A fresh look at the Ramachandran plot and the occurrence of standard structures in proteins

SA Hollingsworth, PA Karplus - 2010 - degruyter.com
The Ramachandran plot is among the most central concepts in structural biology, seen in
publications and textbooks alike. However, with the increasing numbers of known protein …

Molecular spacers for physicochemical investigations based on novel helical and extended peptide structures

C Toniolo, M Crisma, F Formaggio… - Peptide Science …, 2004 - Wiley Online Library
A proper understanding of the detailed nature and mechanism of physicochemical
interactions depends heavily upon our ability to design and synthesize conformationally …

Theoretical and experimental demonstration of the importance of specific nonnative interactions in protein folding

A Zarrine-Afsar, S Wallin, AM Neculai… - Proceedings of the …, 2008 - National Acad Sciences
Many experimental and theoretical studies have suggested a significant role for nonnative
interactions in protein folding pathways, but the energetic contributions of these interactions …

Local protein structures

B Offmann, M Tyagi, AG de Brevern - Current Bioinformatics, 2007 - ingentaconnect.com
Protein structures are classically described as composed of two regular states, the α-helices
and the β-strands and one non-regular and variable state, the coil. Nonetheless, this simple …

Conformational studies on peptides containing α, α-disubstituted α-amino acids: chiral cyclic α, α-disubstituted α-amino acid as an α-helical inducer

Y Demizu, M Doi, M Kurihara, H Okuda… - Organic & …, 2011 - pubs.rsc.org
Four types of α, α-disubstituted amino acids {ie, α-aminoisobutyric acid (Aib), 1-
aminocyclopentanecarboxylic acid (Ac5c),(3S, 4S)-1-amino-(3, 4-dimethoxy) …

Secondary structure adopted by the Gly-Gly-X repetitive regions of dragline spider silk

GM Gray, A Van der Vaart, C Guo, J Jones… - International journal of …, 2016 - mdpi.com
Solid-state NMR and molecular dynamics (MD) simulations are presented to help elucidate
the molecular secondary structure of poly (Gly-Gly-X), which is one of the most common …

Sequence and structure patterns in proteins from an analysis of the shortest helices: implications for helix nucleation

L Pal, P Chakrabarti, G Basu - Journal of molecular biology, 2003 - Elsevier
The shortest helices (three-length 310 and four-length α), most abundant among helices of
different lengths, have been analyzed from a database of protein structures. A characteristic …

Asymmetric 1,4‐Addition Reactions Catalyzed by N‐Terminal Thiourea‐Modified Helical l‐Leu Peptide with Cyclic Amino Acids

K Sato, T Umeno, A Ueda, T Kato… - … –A European Journal, 2021 - Wiley Online Library
N‐terminal thiourea‐modified l‐Leu‐based peptide {(3, 5‐diCF3Ph) NHC (= S)‐(l‐Leu‐l‐
Leu‐Ac5c) 2‐OMe} with five‐membered ring α, α‐disubstituted α‐amino acids (Ac5c) …

Discrete analyses of protein dynamics

TJ Narwani, P Craveur, NK Shinada… - Journal of …, 2020 - Taylor & Francis
Protein structures are highly dynamic macromolecules. This dynamics is often analysed
through experimental and/or computational methods only for an isolated or a limited number …

One‐Handed Helical Screw Direction of Homopeptide Foldamer Exclusively Induced by Cyclic α‐Amino Acid Side‐Chain Chiral Centers

Y Demizu, M Doi, M Kurihara… - … A European Journal, 2012 - Wiley Online Library
Chiral cyclic α, α‐disubstituted amino acids,(3S, 4S)‐and (3R, 4R)‐1‐amino‐3, 4‐(dialkoxy)
cyclopentanecarboxylic acids ((S, S)‐and (R, R)‐Ac5cdOR; R: methyl, methoxymethyl), were …