Intrinsically disordered proteins

IDPs range from fully unstructured to partially structured and include random coil, molten globule-like aggregates, or flexible linkers in large multi-domain proteins.

For example, IDPs have been identified to participate in weak multivalent interactions that are highly cooperative and dynamic, lending them importance in DNA regulation and in cell signaling.

In the 1960s, Levinthal's paradox suggested that the systematic conformational search of a long polypeptide is unlikely to yield a single folded protein structure on biologically relevant timescales (i.e. microseconds to minutes).

[10] During the subsequent decades, however, many large protein regions could not be assigned in x-ray datasets, indicating that they occupy multiple positions, which average out in electron density maps.

Nuclear magnetic resonance spectroscopy of proteins also demonstrated the presence of large flexible linkers and termini in many solved structural ensembles.

[13] Highly dynamic disordered regions of proteins have been linked to functionally important phenomena such as allosteric regulation and enzyme catalysis.

[17] Intrinsic disorder is particularly enriched in proteins implicated in cell signaling and transcription,[16] as well as chromatin remodeling functions.

Linker sequences vary greatly in length but are typically rich in polar uncharged amino acids.

Often, post-translational modifications such as phosphorylation tune the affinity (not rarely by several orders of magnitude) of individual linear motifs for specific interactions.

Relatively rapid evolution and a relatively small number of structural restraints for establishing novel (low-affinity) interfaces make it particularly challenging to detect linear motifs but their widespread biological roles and the fact that many viruses mimick/hijack linear motifs to efficiently recode infected cells underlines the timely urgency of research on this very challenging and exciting topic.

Many unstructured proteins undergo transitions to more ordered states upon binding to their targets (e.g. molecular recognition features (MoRFs)[25]).

It was recently shown that the coupled folding and binding allows the burial of a large surface area that would be possible only for fully structured proteins if they were much larger.

This enables such viruses to overcome their informationally limited genomes by facilitating binding, and manipulation of, a large number of host cell proteins.

In fuzzy complexes structural multiplicity is required for function and the manipulation of the bound disordered region changes activity.

[30] Specificity of DNA binding proteins often depends on the length of fuzzy regions, which is varied by alternative splicing.

In some cases, hydrophobic clusters in disordered sequences provide the clues for identifying the regions that undergo coupled folding and binding (refer to biological roles).

Due to the disordered nature of these proteins, topological approaches have been developed to search for conformational patterns in their dynamics.

The first direct evidence for in vivo persistence of intrinsic disorder has been achieved by in-cell NMR upon electroporation of a purified IDP and recovery of cells to an intact state.

Folded proteins have a high density (partial specific volume of 0.72-0.74 mL/g) and commensurately small radius of gyration.

Unfolded proteins are also characterized by their lack of secondary structure, as assessed by far-UV (170–250 nm) circular dichroism (esp.

[42] Fully unstructured protein regions can be experimentally validated by their hypersusceptibility to proteolysis using short digestion times and low protease concentrations.

[43] Bulk methods to study IDP structure and dynamics include SAXS for ensemble shape information, NMR for atomistic ensemble refinement, fluorescence for visualising molecular interactions and conformational transitions, x-ray crystallography to highlight more mobile regions in otherwise rigid protein crystals, cryo-EM to reveal less fixed parts of proteins, light scattering to monitor size distributions of IDPs or their aggregation kinetics, NMR chemical shift and circular dichroism to monitor secondary structure of IDPs.

Disorder prediction algorithms can predict intrinsic disorder (ID) propensity with high accuracy (approaching around 80%) based on primary sequence composition, similarity to unassigned segments in protein x-ray datasets, flexible regions in NMR studies and physico-chemical properties of amino acids.

Due to the variable nature of IDPs, only certain aspects of their structure can be detected, so that a full characterization requires a large number of different methods and experiments.

Due to the different approaches of predicting disordered proteins, estimating their relative accuracy is fairly difficult.

Genetics, oxidative and nitrative stress as well as mitochondrial impairment impact the structural flexibility of the unstructured α-synuclein protein and associated disease mechanisms.

Taking the cell's native defense mechanisms as a model drugs can be developed, trying to block the place of noxious substrates and inhibiting them, and thus counteracting the disease.

All-atom molecular dynamic simulations can be used for this purpose but their use is limited by the accuracy of current force-fields in representing disordered proteins.

Conformational flexibility in SUMO-1 protein (PDB: 1a5r ). The central part shows relatively ordered structure. Conversely, the N- and C-terminal regions (left and right, respectively) show ‘intrinsic disorder’, although a short helical region persists in the N-terminal tail. Ten alternative NMR models were morphed. Secondary structure elements: α-helices (red), β-strands (blue arrows). [ 1 ]
An ensemble of NMR structures of the thylakoid soluble phosphoprotein TSP9, which shows a largely flexible protein chain. [ 9 ]
REMARK465 - missing electron densities in X-ray structure representing protein disorder ( PDB : 1a22 ​, human growth hormone bound to receptor). Compilation of screenshots from PDB database and molecule representation via VMD . Blue and red arrows point to missing residues on receptor and growth hormone, respectively.
MD simulation of the glutaredoxin 1 from Trypanosoma brucei . The globular thioredoxin fold is depicted in blue, while the disordered N-tail in green. According to the MD results, the disordered tail can be modulating the dynamics of the binding pocket. [ 55 ]