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Related Concept Videos

Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

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...
Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

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...
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

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 form...
Conserved Binding Sites01:49

Conserved Binding Sites

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.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Conserved Binding Sites01:49

Conserved Binding Sites

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.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Signal Sequences and Sorting Receptors01:41

Signal Sequences and Sorting Receptors

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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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
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Signatures of protein biophysics in coding sequence evolution.

Claus O Wilke1, D Allan Drummond

  • 1Center for Computational Biology and Bioinformatics, Institute for Cell and Molecular Biology, and Section of Integrative Biology, The University of Texas at Austin, Austin, TX, USA. cwilke@mail.utexas.edu

Current Opinion in Structural Biology
|April 17, 2010
PubMed
Summary

Molecular evolution is shaped by more than just function. Biophysical processes like protein synthesis and folding also influence gene sequences at both amino acid and nucleotide levels.

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Area of Science:

  • Molecular Biology
  • Evolutionary Biology
  • Biophysics

Background:

  • Traditionally, functional constraints were considered the primary drivers of protein-coding gene evolution.
  • Emerging evidence suggests biophysical processes significantly impact gene evolution.

Purpose of the Study:

  • To explore the influence of biophysical processes on protein-coding gene evolution.
  • To investigate how selection pressures from protein synthesis, folding, and interactions shape gene sequences.
  • To highlight the need for a unifying framework integrating these selection pressures.

Main Methods:

  • Analysis of molecular evolution data.
  • Examination of selection pressures at amino-acid and nucleotide (synonymous sites) levels.
  • Review of existing evidence on biophysical impacts on gene sequences.

Main Results:

  • Biophysical processes, including protein synthesis, folding, and interactions, strongly shape gene evolution.
  • These pressures affect amino-acid sequences and leave detectable marks on synonymous nucleotide sites.
  • Evidence for selection pressures related to protein biophysics is substantial.

Conclusions:

  • Protein-coding gene evolution is influenced by both functional and biophysical constraints.
  • A comprehensive framework is needed to integrate and differentiate the impacts of various selection pressures.
  • Understanding these multifaceted pressures is crucial for a complete picture of molecular evolution.