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Related Concept Videos

Cis-regulatory Sequences02:02

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
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...
Nuclear Localization Signals and Import01:46

Nuclear Localization Signals and Import

Proteins targeted to the nucleus carry short stretches of amino acid sequences called the nuclear localization signal or NLS. Classical nuclear localization signals are of two types: monopartite and bipartite NLS. Monopartite classical NLS (cNLS) consists of a single cluster of 4-8 amino acids. Bipartite cNLS consists of two clusters of  2-3 amino acids and a 9-12 residue long proline-rich linker bridging the two clusters. Signal clusters are rich in positively charged amino acids such as...
Post-translational Translocation of Proteins to the RER01:27

Post-translational Translocation of Proteins to the RER

A sizable fraction of proteins destined for ER are first synthesized in the cell cytosol and then transported across the ER membrane–a process called post-translational translocation. Similar to cotranslationally translocated proteins, these proteins also use the Sec translocon complex to enter the ER lumen.
Targeting proteins to the ER
Hsp40 and Hsp70 chaperone molecules bind the translated proteins in the cytosol to prevent their folding. The chaperone binding helps to keep the signal...
Cotranslational Protein Translocation01:20

Cotranslational Protein Translocation

Translocation of proteins across membranes is an ancient process that occurs even in bacteria and archaebacteria. In fact, the components of the translocation machinery are still conserved between prokaryotes and eukaryotes.
Sec61 channel partners for cotranslational translocation
During cotranslational translocation, the Sec61 channel partners with the signal recognition particle (SRP), the signal recognition particle receptor (SR), and the ribosomes to transport the nascent polypeptide chain...

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Antimicrobial Peptides Produced by Selective Pressure Incorporation of Non-canonical Amino Acids
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Local and nonlocal environments around Cis peptides.

Brent Wathen1, Zongchao Jia

  • 1Department of Biochemistry, Queen's University, Kingston, Ontario, Canada K7L 3N6.

Journal of Proteome Research
|December 14, 2007
PubMed
Summary

Nonlocal factors significantly influence cis peptide bond formation in proteins, contrary to previous assumptions focusing on local aromatic residues. This study reveals distinct structural environments surrounding cis versus trans peptide bonds, impacting protein folding.

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Computational Biology

Background:

  • Most peptide bonds in proteins adopt the trans conformation.
  • The cis peptide bond conformation is less energetically favorable and its formation mechanism is not fully understood.
  • Previous research emphasized the role of local aromatic residues in cis peptide formation.

Purpose of the Study:

  • To conduct a comprehensive statistical analysis of the local and nonlocal environments surrounding cis peptides.
  • To identify structural differences between cis and trans peptide bonds.
  • To investigate the role of nonlocal factors in cis peptide formation.

Main Methods:

  • Statistical analysis of protein structures.
  • Comparison of local and tertiary environments around cis and trans peptide bonds.
  • Analysis of protein secondary and tertiary structure features.

Main Results:

  • Cis peptides exhibit an increased frequency of aromatic residues locally.
  • Nonlocal analysis revealed longer coil regions with more Tyr and Pro residues near cis peptides.
  • Cis peptides were found near large beta-structures and showed nonlocal enrichment of Cys, His, Tyr, and Ser.
  • Cis peptides form fewer medium-range and more long-range contacts than trans peptides.

Conclusions:

  • Nonlocal factors play a crucial, previously underappreciated role in cis peptide formation.
  • Differences in tertiary structure and contact patterns contribute to cis peptide formation.
  • The findings have implications for understanding protein folding mechanisms and potential autocatalytic models.