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Related Concept Videos

Intrinsically Disordered Proteins02:18

Intrinsically Disordered Proteins

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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Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
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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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Within a biological system, the DNA encodes the RNA, and the nucleotide sequence in the RNA further defines the amino acid sequence in the protein. This is referred to as “The Central Dogma of Molecular Biology” - a term coined by Francis Crick.  Central dogma is a firm principle in biology that defines the flow of genetic information within any life form. The two fundamental steps in central dogma are - transcription and translation.
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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

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Published on: July 25, 2013

Analysis and design of disordered polypeptides with optimized sequence patterning properties.

Arjun Singh1, Ali I Ukperaj1, Gabriel F Porto1

  • 1Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey, United States of America.

Plos Computational Biology
|July 8, 2026
PubMed
Summary
This summary is machine-generated.

We developed a new method to compare intrinsically disordered protein (IDP) sequences, enabling the design of novel IDPs with predictable phase separation behavior for various applications.

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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Area of Science:

  • Biophysics
  • Protein Science
  • Computational Biology

Background:

  • Intrinsically disordered proteins (IDPs) undergo liquid-liquid phase separation (LLPS), a process crucial for cellular function.
  • LLPS in IDPs is influenced by single-chain compaction, dictated by amino acid composition and sequence patterning.
  • Current metrics like sequence charge decoration (SCD) and sequence hydropathy decoration (SHD) have limitations in comparing sequences of varying lengths and compositions.

Purpose of the Study:

  • To develop a robust method for comparing sequence patterning across diverse intrinsically disordered protein sequences.
  • To create a computational framework for designing novel IDPs with specific phase separation properties.
  • To enable rational design of IDPs for biomedical and biotechnological applications.

Main Methods:

  • Introduced a shuffle-based normalization scheme for SCD and SHD to enable cross-sequence comparisons.
  • Developed a Monte Carlo-based sequence design algorithm incorporating normalized SCD, SHD, sequence aromatic decoration (SAD), compositional RMSD, and a ΔG predictor.
  • Validated the designed sequences using coarse-grained molecular dynamics (MD) simulations.

Main Results:

  • The normalization scheme effectively allows comparison of sequence patterning between IDPs of significantly different lengths and compositions.
  • The Monte Carlo design algorithm successfully generated novel IDP sequences with desired patterning features.
  • Coarse-grained MD simulations confirmed that the designed IDPs exhibit tunable phase separation behavior.

Conclusions:

  • The developed shuffle-based normalization and design framework provide a powerful tool for understanding and engineering IDP sequence-structure-function relationships.
  • This approach facilitates the rational design of IDPs with predictable phase separation for targeted applications.
  • The study lays the foundation for advancing IDP research in biophysics, medicine, and biotechnology.