including and beyond the accuracy of Cα positioning. Moreover, SPECS delivers superior performance in capturing local quality aspect compared to popular global Cα positioning-based metrics ranging from models at near-experimental accuracies to models with correct overall folds—making it a robust measure suitable for both high- and moderate-resolution models. Finally, SPECS is sensitive to minute variations in side-chain χ angles even for models with perfect Cα trace, revealing the power of including side-chain orientation. Collectively, SPECS is a versatile evaluation metric covering a wide spectrum of protein modeling scenarios and simultaneously captures complementary aspects of structural similarities at multiple levels of granularities. SPECS is freely available at http://watson.cse.eng.auburn.edu/SPECS/.

Effects of molecular weight and structural conformation of multivalent-based elastin-like polypeptides on tumor accumulation and tissue biodistribution.

In order to improve clinical outcomes for novel drug delivery systems, distinct optimization of size, shape, multifunctionality, and site-specificity are of utmost importance. In this study, we designed various multivalent elastin-like polypeptide (ELP)-based tumor-targeting polymers in which multiple copies of IL-4 receptor (IL-4R)-targeting ligand (AP1 peptide) were periodically incorporated into the ELP polymer backbone to enhance the affinity and avidity towards tumor cells expressing high levels of IL-4R. Several ELPs with different molecular sizes and structures ranging from unimer to micelle-forming polymers were evaluated for their tumor accumulation as well as in vivo bio-distribution patterns. Different percentages of cell binding and uptake were detected corresponding to polymer size, number of targeting peptides, or unimer versus micelle structure. As compared to low molecular weight polypeptides, high molecular weight AP1-ELP showed superior binding activity with faster entry and efficient processing in the IL-4R-dependent endocytic pathway. In addition, in vivo studies revealed that the high molecular weight micelle-forming AP1-ELPs (A86 and A100) displayed better tumor penetration and extensive retention in tumor tissue along with reduced non-specific accumulation in vital organs, when compared to low molecular weight non-micelle forming AP1-ELPs. It is suggested that the superior binding activities shown by A86 and A100 may depend on the multiple presentation of ligands upon transition to a micelle-like structure rather than a larger molecular weight. Thus, this study has significance in elucidating the different patterns underlying unimer and micelle-forming ELP-mediated tumor targeting as well as the in vivo biodistribution.