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Related Concept Videos

Single-Strand DNA Binding Proteins01:03

Single-Strand DNA Binding Proteins

For successful DNA replication, the unwinding of double-stranded DNA must be accompanied by stabilization and protection of the separated single strands of the DNA. This crucial task is performed by single-strand DNA-binding (SSB) proteins. They bind to the DNA in a sequence-independent manner, which means that the nitrogenous bases of the DNA need not be present in a specific order for binding of SSB proteins to it. The binding of SSB proteins straightens single-stranded DNA (ssDNA) and makes...
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Topoisomerases are enzymes that relax overwound DNA molecules during various cell processes, including DNA replication and transcription. These enzymes regulate positive and negative DNA supercoiling without changing the nucleotide sequence. DNA overwinding in a clockwise direction results in positively supercoiled DNA, whereas underwinding in a counterclockwise direction produces negatively supercoiled DNA.
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Nucleosome Remodeling02:54

Nucleosome Remodeling

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Restriction enzymes are bacterial enzymes used to cut DNA in a sequence-specific manner. To cleave DNA, they bind to specific palindromic sequences called restriction sites. Such palindromic DNA sequences or inverted repeats are commonly found in regions of functional significance, such as the origin of replication, gene operator sites, and regions containing transcription termination signals.
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Mismatch Repair01:20

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Single-molecule Manipulation of G-quadruplexes by Magnetic Tweezers
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Electrostatic effects in unfolded staphylococcal nuclease.

Nicholas C Fitzkee1, Bertrand García-Moreno E

  • 1Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, USA.

Protein Science : a Publication of the Protein Society
|January 30, 2008
PubMed
Summary

Electrostatic effects in unfolded proteins are significant and impact protein behavior. Structure-based calculations must explicitly include these interactions for accurate protein stability predictions.

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Area of Science:

  • Biophysics
  • Computational Biology
  • Protein Science

Background:

  • Structure-based protein calculations often neglect electrostatic effects in unfolded states.
  • Emerging evidence indicates unfolded proteins are more structured and compact than previously assumed.
  • The validity of neglecting unfolded-state electrostatics requires re-evaluation.

Purpose of the Study:

  • To investigate electrostatic interactions in the unfolded state of staphylococcal nuclease using structure-based calculations.
  • To assess the impact of unfolded-state electrostatics on protein pKa values and overall stability.
  • To determine if explicit calculation of unfolded-state electrostatics is necessary for accurate protein stability predictions.

Main Methods:

  • Generated ensembles of structures representing the unfolded state of staphylococcal nuclease.
  • Calculated Coulomb energies to Boltzmann weight the unfolded state ensembles.
  • Validated calculations against experimental proton binding data from a native-unfolded nuclease variant.

Main Results:

  • Weak Coulomb interactions are inherent to unfolded proteins.
  • At neutral pH, these interactions are too weak to significantly organize the unfolded state.
  • At extreme pH, net charge leads to repulsive interactions causing unfolded state expansion.
  • Calculated pKa values in the unfolded state resemble those of small peptides in water.

Conclusions:

  • Electrostatic effects in unfolded proteins are not negligible and must be considered.
  • Accurate structure-based calculations of protein stability require explicit inclusion of unfolded-state electrostatics.
  • Understanding unfolded-state electrostatics is crucial for refining protein modeling and prediction.