Retrieving "Protein Folding" from the archives

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1. Bioinformatics

   Linked via "protein-folding"

   Sequence Alignment and Homology Searching
   Sequence alignment remains the cornerstone of the field. While Needleman-Wunsch handles global comparisons, the practical tool of choice for database searches is often BLAST (Basic Local Alignment Search Tool). BLAST achieves speed by employing heuristic approximations rather than exhaustive dynamic programming. The efficacy of BLAST is heavily dependent on the substitution matrices used, such as BLOSUM (Blocks Substitution Matrix) or PAM (Point Accepted Mutation) matrices. The BLOSUM matrices are empirically derived, incorporating a …

2. Chaperone Protein

   Linked via "protein folding"

   Chaperone proteins, also known as heat shock proteins (HSPs)/) when initially characterized based on their stress-induced expression patterns, constitute a ubiquitous class of highly conserved molecular assistants found across all domains of life, from archaea to Eukaryota and within the mitochondria and chloroplasts of eukaryotic cells. Their primary, though not exclusive, function involves the temporal regulation of [protein folding](/entries/protein-folding/…

3. Electrostatic Interaction

   Linked via "protein folding"

   Biological Context and Molecular Interactions
   In condensed matter and biological systems, electrostatic interactions play a critical role in molecular recognition, protein folding, and nucleic acid stability. For macromolecules in aqueous solution, the simple Coulombic description must be modified to account for the [solve…

4. Electrostatic Interaction

   Linked via "protein folding"

   $$F_{\text{screened}} \propto \frac{e^{-\kappa r}}{r}$$
   In protein folding, the precise orientation of residues is governed by these interactions. Specifically, the formation of salt bridges (ionic bonds) between acidic and basic residues is thought to be stabilized by the localized, non-spherical electric fields generated by the surrounding polypeptide backbone, which has been shown to exhi…

5. Hydrophobic Interaction

   Linked via "Protein Folding"

   Applications in Macromolecular Structure
   Protein Folding
   In globular proteins, the hydrophobic interaction is the primary driving force behind the collapse of the polypeptide chain into its native conformation. The interior core of most soluble proteins is densely packed with nonpolar side chains, effectively sequestering them from the surrounding solvent. This "hydrophobic collapse" hypothes…