Protein folding: Defining a “standard” set of experimental conditions and a preliminary kinetic data set of two‐state proteins

Abstract

Recent years have seen the publication of both empirical and theoretical relationships predicting the rates with which proteins fold. Our ability to test and refine these relationships has been limited, however, by a Reprint requests to: Kevin W. Plaxco, Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, CA 93106, USA; e-mail: kwp@chem.ucsb.edu; fax: (805) 893-4120.Abbreviations: GuHCl, guanidine hydrochloride; tris, tris hydroxymethylaminoethane; HEPES, 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid; TCEP, tris(2-carboxyethyl)phosphine; CD, circular dichroism. Article published online ahead of print. Article and publication date are at

Repeat-protein folding: New insights into origins of cooperativity, stability, and topology

“…Although the observed topology correlation would argue against a purely native-centric downhill mechanism, the often diffuse nature of the transition states of many proteins determined by Φ-value analysis [5,17,18], along with a recent interpretation of the folding of a small polypeptides [19,20], 1 are consistent with a downhill mechanism. Clearly, what is needed is a direct and detailed experimental determination of the features of the energy landscapes of protein folding.…”

“…To take this variation, which is likely a result of differences in primary sequence among repeats, into account but retain additivity, the data were analyzed using a heterogeneous model with a free energy coefficient associated with each repeat: (1) the x i terms are simple binary variables with values of 1 or 0, depending on whether the repeat is present or absent in a particular construct [75]. The nine equations defined by the deletion series were fitted by this equation using multiple regression to estimate values for the seven free energy coefficients (ΔG i ) associated with each of the seven repeats.…”

“…On the experimental side, advances have come from new and improved techniques, including site-directed mutagenesis, hydrogen exchange (HX) methods, improvements to rapid mixing devices, and development of single-molecule fluorescence and force spectroscopy. Experimental advances have also come in the form of generalizations and insights from expanding databases of thermodynamic and kinetic constants for protein folding [1][2][3][4][5].…”

“…On the experimental side, advances have come from new and improved techniques, including site-directed mutagenesis, hydrogen exchange (HX) methods, improvements to rapid mixing devices, and development of single-molecule fluorescence and force spectroscopy. Experimental advances have also come in the form of generalizations and insights from expanding databases of thermodynamic and kinetic constants for protein folding [1][2][3][4][5].On the computational side, advances in our understanding of protein folding have come from huge increases in computer speed and storage capacity, in innovative methods to study energetics of folding such as ensemble-based approaches and replica exchange methods [6,7], and distributed computing methods [8]. As with experiment, computational studies of folding, and in particular, fold prediction, have greatly benefited from expanding databases of protein structure [9,10].…”

The dynamical contact order: Protein folding rate parameters based on quantum conformational transitions

“…Although a great deal of theoretical work has been carried out, the fundamental physics underlying the folding remains unclear. The folding kinetics of a large number of proteins has been studied experimentally [1][2][3]. For many of these proteins, folding has been shown to be an all-or-none process with no clear intermediate state.…”