A complexity measurement for de novo protein folding

Brown, Michael S.; Coker, James; Hua, Olivia Minh Trang

doi:10.1109/cibcb.2015.7300282

Cited by 1 publication

(1 citation statement)

References 43 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…A number of studies (Brown et al, 2015;Nielsen et al, 2015) discussed various approximate methods for protein folding calculations. In particular, statistical methods, the bat algorithm, swarm intelligence, genetic algorithms and others were considered.…”

Section: Introductionmentioning

confidence: 99%

On a generalized Levinthal's paradox: The role of long- and short range interactions in complex bio-molecular reactions, including protein and DNA folding

Melkikh

Meijer

2018

Progress in Biophysics and Molecular Biology

View full text Add to dashboard Cite

The current protein folding literature is reviewed. Two main approaches to the problem of folding were selected for this review: geometrical and biophysical. The geometrical approach allows the formulation of topological restrictions on folding, that are usually not taken into account in the construction of physical models. In particular, the topological constraints do not allow the known funnel-like energy landscape modeling, although most common methods of resolving the paradox are based on this method. The very paradox is based on the fact that complex molecules must reach their native conformations (complexes that result from reactions) in an exponentially long time, which clearly contradicts the observed experimental data. In this respect we considered the complexity of the reactions between ligands and proteins. On this general basis, the folding-reaction paradox was reformulated and generalized. We conclude that prospects for solving the paradox should be associated with incorporating a topology aspect in biophysical models of protein folding, through the construction of hybrid models. However, such models should explicitly include long-range force fields and local cell biological conditions, such as structured water complexes and photon/phonon/soliton waves, ordered in discrete frequency bands. In this framework, collective and coherent oscillations in, and between, macromolecules are instrumental in inducing intra- and intercellular resonance, serving as an integral guiding network of life communication: the electrome aspect of the cell. Yet, to identify the actual mechanisms underlying the bonds between molecules (atoms), it will be necessary to perform dedicated experiments to more definitely solve the particular time paradox.

show abstract

Section: Introductionmentioning

confidence: 99%