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Related Concept Videos

Amyloid Fibrils03:03

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Amyloid fibrils are aggregates of misfolded proteins.  Under most circumstances, misfolded proteins are either refolded by chaperone proteins or degraded by the proteasome. However, in the case of a mutation or a disease, these proteins can accumulate to form large clusters and often further assemble to form elongated fibers, called fibrils. 
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After folding, the ER assesses the quality of secretory and membrane proteins. The correctly folded proteins are cleared by the calnexin cycle for transport to their final destination, while misfolded proteins are held back in the ER lumen. The ER chaperones attempt to unfold and refold the misfolded proteins but sometimes fail to achieve the correct native conformation. Such terminally misfolded proteins are then exported to the cytosol by ER-associated degradation or ERAD pathway for...
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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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Amino acid biosynthesis is essential for cell growth, protein synthesis, and metabolic regulation. Cells generate essential and non-essential amino acids from metabolic intermediates to sustain vital biological functions. These intermediates originate from key metabolic pathways: glycolysis, the tricarboxylic acid (TCA) cycle, and the pentose phosphate pathway. Important precursors include α-ketoglutarate, pyruvate, oxaloacetate, phosphoenolpyruvate, and erythrose-4-phosphate, which...
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Mitochondrial Precursor Proteins01:39

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Mitochondrial precursors are partially unfolded or loosely folded polypeptide chains. Newly synthesized precursors are inhibited from spontaneously folding into their native conformation by the cytosolic chaperones, heat shock proteins 70 (Hsp70), and mitochondrial import stimulation factors (MSFs). Precursors bound to MSFs are guided to the TOM70-TOM37 receptors, while precursors bound to Hsp70  chaperones are targetted to TOM20-TOM22 receptor complexes.
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Purification and Aggregation of the Amyloid Precursor Protein Intracellular Domain
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Purification and Aggregation of the Amyloid Precursor Protein Intracellular Domain

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Navigating Homogeneous Graph Paths Through Amyloidogenic and Non-Amyloidogenic Hexapeptides.

László Keresztes1, Evelin Szögi1, Bálint Varga1

  • 1PIT Bioinformatics Group, Eötvös University, Budapest, Hungary.

Journal of Computational Chemistry
|October 3, 2025
PubMed
Summary
This summary is machine-generated.

The Budapest Amyloid Predictor (BAP) reveals a connected graph structure for hexapeptides. All predicted amyloidogenic or non-amyloidogenic hexapeptides form distinct connected components, accessible via short paths.

Keywords:
amyloidshexapeptidesmutational graphpeptides

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Rapid Generation of Amyloid from Native Proteins In vitro
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Rapid Generation of Amyloid from Native Proteins In vitro
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Area of Science:

  • Biophysics
  • Computational Biology
  • Bioinformatics

Background:

  • Hexapeptides serve as models for studying polypeptide amyloidogenicity.
  • A vast sequence space of 64 million hexapeptides exists, with limited experimental data.
  • Computational predictors accurately label hexapeptides as amyloidogenic or non-amyloidogenic.

Purpose of the Study:

  • To define and investigate a graph structure connecting hexapeptides based on single residue differences.
  • To demonstrate a novel connectivity property of the Budapest Amyloid Predictor (BAP) within this hexapeptide graph.
  • To explore the implications of this property for understanding amyloidogenic and non-amyloidogenic peptide landscapes.

Main Methods:

  • Construction of a graph where hexapeptides are nodes and edges connect peptides differing by one residue.
  • Utilizing the Budapest Amyloid Predictor (BAP), an artificial intelligence-based tool, to classify hexapeptides.
  • Demonstrating path existence between any two hexapeptides with the same BAP prediction (amyloidogenic or non-amyloidogenic).

Main Results:

  • A graph structure for 64 million hexapeptides was conceptualized.
  • For any two hexapeptides predicted as amyloidogenic by BAP, a path of length at most six exists, composed solely of BAP-predicted amyloidogenic hexapeptides.
  • The same connectivity property holds for hexapeptides predicted as non-amyloidogenic by BAP.
  • This property is inherent to linear Support Vector Machine (SVM) predictors.

Conclusions:

  • The Budapest Amyloid Predictor (BAP) exhibits a significant graph property, connecting all predicted amyloidogenic (or non-amyloidogenic) hexapeptides through short paths.
  • This finding suggests a structured organization within the hexapeptide sequence space concerning amyloidogenicity.
  • The demonstrated property is generalizable to other linear SVM-based predictors, offering insights into amyloid formation mechanisms.