Stereodependent and solvent‐specific formation of unusual β‐structure through side chain‐backbone H‐bonding in C4(<i>S</i>)‐(NH<sub>2</sub>/OH/NHCHO)‐L‐prolyl polypeptides

Bansode, Nitin D.; Madhanagopal, Bharath Raj; Sonar, Mahesh V.; Ganesh, Krishna N.

doi:10.1002/bip.22981

Cited by 4 publications

(6 citation statements)

References 51 publications

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“…Conformation vs Morphology. The observed β-structure in TFE for the cis-4-substituted L/D-prolyl polypeptides correlates well with the self-assembly of these peptides into nanofibers 24,25,30 as seen from the FESEM images. The polypeptides with the PPII form assemble into irregular or spherical nanostructures (Figures 8A,D and 9A,C) in buffer.…”

Section: Effect Of Concentration On Morphology Of L C -Ampsupporting

confidence: 69%

Conformation and Morphology of 4-(NH₂/OH)-Substituted l/d-Prolyl Polypeptides: Effect of Homo- and Heterochiral Backbones on Formation of β-Structures and Nanofibers

Madhanagopal

Bansode

et al. 2020

ACS Omega

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The relative stereochemistry of C2 and C4 in 4-substituted prolyl polypeptides plays an important role in defining the derived conformation in solution. cis -(2 S ,4 S )-Amino/hydroxy- l -prolyl polypeptide ( l C - Amp 9 / l C - Hyp 9 ) shows a PPII conformation in phosphate buffer and a β-structure in a relatively hydrophobic solvent, trifluoroethanol (TFE). It is now demonstrated that the homochiral enantiomeric cis-substituted d -prolyl polypeptide ( d C - Amp 9 / d C - Hyp 9 ) exhibits mirror image β-structures in TFE. In the case of alternating heterochiral prolyl peptides, it is the trans-substituted [ l T (2 S ,4R)- d T (2 R ,4 S )] n prolyl polypeptide that shows β-structures in TFE, while the cis-substituted [ l C (2 S ,4 S )- d C (2 R ,4 R )] n prolyl polypeptide is disordered in both phosphate buffer and TFE. The results highlight the important chirality-specific structural requirements for β-structure formation. The observed conformation in solution (circular dichroism (CD)) is also correlated with the morphology of the self-assemblies (field emission scanning electron microscopy (FESEM)), with the PPII form leading to spherical nanoparticles and β-structures leading to nanofiber formation. The results shed light on the role of relative stereochemistry at C2 and C4 in defining the polyproline peptide conformation in solution and how different conformations drive self-assemblies of peptides toward specific nanostructures.

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Section: Effect Of Concentration On Morphology Of L C -Ampsupporting

confidence: 69%

Conformation and Morphology of 4-(NH₂/OH)-Substituted l/d-Prolyl Polypeptides: Effect of Homo- and Heterochiral Backbones on Formation of β-Structures and Nanofibers

Madhanagopal

Bansode

et al. 2020

ACS Omega

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“…Since β‐strand structure is the least stabilized owing to the carbonyl‐carbonyl interactions, the β‐contribution in the absence of an alternative stabilizing force seems very unlikely. For example, isomerization of some model oligoproline‐based structure into the β‐like antiparallel sheets was reported in nonpolar media, when this was assisted by backbone‐side chain hydrogen bond formation, but not otherwise . Thus, the CD curves in the oligo‐Oic sequences can be attributed to dominating P II helix, which is encapsulated in a hydrophobic shell and is still sensitive to the presence of the polar groups in the solvent via the secondary effects .…”

Section: Discussionmentioning

confidence: 99%

“…The latter were documented only very recently for peptides formed by specific proline analogues. [35][36][37]…”

Section: Hydrophobic Peptidesmentioning

confidence: 99%

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Exploring hydrophobicity limits of polyproline helix with oligomeric octahydroindole‐2‐carboxylic acid

Kubyshkin

Budiša

2018

Journal of Peptide Science

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The polyproline-II helix is the most extended naturally occurring helical structure and is widely present in polar, exposed stretches and "unstructured" denatured regions of polypeptides. Can it be hydrophobic? In this study, we address this question using oligomeric peptides formed by a hydrophobic proline analogue, (2S,3aS,7aS)-octahydroindole-2-carboxylic acid (Oic). Previously, we found the molecular principles underlying the structural stability of the polyproline-II conformation in these oligomers, whereas the hydrophobicity of the peptide constructs remains to be examined. Therefore, we investigated the octan-1-ol/water partitioning and inclusion in detergent micelles of the oligo-Oic peptides. The results showed that the hydrophobicity is remarkably enhanced in longer oligomeric sequences, and the oligo-Oic peptides with 3 to 4 residues and higher are specific towards hydrophobic environments. This contrasts significantly to the parent oligoproline peptides, which were moderately hydrophilic. With these findings, we have demonstrated that the polyproline-II structure is compatible with nonpolar media, whereas additional manipulations of the terminal functionalities feature solubility in extremely nonpolar solvents such as hexane.

