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 …
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 …
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 …
residue X in the peptides NH2‐XAKAAAAKAAAAKAAGY‐CONH2 and in Ac …
Rules for α-helix termination by glycine
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 …
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 …
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 …
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
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 …
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 …
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
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 …
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 …
We identified 2,024 loops of one to eight residues in length, with acceptable main‐chain …