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Related Concept Videos

Protein Organization01:24

Protein Organization

6.2K
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....
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Protein and Protein Structure02:15

Protein and Protein Structure

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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...
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Leaky Scanning02:28

Leaky Scanning

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During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA.  Marilyn Kozak discovered that the sequence RCCAUGG (where R...
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Protein and Protein Structures02:15

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Termination of Translation01:44

Termination of Translation

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The large ribosomal subunit has several important structures essential to translation. These include the peptidyl transferase center (PTC) - which is the site where the peptide bond is formed - and a large, internal, water-filled tube through which the nascent polypeptide moves. This latter structure is called the Peptide Exit Tunnel, and it begins at the PTC and spans the body of the large ribosomal subunit. During translation, as the nascent polypeptide chain is synthesized, it passes through...
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Conservation of Protein Domains Over Different Proteins02:26

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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A Protocol for Computer-Based Protein Structure and Function Prediction
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A Protocol for Computer-Based Protein Structure and Function Prediction

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Bilingual language model for protein sequence and structure.

Michael Heinzinger1, Konstantin Weissenow1, Joaquin Gomez Sanchez1

  • 1School of Computation, Information, and Technology (CIT), Department of Informatics, Bioinformatics & Computational Biology, TUM (Technical University of Munich), 85748 Garching/Munich, Germany.

NAR Genomics and Bioinformatics
|December 5, 2024
PubMed
Summary
This summary is machine-generated.

We developed ProstT5, a novel protein language model (pLM) that integrates 3D structural and 1D sequence data. This approach enhances structure-related predictions and accelerates the analysis of protein structure databases.

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Area of Science:

  • Computational biology
  • Structural bioinformatics
  • Machine learning in genomics

Background:

  • Protein language models (pLMs) have advanced the analysis of protein sequences.
  • AlphaFold2 revolutionized protein structure prediction, generating vast amounts of 3D structural data.
  • Understanding proteins requires integrating their 1D sequence and 3D structural information.

Purpose of the Study:

  • To develop a unified model that simultaneously analyzes both protein sequence and structure data.
  • To leverage pLMs for modeling the dual nature of proteins as sequences and 3D machines.
  • To create a novel approach for translating between 3D structural representations and amino acid sequences.

Main Methods:

  • Encoding protein structures into token sequences using the 3Di-alphabet from Foldseek.
  • Fine-tuning an existing pLM (ProtT5) on a non-redundant dataset from AlphaFoldDB.
  • Developing the Protein 'structure-sequence' T5 (ProstT5) model for joint structure-sequence analysis.

Main Results:

  • ProstT5 demonstrated improved performance on structure-related prediction tasks.
  • Achieved a three orders of magnitude speedup in deriving 3D structural representations (3Di).
  • Established a proof-of-concept for integrating pLMs with large-scale protein structure data.

Conclusions:

  • ProstT5 effectively models both protein sequence and structure, bridging the gap between pLMs and structural bioinformatics.
  • This approach is crucial for future applications, enabling structure-sensitive searches in large metagenomic databases.
  • ProstT5 opens new research avenues in the post-AlphaFold2 era by integrating structural predictions into sequence-based analyses.