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Protein and Protein Structure

Protein and Protein Structure

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...

Protein and Protein Structures

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Protein Organization

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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....

Conservation of Protein Domains Over Different Proteins

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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.
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The flow of genetic information in cells from DNA to mRNA to protein is described by the central dogma, which states that genes specify the sequence of mRNAs, which in turn specify the sequence of amino acids making up all proteins. The decoding of one molecule to another is performed by specific proteins and RNAs. Because the information stored in DNA is so central to cellular function, it makes intuitive sense that the cell would make mRNA copies of this information for protein synthesis...

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Related Experiment Video

Updated: May 26, 2025

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

Toward deep learning sequence-structure co-generation for protein design.

Chentong Wang¹, Sarah Alamdari², Carles Domingo-Enrich²

¹School of Life Sciences, Westlake University, Hangzhou, Zhejiang, 310024, China.

Current Opinion in Structural Biology

|February 21, 2025

Summary

This summary is machine-generated.

Deep generative models can design novel proteins by learning from natural sequences and structures. Emerging co-generation methods, modeling both protein sequence and structure simultaneously, offer more accurate and controllable protein design possibilities.

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Published on: July 16, 2017

Area of Science:

Computational biology
Protein engineering
Artificial intelligence in drug discovery

Background:

Deep generative models are advancing protein design by learning from natural protein data.
Current models often generate protein sequences or structures independently.
Simultaneous co-generation of sequence and structure offers enhanced design control and accuracy.

Purpose of the Study:

To review recent advancements in deep generative models for protein design.
To focus on sequence-structure co-generation methods.
To discuss future opportunities in this field.

Main Methods:

Review of literature on deep generative models for protein design.
Focus on methodologies for simultaneous sequence and structure co-generation.
Analysis of evaluation principles for co-generation models.

Main Results:

Highlighting key methodological and evaluation principles in sequence-structure co-generation.
Summarizing recent breakthroughs in the field.
Identifying current trends and challenges.

Conclusions:

Sequence-structure co-generation represents a promising frontier in protein design.
Further development is needed to fully realize the potential of these models.
Continued research can accelerate the creation of novel proteins with desired functions.