Literature DB >> 21547966

Amino acids with hydrogen-bonding side chains have an intrinsic tendency to sample various turn conformations in aqueous solution.

Andrew Hagarman1, Daniel Mathieu, Siobhan Toal, Thomas J Measey, Harald Schwalbe, Reinhard Schweitzer-Stenner.   

Abstract

Local structure in unfolded proteins, especially turn segments, has been suggested to initiate the hierarchical protein-folding process. To determine the intrinsic propensity to form such turn structures, amide I' band profiles of the Raman, IR, and vibrational circular dichroism (VCD) spectra, and several structure-sensitive NMR J-coupling constants, have been measured for a series of GxG (x=D, N, T, C) peptides, in which the central x residues are abundant in various turn motifs in folded proteins. In addition, we revisited earlier measured GSG experimental data. To check whether this relatively high propensity for these residues to sample turns reflects an intrinsic propensity, the experimental data were analyzed in terms of conformational distributions that can be described as a superposition of two-dimensional Gaussian distributions associated with different so-called mesostates. The analysis reveals that the investigated residues sample dihedral angles similar to those found in the corner residues of various turns, namely, type I/I', II/II', and IV β-turns. Aspartic acid (D) was found to predominantly sample regions attributed to turns, including distributions at the upper border of the upper-right quadrant of the Ramachandran plot, which bear some resemblance to asx-turns observed in proteins. This conformation enables hydrogen bonding between the side-chain carboxylate and the C-terminal amide group. Altogether, the study shows that the high propensity for T, S, C, N, and D to be located in turn motifs reflects, to a substantial degree, an intrinsic property and supports the role of these residues as initiation sites for hierarchical folding processes that can lead to compact structures in the unfolded state of peptides and proteins.
Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Entities:  

Mesh:

Substances:

Year:  2011        PMID: 21547966     DOI: 10.1002/chem.201100016

Source DB:  PubMed          Journal:  Chemistry        ISSN: 0947-6539            Impact factor:   5.236


  15 in total

1.  Conformational distributions of denatured and unstructured proteins are similar to those of 20 × 20 blocked dipeptides.

Authors:  Kwang-Im Oh; Young-Sang Jung; Geum-Sook Hwang; Minhaeng Cho
Journal:  J Biomol NMR       Date:  2012-03-18       Impact factor: 2.835

2.  Dihedral angle preferences of amino acid residues forming various non-local interactions in proteins.

Authors:  Konda Mani Saravanan; Samuel Selvaraj
Journal:  J Biol Phys       Date:  2017-06-02       Impact factor: 1.365

3.  Beyond basins: φ,ψ preferences of a residue depend heavily on the φ,ψ values of its neighbors.

Authors:  Scott A Hollingsworth; Matthew C Lewis; P Andrew Karplus
Journal:  Protein Sci       Date:  2016-07-11       Impact factor: 6.725

4.  Anticooperative Nearest-Neighbor Interactions between Residues in Unfolded Peptides and Proteins.

Authors:  Reinhard Schweitzer-Stenner; Siobhan E Toal
Journal:  Biophys J       Date:  2018-03-13       Impact factor: 4.033

5.  Randomizing of Oligopeptide Conformations by Nearest Neighbor Interactions between Amino Acid Residues.

Authors:  Reinhard Schweitzer-Stenner; Bridget Milorey; Harald Schwalbe
Journal:  Biomolecules       Date:  2022-05-11

6.  pH-Independence of trialanine and the effects of termini blocking in short peptides: a combined vibrational, NMR, UVCD, and molecular dynamics study.

Authors:  Siobhan Toal; Derya Meral; Daniel Verbaro; Brigita Urbanc; Reinhard Schweitzer-Stenner
Journal:  J Phys Chem B       Date:  2013-03-28       Impact factor: 2.991

7.  New Dynamic Rotamer Libraries: Data-Driven Analysis of Side-Chain Conformational Propensities.

Authors:  Clare-Louise Towse; Steven J Rysavy; Ivan M Vulovic; Valerie Daggett
Journal:  Structure       Date:  2016-01-05       Impact factor: 5.006

8.  Circular Permutation of the Trp-cage: Fold Rescue upon Addition of a Hydrophobic Staple.

Authors:  Aimee Byrne; Brandon L Kier; D V Williams; Michele Scian; Niels H Andersen
Journal:  RSC Adv       Date:  2013-11-21       Impact factor: 3.361

9.  Short peptides as predictors for the structure of polyarginine sequences in disordered proteins.

Authors:  Bridget Milorey; Reinhard Schweitzer-Stenner; Brian Andrews; Harald Schwalbe; Brigita Urbanc
Journal:  Biophys J       Date:  2021-01-14       Impact factor: 4.033

10.  Secondary structure, a missing component of sequence-based minimotif definitions.

Authors:  David P Sargeant; Michael R Gryk; Mark W Maciejewski; Vishal Thapar; Vamsi Kundeti; Sanguthevar Rajasekaran; Pedro Romero; Keith Dunker; Shun-Cheng Li; Tomonori Kaneko; Martin R Schiller
Journal:  PLoS One       Date:  2012-12-07       Impact factor: 3.240

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.