Conformational analysis of macromolecules. V. Helical structures of poly-L-aspartic acid and poly-L-glutamic acid, and related compounds

Beware of Cocktails: Chain-Length Bidispersity Triggers Explosive Self-Assembly of Poly-L-Glutamic Acid β2-Fibrils

Chain-length polydispersity is among the least understood factors governing the fibrillation propensity of homopolypeptides. For monodisperse poly-L-glutamic acid (PLGA), the tendency to form fibrils depends of the main-chain length. Long-chained PLGA, so-called (Glu)200, fibrillates more readily than short (Glu)5 fragments. Here we show that conversion of α-helical (Glu)200 into amyloid-like β-fibrils is dramatically accelerated in the presence of intrinsically disordered (Glu)5. While separately self-assembled fibrils of (Glu)200 and (Glu)5 reveal distinct morphological and infrared characteristics, accelerated fibrillation in mixed (Glu)200 and (Glu)5 leads to aggregates similar to neat (Glu)200 fibrils, even in excess of (Glu)5. According to molecular dynamics simulations and circular dichroism measurements, local events of "misfolding transfer" from (Glu)5 to (Glu)200 may play a key role in the initial stages of conformational dynamics underlying the observed phenomenon. Our results highlight chain-length polydispersity as a potent, although so-far unrecognized factor profoundly affecting the fibrillation propensity of homopolypeptides.

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.

My 65 years in protein chemistry

This is a tour of a physical chemist through 65 years of protein chemistry from the time when emphasis was placed on the determination of the size and shape of the protein molecule as a colloidal particle, with an early breakthrough by James Sumner, followed by Linus Pauling and Fred Sanger, that a protein was a real molecule, albeit a macromolecule. It deals with the recognition of the nature and importance of hydrogen bonds and hydrophobic interactions in determining the structure, properties, and biological function of proteins until the present acquisition of an understanding of the structure, thermodynamics, and folding pathways from a linear array of amino acids to a biological entity. Along the way, with a combination of experiment and theoretical interpretation, a mechanism was elucidated for the thrombin-induced conversion of fibrinogen to a fibrin blood clot and for the oxidative-folding pathways of ribonuclease A. Before the atomic structure of a protein molecule was determined by x-ray diffraction or nuclear magnetic resonance spectroscopy, experimental studies of the fundamental interactions underlying protein structure led to several distance constraints which motivated the theoretical approach to determine protein structure, and culminated in the Empirical Conformational Energy Program for Peptides (ECEPP), an all-atom force field, with which the structures of fibrous collagen-like proteins and the 46-residue globular staphylococcal protein A were determined. To undertake the study of larger globular proteins, a physics-based coarse-grained UNited-RESidue (UNRES) force field was developed, and applied to the protein-folding problem in terms of structure, thermodynamics, dynamics, and folding pathways. Initially, single-chain and, ultimately, multiple-chain proteins were examined, and the methodology was extended to protein-protein interactions and to nucleic acids and to protein-nucleic acid interactions. The ultimate results led to an understanding of a variety of biological processes underlying natural and disease phenomena.

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.

From helix-coil transitions to protein folding

An evolution of procedures to simulate protein structure and folding pathways is described. From an initial focus on the helix-coil transition and on hydrogen-bonding and hydrophobic interactions, our original attempts to determine protein structure and folding pathways were based on an experimental approach. Experiments on the oxidative folding of reduced bovine pancreatic ribonuclease A (RNase A) led to a mechanism by which the molecule folded to the native structure by a minimum of four different pathways. The experiments with RNase A were followed by development of a molecular mechanics approach, first, making use of global optimization procedures and then with molecular dynamics (MD), evolving from an all-atom to a united-residue model. This hierarchical MD approach facilitated probing of the folding trajectory to longer time scales than with all-atom MD, and hence led to the determination of complete folding trajectories, thus far for a protein containing as many as 75 amino acid residues. With increasing refinement of the computational procedures, the computed results are coming closer to experimental observations, providing an understanding as to how physics directs the folding process.

Side-chain and backbone ordering in a polypeptide

We report results from multicanonical simulations of polyglutamic acid chains of length of ten residues. For this simple polypeptide we observe a decoupling of backbone and side-chain ordering in the folding process. While the details of the two transitions vary between the peptide in gas phase and in an implicit solvent, our results indicate that, independent of the specific surroundings, upon continuously lowering the temperature side-chain ordering occurs only after the backbone topology is completely formed.

Handedness control of peptide helices by amino acid side-chain chirality: Ile/aIle peptides

A set of four hexapeptide sequences, each characterized by four strongly helicogenic Aib residues and all combinations of two isomeric Ile/aIle residues at positions 2 and 5, was synthesized by solution methods and fully characterized. A detailed solution (by FT-IR absorption, NMR, and CD techniques) and solid/crystalline state (by X-ray diffraction) conformational investigation allowed us to validate our assumption that all four peptides are folded in well-developed 3(10)-helical structures. However, the most relevant conformational conclusion extracted from the present 3D-analysis is that the handedness of the 3(10)-helical structures formed does not seem to be sensitive to the configurational change at the beta-carbon atom of the constituent Ile versus the diastereomeric aIle residues (in other words, the dominant control on this important structural parameter appears to be exerted by the chirality of the amino acid alpha-carbon atom). These results complement published findings on the diverging relative stabilities of the intermolecularly H-bonded beta-sheet structures generated by Ile versus aIle homo-oligopeptides.

