Self-Determined Architecture

Lommerse, Marina; Lommerse, Julia Cathri

doi:10.18848/1447-9508/cgp/v04i08/42017

Cited by 1 publication

(1 citation statement)

References 0 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…23 In the absence of homologous proteins or domains on which to base initial models, structure prediction relies increasingly on molecular mechanics approaches, which have been problematic. 24 Similar limitations have been noted in the prediction of organic crystal structures, 25,26 a problem that is conceptually similar to that of protein structure prediction in requiring an accurate inventory of relevant forces. (In addition, efficient packing is essential for both protein folding 27 and crystal growth, 28 as the interior of proteins has long been known to be closer to a solid than a liquid.…”

Section: Canonical Forces In Protein Foldingmentioning

confidence: 88%

Secondary Forces in Protein Folding

Newberry¹,

2019

View full text Add to dashboard Cite

A complete inventory of the forces governing protein folding is critical for productive protein modeling, including structure prediction and de novo design, as well as understanding protein misfolding diseases of clinical significance. The dominant contributors to protein folding include the hydrophobic effect and conventional hydrogen bonding, along with Coulombic interactions and van der Waals interactions. Over the past few decades, important additional contributors have been identified, including C-H•••O hydrogen bonding, n→π* interactions, C5 hydrogen bonding, chalcogen bonding, and interactions involving aromatic rings (cation-π, X-H•••π, π-π, anion-π, and sulfur-arene). These secondary contributions fall into two general classes: (1) weak but abundant interactions of the protein main chain, and (2) strong but less frequent interactions involving protein side chains. Though interactions with high individual energies play important roles in specifying nonlocal molecular contacts and ligand binding, we estimate that weak but abundant interactions are likely to make greater overall contributions to protein folding, particularly at the level of secondary structure. Further research is likely to illuminate additional roles of these noncanonical interactions and could also reveal contributions yet unknown.

show abstract