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Protein Families

Protein Families

Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism. Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members. If these new proteins contain similar amino acids in key...

Protein Complexes with Interchangeable Parts

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order...

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...

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...

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...

Protein Folding

Protein Folding

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Related Experiment Video

Updated: Jul 31, 2025

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Effector protein structures: a tale of evolutionary relationship.

Ravi Kumar¹, Vishal Acharya¹

¹Functional Genomics and Complex System Lab, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.

Trends in Plant Science

|May 1, 2023

Summary

Fungal effector proteins, crucial for plant disease, share similar structures despite diverse sequences. AlphaFold2 analysis reveals these structural commonalities, aiding in understanding effector evolution and function.

Keywords:

effector evolutionary relationship plant immunity protein disorder protein structure

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Last Updated: Jul 31, 2025

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

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Published on: July 14, 2015

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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Characterization of Proteins by Size-Exclusion Chromatography Coupled to Multi-Angle Light Scattering SEC-MALS

Characterization of Proteins by Size-Exclusion Chromatography Coupled to Multi-Angle Light Scattering SEC-MALS

Published on: June 20, 2019

Area of Science:

Molecular biology
Structural biology
Mycology

Background:

Effector proteins from fungal pathogens exhibit high sequence diversity, complicating functional analysis.
Understanding effector function is critical for developing disease resistance strategies in agriculture.

Purpose of the Study:

To investigate conserved structural features of fungal effector proteins.
To explore the utility of AlphaFold2 in identifying functionally relevant structural similarities among effectors.

Main Methods:

Utilized AlphaFold2 (AF2) for predicting the three-dimensional structures of diverse fungal effector proteins.
Compared predicted effector structures to identify conserved structural motifs and families.
Analyzed sequence-structure relationships to understand evolutionary patterns.

Main Results:

Identified significant structural commonalities among fungal effectors that are not apparent at the sequence level.
Revealed the existence of unique effector families with similar structures but unrelated sequences.
Demonstrated that structural analysis provides a complementary approach to sequence analysis for functional prediction.

Conclusions:

Fungal effector evolution favors structural conservation over sequence conservation.
Structural insights from AF2 can uncover novel effector families and inform functional predictions.
This approach enhances our understanding of fungal-plant interactions and effector-driven pathogenesis.