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Literature DB >> 21618253

Three-residue loop closure in proteins: a new kinematic method reveals a locus of connected loop conformations.

Abstract

The closure of a three-residue loop was studied using a developed kinematic method. It was shown that there are infinite number of three-residue loops (a locus of conformations), which can connect two segments of a polypeptide. This adds to the current understanding of a finite number of conformations for three-residue loop-closure. In the developed method, some of the equations can be solved analytically to reduce the computation cost. Benefiting from the reduced computation time, we determined all the relative positions of two polypeptide segments that can be connected by a three-residue loop.

Entities: Chemical Species

Mesh：

Substances：
Proteins

Year: 2011 PMID： 21618253 PMCID： PMC4154380 DOI： 10.1002/jcc.21812

Source DB: PubMed Journal: J Comput Chem ISSN： 0192-8651 Impact factor: 3.376

12 in total

1. Conformational changes of an ion-channel during gating and emerging electrophysiologic properties: Application of a computational approach to cardiac Kv7.1.

Authors: Ali Nekouzadeh; Yoram Rudy
Journal: Prog Biophys Mol Biol Date: 2015-12-30 Impact factor: 3.667

2. Continuum molecular simulation of large conformational changes during ion-channel gating.

Authors: Ali Nekouzadeh; Yoram Rudy
Journal: PLoS One Date: 2011-05-20 Impact factor: 3.240

3. Clustering and percolation in protein loop structures.

Authors: Xubiao Peng; Jianfeng He; Antti J Niemi
Journal: BMC Struct Biol Date: 2015-10-29

3 in total

Three-residue loop closure in proteins: a new kinematic method reveals a locus of connected loop conformations.

1. Generation of accurate protein loop conformations through low-barrier molecular dynamics.

2. A kinematic view of loop closure.

3. Stereochemistry of polypeptide chain configurations.

4. A hierarchical approach to all-atom protein loop prediction.

5. On the structure of the inverse kinematics map of a fragment of protein backbone.

6. A multiscale model linking ion-channel molecular dynamics and electrostatics to the cardiac action potential.

7. Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling.

8. Prediction of Protein Loop Conformations using the AGBNP Implicit Solvent Model and Torsion Angle Sampling.

9. Toward better refinement of comparative models: predicting loops in inexact environments.

10. High-resolution design of a protein loop.

1. Conformational changes of an ion-channel during gating and emerging electrophysiologic properties: Application of a computational approach to cardiac Kv7.1.

2. Continuum molecular simulation of large conformational changes during ion-channel gating.

3. Clustering and percolation in protein loop structures.