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“…However, it can also be manipulated with the substitution pattern in proline [55,56]. Moreover, it was recently shown that the oligoproline scaffold can also adopt a special type of a β-structure in case of certain chemical analogues [57,58].…”

Section: The Proline Worldmentioning

confidence: 99%

The Alanine World Model for the Development of the Amino Acid Repertoire in Protein Biosynthesis

Kubyshkin

Budiša

2019

IJMS

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A central question in the evolution of the modern translation machinery is the origin and chemical ethology of the amino acids prescribed by the genetic code. The RNA World hypothesis postulates that templated protein synthesis has emerged in the transition from RNA to the Protein World. The sequence of these events and principles behind the acquisition of amino acids to this process remain elusive. Here we describe a model for this process by following the scheme previously proposed by Hartman and Smith, which suggests gradual expansion of the coding space as GC–GCA–GCAU genetic code. We point out a correlation of this scheme with the hierarchy of the protein folding. The model follows the sequence of steps in the process of the amino acid recruitment and fits well with the co-evolution and coenzyme handle theories. While the starting set (GC-phase) was responsible for the nucleotide biosynthesis processes, in the second phase alanine-based amino acids (GCA-phase) were recruited from the core metabolism, thereby providing a standard secondary structure, the α-helix. In the final phase (GCAU-phase), the amino acids were appended to the already existing architecture, enabling tertiary fold and membrane interactions. The whole scheme indicates strongly that the choice for the alanine core was done at the GCA-phase, while glycine and proline remained rudiments from the GC-phase. We suggest that the Protein World should rather be considered the Alanine World, as it predominantly relies on the alanine as the core chemical scaffold.

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Stereodependent and solvent‐specific formation of unusual β‐structure through side chain‐backbone H‐bonding in C4(S)‐(NH₂/OH/NHCHO)‐L‐prolyl polypeptides

Cited by 4 publications

References 51 publications

Conformation and Morphology of 4-(NH₂/OH)-Substituted l/d-Prolyl Polypeptides: Effect of Homo- and Heterochiral Backbones on Formation of β-Structures and Nanofibers

Conformation and Morphology of 4-(NH₂/OH)-Substituted l/d-Prolyl Polypeptides: Effect of Homo- and Heterochiral Backbones on Formation of β-Structures and Nanofibers

Exploring hydrophobicity limits of polyproline helix with oligomeric octahydroindole‐2‐carboxylic acid

The Alanine World Model for the Development of the Amino Acid Repertoire in Protein Biosynthesis

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Stereodependent and solvent‐specific formation of unusual β‐structure through side chain‐backbone H‐bonding in C4(S)‐(NH2/OH/NHCHO)‐L‐prolyl polypeptides

Cited by 4 publications

References 51 publications

Conformation and Morphology of 4-(NH2/OH)-Substituted l/d-Prolyl Polypeptides: Effect of Homo- and Heterochiral Backbones on Formation of β-Structures and Nanofibers

Conformation and Morphology of 4-(NH2/OH)-Substituted l/d-Prolyl Polypeptides: Effect of Homo- and Heterochiral Backbones on Formation of β-Structures and Nanofibers

Exploring hydrophobicity limits of polyproline helix with oligomeric octahydroindole‐2‐carboxylic acid

The Alanine World Model for the Development of the Amino Acid Repertoire in Protein Biosynthesis

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Product

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About

Stereodependent and solvent‐specific formation of unusual β‐structure through side chain‐backbone H‐bonding in C4(S)‐(NH₂/OH/NHCHO)‐L‐prolyl polypeptides

Conformation and Morphology of 4-(NH₂/OH)-Substituted l/d-Prolyl Polypeptides: Effect of Homo- and Heterochiral Backbones on Formation of β-Structures and Nanofibers

Conformation and Morphology of 4-(NH₂/OH)-Substituted l/d-Prolyl Polypeptides: Effect of Homo- and Heterochiral Backbones on Formation of β-Structures and Nanofibers