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Related Concept Videos

Protein Organization01:24

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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Conserved Binding Sites01:49

Conserved Binding Sites

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Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
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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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Intrinsically disordered proteins are a group of proteins that do not fold into specific three-dimensional structures. Their structural flexibility allows them to complement ordered proteins to perform functions that are inaccessible to rigid structures. They are more common in eukaryotes than prokaryotes and may either be exclusively intrinsically disordered or hybrid proteins, consisting of a mix of ordered and disordered regions. The absence of a rigid structure in these proteins can be...
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Signal sequences are short amino acid sequences that guide newly synthesized proteins to their proper location within the cell. Classical signal sequences are fifteen to sixty amino acids long and present at the N-terminus of a polypeptide chain. Each signal sequence has a conserved segment of basic residues towards their N terminus, a hydrophobic core, and a C-terminus rich in polar residues. The C-terminus also contains a signal cleavage site and features a -3 -1 sequence motif. The -3-1...
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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.
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Updated: Jun 13, 2025

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
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epLSAP-Align: a non-sequential protein structural alignment solver with entropy-regularized partial linear sum

Xuechen Zhang1, Zhuoyang Chen2, Junyu Li3

  • 1Department of Electronic and Computational Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China.

Bioinformatics (Oxford, England)
|May 21, 2025
PubMed
Summary
This summary is machine-generated.

A new method, epLSAP-Align, addresses non-sequential protein structure alignment challenges. This approach improves accuracy and efficiency for understanding protein function and evolution.

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Area of Science:

  • Computational biology
  • Structural bioinformatics
  • Protein structure analysis

Background:

  • Three-dimensional protein tertiary structure alignment is crucial for understanding protein function and evolution.
  • Existing sequential alignment algorithms struggle with distantly related structures exhibiting non-sequential similarities.
  • Current non-sequential alignment tools often lack efficiency and accuracy.

Purpose of the Study:

  • To formulate non-sequential protein structure alignment as an Entropy-regularized Partial Linear Sum Assignment Problem (epLSAP).
  • To develop an efficient and accurate solver for non-sequential alignment using Sinkhorn algorithms (epLSAP-Align).

Main Methods:

  • Formulation of non-sequential alignment as the Entropy-regularized Partial Linear Sum Assignment Problem (epLSAP).
  • Development of a solver based on Sinkhorn algorithms, named epLSAP-Align.
  • Integration of epLSAP-Align into existing frameworks (TM-align, MICAN) to create epLSAP-TM and epLSAP-MICAN.

Main Results:

  • epLSAP-Align explicitly models gap penalties, achieves global optimality, and balances coverage and fidelity.
  • epLSAP-TM and epLSAP-MICAN demonstrate superior performance on various benchmark datasets compared to existing non-sequential alignment tools.
  • epLSAP-TM shows a speed improvement of at least 22% over USalign2.

Conclusions:

  • epLSAP-Align offers a novel and effective approach to non-sequential protein structure alignment.
  • The integrated tools epLSAP-TM and epLSAP-MICAN advance the field of structural bioinformatics.
  • The method provides a more accurate and efficient means for analyzing protein structure similarities.