Design of folded peptides

J Venkatraman, SC Shankaramma… - Chemical reviews, 2001 - ACS Publications
The construction of complex protein folds relies on the precise conversion of a linear
polypeptide chain into a compact 3-dimensional structure. The interplay of forces that link …

Aib residues in peptaibiotics and synthetic sequences: analysis of nonhelical conformations

S Aravinda, N Shamala, P Balaram - Chemistry & biodiversity, 2008 - Wiley Online Library
The α‐aminoisobutyric (Aib) residue has generally been considered to be a strongly
helicogenic residue as evidenced by its ability to promote helical folding in synthetic and …

N‐and C‐cap** preferences for all 20 amino acids in α‐helical peptides

AJ Doig, RL Baldwin - Protein Science, 1995 - Wiley Online Library
We have determined the N‐and C‐cap** preferences of all 20 amino acids by substituting
residue X in the peptides NH2‐XAKAAAAKAAAAKAAGY‐CONH2 and in Ac …

Rules for α-helix termination by glycine

R Aurora, R Srinivasan, GD Rose - Science, 1994 - science.org
A predictive rule for protein folding is presented that involves two recurrent glycine-based
motifs that cap the carboxyl termini of α helices. In proteins, helices that terminated in glycine …

Beta-hairpins in proteins revisited: lessons for de novo design.

K Gunasekaran, C Ramakrishnan… - Protein …, 1997 - academic.oup.com
Beta-Hairpins with short connecting loops (1-5 residues) have been identified from a data
set of 250 non-homologous, high resolution (< or= 2.0 A) protein crystal structures. The …

Stereochemical control of peptide folding

R Kaul, P Balaram - Bioorganic & medicinal chemistry, 1999 - Elsevier
Stereochemically constrained amino acid residues that strongly favour specific backbone
conformations may be used to nucleate and stabilize specific secondary structures in …

Stereochemical punctuation marks in protein structures: glycine and proline containing helix stop signals

K Gunasekaran, HA Nagarajaram… - Journal of molecular …, 1998 - Elsevier
An analysis on the nature of α-helix stop signals has been carried out, using a dataset of
1057 helices identified from 250 high resolution (⩽ 2.0 Å), non-homologous, protein crystal …

The occurrence of C H… O hydrogen bonds in α‐helices and helix termini in globular proteins

K Manikandan, S Ramakumar - Proteins: Structure, Function …, 2004 - Wiley Online Library
A comprehensive database analysis of C H… O hydrogen bonds in 3124 α‐helices and
their corresponding helix termini has been carried out from a nonredundant data set of high …

ω-Amino acids in peptide design. Crystal structures and solution conformations of peptide helices containing a β-alanyl-γ-aminobutyryl segment

IL Karle, A Pramanik, A Banerjee… - Journal of the …, 1997 - ACS Publications
Insertion of achiral ω-amino acids into peptide sequences results in replacement of scissile
peptide bonds by proteolytically stable C− C bonds. This provides a convenient means of …

Conformational analysis and clustering of short and medium size loops connecting regular secondary structures: a database for modeling and prediction

LE Donate, SD Rufino, LHJ Canard… - Protein …, 1996 - Wiley Online Library
Loops are regions of nonrepetitive conformation connecting regular secondary structures.
We identified 2,024 loops of one to eight residues in length, with acceptable main‐chain …