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Protein Organization

Protein 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....

Protein Organization

Protein Organization

Protein Organization

Protein Organization

Conservation of Protein Domains Over Different Proteins

Conservation 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...

Conserved Binding Sites

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...

Protein-protein Interfaces

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...

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Related Experiment Video

Updated: Mar 18, 2026

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

Computational protein design for given backbone: recent progresses in general method-related aspects.

Haiyan Liu¹, Quan Chen²

¹School of Life Sciences, University of Science and Technology of China, China; Hefei National Laboratory for Physical Sciences at the Microscales, China; Collaborative Innovation Center of Chemistry for Life Sciences, Hefei, Anhui 230027, China; Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, China.

Current Opinion in Structural Biology

|June 28, 2016

Summary

High success rates in protein design depend on accurate sequence design methods. Energy minimization, energy model quality, backbone flexibility, and post-processing techniques are key factors for improving computational protein design accuracy.

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Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

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Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Published on: January 26, 2024

Area of Science:

Computational biology
Protein engineering
Biophysics

Background:

Achieving high success rates in protein design necessitates reliable methods for designing amino acid sequences that stably fold into desired structures.
Computational protein design, primarily through energy minimization, is a key approach to address this challenge.

Purpose of the Study:

To review recent advancements in computational protein design methods focused on enhancing accuracy.
To highlight critical factors influencing the success of energy minimization approaches in protein sequence design.

Main Methods:

Review of recent progress in computational protein design techniques.
Analysis of the impact of energy model quality and backbone flexibility on design accuracy.
Evaluation of post-processing strategies to boost design effectiveness.

Main Results:

Energy model quality is a critical determinant of design accuracy.
Consideration of backbone flexibility significantly affects design outcomes, even with minor structural adjustments.
Post-processing designed sequences with complementary models can enhance overall design accuracy.

Conclusions:

Improving computational protein design relies on refining energy models and incorporating backbone flexibility.
Post-processing offers a viable strategy to boost the accuracy of designed protein sequences.
Enhanced experimental feedback loops are crucial for advancing computational method development.