PubMed Health⌕ Search
Home/Archive/PubMed

PubMed · 11095708

Three-helix-bundle protein in a Ramachandran model.

A Irbäck·F Sjunnesson·S Wallin
View original source ↗Export metadata ↓

Abstract

We study the thermodynamic behavior of a model protein with 54 amino acids that forms a three-helix bundle in its native state. The model contains three types of amino acids and five to six atoms per amino acid and has the Ramachandran torsional angles phi(i), psi(i) as its degrees of freedom. The force field is based on hydrogen bonds and effective hydrophobicity forces. For a suitable choice of the relative strength of these interactions, we find that the three-helix-bundle protein undergoes an abrupt folding transition from an expanded state to the native state. Also shown is that the corresponding one- and two-helix segments are less stable than the three-helix sequence.

Explore related subjects

Models, MolecularProtein ConformationProteinsThermodynamicsJournal ArticleResearch Support, Non-U.S. Gov't

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

A Irbäck, F Sjunnesson, S Wallin. 2000-12-05. Three-helix-bundle protein in a Ramachandran model.. https://doi.org/10.1073/pnas.240245297

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related citations

PubMed2002

Design of three-dimensional, millimeter-scale models for molecular folding.

This communication describes the fabrication of three-dimensional structures of organic polymers using principles of design inspired by protein folding. The structures consist of rigid polyhedral components with dimensions of a few millimeters ("microdomains"), representing alpha-helical and beta-sheet secondary structures, connected with flexible linkers representing loops or turns. These structures were fabricated from polyurethane using photolithographic and soft lithographic techniques. The surfaces of the microdomains were patterned into hydrophobic and hydrophilic regions, and a hydrophobic photocurable liquid (serving both as lubricant and adhesive) was selectively precipitated onto the hydrophobic areas. The unfolded structures were suspended in water and agitated by tumbling. Self-assembly occurred through coalescence of the thin films of hydrophobic liquid, and was caused by minimization of the free energy of the interface between the liquid adhesive and the water. The self-assembled structures were locked in place by curing the adhesive with UV light. These results demonstrate the use of concepts abstracted from the study of proteins-including attractive hydrophobic interactions, shape complementarity, and conformational constraint-in the self-assembly of complex, three-dimensional structures on the millimeter scale.

Models, Molecular↗
PubMed2001

A dipolar coupling based strategy for simultaneous resonance assignment and structure determination of protein backbones.

A new approach for simultaneous protein backbone resonance assignment and structure determination by NMR is introduced. This approach relies on recent advances in high-resolution NMR spectroscopy that allow observation of anisotropic interactions, such as dipolar couplings, from proteins partially aligned in field ordered media. Residual dipolar couplings are used for both geometric information and a filter in the assembly of residues in a sequential manner. Experimental data were collected in less than one week on a small redox protein, rubredoxin, that was 15N enriched but not enriched above 1% natural abundance in 13C. Given the acceleration possible with partial 13C enrichment, the protocol described should provide a very rapid route to protein structure determination. This is critical for the structural genomics initiative where protein expression and structural determination in a high-throughput manner will be needed.

Models, Molecular↗
PubMed2001

Small molecule somatostatin receptor subtype-2 antagonists.

The first potent small molecule sst2 antagonists are reported. Altering known sst2 agonist molecules yielded compounds with high sst2 binding affinity and full antagonist activity. Compound 7a, for example, displaced somatostatin binding to the sst2 receptor with an IC(50)=2.9 nM and antagonized somatostatin action with an IC(50)=29nM.

Models, Molecular↗