Related Experiment Video
Updated: May 7, 2026
09:51
Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
A comparison of reduced coordinate sets for describing protein structure
Konrad Hinsen1, Shuangwei Hu, Gerald R Kneller
1Centre de Biophysique Moléculaire (CNRS), Rue Charles Sadron, 45071 Orléans, France and Synchrotron SOLEIL, L'Orme des Merisiers, BP 48, 91192 Gif-sur-Yvette, France.
The Journal of Chemical Physics
|October 5, 2013
Summary
Choosing the right coordinates is crucial for simplified protein models. This study reveals that while some coordinate sets like phi/psi torsion angles are insufficient, others, such as those using virtual Cα backbone bonds and torsion angles, provide satisfactory protein structure representations.
Area of Science:
- Computational Biology
- Biophysics
- Structural Bioinformatics
Background:
- All-atom molecular simulations represent proteins with individual atoms, offering detailed interactions but demanding significant computational resources.
- Simplified protein models aim to enhance computational efficiency and physical insight by reducing the number of atoms and internal coordinates.
- These simplified models vary in their geometric and interaction descriptions, necessitating an evaluation of fundamental choices.
Purpose of the Study:
- To investigate the impact of different coordinate sets on protein structure representation in simplified models.
- To identify optimal coordinate choices for accurate and efficient protein simulations.
- To understand the sensitivity of protein structure to variations in angular coordinates.
Main Methods:
- Exploration of various coordinate sets for defining protein structure in simplified models.
- Analysis of the implications of reduced atom representation and fixed internal coordinates on overall protein structure.
- Evaluation of the sufficiency of different angular coordinate choices, including phi/psi torsion angles and virtual Cα backbone bonds.
Main Results:
- Small variations in angular coordinates can cause substantial changes in distant atomic positions.
- The commonly used phi/psi torsion angles alone are insufficient for accurate protein structure representation in simplified models.
- A coordinate set incorporating two degrees of freedom per residue, virtual Cα backbone bonds, and torsion angles demonstrated satisfactory performance.
Conclusions:
- The selection of a coordinate set is a critical decision in developing simplified protein models.
- Careful consideration of angular coordinates is essential to avoid significant structural artifacts.
- The proposed coordinate set offers a promising alternative for efficient and accurate simplified protein simulations.
Related Concept Videos
01:24Protein Organization
Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.
The primary structure of a protein is its amino acid sequence.
01:13Protein Organization
Overview
02:18Fischer Projections
Learning to draw Fischer projections of molecules and understanding their relevance plays a crucial role in the visual depiction of organic molecules. A Fischer projection is a two-dimensional projection on a planar surface to simplify the three-dimensional wedge–dash representation of molecules. This is especially helpful in the case of molecules with multiple chiral centers that can be difficult to draw. Here, all the bonds of interest are represented as horizontal or vertical lines. While...
02:06Newman Projections
Different notations are used to represent the three-dimensional structure of molecules on two-dimensional surfaces. One of the most commonly used representations is the dash-wedge formula. The dashed wedges, solid wedges, and the plane lines indicate the groups situated behind the plane, coming out of the plane, and in the plane, respectively.
The organic molecules rotate across the single bonds leading to numerous temporary three-dimensional structures of varying energy known as conformers.
The organic molecules rotate across the single bonds leading to numerous temporary three-dimensional structures of varying energy known as conformers.
02:26Conservation of Protein Domains Over Different Proteins
Protein domains are small structurally independent units that are part of a single amino acid chain. Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
02:15Protein and Protein Structures
Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme can...
A protein's shape is critical to its function. For example, an enzyme can...