Polyproline II propensities from GGXGG peptides reveal an anticorrelation with β-sheet scales

Abstract

There is growing appreciation of the functional relevance of unfolded proteins in biology. However, unfolded states of proteins have proven inaccessible to the usual techniques for high-resolution structural and energetic characterization. Unfolded states are still generally conceived of as statistical coils, based on the pioneering work of Flory [(1969 T he process by which a protein acquires its native structure is among the most complex reactions known, and challenges remain in defining the nature of the transition state(s), the structure and role of intermediates, and the properties of the starting ensemble of states (1-4). According to Flory (5) and Tanford (6), unfolded proteins can be represented as statistical random coils, in which a given residue has no strong preference for any specific conformation. Confirming earlier conclusions by Tiffany and Krimm (7-9), recent evidence from a variety of spectroscopic probes (10-22), theoretical studies (23-34), and coil library surveys (35-43) consistently point to a major role for the polyproline II (PPII, ⌽ ϭ Ϫ75°, ⌿ ϭ ϩ145°) conformation in oligo-Ala (for review, see ref. 3 and related articles in the same volume), oligo-Lys, and oligo-Glu peptides (44). We have reported that in a seven-Ala peptide model PPII converts to a ␤-like structure with increasing temperature (13). These findings raise several important questions regarding the structure of unfolded proteins: Although alanine is arguably a reasonable model for the unperturbed peptide backbone, is PPII also present in unfolded peptide chains composed of nonalanine nonproline residues? Is there an intrinsic PPII propensity for each individual side chain? If PPII is in equilibrium with ␤-structure, is there a correlation between scales of PPII propensity and analogous ␤-sheet scales? To what extent is PPII sequence and context dependent?Here, we address these questions by analyzing a series of end-blocked host pentapeptides AcGGXGGNH 2 , where X denotes 19 natural amino acids except glycine. Members of the series are found to differ in their extent of PPII conformation as determined by NMR and CD spectroscopy. Our results lead to the following conclusions: PPII is present as a dominant conformation in the majority of AcGGXGGNH 2 peptides. Different side chains show distinct propensities to adopt PPII in these unfolded molecules. Importantly, we find an inverse correlation between the determined PPII scale and the ␤-sheet-forming propensities derived from a zinc-finger model system (45) when 18 aa (except Gly and Pro) are divided into two groups: one, the nonpolar ␤-branched and bulky aromatic residues (VIWFY) and the other all of the remaining side chains. Finally, we find a correlation between our PPII scale in AcGGXGGNH 2 and a PPII scale derived from alternative model peptides such as AcPPPXPPPGYNH 2 (46). Still there are indications that the PPII scale is likely to be sequence and context dependent (47). Materials and MethodsPeptides Synthesis and Purification. Peptides were assembled on Rink Amide res...

Comparison of multiple Amber force fields and development of improved protein backbone parameters

“…The experimental studies of Schweitzer-Stenner & Eker on trialanines 53,54 and tetraalanines 55 in water using polarized Raman, FT-IR and VCD spectroscopy confirm the dominance of PP II conformation in tetraalanines, while a 50:50 mixture of PP II and extended β-strand-like conformations was observed for trialanines. Other studies [56][57][58] , mostly from Kallenbach and colleagues, have confirmed that short alanine peptides form predominantly PP II conformation, which is in temperature dependent equilibrium with extended β-strand conformations. Taken together, these experimental findings suggest that short alanine peptides are found predominantly in PP II -like structures with varying degree of extended β-strand, and possibly smaller fractions of α-helical conformations.…”

Implementation of the SCC-DFTB Method for Hybrid QM/MM Simulations within the Amber Molecular Dynamics Package

“…Recent experimental results suggest that the backbone preferences in proteins are already present in blocked aminoacids. 55,56 A number of experimental 55,[57][58][59][60] and theoretical, [61][62][63][64][65][66][67][68][69][70][71][72][73][74][75][76][77][78] studies indicate that the potential energy surface for AD in vacuum and in solution are considerably different: While in the gas-phase the global minimum is believed to be a C7 eq structure (ϕ− 83°, ψ~73°), 70 interaction with water favors the polyproline-II (P II , (ϕ~−75°, ψ~150°) conformation. 60 AD has also been used previously to investigate the performance of the SCC-DFTB method as compared to different classical force fields.…”

Length Effects in Antimicrobial Peptides of the (RW)nSeries

“…2). The negative band around 200 nm is characteristic of small unfolded peptides, while the band at 225 nm is due to the indole side chain of W (21,57), as seen in the CD spectrum of a peptide such as GGWGG containing a single chiral W residue (44). Each of the five peptides exhibits distinctive CD spectra in the presence of POPG and POPC.…”

“…CD spectroscopy is widely used to analyze the secondary structure of proteins and peptides because it is extremely sensitive to conformational changes. (RW) n in buffer appears to be unfolded due to the negative band around 200 nm that is characteristic of unfolded model peptides (44); the positive band around 225 nm due to the indole side chain is Trp specific (21,57). Peptide interactions with liposomes are accompanied by distinct CD spectral changes.…”