Related Experiment Video
Updated: Jul 10, 2026
09:51
Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
Molecular Architecture and Energy Visualization: Advancing Insights into Protein Structure, Interactions, and
Luis A Landrau Correa1, Owen Borden2, Oscar Claudio Ares2
1Department of Biology, University of Puerto Rico-Río Piedras, San Juan, Puerto Rico. luis.landrau2@upr.edu.
Methods in Molecular Biology (Clifton, N.J.)
|July 9, 2026
Summary
Understanding protein structure is crucial for cellular life. This chapter explores protein organization, folding, and analysis using PyMOL for deeper structural insights.
Area of Science:
- Protein biochemistry
- Structural biology
- Computational biology
Background:
- Proteins are central to cellular functions, driving the need for structural visualization.
- 3D protein structure visualization is essential for structural biology, drug development, and protein design.
- PyMOL is a versatile and user-friendly platform for protein structure analysis.
Purpose of the Study:
- To explain the influence of amino acids on protein structure.
- To describe hierarchical levels of protein organization and folding.
- To highlight key regulatory interactions and PyMOL's analytical capabilities.
Main Methods:
- Explanation of how amino acids determine protein structure.
- Description of hierarchical protein organization (primary, secondary, tertiary, quaternary).
- Illustration of folding pathways driven by energy landscapes.
- Discussion of PyMOL features for structural analysis.
Main Results:
- Amino acids dictate protein structure and function.
- Protein folding follows hierarchical levels influenced by energy landscapes.
- Key interactions like allostery and metal binding are crucial for regulation.
- PyMOL facilitates analysis of pH-dependent states, solvent accessibility, and alignments.
Conclusions:
- PyMOL is a powerful tool for visualizing and analyzing protein structures.
- Understanding protein structure aids in drug development and biological research.
- Detailed structural analysis provides deeper insights into protein function and conformational changes.
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
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.
02:00Molecular Models
Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.
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...
01:19Protein Dynamics in Living Cells
Different fluorescence-based techniques are used to study the protein dynamics in living cells. These techniques include FRAP, FRET, and PET.
Fluorescent recovery after photobleaching (FRAP) is a fluorescent-protein-based detection technique used to quantify protein movement rates within the cell. This method exposes a small portion of the cell to an intense laser beam. The laser beam causes permanent photobleaching of the fluorophore-tagged proteins in the exposed region. As the bleached...
Fluorescent recovery after photobleaching (FRAP) is a fluorescent-protein-based detection technique used to quantify protein movement rates within the cell. This method exposes a small portion of the cell to an intense laser beam. The laser beam causes permanent photobleaching of the fluorophore-tagged proteins in the exposed region. As the bleached...