Conformations and free energy landscapes of polyproline peptides

Abstract

The structure of the proline amino acid allows folded polyproline peptides to exist as both left-(PPII) and right-handed (PPI) helices. We have characterized the free energy landscapes of hexamer, nanomer, and tridecamer polyproline peptides in gas phase and implicit water as well as explicit hexane and 1-propanol for the nanomer. To enhance the sampling provided by regular molecular dynamics, we used the recently developed adaptively biased molecular dynamics method, which describes Landau free energy maps in terms of relevant collective variables. These maps, as a function of the collective variables of handedness, radius of gyration, and three others based on the peptide torsion angle ω, were used to determine the relative stability of the different structures, along with an estimate of the transition pathways connecting the different minima. Results show the existence of several metastable isomers and therefore provide a complementary view to experimental conclusions based on photo-induced electron transfer experiments with regard to the existence of stable heterogeneous subpopulations in PPII polyproline.cis-trans isomerization | left-handed helix | molecular dynamics | PPI | PPII T he concept of molecular chirality is used to describe molecular structures that are not superposable on their mirror images. Chiral molecules are quite prevalent in biological systems, which are primarily homochiral systems. For example, most proteins contain only L-amino acids, while DNA is made up primarily of D-deoxyribose. The relationship between chirality and helical polypeptide structure was first mentioned by Pauling (1) in reference to the α-helix. The naturally occurring L-amino acids predominantly form right-handed helices, whereas their stereoisomers D-amino acids favor left-handed helices. Indeed, right-handed helices are prevalent in biology, not only in peptides (with structural motifs such as α-helix , 3 10 helix, and π helix) but also in the double-helical structure of B-and A-DNA. Although much less common, left-handed helices with the same chiral units as right-handed helices also exist, such as those found in PPII and in Z-DNA.In this paper, we investigate the free energy landscape of several short polyproline peptides. Proline is unique among the natural amino acids in that its side chain is cyclized to the backbone, restricting its backbone dihedral angle to φ = −75• , giving proline an exceptional rigidity and a considerably restricted conformational space. Polyproline is known to form helical structures with two well-characterized conformations: a left-handed polyproline helix (PPII) is formed when the sequential residues all adopt backbone dihedral angles (φ, ψ) of (−75• , 146• ), with all prolyl bonds in the trans-isomer conformation (i.e. backbone dihedral angle ω = 180• ) with 3 residues per turn; and a more compact right-handed polyproline helix (PPI) is formed with all sequential residues adopting dihedral angles of roughly (−75• , 160• ) and all prolyl bonds assume a cis-isomer conformation (i.e. b...

Measuring the Elasticity of Poly‐l‐Proline Helices with Terahertz Spectroscopy

“…The 10 % elongation of the PP‐II helix and concomitant dihedral angle changes resulted in an energy increase within the polypeptide of 10.02 kJ mol −1 per Å of distortion, which serves as a preliminary indicator of the barrier opposing the formation of PP‐I. These results are consistent with previous studies of the poly‐ l ‐proline transformation, which found that large activation energy barriers exist along the conversion coordinate 15, 29…”

Measuring the Elasticity of Poly‐l‐Proline Helices with Terahertz Spectroscopy

“…These results are consistent with previous studies of the poly-l-proline transformation, which found that large activation energy barriers exist along the conversion coordinate. [15,29] Themeasurement of biopolymer elasticity through acombined approach of THz-TDS experiments and ss-DFT simulations enables quantification of molecular rigidities to be achieved in arelatively straightforward way.This methodology has yielded the previously unmeasured Youngs moduli of the widespread poly-l-proline polypeptide in both its helical forms,a nd revealed them to be considerably more elastic than expected. This prompts contemplation of their role as an analytical standard for rigidity.…”

Determining Protein Complex Structures Based on a Bayesian Model of in Vivo Förster Resonance Energy Transfer (FRET) Data

“…To do so, we used MD simulations combined with advanced sampling techniques to explore the conformational landscape of the test structures. Although polyproline peptides have often been employed as a spectroscopic ruler, several experimental (56 -58) and computational (48,57) studies have questioned the role of polyproline as a "rigid rod" in a single dominant conformation. Prolyl isomerization from the trans to cis isomer, whose activation energy is on the order of 10 to 20 kcal/mol (59,60), converts the left-handed polyproline II helix (PPII) to the more compact right-handed polyproline I helix (PPI).…”

“…16 to 40 replicas were used to span a temperature range from 300 to 600 K. A collective variable measuring the number of prolines in cis and trans conformations was used to accelerate proline cis-trans isomerization. For an n-mer peptide, this collective variable was defined (48) as ⍀ ϭ ¥ iϭ1 nϪ1 cos i where the torsional angle formed by the quadruplet C␣-C-N-C␣ was equal to 0°for the cis isomer and to 180°for the trans isomer. The well-tempered (49) variant of metadynamics was used, with a bias factor equal to 30 and an initial depo-sition rate of 1 kJ ⅐ mol Ϫ1 ⅐ ps Ϫ1 .…”