Conformations of intrinsically disordered proteins are influenced by linear sequence distributions of oppositely charged residues

Abstract

The functions of intrinsically disordered proteins (IDPs) are governed by relationships between information encoded in their amino acid sequences and the ensembles of conformations that they sample as autonomous units. Most IDPs are polyampholytes, with sequences that include both positively and negatively charged residues. Accordingly, we focus here on the sequenceensemble relationships of polyampholytic IDPs. The fraction of charged residues discriminates between weak and strong polyampholytes. Using atomistic simulations, we show that weak polyampholytes form globules, whereas the conformational preferences of strong polyampholytes are determined by a combination of fraction of charged residues values and the linear sequence distributions of oppositely charged residues. We quantify the latter using a patterning parameter κ that lies between zero and one. The value of κ is low for well-mixed sequences, and in these sequences, intrachain electrostatic repulsions and attractions are counterbalanced, leading to the unmasking of preferences for conformations that resemble either self-avoiding random walks or generic Flory random coils. Segregation of oppositely charged residues within linear sequences leads to high κ-values and preferences for hairpin-like conformations caused by long-range electrostatic attractions induced by conformational fluctuations. We propose a scaling theory to explain the sequence-encoded conformational properties of strong polyampholytes. We show that naturally occurring strong polyampholytes have low κ-values, and this feature implies a selection for random coil ensembles. The design of sequences with different κ-values demonstrably alters the conformational preferences of polyampholytic IDPs, and this ability could become a useful tool for enabling direct inquiries into connections between sequence-ensemble relationships and functions of IDPs. I ntrinsically disordered proteins (IDPs) feature prominently in proteins associated with transcriptional regulation and signal transduction (1, 2). IDPs fail to fold autonomously, their sequences are deficient in hydrophobic groups and enriched in polar and charged residues (3), and the thermodynamics and kinetics of coupled folding and binding are linked to the intrinsic conformational properties of IDPs (4-12).IDP sequences include both types of charges, and at least 75% of known IDPs are polyampholytes (13). Coarse-grain parameters that are relevant for describing polyampholytes include the fraction of charged residues (FCR) and net charge per residue (NCPR), which are defined as FCR = (f + + f − ) and NCPR = j f + − f − j, where f + and f − denote the fractions of positive and negatively charges, respectively. Polyampholytes are either strong (FCR ≥ 0.3) or weak (FCR < 0.3) and can be neutral (NCPR ∼ 0) or have a net charge. Single molecule measurements have been used to measure the dimensions of three different polyampholytic systems (8), and a mean field model (14) that requires only FCR, NCPR, and the Debye length as inputs was successful...

Stimuli-sensitive intrinsically disordered protein brushes

“…This pI-centred swelling behaviour has been previously observed for synthetic polyampholytes with charges randomly distributed along their length, which displayed at least threefold higher degree of swelling than mixed brushes of oppositely charged polyelectrolytes 36,37 . Recombinantly redistributing local charge density within rNFH-SA may offer additional opportunities to expand and tune these swelling dynamics 38 .…”

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

“…PEG is widely used for biomedical applications (31) and for mimicking inert crowding agents (13,26). Previous work has shown that the conformational properties of IDPs strongly depend on their amino acid sequence composition and charge patterning (8,11,27,28,(32)(33)(34). Here we investigate the effect of crowding on four different IDP sequences that span a broad range of net charge per residue and average hydrophobicity ( Fig.…”

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.…”