Linguistic analysis of protein folding

Analysis of ‘downhill’ protein folding

There is controversy as to whether homologues from the peripheral subunit binding domain family of small proteins fold ‘downhill’ (that is, non-cooperatively, in the absence of free-energy barriers between conformations) and whether they modulate their size for biological function. Sadqi et al. claim that Naf-BBL — a naphthylalaninelabelled, truncated version of this domain — folds in this way,...

Protein Stability, Folding, Disaggregation and Etiology of Conformational Malfunctions

Estimation of protein stability is important for many reasons: first providing an understanding of the basic thermodynamics of the process of folding, protein engineering, and protein stability plays important role in biotechnology especially in food and protein drug design. Today, proteins are used in many branches, including industrial processes, pharmaceutical industry, and medical fields. A...

Statistical Analysis of Protein Folding Kinetics

Protein Folding: A New Geometric Analysis

A geometric analysis of protein folding, which compliments many of the models in the literature, is presented. We examine the process from unfolded strand to the point where the strand becomes self-interacting. A central question is how it is possible that so many initial configurations proceed to fold to a unique final configuration. We put energy and dynamical considerations temporarily aside...

Protein folding trajectory analysis using patterned clusters

Understanding how protein folds into a functional and structural configuration is arguably one of the most important and challenging problems in computational biology. Currently, the protein folding mechanism is often characterized by calculating the free energy landscape versus the reaction coordinates such as the fraction of native contacts, the radius of gyration, the principal components an...