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Related Concept Videos

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.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
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Evolutionary Relationships through Genome Comparisons02:54

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Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
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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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Gene Evolution - Fast or Slow?02:05

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The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
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Signal Sequences and Sorting Receptors01:41

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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 Families02:47

Protein Families

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Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key...
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Updated: May 21, 2025

Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation
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Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation

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Anticipating protein evolution with successor sequence predictor.

Rayyan Tariq Khan1,2, Pavel Kohout1,2, Milos Musil1,2,3

  • 1Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic.

Journal of Cheminformatics
|March 22, 2025
PubMed
Summary
This summary is machine-generated.

The Successor Sequence Predictor (SSP) offers a novel in silico method for protein design, predicting future amino acid substitutions to enhance protein properties. This computational tool aids in protein engineering, reducing the need for resource-intensive experimental evolution.

Keywords:
ActivityAdaptationEvolutionEvolutionary trajectoryProtein designSolubilityThermostability

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Area of Science:

  • Computational biology
  • Protein engineering
  • Evolutionary biology

Background:

  • Predicting protein evolution is challenging due to limitations in theoretical models and resource-intensive experimental techniques like directed evolution.
  • Existing methods are often descriptive rather than predictive, requiring significant researcher intervention for protein modification.

Purpose of the Study:

  • To introduce the Successor Sequence Predictor (SSP), an in silico method for protein design.
  • To provide a predictive tool that reconstructs protein evolutionary history and suggests beneficial amino acid substitutions.
  • To enhance protein engineering by improving properties like thermostability, activity, and solubility.

Main Methods:

  • Developed an in silico protein design method, the Successor Sequence Predictor (SSP).
  • SSP reconstructs a protein's evolutionary history.
  • Identifies trends in evolutionary history using physicochemical descriptors to predict future amino acid substitutions.

Main Results:

  • SSP predicts amino acid substitutions that enhance protein properties such as thermostability, activity, and solubility.
  • The method advances protein evolution prediction at the amino acid level.
  • Successfully integrates ancestral sequence reconstruction with in silico modeling of evolutionary trends.

Conclusions:

  • SSP is a generalizable and predictive tool for protein engineering.
  • This approach reduces reliance on resource-intensive directed evolution techniques.
  • Enables the development of practically useful enhanced specialized proteins.