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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

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 and Protein Structures

Protein and Protein Structures

Protein Complexes with Interchangeable Parts

Protein Complexes with Interchangeable Parts

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...

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Related Experiment Video

Updated: Jan 16, 2026

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

Jointly Embedding Protein Structures and Sequences through Residue Level Alignment.

Foster Birnbaum¹, Saachi Jain², Aleksander Madry²

¹Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA and Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.

|October 6, 2025

Summary

This summary is machine-generated.

Scientists developed residue level alignment (RLA), a new method to link protein sequences and structures. RLA efficiently identifies potential protein binders, accelerating drug discovery.

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Last Updated: Jan 16, 2026

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

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Published on: July 14, 2015

A Protocol for Computer-Based Protein Structure and Function Prediction

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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

Area of Science:

Biochemistry
Structural Biology
Computational Biology

Background:

Protein function is intrinsically linked to its sequence and structure.
Experimental determination of protein structures is challenging and time-consuming.
Protein sequences are abundant but do not directly reveal biochemical functions.

Purpose of the Study:

To develop a self-supervised method for aligning protein sequence and structure embedding spaces.
To enable similarity measurement between protein sequences and structures.
To apply the method for efficient binder design.

Main Methods:

Proposed residue level alignment (RLA), a self-supervised objective.
Integrated sequence and structure encoders into a shared latent space.
Utilized RLA embeddings to calculate sequence-structure similarity scores.

Main Results:

RLA successfully enriches sequence encoders with spatial information.
RLA similarity scores effectively identify true binders from designed sets.
RLA performs comparably to existing methods but is significantly faster.
RLA is effective even with only backbone structure information.

Conclusions:

RLA provides a powerful new tool for aligning protein sequence and structure representations.
RLA significantly accelerates the screening process in binder design pipelines.
The method offers a faster and efficient alternative for identifying potential protein binders.