Screw-sense inversion characteristic of ?-helical poly(?-p-chlorobenzylL-aspartate) and comparison with other related polyaspartates

This is one of a series of studies on the reversal of the helix sense of polyaspartates originated from the pioneering work of Goodman and his associates in 1960s. Poly(beta-p-chlorobenzyl L-aspartate) (PClBLA) is one of the well-studied polyaspartate derivatives in both solution and the solid state. The chemical structure of PClBLA differs from those of poly(beta-benzyl L-aspartate) (PBLA) and poly(beta-phenethyl L-aspartate) (PPLA) only at the terminal of the relatively long side chain. PBLA takes a left-handed form (L) in conventional helicoidal solvents and does not exhibit any screw-sense inversion. In contrast to PBLA, both PClBLA and PPLA form a right-handed helix (R) in chlorinated alkane solvents and exhibits a reversal of alpha-helix sense at higher temperatures. Yet the transition behaviors in the presence of denaturant acid are quite different between these two polymers. While PPLA exhibits transitions such as R --> L --> coil by lowering temperature, PClBLA directly goes into the coil state without showing the reentrant L form. The cause of these phenomenological differences among these polymers has been investigated by constructing the phase diagram.

Evolution of physics-based methodology for exploring the conformational energy landscape of proteins

The evolution of our physics-based computational methods for determining protein conformation without the introduction of secondary-structure predictions, homology modeling, threading, or fragment coupling is described. Initial use of a hard-sphere potential captured much of the structural properties of polypeptide chains, and subsequent more refined force fields, together with efficient methods of global optimization provide indications that progress is being made toward an understanding of the interresidue interactions that underlie protein folding.

Structural study of poly(beta-benzyl-L-aspartate) monolayers at air-liquid interfaces

As normally studied, in the solid state or in solution, poly(beta-benzyl-L-aspartate) (PBLA) differs from the other helical polyamino acids in that its alpha-helical conformation is most stable in the left-handed rather than in the right-handed form. The slightly lower energy per residue for the left-handed form in PBLA is easily perturbed, however. The helical screw sense can be inverted in a polar environment and, upon heating above 100 degrees C, a distorted left-handed helix or omega-helix is irreversibly formed. From external reflectance Fourier transform infrared measurements at the air-water interface, the conformation of PBLA in the monolayer state is directly established for the first time. The infrared frequencies of the amide bands suggest that right-handed alpha-helices are formed on the surface of water immediately after spreading the monolayers and independently of the polypeptide conformational distribution in the spreading solution. The right-handed helical form prevails throughout the slow compression of the Langmuir monolayers to collapsed films. The helical screw sense can be reversed by lowering the polarity of the aqueous phase. In addition, an alternate conformation similar to the omega-helix forms on addition of small amounts of isopropanol to the aqueous subphase, and appears to be an intermediate in the helix-helix transition.

Energy of stabilization of the right-handed beta alpha beta crossover in proteins

An explanation in terms of conformational energies is provided for the observed nearly exclusive preference of the beta alpha beta structure for forming a right-handed, rather than a left-handed, crossover connection. Conformational energy computations have been carried out on a model beta alpha beta structure, consisting of two six-residue Val beta-strands and of a 12-residue Ala alpha-helix, connected by two flexible four-residue Ala links to the strands. The energy of the most favorable right-handed crossover is 15.51 kcal/mol lower than that of the corresponding left-handed cross-over. The right-handed crossover is a strain-free structure. Its energy of stabilization arises largely from the interactions of the two beta-strands with one another and with the alpha-helix. On the other hand, the left-handed crossover is either disrupted after energy minimization or it remains conformationally strained, as indicated by an energetically unfavorable left twisting of the beta-sheet and by the presence of high-energy local residue conformations. In the energetically most favorable right-handed crossover, the right twisting of the beta-sheet and its manner of interacting with the alpha-helix are identical with those computed earlier for isolated beta-sheets and for packed alpha/beta structures. This result supports a proposed principle that it is possible to account for the main features of frequently occurring structural arrangements in globular proteins in terms of the properties of their component structural elements.

Reversal in helix sense of copoly(beta-alkyl-L-aspartate-beta-benzyl-L-aspartate)

The conformation of copoly(beta-alkyl-L-aspartate-beta-benzyl-L-aspartate), in which the alkyl group is ethyl, propyl, butyl, hexyl, nonyl, dodecyl, or stearyl, was studied in solution and the solid state by optical rotatory dispersion and circular dichroism methods. The helix sense of the copolyaspartate studied here is transformed from a left-handed to right-handed alpha-helix as the degree of alkylation increases. Reversal in helix sense occurs, i.e., the left-handed alpha-helix based on the handedness of poly(beta-benzyl-L-aspartate) is transformed into a right-handed alpha-helix with increase in alkyl groups with right-handed nature. Reversal in helix sense is also observed for copolyaspartates with an intermediate or high degree of alkylation as temperature rises. Copolyaspartates with hexyl, nonyl, or dodecyl groups exhibit an induced circular dichroism around 230-238 nm and can form an ordered side chain structure which is broken down at high temperature. One has to consider the conformation of the omega-helix and beta-form of the copolyaspartates in the solid state in addition to the reversal in helix sense. Copolyaspartates with a low degree of alkylation are in the alpha-helical conformation over the low temperature range and adopt the omega-helical conformation in the high temperature range, indicative of a thermal alpha-omega transition. A small number of alkyl groups can be incorporated into the benzene ring stacking of the omega-helix, but not a large number. All the copolyaspartates can assume the beta-form at high temperatures. The helix conformation is not significantly affected by the formation of side chain crystals of the copolyaspartate with a large number of stearyl groups, in contrast to copolyglutamate.