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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.
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Updated: Jan 1, 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

Protein Structure from Experimental Evolution.

Michael A Stiffler¹, Frank J Poelwijk¹, Kelly P Brock²

¹cBio Center, Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Cell Biology, Harvard Medical School, Boston, MA, USA; Broad Institute, Cambridge, MA, USA.

|December 16, 2019

Summary

This summary is machine-generated.

Experimental evolution generated functional protein sequences encoding structural information. This new method, 3Dseq, uses evolutionary coupling analysis and computational folding to determine protein structures from evolved sequences.

Keywords:

Experimental evolution aminoglycoside acetyltransferase beta-lactamase co-evolution deep sequencing evolutionary couplings maximum entropy mutagenesis protein structure protein structure determination

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Published on: July 16, 2017

Area of Science:

Biochemistry
Structural Biology
Evolutionary Biology

Background:

Natural evolution encodes biomolecular structure and function in genetic records.
Co-variation analysis of natural protein families aids 3D structure computation.

Purpose of the Study:

To explore experimental evolution for generating protein sequence information encoding structural constraints.
To develop a novel method for protein structure determination using experimental evolution and sequence analysis.

Main Methods:

Performed multiple cycles of in vitro mutagenesis and functional selection on antibiotic resistance genes (β-lactamase PSE1, acetyltransferase AAC6) in Escherichia coli.
Applied evolutionary coupling analysis to inferred residue interaction constraints from evolved sequences.
Utilized computational protein folding with inferred constraints to predict 3D structures.

Main Results:

Obtained hundreds of thousands of diverse, functional protein sequences through experimental evolution.
Inferred residue interaction constraints that agreed with known 3D structural contacts.
Successfully predicted 3D protein structures with folds matching natural relatives using computational methods.

Conclusions:

Experimental evolution can generate functional sequences that encode structural information, mirroring natural evolution.
The developed method (3Dseq) provides a novel experimental approach for protein structure determination.
This work integrates evolutionary experiments with sequence analysis for advancing structural biology.