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Sequence-structure-function relationships in the microbial protein universe.

Julia Koehler Leman1,2, Pawel Szczerbiak3, P Douglas Renfrew4,5

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|April 26, 2023
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Summary
This summary is machine-generated.

This study reveals that diverse protein sequences and structures can perform similar functions, expanding our understanding beyond sequence-based predictions. It introduces a new database of protein structures and functions for broader biological context.

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Area of Science:

  • Structural Biology
  • Bioinformatics
  • Genomics

Background:

  • Traditional structural biology assumes sequence similarity dictates structure and function.
  • This assumption limits exploration of the full protein universe.
  • Alternative pathways for protein function exist, independent of sequence homology.

Purpose of the Study:

  • To explore protein universe regions where function is independent of sequence and structure.
  • To predict and functionally annotate protein structures for diverse microbial proteomes.
  • To create a database complementing existing resources like AlphaFold.

Main Methods:

  • Prediction of ~200,000 protein structures using the World Community Grid.
  • Functional annotation of predicted structures on a per-residue basis.
  • Comparative analysis with the AlphaFold database for coverage and diversity.

Main Results:

  • Identification of 148 novel protein folds.
  • Mapping of specific functions to structural motifs.
  • Demonstration of a continuous and saturated protein structural space.
  • Creation of a database with broad genomic and sequence diversity.

Conclusions:

  • Protein function can be achieved through diverse sequences and structures.
  • A shift towards sequence-structure-function based meta-omics is needed.
  • The predicted structural models offer complementary insights to existing databases.