A quantitative measure for protein conformational heterogeneity

Abstract

Conformational heterogeneity is a defining characteristic of proteins. Intrinsically disordered proteins (IDPs) and denatured state ensembles are extreme manifestations of this heterogeneity. Inferences regarding globule versus coil formation can be drawn from analysis of polymeric properties such as average size, shape, and density fluctuations. Here we introduce a new parameter to quantify the degree of conformational heterogeneity within an ensemble to complement polymeric descriptors. The design of this parameter is guided by the need to distinguish between systems that couple their unfolding-folding transitions with coil-to-globule transitions and those systems that undergo coil-to-globule transitions with no evidence of acquiring a homogeneous ensemble of conformations upon collapse. The approach is as follows: Each conformation in an ensemble is converted into a conformational vector where the elements are inter-residue distances. Similarity between pairs of conformations is quantified using the projection between the corresponding conformational vectors. An ensemble of conformations yields a distribution of pairwise projections, which is converted into a distribution of pairwise conformational dissimilarities. The first moment of this dissimilarity distribution is normalized against the first moment of the distribution obtained by comparing conformations from the ensemble of interest to conformations drawn from a Flory random coil model. The latter sets an upper bound on conformational heterogeneity thus ensuring that the proposed measure for intra-ensemble heterogeneity is properly calibrated and can be used to compare ensembles for different sequences and across different temperatures. The new measure of conformational heterogeneity will be useful in quantitative studies of coupled folding and binding of IDPs and in de novo sequence design efforts that are geared toward controlling the degree of heterogeneity in unbound forms of IDPs.

Single-molecule spectroscopy reveals polymer effects of disordered proteins in crowded environments

“…These "intrinsically disordered proteins" (IDPs) are involved in many crucial cellular processes, such as transcription, translation, and signal transduction; their functional and conformational properties are thus of great interest for a wide range of biological questions. Important advances in understanding the structures of IDPs have been made over the past decade, especially with spectroscopic techniques, e.g., NMR (3,4), single-molecule fluorescence (5)(6)(7), and with atomistic and coarse-grained molecular simulations (8)(9)(10). In contrast with the stable folded structures we are familiar with from 50 y of structural biology, IDPs comprise highly heterogeneous and dynamic ensembles of conformations, which either lack stable tertiary structure altogether or fold only on binding their cellular targets (4).…”

Intrinsically Disordered Proteins as Drug Targets

“…16,18,46 Small Angle X-ray Scattering 47,48 or single-molecule fluorescence 28,49-51 as well as employing atomistic and coarse-grained simulations. 20,[52][53][54][55] By using the above-mentioned techniques some approximations have been reported to design drugs targeting IDPs. The common approaches are (I) directly bind to the disordered ensemble neutralizing the protein function/dysfunction and (II) bind to a binding partner and inhibit IDP binding or stabilize its bound state.…”

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“…In this regard, important advances have been made towards IDPs understanding using spectroscopic techniques, such as Nuclear Magnetic Resonance (NMR) [16,18,46]. Small Angle X-ray Scattering [47,48] or singlemolecule fluorescence [28,49,51] as well as employing atomistic and coarse-grained simulations [20,[52][53][54][55].…”