𝔖 Bobbio Scriptorium
✦   LIBER   ✦

Reconstruction of protein conformations from estimated positions of the Cα coordinates

✍ Scribed by Philip W. Payne

Publisher
Cold Spring Harbor Laboratory Press
Year
2008
Tongue
English
Weight
1013 KB
Volume
2
Category
Article
ISSN
0961-8368

No coin nor oath required. For personal study only.

✦ Synopsis

Abstract

Protein C~α~ coordinates are used to accurately reconstruct complete protein backbones and side‐chain directions. This work employs potentials of mean force to align semirigid peptide groups around the axes that connect successive C~α~ atoms. The algorithm works well for all residue types and secondary structure classes and is stable for imprecise C~α~ coordinates. Tests on known protein structures show that root mean square errors in predicted main‐chain and C~β~ coordinates are usually less than 0.3 Å. These results are significantly more accurate than can be obtained from competing approaches, such as modeling of backbone conformations from structurally homologous fragments.

📜 SIMILAR VOLUMES

The reconstruction of side-chain conform
The reconstruction of side-chain conformations from protein Cα coordinates
✍ Kaiwan Gan; James M. Coxon; A. John McKinnon; Gillian H. Worth 📂 Article 📅 1997 🏛 Wiley (John Wiley & Sons) 🌐 English ⚖ 216 KB 👁 1 views

A model of nine proteins including side-chain atoms have been built from the known C a coordinates and amino acid sequences using a Monte Carlo Protein Building Annealing method. The Cartesian coordinates for the side-chain atoms were established with bond lengths and angles selected randomly from w

The reconstruction of a protein backbone
The reconstruction of a protein backbone from Cα coordinates
✍ Kaiwan Gan; Peter Alexander; James M. Coxon; A. John McKinnon; Gillian H. Worth 📂 Article 📅 1997 🏛 Wiley (John Wiley & Sons) 🌐 English ⚖ 87 KB

A Monte Carlo Protein Building method to construct the backbone and C b atomic coordinates from known C a coordinates is reported. The method selects values of dihedral angles from ranges established from a statistical analysis of the relationship between dihedral angles of the backbone and C a coor

Reconstruction of the 3D coordinates of
Reconstruction of the 3D coordinates of α-carbon atoms of proteins from a pair of stereographic figures
✍ Yoriko Iwata; Atsushi Kasuya; Schuichi Miyamoto 📂 Article 📅 1996 🏛 Springer Netherlands 🌐 English ⚖ 845 KB

In an attempt to promptly use the experimentally determined structures of proteins in modeling studies, we have developed the program ReconstCcl to generate the 3D coordinates of a-carbon atoms from a pair of stereographic figures. Calculations of the 3D coordinates were performed by estimating the

Conformational analysis of the Gαs prote
Conformational analysis of the Gαs protein C-terminal region
✍ Anna Maria D'ursi; Stefania Albrizio; Giovanni Greco; Sonia Mazzeo; Maria R. Maz 📂 Article 📅 2002 🏛 John Wiley and Sons 🌐 English ⚖ 484 KB

The C-terminal domain of the heterotrimeric G protein a-subunits plays a key role in selective activation of G proteins by their cognate receptors. Several C-terminal fragments of Galpha(s) (from 11 to 21 residues) were recently synthesized. The ability of these peptides to stimulate agonist binding

Structural versatility of peptides from
Structural versatility of peptides from Cα,α-disubstituted glycines: Preferred conformation of the Cα,α-diphenylglycine residue
✍ M. Crisma; G. Valle; G. M. Bonora; E. De Menego; C. Toniolo; F. Lelj; V. Barone; 📂 Article 📅 1990 🏛 Wiley (John Wiley & Sons) 🌐 English ⚖ 751 KB

## Abstract The preferred conformation of the C^α,α^‐diphenylglycine residue was determined in simple derivatives and dipeptides. The dipeptides were synthesized by the 5(4__H__)‐oxazolone (from the N‐__para__‐bromobenzoylated amino acid) method. This activated intermediate and a reaction by‐produc